Starting phenix.real_space_refine on Sun May 18 05:45:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vht_43241/05_2025/8vht_43241.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vht_43241/05_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_43241/05_2025/8vht_43241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vht_43241/05_2025/8vht_43241.map" model { file = "/net/cci-nas-00/data/ceres_data/8vht_43241/05_2025/8vht_43241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vht_43241/05_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-5687/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: 9.41, per 1000 atoms: 0.57 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: 4.00 Conformation dependent library (CDL) restraints added in 2.0 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: 1.69 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: 5.50 Time building geometry restraints manager: 4.71 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: 4.030 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: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 36.790 Find NCS groups from input model: 0.330 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.220 ------------------------------------------------------------------------------- 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 : 1.706 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: 0.2923 time to fit residues: 105.4724 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 : 1.658 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.165885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.118911 restraints weight = 19118.383| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.52 r_work: 0.2774 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 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 1.90331 ( 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 : 1.659 Fit side-chains REVERT: A 569 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8703 (mp) REVERT: A 850 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7955 (t80) REVERT: B 733 MET cc_start: 0.8207 (mtp) cc_final: 0.7552 (mtp) REVERT: B 832 ARG cc_start: 0.7612 (ttp80) cc_final: 0.7217 (ptt90) REVERT: D 309 ILE cc_start: 0.8330 (mm) cc_final: 0.8097 (mm) REVERT: D 720 ARG cc_start: 0.8823 (ttt90) cc_final: 0.8623 (ttm170) REVERT: D 814 ARG cc_start: 0.6101 (tpt-90) cc_final: 0.5863 (tpt-90) REVERT: D 832 ARG cc_start: 0.7596 (ttp80) cc_final: 0.6998 (ptt90) REVERT: D 870 ILE cc_start: 0.7317 (OUTLIER) cc_final: 0.6970 (mt) outliers start: 42 outliers final: 26 residues processed: 271 average time/residue: 0.2908 time to fit residues: 117.1181 Evaluate side-chains 263 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 1.909 ------------------------------------------------------------------------------- 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: 3.9990 chunk 81 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 87 optimal weight: 0.0770 chunk 152 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.165468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.121102 restraints weight = 19039.421| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.50 r_work: 0.2755 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17067 Z= 0.153 Angle : 0.542 6.471 23238 Z= 0.277 Chirality : 0.043 0.155 2550 Planarity : 0.004 0.045 2922 Dihedral : 4.256 58.542 2373 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.31 % Allowed : 13.00 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.91 (0.19), residues: 2037 helix: 2.14 (0.16), residues: 1089 sheet: 1.26 (0.47), residues: 120 loop : 0.15 (0.22), residues: 828 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 0.012 0.001 PHE B1016 TYR 0.011 0.001 TYR A 288 ARG 0.003 0.000 ARG A 720 Details of bonding type rmsd link_BETA1-4 : bond 0.00178 ( 3) link_BETA1-4 : angle 1.95608 ( 9) hydrogen bonds : bond 0.04500 ( 867) hydrogen bonds : angle 3.75213 ( 2583) covalent geometry : bond 0.00373 (17064) covalent geometry : angle 0.54065 (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: 59 poor density : 249 time to evaluate : 1.946 Fit side-chains revert: symmetry clash REVERT: A 452 MET cc_start: 0.9152 (tpp) cc_final: 0.8880 (tpt) REVERT: A 569 