Starting phenix.real_space_refine on Mon Aug 25 02:40:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gs6_34221/08_2025/8gs6_34221.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gs6_34221/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8gs6_34221/08_2025/8gs6_34221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gs6_34221/08_2025/8gs6_34221.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gs6_34221/08_2025/8gs6_34221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gs6_34221/08_2025/8gs6_34221.map" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 6.24, per 1000 atoms: 0.25 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: 2.09 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.22 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: 5.82 Time building geometry restraints manager: 2.84 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 1309)) selection = (chain 'B' and (resid 25 through 137 or resid 166 through 618 or resid 632 throu \ gh 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 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: 3.940 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.200 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.950 ------------------------------------------------------------------------------- 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 : 6.21 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.005 0.001 ARG A 24 TYR 0.023 0.001 TYR C 756 PHE 0.035 0.002 PHE A 906 TRP 0.027 0.002 TRP B 886 HIS 0.010 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00413 (25100) covalent geometry : angle 0.62139 (34138) SS BOND : bond 0.00541 ( 40) SS BOND : angle 1.95623 ( 80) hydrogen bonds : bond 0.19968 ( 934) hydrogen bonds : angle 7.24923 ( 2544) link_BETA1-4 : bond 0.00812 ( 5) link_BETA1-4 : angle 3.14306 ( 15) link_NAG-ASN : bond 0.00748 ( 36) link_NAG-ASN : angle 6.00441 ( 108) *********************** 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 : 0.905 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: 0.7135 time to fit residues: 122.7774 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 : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 A 690 GLN B 125 ASN B 439 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B1083 HIS C 125 ASN C 394 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.106073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.076415 restraints weight = 53110.550| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 3.05 r_work: 0.3057 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25181 Z= 0.135 Angle : 0.648 16.533 34341 Z= 0.322 Chirality : 0.047 0.466 3987 Planarity : 0.004 0.053 4344 Dihedral : 7.592 59.757 4139 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.82 % Allowed : 5.91 % Favored : 93.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.15), residues: 3006 helix: 2.20 (0.20), residues: 693 sheet: 0.28 (0.20), residues: 665 loop : -1.57 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.023 0.001 TYR B 170 PHE 0.018 0.001 PHE A 906 TRP 0.015 0.001 TRP B 886 HIS 0.006 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00302 (25100) covalent geometry : angle 0.58799 (34138) SS BOND : bond 0.00427 ( 40) SS BOND : angle 1.61234 ( 80) hydrogen bonds : bond 0.05701 ( 934) hydrogen bonds : angle 5.49709 ( 2544) link_BETA1-4 : bond 0.00551 ( 5) link_BETA1-4 : angle 1.87084 ( 15) link_NAG-ASN : bond 0.00715 ( 36) link_NAG-ASN : angle 4.65767 ( 108) *********************** 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 135 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 740 MET cc_start: 0.9321 (tpt) cc_final: 0.9038 (tpp) REVERT: B 1101 HIS cc_start: 0.7831 (OUTLIER) cc_final: 0.7571 (t-170) REVERT: C 170 TYR cc_start: 0.6862 (t80) cc_final: 0.6582 (t80) REVERT: C 389 ASP cc_start: 0.8227 (m-30) cc_final: 0.7475 (OUTLIER) REVERT: C 474 GLN cc_start: 0.6822 (pp30) cc_final: 0.6550 (pm20) REVERT: C 489 TYR cc_start: 0.7430 (m-80) cc_final: 0.7039 (m-80) REVERT: C 759 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7005 (m-10) REVERT: C 900 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7475 (mtt) outliers start: 22 outliers final: 5 residues processed: 125 average time/residue: 0.6960 time to fit residues: 100.7605 Evaluate side-chains 104 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 84 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 246 optimal weight: 0.0470 chunk 110 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 339 HIS B 422 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.104205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.074260 restraints weight = 53137.818| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.04 r_work: 0.3032 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25181 Z= 0.186 Angle : 0.657 15.994 34341 Z= 0.329 Chirality : 0.048 0.421 3987 Planarity : 0.004 0.052 4344 Dihedral : 7.316 59.539 4139 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.05 % Allowed : 8.83 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.15), residues: 3006 helix: 2.01 (0.20), residues: 697 sheet: 0.22 (0.20), residues: 672 loop : -1.58 (0.14), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 24 TYR 0.016 0.001 TYR B 170 PHE 0.024 0.002 PHE B 906 TRP 0.018 0.002 TRP B 886 HIS 0.005 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00446 (25100) covalent geometry : angle 0.60299 (34138) SS BOND : bond 0.00489 ( 40) SS BOND : angle 1.82719 ( 80) hydrogen bonds : bond 0.06361 ( 934) hydrogen bonds : angle 5.33059 ( 2544) link_BETA1-4 : bond 0.00730 ( 5) link_BETA1-4 : angle 1.66445 ( 15) link_NAG-ASN : bond 0.00627 ( 36) link_NAG-ASN : angle 4.39427 ( 108) *********************** 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 129 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.9366 (tpt) cc_final: 0.9091 (tpp) REVERT: C 170 TYR cc_start: 0.7108 (t80) cc_final: 0.6831 (t80) REVERT: C 389 ASP cc_start: 0.8261 (m-30) cc_final: 0.7551 (OUTLIER) REVERT: C 489 TYR cc_start: 0.7496 (m-80) cc_final: 0.7110 (m-80) REVERT: C 759 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7263 (m-10) outliers start: 28 outliers final: 10 residues processed: 121 average time/residue: 0.6329 time to fit residues: 89.6700 Evaluate side-chains 108 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 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 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 934 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 99 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 160 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 183 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN C 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.104713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.074878 restraints weight = 52914.089| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.03 r_work: 0.3026 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25181 Z= 0.149 Angle : 0.622 15.302 34341 Z= 0.310 Chirality : 0.047 0.391 3987 Planarity : 0.004 0.052 4344 Dihedral : 7.020 59.581 4139 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.20 % Allowed : 10.81 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.15), residues: 3006 helix: 2.07 (0.20), residues: 697 sheet: 0.30 (0.20), residues: 652 loop : -1.55 (0.14), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 24 TYR 0.023 0.001 TYR C1138 PHE 0.018 0.001 PHE B 906 TRP 0.016 0.001 TRP C 886 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00350 (25100) covalent geometry : angle 0.57043 (34138) SS BOND : bond 0.00415 ( 40) SS BOND : angle 1.63476 ( 80) hydrogen bonds : bond 0.05703 ( 934) hydrogen bonds : angle 5.11289 ( 2544) link_BETA1-4 : bond 0.00626 ( 5) link_BETA1-4 : angle 1.46838 ( 15) link_NAG-ASN : bond 0.00648 ( 36) link_NAG-ASN : angle 4.21188 ( 108) *********************** 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 134 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.9352 (tpt) cc_final: 0.9050 (tpp) REVERT: B 474 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7781 (pp30) REVERT: C 170 TYR cc_start: 0.7034 (t80) cc_final: 0.6742 (t80) REVERT: C 389 ASP cc_start: 0.8253 (m-30) cc_final: 0.7519 (OUTLIER) REVERT: C 489 TYR cc_start: 0.7479 (m-80) cc_final: 0.7138 (m-80) REVERT: C 759 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7332 (m-10) outliers start: 32 outliers final: 14 residues processed: 127 average time/residue: 0.5530 time to fit residues: 81.6550 Evaluate side-chains 111 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 525 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 474 GLN 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 483 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 283 optimal weight: 0.5980 chunk 184 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 153 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 219 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 304 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 chunk 232 optimal weight: 5.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN C 125 ASN C 271 GLN C 644 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.102605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.072600 restraints weight = 53033.318| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.01 r_work: 0.2982 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 25181 Z= 0.241 Angle : 0.690 15.452 34341 Z= 0.348 Chirality : 0.049 0.377 3987 Planarity : 0.005 0.055 4344 Dihedral : 7.082 59.902 4139 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.65 % Allowed : 11.82 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.15), residues: 3006 helix: 1.82 (0.20), residues: 696 sheet: 0.18 (0.20), residues: 690 loop : -1.69 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 24 TYR 0.019 0.002 TYR C 636 PHE 0.022 0.002 PHE B 906 TRP 0.025 0.002 TRP C 886 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00590 (25100) covalent geometry : angle 0.63929 (34138) SS BOND : bond 0.00634 ( 40) SS BOND : angle 2.08348 ( 80) hydrogen bonds : bond 0.06939 ( 934) hydrogen bonds : angle 5.28528 ( 2544) link_BETA1-4 : bond 0.00439 ( 5) link_BETA1-4 : angle 1.39858 ( 15) link_NAG-ASN : bond 0.00601 ( 36) link_NAG-ASN : angle 4.30872 ( 108) *********************** 