Starting phenix.real_space_refine on Sat Jun 14 21:58:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vht_43241/06_2025/8vht_43241.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vht_43241/06_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_43241/06_2025/8vht_43241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vht_43241/06_2025/8vht_43241.map" model { file = "/net/cci-nas-00/data/ceres_data/8vht_43241/06_2025/8vht_43241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vht_43241/06_2025/8vht_43241.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.033 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.73, per 1000 atoms: 0.59 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: 3.95 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.64 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: 5.17 Time building geometry restraints manager: 4.69 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: 0.10 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: 4.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 37.560 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.760 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (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 TRP 0.024 0.001 TRP A 837 HIS 0.003 0.001 HIS A1023 PHE 0.009 0.001 PHE A1016 TYR 0.014 0.001 TYR B 271 ARG 0.005 0.000 ARG B 720 Details of bonding type rmsd link_BETA1-4 : bond 0.00169 ( 3) link_BETA1-4 : angle 1.41489 ( 9) hydrogen bonds : bond 0.13259 ( 867) hydrogen bonds : angle 5.18322 ( 2583) covalent geometry : bond 0.00261 (17064) covalent geometry : angle 0.54101 (23229) *********************** 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 : 1.715 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: 0.2939 time to fit residues: 104.9906 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 : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 85 optimal weight: 0.4980 chunk 52 optimal weight: 0.0170 chunk 104 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 ASN A1005 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3808 r_free = 0.3808 target = 0.167948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.125823 restraints weight = 19107.087| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.44 r_work: 0.2806 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1041 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= 0.154 Angle : 0.555 6.043 23238 Z= 0.283 Chirality : 0.043 0.159 2550 Planarity : 0.005 0.044 2922 Dihedral : 4.305 55.682 2373 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.35 % Allowed : 13.05 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.19), residues: 2037 helix: 2.03 (0.16), residues: 1086 sheet: 1.31 (0.46), residues: 120 loop : 0.31 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 837 HIS 0.004 0.001 HIS D 531 PHE 0.013 0.001 PHE B 830 TYR 0.016 0.002 TYR D 998 ARG 0.003 0.000 ARG B 720 Details of bonding type rmsd link_BETA1-4 : bond 0.00146 ( 3) link_BETA1-4 : angle 1.90328 ( 9) hydrogen bonds : bond 0.04514 ( 867) hydrogen bonds : angle 3.85476 ( 2583) covalent geometry : bond 0.00366 (17064) covalent geometry : angle 0.55344 (23229) *********************** 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 286 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 244 time to evaluate : 1.815 Fit side-chains REVERT: A 569 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.8697 (mp) REVERT: A 850 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7959 (t80) REVERT: B 733 MET cc_start: 0.8186 (mtp) cc_final: 0.7526 (mtp) REVERT: B 832 ARG cc_start: 0.7596 (ttp80) cc_final: 0.7202 (ptt90) REVERT: D 309 ILE cc_start: 0.8346 (mm) cc_final: 0.8111 (mm) REVERT: D 814 ARG cc_start: 0.6104 (tpt-90) cc_final: 0.5867 (tpt-90) REVERT: D 832 ARG cc_start: 0.7574 (ttp80) cc_final: 0.6978 (ptt90) REVERT: D 870 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.6972 (mt) outliers start: 42 outliers final: 26 residues processed: 271 average time/residue: 0.3029 time to fit residues: 122.1939 Evaluate side-chains 264 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 235 time to evaluate : 1.942 ------------------------------------------------------------------------------- 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 497 MET Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 569 LEU 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 875 CYS 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 109 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 152 optimal weight: 0.7980 chunk 140 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.165094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.119049 