Starting phenix.real_space_refine on Fri May 23 22:39:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gs6_34221/05_2025/8gs6_34221.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gs6_34221/05_2025/8gs6_34221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gs6_34221/05_2025/8gs6_34221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gs6_34221/05_2025/8gs6_34221.map" model { file = "/net/cci-nas-00/data/ceres_data/8gs6_34221/05_2025/8gs6_34221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gs6_34221/05_2025/8gs6_34221.cif" } resolution = 2.86 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= 0.017 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 114 5.16 5 C 15679 2.51 5 N 4031 2.21 5 O 4714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24538 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 8420 Classifications: {'peptide': 1075} Link IDs: {'PTRANS': 54, 'TRANS': 1020} Chain breaks: 5 Chain: "B" Number of atoms: 7696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7696 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 51, 'TRANS': 930} Chain breaks: 10 Chain: "C" Number of atoms: 7848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7848 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 50, 'TRANS': 950} Chain breaks: 8 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 13.95, per 1000 atoms: 0.57 Number of scatterers: 24538 At special positions: 0 Unit cell: (134.67, 135.675, 165.825, 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 114 16.00 O 4714 8.00 N 4031 7.00 C 15679 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1134 " " NAG A1308 " - " ASN A 234 " " NAG A1309 " - " ASN A 122 " " NAG A1310 " - " ASN A 165 " " NAG A1311 " - " ASN A 282 " " NAG A1312 " - " ASN A1098 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B1074 " " NAG B1305 " - " ASN B1134 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B1098 " " NAG B1309 " - " ASN B 801 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1134 " " NAG C1309 " - " ASN C 234 " " NAG C1310 " - " ASN C1098 " " NAG D 1 " - " ASN A 801 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN C 717 " " NAG H 1 " - " ASN C 801 " Time building additional restraints: 5.72 Conformation dependent library (CDL) restraints added in 2.9 seconds 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5732 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 51 sheets defined 26.7% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.711A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.693A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.634A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.641A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 630 through 636 removed outlier: 4.080A pdb=" N TYR A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.664A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 837 through 843 Processing helix chain 'A' and resid 844 through 847 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.812A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.633A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.381A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.766A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.549A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.085A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.861A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.876A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.588A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.203A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.930A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 760 removed outlier: 7.864A pdb=" N SER B 758 " --> pdb=" O GLN B 755 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE B 759 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS B 760 " --> pdb=" O GLY B 757 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 755 through 760' Processing helix chain 'B' and resid 761 through 783 removed outlier: 3.701A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.384A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.675A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.917A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.534A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.714A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.488A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.740A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 Processing helix chain 'C' and resid 811 through 815 removed outlier: 3.514A pdb=" N ARG C 815 " --> pdb=" O