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 141 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 97 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8046 (tpp-160) REVERT: A 740 MET cc_start: 0.9436 (tpt) cc_final: 0.9151 (tpp) REVERT: B 117 LEU cc_start: 0.8002 (tm) cc_final: 0.7707 (tt) REVERT: B 346 ARG cc_start: 0.7413 (mmp-170) cc_final: 0.7179 (mmm160) REVERT: B 987 PRO cc_start: 0.7686 (Cg_exo) cc_final: 0.7400 (Cg_endo) REVERT: C 389 ASP cc_start: 0.8334 (m-30) cc_final: 0.7653 (OUTLIER) REVERT: C 489 TYR cc_start: 0.7497 (m-80) cc_final: 0.7142 (m-80) REVERT: C 493 GLN cc_start: 0.7322 (tm-30) cc_final: 0.6662 (tm-30) REVERT: C 759 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7563 (m-10) REVERT: C 1092 GLU cc_start: 0.8033 (tp30) cc_final: 0.7794 (tp30) outliers start: 44 outliers final: 17 residues processed: 135 average time/residue: 0.5758 time to fit residues: 91.3094 Evaluate side-chains 112 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 203 ILE Chi-restraints excluded: chain B residue 503 VAL 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 Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 289 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 302 optimal weight: 3.9990 chunk 278 optimal weight: 0.8980 chunk 296 optimal weight: 0.8980 chunk 262 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN C 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.104665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.074869 restraints weight = 53009.509| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.04 r_work: 0.3026 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1445 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= 0.126 Angle : 0.617 15.990 34341 Z= 0.306 Chirality : 0.046 0.368 3987 Planarity : 0.004 0.053 4344 Dihedral : 6.795 59.320 4139 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.01 % Allowed : 13.21 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.15), residues: 3006 helix: 2.12 (0.20), residues: 696 sheet: 0.32 (0.20), residues: 652 loop : -1.57 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1107 TYR 0.021 0.001 TYR C1138 PHE 0.011 0.001 PHE C 32 TRP 0.016 0.001 TRP C 886 HIS 0.003 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00284 (25100) covalent geometry : angle 0.56645 (34138) SS BOND : bond 0.00469 ( 40) SS BOND : angle 1.67665 ( 80) hydrogen bonds : bond 0.05423 ( 934) hydrogen bonds : angle 5.00451 ( 2544) link_BETA1-4 : bond 0.00659 ( 5) link_BETA1-4 : angle 1.38728 ( 15) link_NAG-ASN : bond 0.00633 ( 36) link_NAG-ASN : angle 4.14966 ( 108) *********************** 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 129 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8170 (tpp-160) REVERT: A 740 MET cc_start: 0.9383 (tpt) cc_final: 0.9077 (tpp) REVERT: B 117 LEU cc_start: 0.8016 (tm) cc_final: 0.7750 (tt) REVERT: B 346 ARG cc_start: 0.7365 (mmp-170) cc_final: 0.7113 (mmm160) REVERT: B 979 ASP cc_start: 0.8388 (m-30) cc_final: 0.7915 (t0) REVERT: C 389 ASP cc_start: 0.8227 (m-30) cc_final: 0.7519 (OUTLIER) REVERT: C 489 TYR cc_start: 0.7429 (m-80) cc_final: 0.7118 (m-80) REVERT: C 493 GLN cc_start: 0.7106 (tm-30) cc_final: 0.6504 (tm-30) REVERT: C 759 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7416 (m-10) REVERT: C 988 GLU cc_start: 0.8054 (mp0) cc_final: 0.7612 (pm20) outliers start: 27 outliers final: 17 residues processed: 121 average time/residue: 0.6268 time to fit residues: 88.5077 Evaluate side-chains 114 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 878 LEU Chi-restraints excluded: chain B residue 203 ILE 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 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 934 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 27 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 297 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 231 optimal weight: 0.7980 chunk 244 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 125 ASN C 804 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.102490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.072408 restraints weight = 53260.812| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.04 r_work: 0.2981 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 25181 Z= 0.231 Angle : 0.686 15.318 34341 Z= 0.344 Chirality : 0.049 0.359 3987 Planarity : 0.005 0.056 4344 Dihedral : 6.896 59.784 4139 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.27 % Allowed : 14.18 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.15), residues: 3006 helix: 1.76 (0.20), residues: 703 sheet: 0.26 (0.20), residues: 671 loop : -1.71 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 24 TYR 0.019 0.002 TYR C 636 PHE 0.018 0.002 PHE B 906 TRP 0.024 0.002 TRP C 886 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00561 (25100) covalent geometry : angle 0.63648 (34138) SS BOND : bond 0.00549 ( 40) SS BOND : angle 2.04153 ( 80) hydrogen bonds : bond 0.06836 ( 934) hydrogen bonds : angle 5.21972 ( 2544) link_BETA1-4 : bond 0.00537 ( 5) link_BETA1-4 : angle 1.34902 ( 15) link_NAG-ASN : bond 0.00597 ( 36) link_NAG-ASN : angle 4.24772 ( 108) *********************** 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 132 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 498 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8131 (tpp-160) REVERT: A 740 MET cc_start: 0.9448 (tpt) cc_final: 0.9092 (tpp) REVERT: B 117 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7783 (tt) REVERT: B 987 PRO cc_start: 0.7579 (Cg_exo) cc_final: 0.7289 (Cg_endo) REVERT: C 389 ASP cc_start: 0.8337 (m-30) cc_final: 0.7708 (OUTLIER) REVERT: C 489 TYR cc_start: 0.7450 (m-80) cc_final: 0.7106 (m-80) REVERT: C 493 GLN cc_start: 0.7116 (tm-30) cc_final: 0.6733 (tm-30) REVERT: C 759 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7545 (m-10) outliers start: 34 outliers final: 22 residues processed: 123 average time/residue: 0.6181 time to fit residues: 88.9085 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 : 0.738 ------------------------------------------------------------------------------- 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 A residue 878 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 267 VAL 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 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 934 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 17 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 192 optimal weight: 0.6980 chunk 282 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 205 optimal weight: 6.9990 chunk 240 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 242 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 198 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 606 ASN C 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.105006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.075336 restraints weight = 52985.919| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.02 r_work: 0.3035 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1563 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= 0.119 Angle : 0.612 14.772 34341 Z= 0.302 Chirality : 0.046 0.357 3987 Planarity : 0.004 0.053 4344 Dihedral : 6.580 59.652 4139 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.31 % Allowed : 14.52 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.15), residues: 3006 helix: 2.11 (0.20), residues: 702 sheet: 0.36 (0.20), residues: 661 loop : -1.51 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.023 0.001 TYR C1138 PHE 0.011 0.001 PHE C1121 TRP 0.013 0.001 TRP C 886 HIS 0.002 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00264 (25100) covalent geometry : angle 0.56429 (34138) SS BOND : bond 0.00442 ( 40) SS BOND : angle 1.59159 ( 80) hydrogen bonds : bond 0.05148 ( 934) hydrogen bonds : angle 4.91074 ( 2544) link_BETA1-4 : bond 0.00684 ( 5) link_BETA1-4 : angle 1.38204 ( 15) link_NAG-ASN : bond 0.00653 ( 36) link_NAG-ASN : angle 4.03858 ( 108) *********************** 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 140 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8186 (tpp-160) REVERT: A 590 CYS cc_start: 0.4852 (m) cc_final: 0.4602 (m) REVERT: A 740 MET cc_start: 0.9377 (tpt) cc_final: 0.9071 (tpp) REVERT: B 117 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7703 (tt) REVERT: B 979 ASP cc_start: 0.8363 (m-30) cc_final: 0.7901 (t0) REVERT: C 389 ASP cc_start: 0.8199 (m-30) cc_final: 0.7590 (t0) REVERT: C 489 TYR cc_start: 0.7391 (m-80) cc_final: 0.7097 (m-80) REVERT: C 759 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7465 (m-10) outliers start: 35 outliers final: 19 residues processed: 132 average time/residue: 0.6132 time to fit residues: 95.2566 Evaluate side-chains 121 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 878 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 CYS 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 934 ILE 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 81 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 242 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 245 optimal weight: 10.0000 chunk 260 optimal weight: 0.0570 chunk 248 optimal weight: 4.9990 chunk 264 optimal weight: 2.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 271 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.103982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.074078 restraints weight = 53247.226| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.04 r_work: 0.3013 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1606 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 : 0.636 14.828 34341 Z= 0.316 Chirality : 0.047 0.369 3987 Planarity : 0.004 0.054 4344 Dihedral : 6.556 59.746 4139 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.16 % Allowed : 15.15 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.15), residues: 3006 helix: 2.10 (0.20), residues: 697 sheet: 0.35 (0.20), residues: 662 loop : -1.54 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.018 0.001 TYR A 449 PHE 0.012 0.001 PHE B1121 TRP 0.016 0.001 TRP C 886 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00373 (25100) covalent geometry : angle 0.58923 (34138) SS BOND : bond 0.00448 ( 40) SS BOND : angle 1.72106 ( 80) hydrogen bonds : bond 0.05721 ( 934) hydrogen