restraints weight = 19060.073| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.51 r_work: 0.2754 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1519 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= 0.144 Angle : 0.533 6.456 23238 Z= 0.272 Chirality : 0.042 0.156 2550 Planarity : 0.004 0.045 2922 Dihedral : 4.203 57.997 2373 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.25 % Allowed : 13.00 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.19), residues: 2037 helix: 2.15 (0.16), residues: 1092 sheet: 1.27 (0.47), residues: 120 loop : 0.19 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 911 HIS 0.004 0.001 HIS B 531 PHE 0.013 0.001 PHE B1016 TYR 0.011 0.001 TYR A 288 ARG 0.004 0.000 ARG A 720 Details of bonding type rmsd link_BETA1-4 : bond 0.00187 ( 3) link_BETA1-4 : angle 1.88404 ( 9) hydrogen bonds : bond 0.04365 ( 867) hydrogen bonds : angle 3.71488 ( 2583) covalent geometry : bond 0.00347 (17064) covalent geometry : angle 0.53172 (23229) *********************** 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 308 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 250 time to evaluate : 2.035 Fit side-chains revert: symmetry clash REVERT: A 452 MET cc_start: 0.9153 (tpp) cc_final: 0.8894 (tpt) REVERT: A 569 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8663 (mp) REVERT: A 733 MET cc_start: 0.8356 (mtp) cc_final: 0.8128 (mtt) REVERT: A 850 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7983 (t80) REVERT: A 983 THR cc_start: 0.7587 (OUTLIER) cc_final: 0.6742 (m) REVERT: A 984 LEU cc_start: 0.8012 (tt) cc_final: 0.7660 (tp) REVERT: B 392 ASP cc_start: 0.9157 (OUTLIER) cc_final: 0.8859 (m-30) REVERT: B 396 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8723 (ttt) REVERT: B 714 GLN cc_start: 0.7493 (tp40) cc_final: 0.7236 (tm-30) REVERT: B 718 GLU cc_start: 0.8262 (tt0) cc_final: 0.7968 (tt0) REVERT: B 733 MET cc_start: 0.8335 (mtp) cc_final: 0.7733 (mtp) REVERT: B 832 ARG cc_start: 0.7623 (ttp80) cc_final: 0.7189 (ptt90) REVERT: D 309 ILE cc_start: 0.8297 (mm) cc_final: 0.8066 (mm) REVERT: D 714 GLN cc_start: 0.7804 (tm-30) cc_final: 0.7411 (tm-30) REVERT: D 832 ARG cc_start: 0.7647 (ttp80) cc_final: 0.7108 (ptt90) REVERT: D 870 ILE cc_start: 0.7380 (OUTLIER) cc_final: 0.7046 (mt) REVERT: D 924 GLN cc_start: 0.7870 (pt0) cc_final: 0.7277 (mt0) outliers start: 58 outliers final: 35 residues processed: 288 average time/residue: 0.3237 time to fit residues: 141.6243 Evaluate side-chains 277 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 236 time to evaluate : 1.897 ------------------------------------------------------------------------------- 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 530 GLN Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 608 THR 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 975 THR Chi-restraints excluded: chain A residue 983 THR 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 396 MET 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 875 CYS 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 356 SER Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 521 VAL 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 904 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 161 optimal weight: 0.7980 chunk 186 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 202 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.163538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.115710 restraints weight = 19117.246| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.57 r_work: 0.2722 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17067 Z= 0.155 Angle : 0.545 6.668 23238 Z= 0.277 Chirality : 0.043 0.162 2550 Planarity : 0.004 0.048 2922 Dihedral : 4.263 59.850 2373 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.19), residues: 2037 helix: 2.07 (0.16), residues: 1095 sheet: 1.21 (0.46), residues: 120 loop : 0.14 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 911 HIS 0.003 0.001 HIS B 531 PHE 0.010 0.001 PHE A 415 TYR 0.012 0.001 TYR D 858 ARG 0.003 0.000 ARG A 720 Details of bonding type rmsd link_BETA1-4 : bond 0.00225 ( 3) link_BETA1-4 : angle 1.99411 ( 9) hydrogen bonds : bond 0.04406 ( 867) hydrogen bonds : angle 3.69569 ( 2583) covalent geometry : bond 0.00381 (17064) covalent geometry : angle 0.54346 (23229) *********************** 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 296 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 238 time to evaluate : 1.828 Fit side-chains revert: symmetry clash REVERT: A 452 MET cc_start: 0.9144 (tpp) cc_final: 0.8901 (tpt) REVERT: A 569 