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.8673 (mp) REVERT: A 850 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.8006 (t80) REVERT: A 983 THR cc_start: 0.7594 (OUTLIER) cc_final: 0.6766 (m) REVERT: A 984 LEU cc_start: 0.7991 (tt) cc_final: 0.7629 (tp) REVERT: B 392 ASP cc_start: 0.9152 (OUTLIER) cc_final: 0.8806 (m-30) REVERT: B 396 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8721 (ttt) REVERT: B 714 GLN cc_start: 0.7496 (tp40) cc_final: 0.7246 (tm-30) REVERT: B 718 GLU cc_start: 0.8268 (tt0) cc_final: 0.7973 (tt0) REVERT: B 733 MET cc_start: 0.8266 (mtp) cc_final: 0.7681 (mtp) REVERT: B 832 ARG cc_start: 0.7628 (ttp80) cc_final: 0.7192 (ptt90) REVERT: D 309 ILE cc_start: 0.8272 (mm) cc_final: 0.8041 (mm) REVERT: D 832 ARG cc_start: 0.7639 (ttp80) cc_final: 0.7097 (ptt90) REVERT: D 870 ILE cc_start: 0.7356 (OUTLIER) cc_final: 0.7024 (mt) REVERT: D 924 GLN cc_start: 0.7845 (pt0) cc_final: 0.7252 (mt0) outliers start: 59 outliers final: 36 residues processed: 287 average time/residue: 0.2711 time to fit residues: 118.8739 Evaluate side-chains 276 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 234 time to evaluate : 1.835 ------------------------------------------------------------------------------- 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 645 LEU Chi-restraints excluded: chain D residue 716 SER Chi-restraints excluded: chain D residue 778 GLU Chi-restraints excluded: chain D residue 831 SER Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 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: 0.8980 chunk 186 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 202 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.163311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.114883 restraints weight = 19117.308| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.55 r_work: 0.2722 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1875 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= 0.158 Angle : 0.548 6.681 23238 Z= 0.279 Chirality : 0.043 0.166 2550 Planarity : 0.004 0.047 2922 Dihedral : 4.288 58.658 2373 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.97 % Allowed : 13.73 % Favored : 83.31 % 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: 1.82 (0.19), residues: 2037 helix: 2.05 (0.16), residues: 1095 sheet: 1.16 (0.46), residues: 120 loop : 0.12 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 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 0.004 0.000 ARG D 720 Details of bonding type rmsd link_BETA1-4 : bond 0.00049 ( 3) link_BETA1-4 : angle 1.97294 ( 9) hydrogen bonds : bond 0.04445 ( 867) hydrogen bonds : angle 3.71096 ( 2583) covalent geometry : bond 0.00385 (17064) covalent geometry : angle 0.54671 (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 291 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 238 time to evaluate : 1.774 Fit side-chains revert: symmetry clash REVERT: A 569 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8701 (mp) REVERT: A 850 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.8016 (t80) REVERT: A 855 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8410 (t) REVERT: B 392 ASP cc_start: 0.9180 (OUTLIER) cc_final: 0.8855 (m-30) REVERT: B 396 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8717 (ttt) REVERT: B 714 GLN cc_start: 0.7506 (tp40) cc_final: 0.7269 (tm-30) REVERT: B 718 GLU cc_start: 0.8311 (tt0) cc_final: 0.8013 (tt0) REVERT: B 733 MET cc_start: 0.8239 (mtp) cc_final: 0.7719 (mtp) REVERT: B 832 ARG cc_start: 0.7711 (ttp80) cc_final: 0.7215 (ptt90) REVERT: D 290 ILE cc_start: 0.7810 (mm) cc_final: 0.7439 (tp) REVERT: D 832 ARG cc_start: 0.7669 (ttp80) cc_final: 0.7041 (ptt90) REVERT: D 924 GLN cc_start: 0.7799 (pt0) cc_final: 0.7290 (mt0) outliers start: 53 outliers final: 39 residues processed: 271 average time/residue: 0.2846 time to fit residues: 115.6108 Evaluate side-chains 273 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 229 time to evaluate : 1.677 ------------------------------------------------------------------------------- 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 975 THR Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 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 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 