bonds : angle 4.97579 ( 2544) link_BETA1-4 : bond 0.00614 ( 5) link_BETA1-4 : angle 1.31450 ( 15) link_NAG-ASN : bond 0.00613 ( 36) link_NAG-ASN : angle 4.06748 ( 108) *********************** 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 132 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8155 (tpp-160) REVERT: A 590 CYS cc_start: 0.4909 (m) cc_final: 0.4681 (m) REVERT: A 740 MET cc_start: 0.9395 (tpt) cc_final: 0.9095 (tpp) REVERT: B 117 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7697 (tt) REVERT: B 979 ASP cc_start: 0.8402 (m-30) cc_final: 0.7919 (t0) REVERT: C 389 ASP cc_start: 0.8247 (m-30) cc_final: 0.7598 (OUTLIER) REVERT: C 489 TYR cc_start: 0.7369 (m-80) cc_final: 0.7090 (m-80) REVERT: C 759 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7440 (m-10) outliers start: 31 outliers final: 23 residues processed: 125 average time/residue: 0.6313 time to fit residues: 92.6016 Evaluate side-chains 124 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 A residue 878 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 CYS 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 934 ILE 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 164 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 chunk 228 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 292 optimal weight: 0.2980 chunk 281 optimal weight: 0.7980 chunk 160 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 301 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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** C 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.105525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.075830 restraints weight = 52973.570| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.03 r_work: 0.3048 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25181 Z= 0.115 Angle : 0.608 14.579 34341 Z= 0.299 Chirality : 0.046 0.354 3987 Planarity : 0.004 0.052 4344 Dihedral : 6.404 58.660 4139 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.16 % Allowed : 15.19 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.16), residues: 3006 helix: 2.27 (0.20), residues: 697 sheet: 0.43 (0.20), residues: 673 loop : -1.46 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1107 TYR 0.024 0.001 TYR C1138 PHE 0.018 0.001 PHE B 168 TRP 0.012 0.001 TRP C 886 HIS 0.002 0.000 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00256 (25100) covalent geometry : angle 0.56102 (34138) SS BOND : bond 0.00526 ( 40) SS BOND : angle 1.66891 ( 80) hydrogen bonds : bond 0.04868 ( 934) hydrogen bonds : angle 4.83438 ( 2544) link_BETA1-4 : bond 0.00642 ( 5) link_BETA1-4 : angle 1.31359 ( 15) link_NAG-ASN : bond 0.00664 ( 36) link_NAG-ASN : angle 3.94932 ( 108) ********************** 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 133 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8036 (tpp-160) REVERT: A 590 CYS cc_start: 0.4838 (m) cc_final: 0.4633 (m) REVERT: A 740 MET cc_start: 0.9345 (tpt) cc_final: 0.9011 (tpp) REVERT: B 117 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7743 (tt) REVERT: B 979 ASP cc_start: 0.8336 (m-30) cc_final: 0.7887 (t0) REVERT: C 389 ASP cc_start: 0.8198 (m-30) cc_final: 0.7572 (t0) REVERT: C 489 TYR cc_start: 0.7345 (m-80) cc_final: 0.7079 (m-80) REVERT: C 759 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7489 (m-10) outliers start: 31 outliers final: 19 residues processed: 124 average time/residue: 0.6490 time to fit residues: 94.0772 Evaluate side-chains 120 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 A residue 878 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 CYS 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 934 ILE 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 158 optimal weight: 8.9990 chunk 298 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 219 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 = 0.3675 r_free = 0.3675 target = 0.103274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.073408 restraints weight = 53397.212| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.02 r_work: 0.2991 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 25181 Z= 0.217 Angle : 0.679 15.372 34341 Z= 0.339 Chirality : 0.049 0.586 3987 Planarity : 0.004 0.057 4344 Dihedral : 6.626 59.675 4139 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.12 % Allowed : 15.26 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.15), residues: 3006 helix: 1.97 (0.20), residues: 697 sheet: 0.34 (0.20), residues: 670 loop : -1.58 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 24 TYR 0.017 0.002 TYR A 449 PHE 0.016 0.002 PHE B 175 TRP 0.020 0.002 TRP C 886 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00530 (25100) covalent geometry : angle 0.63173 (34138) SS BOND : bond 0.00581 ( 40) SS BOND : angle 2.01895 ( 80) hydrogen bonds : bond 0.06451 ( 934) hydrogen bonds : angle 5.10631 ( 2544) link_BETA1-4 : bond 0.00755 ( 5) link_BETA1-4 : angle 1.32791 ( 15) link_NAG-ASN : bond 0.00635 ( 36) link_NAG-ASN : angle 4.14848 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6343.37 seconds wall clock time: 109 minutes 29.58 seconds (6569.58 seconds total)