Starting phenix.real_space_refine on Sat Aug 8 04:08:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yw0_73535/08_2026/9yw0_73535.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yw0_73535/08_2026/9yw0_73535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yw0_73535/08_2026/9yw0_73535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yw0_73535/08_2026/9yw0_73535.map" model { file = "/net/cci-nas-00/data/ceres_data/9yw0_73535/08_2026/9yw0_73535.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yw0_73535/08_2026/9yw0_73535.cif" } resolution = 2.5 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= 0.015 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 109 5.16 5 C 15861 2.51 5 N 4036 2.21 5 O 4821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24827 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8042 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 8 Chain: "B" Number of atoms: 8070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8070 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 53, 'TRANS': 974} Chain breaks: 11 Chain: "C" Number of atoms: 8071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8071 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 56, 'TRANS': 972} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 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: "I" 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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: 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: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.69, per 1000 atoms: 0.23 Number of scatterers: 24827 At special positions: 0 Unit cell: (128.96, 138.944, 198.848, 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 109 16.00 O 4821 8.00 N 4036 7.00 C 15861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 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 A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 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=2.03 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=2.02 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=2.03 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 354 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 343 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 717 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 282 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 354 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 234 " " NAG D 1 " - " ASN A1134 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN B1098 " " NAG I 1 " - " ASN B1134 " " NAG J 1 " - " ASN B 331 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN C1098 " " NAG M 1 " - " ASN C1134 " " NAG N 1 " - " ASN C 801 " " NAG O 1 " - " ASN C 717 " Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.0 seconds 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5780 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 44 sheets defined 27.2% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.712A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.538A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.604A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 827 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.717A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.069A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 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 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.455A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1150 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.929A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.782A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 626 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.671A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 836 through 840 Processing helix chain 'B' and resid 849 through 856 removed outlier: 3.613A pdb=" N GLN B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) 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 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.151A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 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: 3.927A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1149 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.715A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 removed outlier: 4.235A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 389' Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 627 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.541A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 815 removed outlier: 3.624A pdb=" N LYS C 814 " --> pdb=" O LYS C 811 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG C 815 " --> pdb=" O PRO C 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 811 through 815' Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.142A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' 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 Processing helix chain 'C' and resid 1139 through 1150 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 7.695A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.871A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.825A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.942A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.937A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.248A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.085A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.615A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.615A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.404A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AB9, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.646A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.801A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 204 through 208 removed outlier: 3.607A pdb=" N VAL B 193 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR B 208 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 103 through 107 removed outlier: 3.759A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.865A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.190A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.853A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 376 through 379 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.035A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.606A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.606A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.226A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 29 through 30 removed outlier: 7.837A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.695A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.136A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.896A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE1, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.130A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.800A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.800A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.303A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 1011 hydrogen bonds defined for protein. 