778 GLU Chi-restraints excluded: chain D residue 831 SER Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 975 THR Chi-restraints excluded: chain D residue 1028 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 88 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 HIS A 816 ASN B 817 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.171252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.139421 restraints weight = 18933.510| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.12 r_work: 0.2695 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17067 Z= 0.165 Angle : 0.558 6.706 23238 Z= 0.282 Chirality : 0.043 0.156 2550 Planarity : 0.004 0.048 2922 Dihedral : 4.217 48.976 2373 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.59 % Allowed : 13.28 % Favored : 83.14 % 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: 1.79 (0.19), residues: 2037 helix: 2.02 (0.16), residues: 1107 sheet: 1.11 (0.46), residues: 120 loop : 0.09 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 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 0.004 0.000 ARG A 720 Details of bonding type rmsd link_BETA1-4 : bond 0.00277 ( 3) link_BETA1-4 : angle 1.99315 ( 9) hydrogen bonds : bond 0.04491 ( 867) hydrogen bonds : angle 3.71970 ( 2583) covalent geometry : bond 0.00409 (17064) covalent geometry : angle 0.55685 (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 300 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 236 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 ILE cc_start: 0.8447 (mm) cc_final: 0.8178 (mm) REVERT: A 569 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8682 (mp) REVERT: A 612 ASP cc_start: 0.8782 (m-30) cc_final: 0.8488 (m-30) REVERT: A 850 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.8123 (t80) REVERT: A 855 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8463 (t) REVERT: B 392 ASP cc_start: 0.9207 (OUTLIER) cc_final: 0.8816 (m-30) REVERT: B 396 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8750 (ttt) REVERT: B 718 GLU cc_start: 0.8198 (tt0) cc_final: 0.7851 (tt0) REVERT: B 733 MET cc_start: 0.8288 (mtp) cc_final: 0.7786 (mtp) REVERT: B 832 ARG cc_start: 0.7799 (ttp80) cc_final: 0.7352 (ptt90) REVERT: D 290 ILE cc_start: 0.7737 (mm) cc_final: 0.7361 (tp) REVERT: D 832 ARG cc_start: 0.7767 (ttp80) cc_final: 0.7348 (ptt90) REVERT: D 924 GLN cc_start: 0.7843 (pt0) cc_final: 0.7401 (mt0) outliers start: 64 outliers final: 47 residues processed: 277 average time/residue: 0.2656 time to fit residues: 112.2146 Evaluate side-chains 278 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 226 time to evaluate : 1.774 ------------------------------------------------------------------------------- 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 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 273 MET Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 396 MET 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 B residue 1028 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 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 875 CYS Chi-restraints excluded: chain D residue 904 THR Chi-restraints excluded: chain D residue 975 THR Chi-restraints excluded: chain D residue 1028 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 141 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 120 optimal weight: 0.0370 chunk 183 optimal weight: 1.9990 chunk 179 optimal weight: 0.3980 chunk 112 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 ASN D 605 ASN D 614 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.163904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.115740 restraints weight = 19179.866| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.52 r_work: 0.2748 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2213 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= 0.123 Angle : 0.526 9.610 23238 Z= 0.266 Chirality : 0.042 0.157 2550 Planarity : 0.004 0.048 2922 Dihedral : 4.005 37.733 2373 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.75 % Allowed : 14.68 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.06 (0.16), residues: 1113 sheet: 1.06 (0.46), residues: 120 loop : 0.14 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 911 HIS 0.002 0.001 HIS B 531 PHE 0.011 