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.8703 (mp) REVERT: A 850 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.8039 (t80) REVERT: B 392 ASP cc_start: 0.9175 (OUTLIER) cc_final: 0.8882 (m-30) REVERT: B 396 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8719 (ttt) REVERT: B 714 GLN cc_start: 0.7513 (tp40) cc_final: 0.7279 (tm-30) REVERT: B 718 GLU cc_start: 0.8301 (tt0) cc_final: 0.8004 (tt0) REVERT: B 733 MET cc_start: 0.8241 (mtp) cc_final: 0.7683 (mtp) REVERT: B 832 ARG cc_start: 0.7662 (ttp80) cc_final: 0.7204 (ptt90) REVERT: D 290 ILE cc_start: 0.7777 (mm) cc_final: 0.7394 (tp) REVERT: D 309 ILE cc_start: 0.8285 (mm) cc_final: 0.8084 (mm) REVERT: D 714 GLN cc_start: 0.7689 (tm-30) cc_final: 0.7337 (tm-30) REVERT: D 832 ARG cc_start: 0.7664 (ttp80) cc_final: 0.7031 (ptt90) REVERT: D 924 GLN cc_start: 0.7816 (pt0) cc_final: 0.7271 (mt0) outliers start: 58 outliers final: 43 residues processed: 275 average time/residue: 0.3632 time to fit residues: 150.5877 Evaluate side-chains 278 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 231 time to evaluate : 1.943 ------------------------------------------------------------------------------- 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 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 358 VAL 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 875 CYS 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 274 VAL Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 521 VAL 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 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 88 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.161085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.125449 restraints weight = 19258.041| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.28 r_work: 0.2889 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 17067 Z= 0.235 Angle : 0.617 9.456 23238 Z= 0.314 Chirality : 0.046 0.165 2550 Planarity : 0.005 0.048 2922 Dihedral : 4.491 51.126 2373 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.75 % Allowed : 13.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.19), residues: 2037 helix: 1.90 (0.16), residues: 1107 sheet: 1.03 (0.46), residues: 120 loop : -0.01 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 428 HIS 0.004 0.001 HIS D 494 PHE 0.011 0.002 PHE B 727 TYR 0.015 0.002 TYR B 858 ARG 0.005 0.001 ARG B 635 Details of bonding type rmsd link_BETA1-4 : bond 0.00119 ( 3) link_BETA1-4 : angle 2.32987 ( 9) hydrogen bonds : bond 0.05214 ( 867) hydrogen bonds : angle 3.91658 ( 2583) covalent geometry : bond 0.00593 (17064) covalent geometry : angle 0.61562 (23229) *********************** 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 304 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 237 time to evaluate : 1.965 Fit side-chains revert: symmetry clash REVERT: A 569 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.8692 (mp) REVERT: A 612 ASP cc_start: 0.8784 (m-30) cc_final: 0.8463 (m-30) REVERT: A 850 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.8127 (t80) REVERT: A 855 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8444 (t) REVERT: B 392 ASP cc_start: 0.9232 (OUTLIER) cc_final: 0.8817 (m-30) REVERT: B 396 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8752 (ttt) REVERT: B 476 GLU cc_start: 0.6519 (pm20) cc_final: 0.6306 (pm20) REVERT: B 718 GLU cc_start: 0.8330 (tt0) cc_final: 0.8006 (tt0) REVERT: B 733 MET cc_start: 0.8312 (mtp) cc_final: 0.7907 (mtt) REVERT: B 832 ARG cc_start: 0.7816 (ttp80) cc_final: 0.7382 (ptt90) REVERT: B 870 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7339 (mt) REVERT: D 290 ILE cc_start: 0.7803 (mm) cc_final: 0.7471 (tp) REVERT: D 714 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7423 (tm-30) REVERT: D 733 MET cc_start: 0.8198 (mtp) cc_final: 0.7703 (mtt) REVERT: D 832 ARG cc_start: 0.7802 (ttp80) cc_final: 0.7343 (ptt90) REVERT: D 924 GLN cc_start: 0.7913 (pt0) cc_final: 0.7372 (mt0) outliers start: 67 outliers final: 48 residues processed: 279 average time/residue: 0.2776 time to fit residues: 117.2335 Evaluate side-chains 278 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 224 time to evaluate : 1.878 ------------------------------------------------------------------------------- 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 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 396 MET 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 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 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 308 GLU 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 521 VAL 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 831 SER 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 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 141 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 183 optimal weight: 0.5980 chunk 179 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 133 optimal weight: 8.