PRO C 812 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.577A pdb=" N PHE C 855 " --> pdb=" O CYS C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.616A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 890' Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 940 removed outlier: 3.760A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.569A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 30 removed outlier: 8.212A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.439A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.975A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 279 removed outlier: 7.145A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.081A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.712A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.744A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.623A pdb=" N PHE A 541 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 553 through 554 removed outlier: 3.716A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.995A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.710A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 717 through 722 Processing sheet with id=AB7, first strand: chain 'A' and resid 717 through 722 removed outlier: 5.895A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.738A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.612A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AC2, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.535A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 224 through 229 removed outlier: 7.532A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 169 through 172 removed outlier: 3.598A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.405A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.621A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 539 through 543 removed outlier: 3.553A pdb=" N PHE B 541 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.727A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.661A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.194A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.598A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.532A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 104 through 107 removed outlier: 3.598A pdb=" N GLN C 239 " --> pdb=" O ILE C 105 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 118 through 121 removed outlier: 3.676A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.536A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.646A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE8, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 539 through 543 removed outlier: 3.735A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.007A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 713 removed outlier: 4.442A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 722 Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 722 removed outlier: 7.314A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.737A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.117A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 946 hydrogen bonds defined for protein. 2544 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: 10.39 Time building geometry restraints manager: 6.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7760 1.34 - 1.47: 6440 1.47 - 1.60: 10758 1.60 - 1.72: 0 1.72 - 1.85: 142 Bond restraints: 25100 Sorted by residual: bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.502 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C1 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.62e+00 bond pdb=" C1 NAG D 1 " pdb=" C2 NAG D 1 " ideal model delta sigma weight residual 1.532 1.487 0.045 2.00e-02 2.50e+03 4.98e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.12e+00 ... (remaining 25095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 33361 1.85 - 3.69: 688 3.69 - 5.54: 72 5.54 - 7.39: 11 7.39 - 9.24: 6 Bond angle restraints: 34138 Sorted by residual: angle pdb=" C THR C 716 " pdb=" N ASN C 717 " pdb=" CA ASN C 717 " ideal model delta sigma weight residual 121.75 129.71 -7.96 1.73e+00 3.34e-01 2.12e+01 angle pdb=" N GLY C1099 " pdb=" CA GLY C1099 " pdb=" C GLY C1099 " ideal model delta sigma weight residual 113.18 103.94 9.24 2.37e+00 1.78e-01 1.52e+01 angle pdb=" CB ASN C 717 " pdb=" CG ASN C 717 " pdb=" ND2 ASN C 717 " ideal model delta sigma weight residual 116.40 110.75 5.65 1.50e+00 4.44e-01 1.42e+01 angle pdb=" C ASN A1134 " pdb=" CA ASN A1134 " pdb=" CB ASN A1134 " ideal model delta sigma