0.001 PHE A 415 TYR 0.010 0.001 TYR B 858 ARG 0.004 0.000 ARG D 814 Details of bonding type rmsd link_BETA1-4 : bond 0.00119 ( 3) link_BETA1-4 : angle 1.73370 ( 9) hydrogen bonds : bond 0.04015 ( 867) hydrogen bonds : angle 3.59194 ( 2583) covalent geometry : bond 0.00290 (17064) covalent geometry : angle 0.52483 (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 280 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 ILE cc_start: 0.8343 (mm) cc_final: 0.8048 (mm) REVERT: A 329 GLU cc_start: 0.8442 (tt0) cc_final: 0.8236 (pt0) REVERT: A 356 SER cc_start: 0.8135 (t) cc_final: 0.7785 (m) REVERT: A 569 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8587 (mp) REVERT: A 612 ASP cc_start: 0.8772 (m-30) cc_final: 0.8449 (m-30) REVERT: A 850 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.8080 (t80) REVERT: A 855 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8391 (t) REVERT: B 356 SER cc_start: 0.8322 (OUTLIER) cc_final: 0.7953 (m) REVERT: B 392 ASP cc_start: 0.9183 (OUTLIER) cc_final: 0.8858 (m-30) REVERT: B 476 GLU cc_start: 0.6014 (pm20) cc_final: 0.5756 (pm20) REVERT: B 583 LYS cc_start: 0.8894 (mtpt) cc_final: 0.8251 (mmtm) REVERT: B 718 GLU cc_start: 0.8337 (tt0) cc_final: 0.8020 (tt0) REVERT: B 733 MET cc_start: 0.8205 (mtp) cc_final: 0.7679 (mtp) REVERT: B 832 ARG cc_start: 0.7755 (ttp80) cc_final: 0.7115 (ptt90) REVERT: B 837 TRP cc_start: 0.8115 (p90) cc_final: 0.7882 (p90) REVERT: D 290 ILE cc_start: 0.7921 (mm) cc_final: 0.7508 (tp) REVERT: D 832 ARG cc_start: 0.7669 (ttp80) cc_final: 0.7088 (ptt90) outliers start: 49 outliers final: 38 residues processed: 263 average time/residue: 0.2805 time to fit residues: 111.4703 Evaluate side-chains 270 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 227 time to evaluate : 1.879 ------------------------------------------------------------------------------- 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 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 875 CYS Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 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 778 GLU Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 875 CYS Chi-restraints excluded: chain D residue 904 THR Chi-restraints excluded: chain D residue 975 THR Chi-restraints excluded: chain D residue 1028 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 68 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 42 optimal weight: 0.0370 chunk 146 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 179 optimal weight: 0.8980 chunk 174 optimal weight: 0.9990 chunk 110 optimal weight: 0.0030 overall best weight: 0.4868 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.163755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.115417 restraints weight = 19149.852| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.51 r_work: 0.2751 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2332 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= 0.126 Angle : 0.527 7.921 23238 Z= 0.266 Chirality : 0.042 0.166 2550 Planarity : 0.004 0.048 2922 Dihedral : 3.835 23.946 2373 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.19 % Allowed : 13.95 % Favored : 82.86 % 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: 1.91 (0.19), residues: 2037 helix: 2.14 (0.16), residues: 1110 sheet: 1.03 (0.46), residues: 120 loop : 0.14 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 911 HIS 0.002 0.001 HIS B 531 PHE 0.009 0.001 PHE A 415 TYR 0.011 0.001 TYR D 858 ARG 0.005 0.000 ARG A 720 Details of bonding type rmsd link_BETA1-4 : bond 0.00117 ( 3) link_BETA1-4 : angle 1.68864 ( 9) hydrogen bonds : bond 0.03964 ( 867) hydrogen bonds : angle 3.57677 ( 2583) covalent geometry : bond 0.00298 (17064) covalent geometry : angle 0.52593 (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 287 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 230 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 ILE cc_start: 0.8345 (mm) cc_final: 0.8049 (mm) REVERT: A 356 SER cc_start: 0.8158 (t) cc_final: 0.7735 (m) REVERT: A 569 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8640 (mp) REVERT: A 612 ASP cc_start: 0.8761 (m-30) cc_final: 0.8437 (m-30) REVERT: A 714 GLN cc_start: 0.7694 (tm-30) cc_final: 0.7399 (tm-30) REVERT: A 850 