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 ASN B 817 GLN D 614 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.169256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.131847 restraints weight = 18951.256| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.32 r_work: 0.2801 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2319 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= 0.147 Angle : 0.549 9.052 23238 Z= 0.279 Chirality : 0.043 0.163 2550 Planarity : 0.004 0.048 2922 Dihedral : 4.262 42.267 2373 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.14 % Allowed : 14.34 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.19), residues: 2037 helix: 1.95 (0.16), residues: 1110 sheet: 0.99 (0.46), residues: 120 loop : 0.05 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 911 HIS 0.003 0.001 HIS B 531 PHE 0.011 0.001 PHE A 415 TYR 0.012 0.001 TYR B 858 ARG 0.003 0.000 ARG A 720 Details of bonding type rmsd link_BETA1-4 : bond 0.00167 ( 3) link_BETA1-4 : angle 1.95747 ( 9) hydrogen bonds : bond 0.04419 ( 867) hydrogen bonds : angle 3.74636 ( 2583) covalent geometry : bond 0.00358 (17064) covalent geometry : angle 0.54742 (23229) *********************** 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 283 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 227 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 ILE cc_start: 0.8329 (mm) cc_final: 0.8079 (mm) REVERT: A 569 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8636 (mp) REVERT: A 612 ASP cc_start: 0.8785 (m-30) cc_final: 0.8459 (m-30) REVERT: A 714 GLN cc_start: 0.7733 (tm-30) cc_final: 0.7401 (tm-30) REVERT: A 850 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8160 (t80) REVERT: A 855 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8378 (t) REVERT: B 392 ASP cc_start: 0.9185 (OUTLIER) cc_final: 0.8825 (m-30) REVERT: B 476 GLU cc_start: 0.6600 (pm20) cc_final: 0.6335 (pm20) REVERT: B 583 LYS cc_start: 0.8863 (mtpt) cc_final: 0.8254 (mmtm) REVERT: B 718 GLU cc_start: 0.8300 (tt0) cc_final: 0.7991 (tt0) REVERT: B 733 MET cc_start: 0.8271 (mtp) cc_final: 0.7804 (mtp) REVERT: B 832 ARG cc_start: 0.7769 (ttp80) cc_final: 0.7177 (ptt90) REVERT: D 290 ILE cc_start: 0.7852 (mm) cc_final: 0.7536 (tp) REVERT: D 714 GLN cc_start: 0.7618 (tm-30) cc_final: 0.7285 (tm-30) REVERT: D 832 ARG cc_start: 0.7694 (ttp80) cc_final: 0.7230 (ptt90) outliers start: 56 outliers final: 44 residues processed: 262 average time/residue: 0.2796 time to fit residues: 111.1113 Evaluate side-chains 269 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 221 time to evaluate : 2.001 ------------------------------------------------------------------------------- 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 316 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 870 ILE 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 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 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 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 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 497 MET Chi-restraints excluded: chain D residue 521 VAL 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 855 THR Chi-restraints excluded: chain D residue 860 VAL 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 68 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 42 optimal weight: 5.9990 chunk 146 optimal weight: 0.1980 chunk 126 optimal weight: 0.9980 chunk 179 optimal weight: 0.8980 chunk 174 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 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 B 817 GLN D 592 GLN D 605 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.162349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.114408 restraints weight = 19158.539| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.51 r_work: 0.2726 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2462 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= 0.151 Angle : 0.550 8.153 23238 Z= 0.278 Chirality : 0.043 0.168 2550 Planarity : 0.004 0.048 2922 Dihedral : 4.087 31.860 2373 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.31 % Allowed : 14.01 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.19), residues: 2037 helix: 2.02 (0.16), residues: 1107 sheet: 0.93 (0.46), residues: 120 loop : -0.01 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 