weight residual 109.80 115.69 -5.89 1.64e+00 3.72e-01 1.29e+01 angle pdb=" CA ASN C 717 " pdb=" CB ASN C 717 " pdb=" CG ASN C 717 " ideal model delta sigma weight residual 112.60 116.08 -3.48 1.00e+00 1.00e+00 1.21e+01 ... (remaining 34133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 13823 17.96 - 35.91: 1294 35.91 - 53.87: 246 53.87 - 71.82: 88 71.82 - 89.78: 25 Dihedral angle restraints: 15476 sinusoidal: 6570 harmonic: 8906 Sorted by residual: dihedral pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " pdb=" SG CYS A 851 " pdb=" CB CYS A 851 " ideal model delta sinusoidal sigma weight residual -86.00 -168.41 82.41 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual -86.00 -9.59 -76.41 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -150.60 64.60 1 1.00e+01 1.00e-02 5.48e+01 ... (remaining 15473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 3967 0.165 - 0.331: 15 0.331 - 0.496: 1 0.496 - 0.662: 0 0.662 - 0.827: 4 Chirality restraints: 3987 Sorted by residual: chirality pdb=" C1 NAG B1309 " pdb=" ND2 ASN B 801 " pdb=" C2 NAG B1309 " pdb=" O5 NAG B1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" C1 NAG C1310 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG C1310 " pdb=" O5 NAG C1310 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.55e+01 ... (remaining 3984 not shown) Planarity restraints: 4380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 717 " -0.052 2.00e-02 2.50e+03 5.48e-02 3.75e+01 pdb=" CG ASN C 717 " 0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN C 717 " -0.032 2.00e-02 2.50e+03 pdb=" ND2 ASN C 717 " 0.052 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1098 " 0.003 2.00e-02 2.50e+03 4.21e-02 2.22e+01 pdb=" CG ASN B1098 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN B1098 " -0.049 2.00e-02 2.50e+03 pdb=" ND2 ASN B1098 " 0.051 2.00e-02 2.50e+03 pdb=" C1 NAG B1308 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 717 " -0.019 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" CG ASN C 717 " 0.067 2.00e-02 2.50e+03 pdb=" OD1 ASN C 717 " -0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN C 717 " -0.021 2.00e-02 2.50e+03 ... (remaining 4377 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 628 2.69 - 3.24: 23049 3.24 - 3.80: 35295 3.80 - 4.35: 45824 4.35 - 4.90: 79734 Nonbonded interactions: 184530 Sorted by model distance: nonbonded pdb=" NE2 GLN C 804 " pdb=" OE1 GLN C 935 " model vdw 2.140 3.120 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.167 3.040 nonbonded pdb=" OD1 ASP A 142 " pdb=" OG SER A 155 " model vdw 2.169 3.040 nonbonded pdb=" OD1 ASN B 801 " pdb=" N2 NAG B1309 " model vdw 2.170 3.120 nonbonded pdb=" NE2 HIS A 625 " pdb=" OE1 GLN A 628 " model vdw 2.173 3.120 ... (remaining 184525 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 65 or resid 87 through 95 or resid 102 through \ 109 or resid 116 through 137 or resid 166 through 210 or resid 216 through 243 o \ r resid 264 through 618 or resid 632 through 675 or resid 690 through 827 or res \ id 848 through 1139 or resid 1301 through 1309)) selection = (chain 'B' and (resid 25 through 137 or resid 166 through 618 or resid 632 throu \ gh 1139 or resid 1301 through 1309)) selection = (chain 'C' and (resid 25 through 65 or resid 87 through 95 or resid 102 through \ 109 or resid 116 through 210 or resid 216 through 262 or resid 264 through 618 o \ r resid 632 through 675 or resid 690 through 827 or resid 848 through 1139 or re \ sid 1301 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 2.770 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: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 54.020 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 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 : 0.004 0.096 25181 Z= 0.186 Angle : 0.714 22.766 34341 Z= 0.343 Chirality : 0.054 0.827 3987 Planarity : 0.004 0.067 4344 Dihedral : 14.844 89.776 9624 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 3006 helix: 2.19 (0.20), residues: 706 sheet: -0.07 (0.21), residues: 647 loop : -1.59 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 886 HIS 0.010 0.001 HIS B1101 PHE 0.035 0.002 PHE A 906 TYR 0.023 0.001 TYR C 756 ARG 0.005 0.001 ARG A 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00748 ( 36) link_NAG-ASN : angle 6.00441 ( 108) link_BETA1-4 : bond 0.00812 ( 5) link_BETA1-4 : angle 3.14306 ( 15) hydrogen bonds : bond 0.19968 ( 934) hydrogen bonds : angle 7.24923 ( 2544) SS BOND : bond 0.00541 ( 40) SS BOND : angle 1.95623 ( 80) covalent geometry : bond 0.00413 (25100) covalent geometry : angle 