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.8014 (t80) REVERT: A 855 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8414 (t) REVERT: B 356 SER cc_start: 0.8311 (OUTLIER) cc_final: 0.7937 (m) REVERT: B 392 ASP cc_start: 0.9191 (OUTLIER) cc_final: 0.8880 (m-30) REVERT: B 583 LYS cc_start: 0.8900 (mtpt) cc_final: 0.8287 (mmtm) REVERT: B 718 GLU cc_start: 0.8238 (tt0) cc_final: 0.7933 (tt0) REVERT: B 733 MET cc_start: 0.8213 (mtp) cc_final: 0.7700 (mtp) REVERT: B 832 ARG cc_start: 0.7779 (ttp80) cc_final: 0.7164 (ptt90) REVERT: D 290 ILE cc_start: 0.7922 (mm) cc_final: 0.7541 (tp) REVERT: D 832 ARG cc_start: 0.7677 (ttp80) cc_final: 0.7103 (ptt90) outliers start: 57 outliers final: 45 residues processed: 267 average time/residue: 0.2823 time to fit residues: 114.9048 Evaluate side-chains 276 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 226 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 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 823 LEU Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 497 MET Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 817 GLN Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 875 CYS Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 530 GLN Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 778 GLU Chi-restraints excluded: chain D residue 831 SER Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 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: 0.7980 chunk 80 optimal weight: 0.3980 chunk 105 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 30 optimal weight: 0.0670 chunk 101 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 592 GLN ** D 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 = 0.3759 r_free = 0.3759 target = 0.163493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.115711 restraints weight = 19054.582| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.49 r_work: 0.2810 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2413 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= 0.140 Angle : 0.536 8.594 23238 Z= 0.271 Chirality : 0.042 0.168 2550 Planarity : 0.004 0.048 2922 Dihedral : 3.846 23.304 2373 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.08 % Allowed : 14.12 % Favored : 82.80 % 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: 1.88 (0.19), residues: 2037 helix: 2.13 (0.16), residues: 1110 sheet: 1.03 (0.46), residues: 120 loop : 0.09 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 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 0.004 0.000 ARG A 720 Details of bonding type rmsd link_BETA1-4 : bond 0.00075 ( 3) link_BETA1-4 : angle 1.71090 ( 9) hydrogen bonds : bond 0.04080 ( 867) hydrogen bonds : angle 3.60764 ( 2583) covalent geometry : bond 0.00339 (17064) covalent geometry : angle 0.53538 (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 275 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 220 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 ILE cc_start: 0.8346 (mm) cc_final: 0.8051 (mm) REVERT: A 356 SER cc_start: 0.8158 (OUTLIER) cc_final: 0.7752 (m) REVERT: A 569 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8647 (mp) REVERT: A 612 ASP cc_start: 0.8765 (m-30) cc_final: 0.8435 (m-30) REVERT: A 714 GLN cc_start: 0.7710 (tm-30) cc_final: 0.7392 (tm-30) REVERT: A 850 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.7997 (t80) REVERT: A 855 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8434 (t) REVERT: B 356 SER cc_start: 0.8332 (OUTLIER) cc_final: 0.7960 (m) REVERT: B 392 ASP cc_start: 0.9210 (OUTLIER) cc_final: 0.8869 (m-30) REVERT: B 476 GLU cc_start: 0.6138 (pm20) cc_final: 0.5838 (pm20) REVERT: B 583 LYS cc_start: 0.8902 (mtpt) cc_final: 0.8303 (mmtm) REVERT: B 718 GLU cc_start: 0.8290 (tt0) cc_final: 0.7973 (tt0) REVERT: B 733 MET cc_start: 0.8227 (mtp) cc_final: 0.7723 (mtp) REVERT: B 832 ARG cc_start: 0.7775 (ttp80) cc_final: 0.7194 (ptt90) REVERT: D 290 ILE cc_start: 0.7925 (mm) cc_final: 0.7550 (tp) REVERT: D 832 ARG cc_start: 0.7704 (ttp80) cc_final: 0.7142 (ptt90) outliers start: 55 outliers final: 43 residues processed: 259 average time/residue: 0.2765 time to fit residues: 109.3753 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 : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 