911 HIS 0.003 0.001 HIS B 531 PHE 0.010 0.001 PHE A 415 TYR 0.012 0.001 TYR D 858 ARG 0.004 0.000 ARG A 720 Details of bonding type rmsd link_BETA1-4 : bond 0.00068 ( 3) link_BETA1-4 : angle 1.90349 ( 9) hydrogen bonds : bond 0.04366 ( 867) hydrogen bonds : angle 3.71649 ( 2583) covalent geometry : bond 0.00368 (17064) covalent geometry : angle 0.54835 (23229) *********************** 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 285 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 226 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 ILE cc_start: 0.8341 (mm) cc_final: 0.8065 (mm) REVERT: A 569 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8655 (mp) REVERT: A 612 ASP cc_start: 0.8840 (m-30) cc_final: 0.8515 (m-30) REVERT: A 714 GLN cc_start: 0.7750 (tm-30) cc_final: 0.7384 (tm-30) REVERT: A 850 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8143 (t80) REVERT: A 855 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8437 (t) REVERT: B 356 SER cc_start: 0.8459 (OUTLIER) cc_final: 0.8063 (m) REVERT: B 392 ASP cc_start: 0.9254 (OUTLIER) cc_final: 0.8897 (m-30) REVERT: B 476 GLU cc_start: 0.6625 (pm20) cc_final: 0.6246 (pm20) REVERT: B 583 LYS cc_start: 0.8917 (mtpt) cc_final: 0.8283 (mmtm) REVERT: B 718 GLU cc_start: 0.8312 (tt0) cc_final: 0.8003 (tt0) REVERT: B 733 MET cc_start: 0.8294 (mtp) cc_final: 0.7789 (mtp) REVERT: B 832 ARG cc_start: 0.7830 (ttp80) cc_final: 0.7201 (ptt90) REVERT: B 837 TRP cc_start: 0.8077 (p90) cc_final: 0.7852 (p90) REVERT: D 290 ILE cc_start: 0.7864 (mm) cc_final: 0.7561 (tp) REVERT: D 832 ARG cc_start: 0.7747 (ttp80) cc_final: 0.7159 (ptt90) outliers start: 59 outliers final: 48 residues processed: 264 average time/residue: 0.2819 time to fit residues: 111.6776 Evaluate side-chains 274 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 221 time to evaluate : 1.790 ------------------------------------------------------------------------------- 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 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 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 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 817 GLN 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 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 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 356 SER Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 521 VAL 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 94 optimal weight: 0.5980 chunk 80 optimal weight: 0.3980 chunk 105 optimal weight: 0.5980 chunk 187 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.162666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.114984 restraints weight = 19038.845| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.51 r_work: 0.2739 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2496 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= 0.140 Angle : 0.541 8.374 23238 Z= 0.274 Chirality : 0.042 0.168 2550 Planarity : 0.004 0.048 2922 Dihedral : 4.025 30.345 2373 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.14 % Allowed : 14.62 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.19), residues: 2037 helix: 2.05 (0.16), residues: 1107 sheet: 0.93 (0.46), residues: 120 loop : 0.00 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 911 HIS 0.003 0.001 HIS B 531 PHE 0.010 0.001 PHE A 415 TYR 0.011 0.001 TYR D 858 ARG 0.003 0.000 ARG A 720 Details of bonding type rmsd link_BETA1-4 : bond 0.00104 ( 3) link_BETA1-4 : angle 1.81524 ( 9) hydrogen bonds : bond 0.04234 ( 867) hydrogen bonds : angle 3.67552 ( 2583) covalent geometry : bond 0.00335 (17064) covalent geometry : angle 0.53945 (23229) *********************** 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: 56 poor density : 220 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 ILE cc_start: 0.8338 (mm) cc_final: 0.8063 (mm) REVERT: A 569 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8604 (mp) REVERT: A 612 ASP cc_start: 0.8839 (m-30) cc_final: 0.8526 (m-30) REVERT: A 714 GLN cc_start: 0.7750 (tm-30) cc_final: 0.7397 (tm-30) REVERT: A 850 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.8122 (t80) REVERT: A 855 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8424 (t) REVERT: B 356 SER cc_start: 0.8386 (OUTLIER) cc_final: 0.8008 (m) REVERT: B 392 ASP cc_start: 0.9240 (OUTLIER) cc_final: 0.8886 (m-30) REVERT: B 476 GLU cc_start: 0.6601 (pm20) cc_final: 0.6211 (pm20) REVERT: B 583 LYS cc_start: 0.8916 (mtpt) cc_final: 0.8292 (mmtm) REVERT: B 718 GLU cc_start: 0.8257 (tt0) cc_final: 0.7934 (tt0) REVERT: B 733 MET cc_start: 0.8271 (mtp) cc_final: 0.7763 (mtp) REVERT: B 832 ARG