0.62139 (34138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8851 (tpt) cc_final: 0.8565 (tpp) REVERT: C 389 ASP cc_start: 0.7586 (m-30) cc_final: 0.7371 (OUTLIER) REVERT: C 474 GLN cc_start: 0.6919 (pp30) cc_final: 0.6664 (pm20) outliers start: 0 outliers final: 1 residues processed: 150 average time/residue: 1.3708 time to fit residues: 237.5363 Evaluate side-chains 100 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 257 optimal weight: 0.0770 chunk 231 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 239 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 177 optimal weight: 0.0070 chunk 276 optimal weight: 0.5980 overall best weight: 0.9158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN B 125 ASN B 439 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS C 125 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.106228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.076665 restraints weight = 52976.108| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.04 r_work: 0.3074 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25181 Z= 0.129 Angle : 0.649 16.547 34341 Z= 0.323 Chirality : 0.048 0.468 3987 Planarity : 0.004 0.053 4344 Dihedral : 7.663 59.952 4139 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.79 % Allowed : 5.69 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 3006 helix: 2.20 (0.20), residues: 699 sheet: 0.37 (0.21), residues: 655 loop : -1.55 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 886 HIS 0.005 0.001 HIS A1083 PHE 0.017 0.001 PHE B 906 TYR 0.025 0.001 TYR B 170 ARG 0.004 0.000 ARG A 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00766 ( 36) link_NAG-ASN : angle 4.71159 ( 108) link_BETA1-4 : bond 0.00584 ( 5) link_BETA1-4 : angle 1.63691 ( 15) hydrogen bonds : bond 0.05688 ( 934) hydrogen bonds : angle 5.52938 ( 2544) SS BOND : bond 0.00420 ( 40) SS BOND : angle 1.59449 ( 80) covalent geometry : bond 0.00284 (25100) covalent geometry : angle 0.58835 (34138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 3.007 Fit side-chains revert: symmetry clash REVERT: A 740 MET cc_start: 0.9316 (tpt) cc_final: 0.9038 (tpp) REVERT: B 1101 HIS cc_start: 0.7753 (OUTLIER) cc_final: 0.7500 (t-170) REVERT: C 170 TYR cc_start: 0.6940 (t80) cc_final: 0.6644 (t80) REVERT: C 389 ASP cc_start: 0.8195 (m-30) cc_final: 0.7475 (OUTLIER) REVERT: C 474 GLN cc_start: 0.6750 (pp30) cc_final: 0.6497 (pm20) REVERT: C 489 TYR cc_start: 0.7436 (m-80) cc_final: 0.7038 (m-80) REVERT: C 759 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.6926 (m-10) REVERT: C 900 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7488 (mtt) outliers start: 21 outliers final: 5 residues processed: 124 average time/residue: 1.3581 time to fit residues: 197.4892 Evaluate side-chains 108 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 242 optimal weight: 0.6980 chunk 276 optimal weight: 6.9990 chunk 171 optimal weight: 0.0020 chunk 145 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 228 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A1010 GLN B 422 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 394 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.105405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.075658 restraints weight = 52826.575| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.03 r_work: 0.3041 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25181 Z= 0.144 Angle : 0.623 15.661 34341 Z= 0.311 Chirality : 0.047 0.411 3987 Planarity : 0.004 0.052 4344 Dihedral : 7.193 59.452 4139 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.12 % Allowed : 8.23 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 3006 helix: 2.15 (0.20), residues: 697 sheet: 0.33 (0.20), residues: 674 loop : -1.53 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 886 HIS 0.004 0.001 HIS B1058 PHE 0.020 0.001 PHE B 906 TYR 0.017 0.001 TYR B 170 ARG 0.004 0.000 ARG A 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00648 ( 36) link_NAG-ASN : angle 4.27809 ( 108) link_BETA1-4 : bond 0.00799 ( 5) link_BETA1-4 : angle 1.70243 ( 15) hydrogen bonds : bond 0.05670 ( 934) hydrogen bonds : angle 5.19615 ( 2544) SS BOND : bond 0.00390 ( 40) SS BOND : angle 1.68978 ( 80) covalent geometry : bond 0.00334 (25100) covalent geometry : angle 0.56971 (34138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.9333 (tpt) cc_final: 0.9021 (tpp) REVERT: C 170 TYR cc_start: 0.7034 (t80) cc_final: 0.6794 (t80) REVERT: C 389 ASP cc_start: 0.8178 (m-30) cc_final: 0.7429 (OUTLIER) REVERT: C 489 TYR cc_start: 0.7454 (m-80) cc_final: 0.7077 (m-80) REVERT: C 759 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7186 (m-10) outliers start: 30 outliers final: 11 residues processed: 127 average time/residue: 1.2976 time to fit residues: 193.3898 Evaluate side-chains 109 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 83 optimal weight: 0.5980 chunk 197 optimal weight: 3.9990 chunk 172 optimal weight: 0.0370 chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 0.0970 chunk 279 optimal weight: 3.9990 chunk 259 optimal weight: 0.0570 chunk 267 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 1 optimal weight: 0.0370 overall best weight: 0.1652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 394 ASN B 474 GLN B1101 HIS C 125 ASN C 409 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.108545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.079158 restraints weight = 53155.231| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.05 r_work: 0.3133 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25181 Z= 0.102 Angle : 0.574 14.654 34341 Z= 0.282 Chirality : 0.045 0.381 3987 Planarity : 0.004 0.050 4344 Dihedral : 6.684 56.852 4139 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.90 % Allowed : 10.03 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 3006 helix: 2.44 (0.20), residues: 695 sheet: 0.61 (0.21), residues: 644 loop : -1.44 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.008 0.000 HIS B1101 PHE 0.012 0.001 PHE B 175 TYR 0.020 0.001 TYR C1138 ARG 0.003 0.000 ARG A 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00755 ( 36) link_NAG-ASN : angle 4.04416 ( 108) link_BETA1-4 : bond 0.00775 ( 5) link_BETA1-4 : angle 1.62302 ( 15) hydrogen bonds : bond 0.04133 ( 934) hydrogen bonds : angle 4.82287 ( 2544) SS BOND : bond 0.00297 ( 40) SS BOND : angle 1.20397 ( 80) covalent geometry : bond 0.00205 (25100) covalent geometry : angle 0.52449 (34138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 2.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 CYS cc_start: 0.4446 (m) cc_final: 0.4235 (m) REVERT: B 346 ARG cc_start: 0.7411 (mmp-170) cc_final: 0.7154 (mmm160) REVERT: B 474 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7829 (pp30) REVERT: B 979 ASP cc_start: 0.8285 (m-30) cc_final: 0.7911 (t0) REVERT: C 170 TYR cc_start: 0.6868 (t80) cc_final: 0.6515 (t80) REVERT: C 389 ASP cc_start: 0.8118 (m-30) cc_final: 0.7393 (t0) REVERT: C 489 TYR cc_start: 0.7407 (m-80) cc_final: 0.7090 (m-80) REVERT: C 759 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.6904 (m-10) outliers start: 24 outliers final: 7 residues processed: 129 average time/residue: 1.2728 time to fit residues: 194.7968 Evaluate side-chains 109 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 2.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 759 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 189 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 210 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 253 optimal weight: 0.9980 chunk 185 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1101 HIS C 125 ASN C 271 GLN C 804 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.106027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.076204 restraints weight = 53197.362| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.04 r_work: 0.3074 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25181 Z= 0.142 Angle : 0.600 14.699 34341 Z= 0.298 Chirality : 0.046 0.359 3987 Planarity : 0.004 0.053 4344 Dihedral : 6.655 58.984 4139 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.27 % Allowed : 10.89 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.15), residues: 3006 helix: 2.23 (0.20), residues: 706 sheet: 0.53 (0.21), residues: 646 loop : -1.40 (0.14), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 886 HIS 0.009 0.001 HIS B1101 PHE 0.015 0.001 PHE B 906 TYR 0.018 0.001 TYR C1138 ARG 0.004 0.000 ARG A1091 Details of bonding type rmsd link_NAG-ASN : bond 0.00623 ( 36) link_NAG-ASN : angle 4.02490 ( 108) link_BETA1-4 : bond 0.00631 ( 5) link_BETA1-4 : angle 1.49714 ( 15) hydrogen bonds : bond 0.05214 ( 934) hydrogen bonds : angle 4.90726 ( 2544) SS BOND : bond 0.00462 ( 40) SS BOND : angle 1.67951 ( 80) covalent geometry : bond 0.00334 (25100) covalent geometry : angle 0.55124 (34138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8051 (tpp-160) REVERT: A 590 CYS cc_start: 0.4616 (m) cc_final: 0.4368 (m) REVERT: B 117 LEU cc_start: 0.8039 (tm) cc_final: 0.7751 (tt) REVERT: B 346 ARG cc_start: 0.7433 (mmp-170) cc_final: 0.7168 (mmm160) REVERT: C 170 TYR cc_start: 0.6921 (t80) cc_final: 