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 273 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 497 MET Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 875 CYS Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 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 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 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: 0.6980 chunk 68 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 32 optimal weight: 0.3980 chunk 179 optimal weight: 0.3980 chunk 122 optimal weight: 0.1980 chunk 154 optimal weight: 0.0030 chunk 24 optimal weight: 0.4980 chunk 43 optimal weight: 0.0770 chunk 18 optimal weight: 1.9990 overall best weight: 0.2148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 GLN ** D 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 = 0.3781 r_free = 0.3781 target = 0.165479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.117463 restraints weight = 19203.059| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.54 r_work: 0.2770 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17067 Z= 0.107 Angle : 0.515 9.464 23238 Z= 0.259 Chirality : 0.041 0.163 2550 Planarity : 0.004 0.047 2922 Dihedral : 3.682 24.146 2373 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.52 % Allowed : 14.90 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.03 (0.19), residues: 2037 helix: 2.25 (0.16), residues: 1107 sheet: 1.08 (0.47), residues: 120 loop : 0.17 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 911 HIS 0.002 0.000 HIS B 531 PHE 0.009 0.001 PHE A 415 TYR 0.010 0.001 TYR D 858 ARG 0.005 0.000 ARG D 720 Details of bonding type rmsd link_BETA1-4 : bond 0.00254 ( 3) link_BETA1-4 : angle 1.48702 ( 9) hydrogen bonds : bond 0.03580 ( 867) hydrogen bonds : angle 3.47879 ( 2583) covalent geometry : bond 0.00240 (17064) covalent geometry : angle 0.51403 (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 266 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 1.721 Fit side-chains revert: symmetry clash REVERT: A 313 ILE cc_start: 0.8314 (mm) cc_final: 0.8003 (mm) REVERT: A 356 SER cc_start: 0.7969 (t) cc_final: 0.7568 (m) REVERT: A 509 ASP cc_start: 0.8847 (p0) cc_final: 0.8526 (p0) REVERT: A 612 ASP cc_start: 0.8793 (m-30) cc_final: 0.8476 (m-30) REVERT: A 714 GLN cc_start: 0.7712 (tm-30) cc_final: 0.7358 (tm-30) REVERT: A 850 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.8007 (t80) REVERT: A 855 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8396 (t) REVERT: B 356 SER cc_start: 0.8169 (t) cc_final: 0.7843 (m) REVERT: B 392 ASP cc_start: 0.9134 (OUTLIER) cc_final: 0.8879 (m-30) REVERT: B 476 GLU cc_start: 0.6146 (pm20) cc_final: 0.5844 (pm20) REVERT: B 583 LYS cc_start: 0.8961 (mtpt) cc_final: 0.8309 (mmtm) REVERT: B 718 GLU cc_start: 0.8258 (tt0) cc_final: 0.7957 (tt0) REVERT: B 733 MET cc_start: 0.8272 (mtp) cc_final: 0.7760 (mtp) REVERT: B 832 ARG cc_start: 0.7739 (ttp80) cc_final: 0.7096 (ptt90) REVERT: D 290 ILE cc_start: 0.7959 (mm) cc_final: 0.7578 (tp) REVERT: D 832 ARG cc_start: 0.7651 (ttp80) cc_final: 0.7128 (ptt90) outliers start: 45 outliers final: 40 residues processed: 251 average time/residue: 0.2735 time to fit residues: 105.2813 Evaluate side-chains 258 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 215 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 392 ASP 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 823 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 875 CYS Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 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 778 GLU Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 875 CYS Chi-restraints excluded: chain D residue 904 THR Chi-restraints excluded: chain D residue 975 THR 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: 0.7980 chunk 1 optimal weight: 0.4980 chunk 198 optimal weight: 10.0000 chunk 37 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 32 optimal weight: 0.0370 chunk 30 optimal weight: 0.4980 chunk 173 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 924 GLN ** D 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 = 0.3769 r_free = 0.3769 target = 0.164368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.116778 restraints weight = 19143.693| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.52 