cc_start: 0.7831 (ttp80) cc_final: 0.7224 (ptt90) REVERT: B 837 TRP cc_start: 0.8134 (p90) cc_final: 0.7901 (p90) REVERT: D 290 ILE cc_start: 0.7864 (mm) cc_final: 0.7567 (tp) REVERT: D 832 ARG cc_start: 0.7698 (ttp80) cc_final: 0.7122 (ptt90) outliers start: 56 outliers final: 48 residues processed: 257 average time/residue: 0.2861 time to fit residues: 111.0534 Evaluate side-chains 274 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 221 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 262 SER 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 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 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 855 THR Chi-restraints excluded: chain B residue 870 ILE 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 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 497 MET Chi-restraints excluded: chain D residue 521 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 143 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 32 optimal weight: 0.0060 chunk 179 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 154 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 43 optimal weight: 0.0270 chunk 18 optimal weight: 0.8980 overall best weight: 0.4254 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.163510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.116106 restraints weight = 19200.099| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.54 r_work: 0.2745 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17067 Z= 0.120 Angle : 0.526 9.009 23238 Z= 0.266 Chirality : 0.042 0.167 2550 Planarity : 0.004 0.048 2922 Dihedral : 3.866 25.847 2373 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.03 % Allowed : 14.68 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.19), residues: 2037 helix: 2.13 (0.16), residues: 1107 sheet: 0.91 (0.46), residues: 120 loop : 0.07 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 911 HIS 0.002 0.001 HIS B 531 PHE 0.011 0.001 PHE A 415 TYR 0.011 0.001 TYR B 858 ARG 0.003 0.000 ARG A 720 Details of bonding type rmsd link_BETA1-4 : bond 0.00127 ( 3) link_BETA1-4 : angle 1.65310 ( 9) hydrogen bonds : bond 0.03925 ( 867) hydrogen bonds : angle 3.59595 ( 2583) covalent geometry : bond 0.00281 (17064) covalent geometry : angle 0.52486 (23229) *********************** 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: 54 poor density : 223 time to evaluate : 1.982 Fit side-chains revert: symmetry clash REVERT: A 356 SER cc_start: 0.8132 (OUTLIER) cc_final: 0.7706 (m) REVERT: A 569 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8626 (mp) REVERT: A 612 ASP cc_start: 0.8838 (m-30) cc_final: 0.8525 (m-30) REVERT: A 714 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7396 (tm-30) REVERT: A 850 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.8048 (t80) REVERT: A 855 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8426 (t) REVERT: B 356 SER cc_start: 0.8291 (OUTLIER) cc_final: 0.7922 (m) REVERT: B 392 ASP cc_start: 0.9214 (OUTLIER) cc_final: 0.8903 (m-30) REVERT: B 476 GLU cc_start: 0.6617 (pm20) cc_final: 0.6228 (pm20) REVERT: B 583 LYS cc_start: 0.8926 (mtpt) cc_final: 0.8271 (mmtm) REVERT: B 718 GLU cc_start: 0.8271 (tt0) cc_final: 0.7961 (tt0) REVERT: B 733 MET cc_start: 0.8258 (mtp) cc_final: 0.7814 (mtp) REVERT: B 832 ARG cc_start: 0.7824 (ttp80) cc_final: 0.7232 (ptt90) REVERT: D 290 ILE cc_start: 0.7948 (mm) cc_final: 0.7589 (tp) REVERT: D 832 ARG cc_start: 0.7722 (ttp80) cc_final: 0.7189 (ptt90) outliers start: 54 outliers final: 43 residues processed: 258 average time/residue: 0.2808 time to fit residues: 109.4348 Evaluate side-chains 267 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 SER 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 975 THR Chi-restraints excluded: chain A residue 1010 LEU 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 870 ILE 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 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 530 GLN 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 871 LEU Chi-restraints excluded: chain D residue 875 CYS Chi-restraints excluded: chain D residue 975 THR Chi-restraints excluded: chain D residue 1028 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 182 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 198 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 32 optimal weight: 0.0000 chunk 30 optimal weight: 0.0970 chunk 173 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 817 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.163207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.114996 restraints weight = 