0.6698 (t80) REVERT: C 389 ASP cc_start: 0.8224 (m-30) cc_final: 0.7489 (t0) REVERT: C 458 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8741 (pptt) REVERT: C 489 TYR cc_start: 0.7414 (m-80) cc_final: 0.7132 (m-80) REVERT: C 759 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7129 (m-10) outliers start: 34 outliers final: 13 residues processed: 125 average time/residue: 1.1705 time to fit residues: 174.2058 Evaluate side-chains 113 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 759 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 7 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 294 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 266 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 226 optimal weight: 0.3980 chunk 121 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN B 339 HIS B1101 HIS C 125 ASN C 644 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.103309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.073174 restraints weight = 53129.159| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.04 r_work: 0.2994 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25181 Z= 0.225 Angle : 0.675 15.082 34341 Z= 0.338 Chirality : 0.049 0.358 3987 Planarity : 0.004 0.054 4344 Dihedral : 6.879 59.904 4139 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.50 % Allowed : 11.75 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 3006 helix: 1.98 (0.20), residues: 696 sheet: 0.30 (0.20), residues: 681 loop : -1.55 (0.14), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 886 HIS 0.008 0.001 HIS B1101 PHE 0.026 0.002 PHE B 906 TYR 0.018 0.002 TYR A 266 ARG 0.005 0.000 ARG A 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00599 ( 36) link_NAG-ASN : angle 4.17155 ( 108) link_BETA1-4 : bond 0.00536 ( 5) link_BETA1-4 : angle 1.36610 ( 15) hydrogen bonds : bond 0.06671 ( 934) hydrogen bonds : angle 5.17814 ( 2544) SS BOND : bond 0.00539 ( 40) SS BOND : angle 1.91945 ( 80) covalent geometry : bond 0.00549 (25100) covalent geometry : angle 0.62743 (34138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 2.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8055 (tpp-160) REVERT: A 590 CYS cc_start: 0.4756 (m) cc_final: 0.4555 (m) REVERT: B 117 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7777 (tt) REVERT: C 170 TYR cc_start: 0.7036 (t80) cc_final: 0.6774 (t80) REVERT: C 389 ASP cc_start: 0.8293 (m-30) cc_final: 0.7568 (OUTLIER) REVERT: C 489 TYR cc_start: 0.7421 (m-80) cc_final: 0.7123 (m-80) REVERT: C 493 GLN cc_start: 0.7206 (tm-30) cc_final: 0.6386 (tm-30) REVERT: C 759 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7570 (m-10) outliers start: 40 outliers final: 17 residues processed: 131 average time/residue: 1.2606 time to fit residues: 195.0770 Evaluate side-chains 113 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 759 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 98 optimal weight: 0.7980 chunk 247 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 282 optimal weight: 0.7980 chunk 284 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 278 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 272 optimal weight: 0.8980 chunk 303 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1101 HIS C 125 ASN C 271 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.105102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.075282 restraints weight = 53242.062| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.04 r_work: 0.3034 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25181 Z= 0.127 Angle : 0.611 15.447 34341 Z= 0.303 Chirality : 0.046 0.354 3987 Planarity : 0.004 0.053 4344 Dihedral : 6.670 59.190 4139 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.08 % Allowed : 12.94 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.15), residues: 3006 helix: 2.15 (0.20), residues: 701 sheet: 0.36 (0.20), residues: 652 loop : -1.48 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 886 HIS 0.004 0.001 HIS B1101 PHE 0.011 0.001 PHE B1121 TYR 0.013 0.001 TYR A1067 ARG 0.003 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00638 ( 36) link_NAG-ASN : angle 4.04844 ( 108) link_BETA1-4 : bond 0.00629 ( 5) link_BETA1-4 : angle 1.37627 ( 15) hydrogen bonds : bond 0.05340 ( 934) hydrogen bonds : angle 4.92126 ( 2544) SS BOND : bond 0.00429 ( 40) SS BOND : angle 1.61369 ( 80) covalent geometry : bond 0.00291 (25100) covalent geometry : angle 0.56301 (34138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8170 (tpp-160) REVERT: A 590 CYS cc_start: 0.4799 (m) cc_final: 0.4535 (m) REVERT: B 117 