r_work: 0.2762 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 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= 0.124 Angle : 0.530 8.972 23238 Z= 0.266 Chirality : 0.042 0.175 2550 Planarity : 0.004 0.048 2922 Dihedral : 3.682 24.196 2373 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.63 % Allowed : 14.57 % Favored : 82.80 % 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: 2.01 (0.19), residues: 2037 helix: 2.21 (0.16), residues: 1113 sheet: 1.10 (0.47), residues: 120 loop : 0.17 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 837 HIS 0.002 0.001 HIS B 531 PHE 0.010 0.001 PHE A 415 TYR 0.011 0.001 TYR D 858 ARG 0.006 0.000 ARG D 814 Details of bonding type rmsd link_BETA1-4 : bond 0.00192 ( 3) link_BETA1-4 : angle 1.57857 ( 9) hydrogen bonds : bond 0.03796 ( 867) hydrogen bonds : angle 3.52801 ( 2583) covalent geometry : bond 0.00295 (17064) covalent geometry : angle 0.52874 (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 265 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 218 time to evaluate : 1.685 Fit side-chains revert: symmetry clash REVERT: A 313 ILE cc_start: 0.8354 (mm) cc_final: 0.8044 (mm) REVERT: A 356 SER cc_start: 0.8038 (OUTLIER) cc_final: 0.7628 (m) REVERT: A 476 GLU cc_start: 0.6163 (pm20) cc_final: 0.5881 (pm20) REVERT: A 509 ASP cc_start: 0.8844 (p0) cc_final: 0.8490 (p0) REVERT: A 612 ASP cc_start: 0.8750 (m-30) cc_final: 0.8429 (m-30) REVERT: A 714 GLN cc_start: 0.7720 (tm-30) cc_final: 0.7368 (tm-30) REVERT: A 850 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7989 (t80) REVERT: A 855 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8445 (t) REVERT: B 356 SER cc_start: 0.8156 (t) cc_final: 0.7804 (m) REVERT: B 392 ASP cc_start: 0.9108 (OUTLIER) cc_final: 0.8819 (m-30) REVERT: B 476 GLU cc_start: 0.6219 (pm20) cc_final: 0.5942 (pm20) REVERT: B 583 LYS cc_start: 0.8940 (mtpt) cc_final: 0.8280 (mmtm) REVERT: B 718 GLU cc_start: 0.8271 (tt0) cc_final: 0.7988 (tt0) REVERT: B 733 MET cc_start: 0.8218 (mtp) cc_final: 0.7719 (mtp) REVERT: B 832 ARG cc_start: 0.7801 (ttp80) cc_final: 0.7228 (ptt90) REVERT: D 290 ILE cc_start: 0.7945 (mm) cc_final: 0.7556 (tp) REVERT: D 832 ARG cc_start: 0.7650 (ttp80) cc_final: 0.7160 (ptt90) outliers start: 47 outliers final: 42 residues processed: 251 average time/residue: 0.2754 time to fit residues: 104.6285 Evaluate side-chains 264 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 218 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 497 MET Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 875 CYS Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 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 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 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: 0.8980 chunk 28 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 30 optimal weight: 0.0370 chunk 55 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 201 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 605 ASN ** D 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 = 0.3853 r_free = 0.3853 target = 0.171205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.131722 restraints weight = 18818.079| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.37 r_work: 0.2790 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17067 Z= 0.156 Angle : 0.562 9.442 23238 Z= 0.284 Chirality : 0.043 0.176 2550 Planarity : 0.004 0.047 2922 Dihedral : 3.846 24.503 2373 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.91 % Allowed : 14.40 % 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: 1.95 (0.19), residues: 2037 helix: 2.24 (0.16), residues: 1101 sheet: 1.07 (0.46), residues: 120 loop : 0.04 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 837 HIS 0.003 0.001 HIS B 531 PHE 0.009 0.001 PHE A 415 TYR 0.013 0.001 TYR D 858 ARG 0.004 0.000 ARG A 720 Details of bonding type rmsd link_BETA1-4 : bond 0.00126 ( 3) link_BETA1-4 : angle 1.83291 ( 9) hydrogen bonds : bond 0.04278 ( 867) hydrogen bonds : angle 3.66052 ( 2583) covalent geometry : bond 0.00383 (17064) covalent geometry : angle 0.56131 (23229) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8825.14 seconds wall clock time: 153 minutes 26.27 seconds (9206.27 seconds total)