19160.249| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.50 r_work: 0.2745 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2579 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= 0.132 Angle : 0.543 9.685 23238 Z= 0.273 Chirality : 0.042 0.172 2550 Planarity : 0.004 0.048 2922 Dihedral : 3.842 24.375 2373 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.91 % Allowed : 14.68 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.19), residues: 2037 helix: 2.18 (0.16), residues: 1101 sheet: 0.96 (0.47), residues: 120 loop : 0.02 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 911 HIS 0.003 0.001 HIS B 531 PHE 0.010 0.001 PHE A 415 TYR 0.011 0.001 TYR B 858 ARG 0.003 0.000 ARG A 635 Details of bonding type rmsd link_BETA1-4 : bond 0.00232 ( 3) link_BETA1-4 : angle 1.70146 ( 9) hydrogen bonds : bond 0.03995 ( 867) hydrogen bonds : angle 3.61757 ( 2583) covalent geometry : bond 0.00315 (17064) covalent geometry : angle 0.54213 (23229) ********************** 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 275 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 223 time to evaluate : 1.930 Fit side-chains revert: symmetry clash REVERT: A 356 SER cc_start: 0.8120 (OUTLIER) cc_final: 0.7685 (m) REVERT: A 476 GLU cc_start: 0.6214 (pm20) cc_final: 0.5982 (pm20) REVERT: A 569 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8611 (mp) REVERT: A 612 ASP cc_start: 0.8830 (m-30) cc_final: 0.8513 (m-30) REVERT: A 714 GLN cc_start: 0.7730 (tm-30) cc_final: 0.7382 (tm-30) REVERT: A 850 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.8027 (t80) REVERT: A 855 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8422 (t) REVERT: B 356 SER cc_start: 0.8280 (OUTLIER) cc_final: 0.7902 (m) REVERT: B 392 ASP cc_start: 0.9218 (OUTLIER) cc_final: 0.8898 (m-30) REVERT: B 476 GLU cc_start: 0.6613 (pm20) cc_final: 0.6220 (pm20) REVERT: B 583 LYS cc_start: 0.8935 (mtpt) cc_final: 0.8302 (mmtm) REVERT: B 718 GLU cc_start: 0.8242 (tt0) cc_final: 0.7941 (tt0) REVERT: B 733 MET cc_start: 0.8233 (mtp) cc_final: 0.7745 (mtp) REVERT: B 832 ARG cc_start: 0.7812 (ttp80) cc_final: 0.7258 (ptt90) REVERT: D 290 ILE cc_start: 0.7956 (mm) cc_final: 0.7606 (tp) REVERT: D 832 ARG cc_start: 0.7734 (ttp80) cc_final: 0.7204 (ptt90) outliers start: 52 outliers final: 44 residues processed: 258 average time/residue: 0.2868 time to fit residues: 111.7622 Evaluate side-chains 270 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 220 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 SER 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 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 975 THR Chi-restraints excluded: chain A residue 1010 LEU 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 817 GLN Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 870 ILE 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 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 530 GLN Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 778 GLU 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 975 THR Chi-restraints excluded: chain D residue 1028 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 52 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 55 optimal weight: 0.0170 chunk 119 optimal weight: 3.9990 chunk 154 optimal weight: 0.0270 chunk 201 optimal weight: 8.9990 chunk 113 optimal weight: 0.9980 chunk 100 optimal weight: 0.4980 chunk 99 optimal weight: 0.6980 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 817 GLN ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.164055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.116140 restraints weight = 19134.527| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.51 r_work: 0.2764 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17067 Z= 0.112 Angle : 0.526 9.800 23238 Z= 0.264 Chirality : 0.041 0.171 2550 Planarity : 0.004 0.048 2922 Dihedral : 3.783 24.659 2373 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.86 % Allowed : 14.73 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.19), residues: 2037 helix: 2.23 (0.16), residues: 1101 sheet: 0.97 (0.47), residues: 120 loop : 0.07 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 837 HIS 0.002 0.001 HIS B 531 PHE 0.010 0.001 PHE A 415 TYR 0.010 0.001 TYR B 858 ARG 0.003 0.000 ARG A 720 Details of bonding type rmsd link_BETA1-4 : bond 0.00265 ( 3) link_BETA1-4 : angle 1.58277 ( 9) hydrogen bonds : bond 0.03781 ( 867) hydrogen bonds : angle 3.56006 ( 2583) covalent geometry : bond 0.00253 (17064) covalent geometry : angle 0.52563 (23229) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10777.26 seconds wall clock time: 189 minutes 32.68 seconds (11372.68 seconds total)