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7760 (tt) REVERT: B 346 ARG cc_start: 0.7459 (mmp-170) cc_final: 0.7206 (mmm160) REVERT: B 979 ASP cc_start: 0.8360 (m-30) cc_final: 0.7905 (t0) REVERT: C 170 TYR cc_start: 0.6934 (t80) cc_final: 0.6666 (t80) REVERT: C 389 ASP cc_start: 0.8190 (m-30) cc_final: 0.7521 (t0) REVERT: C 489 TYR cc_start: 0.7346 (m-80) cc_final: 0.7060 (m-80) REVERT: C 493 GLN cc_start: 0.7062 (tm-30) cc_final: 0.6327 (tm-30) REVERT: C 759 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7476 (m-10) outliers start: 29 outliers final: 18 residues processed: 122 average time/residue: 1.2497 time to fit residues: 179.9223 Evaluate side-chains 117 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 759 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 96 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 chunk 49 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 233 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1101 HIS C 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.104425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.074479 restraints weight = 53051.440| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.04 r_work: 0.3041 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 0.050 25181 Z= 0.157 Angle : 0.628 14.761 34341 Z= 0.312 Chirality : 0.047 0.345 3987 Planarity : 0.004 0.054 4344 Dihedral : 6.638 59.605 4139 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.31 % Allowed : 13.32 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.15), residues: 3006 helix: 2.09 (0.20), residues: 701 sheet: 0.40 (0.20), residues: 672 loop : -1.52 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 886 HIS 0.004 0.001 HIS B1101 PHE 0.014 0.001 PHE B 906 TYR 0.024 0.001 TYR C1138 ARG 0.003 0.000 ARG A 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00611 ( 36) link_NAG-ASN : angle 4.03407 ( 108) link_BETA1-4 : bond 0.00593 ( 5) link_BETA1-4 : angle 1.33566 ( 15) hydrogen bonds : bond 0.05698 ( 934) hydrogen bonds : angle 4.94895 ( 2544) SS BOND : bond 0.00442 ( 40) SS BOND : angle 1.69752 ( 80) covalent geometry : bond 0.00375 (25100) covalent geometry : angle 0.58106 (34138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8174 (tpp-160) REVERT: A 590 CYS cc_start: 0.4775 (m) cc_final: 0.4527 (m) REVERT: B 117 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7799 (tt) REVERT: B 346 ARG cc_start: 0.7479 (mmp-170) cc_final: 0.7220 (mmm160) REVERT: B 979 ASP cc_start: 0.8380 (m-30) cc_final: 0.7946 (t0) REVERT: C 170 TYR cc_start: 0.7056 (t80) cc_final: 0.6811 (t80) REVERT: C 389 ASP cc_start: 0.8211 (m-30) cc_final: 0.7567 (t0) REVERT: C 489 TYR cc_start: 0.7366 (m-80) cc_final: 0.7096 (m-80) REVERT: C 493 GLN cc_start: 0.7165 (tm-30) cc_final: 0.6510 (tm-30) REVERT: C 759 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7413 (m-10) outliers start: 35 outliers final: 22 residues processed: 125 average time/residue: 1.1709 time to fit residues: 174.6580 Evaluate side-chains 122 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 140 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 279 optimal weight: 2.9990 chunk 304 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 272 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 125 ASN C 919 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.103508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.073466 restraints weight = 53167.016| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.04 r_work: 0.3021 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 25181 Z= 0.187 Angle : 0.658 14.921 34341 Z= 0.328 Chirality : 0.048 0.352 3987 Planarity : 0.004 0.057 4344 Dihedral : 6.720 59.963 4139 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.20 % Allowed : 13.69 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.15), residues: 3006 helix: 1.96 (0.20), residues: 701 sheet: 0.36 (0.20), residues: 671 loop : -1.57 (0.14), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 886 HIS 0.005 0.001 HIS B1058 PHE 0.017 0.001 PHE B 175 TYR 0.015 0.001 TYR C 636 ARG 0.004 0.000 ARG A 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00616 ( 36) link_NAG-ASN : angle 4.10997 ( 108) link_BETA1-4 : bond 0.00633 ( 5) link_BETA1-4 : angle 1.30681 ( 15) hydrogen bonds : bond 0.06287 ( 934) hydrogen bonds : angle 5.07398 ( 2544) SS BOND : bond 0.00497 ( 40) SS BOND : angle 1.83599 ( 80) covalent geometry : bond 0.00451 (25100) covalent geometry : angle 0.61073 (34138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 2.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8011 (tpp-160) REVERT: A 590 CYS cc_start: 0.4967 (m) cc_final: 0.4726 (m) REVERT: B 117 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7821 (tt) REVERT: B 346 ARG cc_start: 0.7520 (mmp-170) cc_final: 0.7250 (mmm160) REVERT: B 780 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8505 (mm-30) REVERT: C 170 TYR cc_start: 0.7128 (t80) cc_final: 0.6887 (t80) REVERT: C 389 ASP cc_start: 0.8272 (m-30) cc_final: 0.7653 (OUTLIER) REVERT: C 489 TYR cc_start: 0.7355 (m-80) cc_final: 0.7077 (m-80) REVERT: C 759 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7607 (m-10) outliers start: 32 outliers final: 21 residues processed: 122 average time/residue: 1.1577 time to fit residues: 168.2239 Evaluate side-chains 120 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 52 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 168 optimal weight: 0.0970 chunk 55 optimal weight: 2.9990 chunk 296 optimal weight: 0.7980 chunk 232 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 249 optimal weight: 3.9990 chunk 268 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B1101 HIS C 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.105494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.075763 restraints weight = 53120.500| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.03 r_work: 0.3063 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25181 Z= 0.118 Angle : 0.610 16.178 34341 Z= 0.300 Chirality : 0.046 0.345 3987 Planarity : 0.004 0.057 4344 Dihedral : 6.471 59.694 4139 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.97 % Allowed : 14.07 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 3006 helix: 2.23 (0.20), residues: 701 sheet: 0.50 (0.21), residues: 645 loop : -1.46 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 886 HIS 0.007 0.001 HIS B1101 PHE 0.013 0.001 PHE B 175 TYR 0.023 0.001 TYR C1138 ARG 0.003 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00655 ( 36) link_NAG-ASN : angle 3.95950 ( 108) link_BETA1-4 : bond 0.00692 ( 5) link_BETA1-4 : angle 1.38320 ( 15) hydrogen bonds : bond 0.04989 ( 934) hydrogen bonds : angle 4.83081 ( 2544) SS BOND : bond 0.00394 ( 40) SS BOND : angle 1.50457 ( 80) covalent geometry : bond 0.00266 (25100) covalent geometry : angle 0.56446 (34138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8154 (tpp-160) REVERT: A 590 CYS cc_start: 0.4740 (m) cc_final: 0.4499 (m) REVERT: B 41 LYS cc_start: 0.8303 (tptt) cc_final: 0.7219 (tmtt) REVERT: B 117 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7815 (tt) REVERT: B 979 ASP cc_start: 0.8350 (m-30) cc_final: 0.7940 (t0) REVERT: C 170 TYR cc_start: 0.7107 (t80) cc_final: 0.6795 (t80) REVERT: C 389 ASP cc_start: 0.8208 (m-30) cc_final: 0.7580 (t0) REVERT: C 489 TYR cc_start: 0.7363 (m-80) cc_final: 0.7099 (m-80) REVERT: C 759 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7534 (m-10) outliers start: 26 outliers final: 20 residues processed: 120 average time/residue: 1.1915 time to fit residues: 170.0625 Evaluate side-chains 120 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 154 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 209 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 268 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 276 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.104483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.074519 restraints weight = 53196.170| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.06 r_work: 0.3043 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25181 Z= 0.158 Angle : 0.636 14.554 34341 Z= 0.314 Chirality : 0.047 0.341 3987 Planarity : 0.004 0.056 4344 Dihedral : 6.519 59.716 4139 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.08 % Allowed : 14.03 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.15), residues: 3006 helix: 2.14 (0.20), residues: 701 sheet: 0.42 (0.20), residues: 649 loop : -1.46 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 886 HIS 0.009 0.001 HIS B1101 PHE 0.014 0.001 PHE B 175 TYR 0.018 0.001 TYR A 449 ARG 0.003 0.000 ARG A 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00612 ( 36) link_NAG-ASN : angle 3.98245 ( 108) link_BETA1-4 : bond 0.00613 ( 5) link_BETA1-4 : angle 1.35817 ( 15) hydrogen bonds : bond 0.05563 ( 934) hydrogen bonds : angle 4.91076 ( 2544) SS BOND : bond 0.00532 ( 40) SS BOND : angle 1.81421 ( 80) covalent geometry : bond 0.00376 (25100) covalent geometry : angle 0.59018 (34138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12951.64 seconds wall clock time: 224 minutes 43.76 seconds (13483.76 seconds total)