2829 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: 6.35 Time building geometry restraints manager: 2.93 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: 7757 1.34 - 1.46: 5923 1.46 - 1.58: 11585 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 25401 Sorted by residual: bond pdb=" N VAL A 130 " pdb=" CA VAL A 130 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.32e+00 bond pdb=" N ILE A 128 " pdb=" CA ILE A 128 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.29e-02 6.01e+03 7.57e+00 bond pdb=" N ASN A 164 " pdb=" CA ASN A 164 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.22e-02 6.72e+03 6.95e+00 bond pdb=" N GLN A 115 " pdb=" CA GLN A 115 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.48e+00 bond pdb=" N LEU A 117 " pdb=" CA LEU A 117 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.25e-02 6.40e+03 6.38e+00 ... (remaining 25396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 34295 2.63 - 5.26: 237 5.26 - 7.90: 10 7.90 - 10.53: 6 10.53 - 13.16: 3 Bond angle restraints: 34551 Sorted by residual: angle pdb=" CB MET C 153 " pdb=" CG MET C 153 " pdb=" SD MET C 153 " ideal model delta sigma weight residual 112.70 124.85 -12.15 3.00e+00 1.11e-01 1.64e+01 angle pdb=" CA LEU B 117 " pdb=" CB LEU B 117 " pdb=" CG LEU B 117 " ideal model delta sigma weight residual 116.30 129.46 -13.16 3.50e+00 8.16e-02 1.41e+01 angle pdb=" CA LEU B1141 " pdb=" CB LEU B1141 " pdb=" CG LEU B1141 " ideal model delta sigma weight residual 116.30 129.04 -12.74 3.50e+00 8.16e-02 1.33e+01 angle pdb=" N LYS A 113 " pdb=" CA LYS A 113 " pdb=" C LYS A 113 " ideal model delta sigma weight residual 112.89 108.54 4.35 1.24e+00 6.50e-01 1.23e+01 angle pdb=" N GLN A 134 " pdb=" CA GLN A 134 " pdb=" C GLN A 134 " ideal model delta sigma weight residual 111.07 107.33 3.74 1.07e+00 8.73e-01 1.22e+01 ... (remaining 34546 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 14061 17.97 - 35.95: 1279 35.95 - 53.92: 271 53.92 - 71.89: 77 71.89 - 89.87: 30 Dihedral angle restraints: 15718 sinusoidal: 6742 harmonic: 8976 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -159.59 73.59 1 1.00e+01 1.00e-02 6.89e+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 -40.81 -45.19 1 1.00e+01 1.00e-02 2.83e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -41.98 -44.02 1 1.00e+01 1.00e-02 2.70e+01 ... (remaining 15715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3184 0.047 - 0.094: 584 0.094 - 0.141: 260 0.141 - 0.188: 12 0.188 - 0.235: 3 Chirality restraints: 4043 Sorted by residual: chirality pdb=" C2 NAG D 2 " pdb=" C1 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" N2 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.26 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CG LEU B 117 " pdb=" CB LEU B 117 " pdb=" CD1 LEU B 117 " pdb=" CD2 LEU B 117 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.88e-01 ... (remaining 4040 not shown) Planarity restraints: 4421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 428 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.89e+00 pdb=" C ASP A 428 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP A 428 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE A 429 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 571 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.13e+00 pdb=" C ASP A 571 " -0.039 2.00e-02 2.50e+03 pdb=" O ASP A 571 " 0.015 2.00e-02 2.50e+03 pdb=" N THR A 572 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 452 " 0.010 2.00e-02 2.50e+03 1.10e-02 3.00e+00 pdb=" CG TRP A 452 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 452 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 452 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 452 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 452 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 452 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 452 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 452 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 452 " -0.001 2.00e-02 2.50e+03 ... (remaining 4418 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1544 2.73 - 3.28: 24282 3.28 - 3.82: 42004 3.82 - 4.36: 50134 4.36 - 4.90: 86551 Nonbonded interactions: 204515 Sorted by model distance: nonbonded pdb=" OG1 THR B 114 " pdb=" O PHE B 133 " model vdw 2.192 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" OD2 ASP B 53 " model vdw 2.240 3.040 nonbonded pdb=" OE1 GLN B1002 " pdb=" NE2 GLN C1005 " model vdw 2.245 3.120 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.247 3.040 nonbonded pdb=" OD1 ASN C 801 " pdb=" OG SER C 803 " model vdw 2.259 3.040 ... (remaining 204510 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 26 through 65 or resid 82 through 138 or resid 154 through \ 160 or resid 167 through 172 or resid 190 through 208 or resid 215 through 241 \ or resid 264 through 356 or resid 360 through 387 or resid 391 through 676 or re \ sid 689 through 1305)) selection = (chain 'B' and (resid 26 through 65 or resid 82 through 138 or resid 154 through \ 676 or resid 689 through 828 or resid 855 through 1305)) selection = (chain 'C' and (resid 26 through 65 or resid 82 through 138 or resid 154 through \ 160 or resid 167 through 172 or resid 190 through 208 or resid 215 through 241 \ or resid 264 through 356 or resid 360 through 387 or resid 391 through 828 or re \ sid 855 through 1305)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 5.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 25.350 Find NCS groups from input model: 0.670 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: 0.010 Load rotamer database and sin/cos tables:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 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 : 0.002 0.040 25486 Z= 0.127 Angle : 0.537 13.162 34767 Z= 0.278 Chirality : 0.043 0.235 4043 Planarity : 0.003 0.044 4387 Dihedral : 14.667 89.867 9821 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.16 % Favored : 95.80 % Rotamer: Outliers : 0.96 % Allowed : 18.37 % Favored : 80.67 % 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 are not related in a simple way. whole: 0.25 (0.15), residues: 3026 helix: 2.99 (0.19), residues: 695 sheet: -0.18 (0.20), residues: 578 loop : -0.92 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 983 TYR 0.017 0.001 TYR B 904 PHE 0.026 0.001 PHE A 371 TRP 0.029 0.001 TRP A 452 HIS 0.001 0.000 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.13 (25401) covalent geometry : angle 0.52819 / 0.28 (34551) SS BOND : bond 0.00250 / 0.15 ( 39) SS BOND : angle 0.65585 / 0.47 ( 78) hydrogen bonds : bond 0.15188 / 9.60 ( 982) hydrogen bonds : angle 7.51909 / 5.27 ( 2829) link_BETA1-4 : bond 0.00395 / 0.24 ( 12) link_BETA1-4 : angle 1.30966 / 0.75 ( 36) link_NAG-ASN : bond 0.00233 / 0.14 ( 34) link_NAG-ASN : angle 1.68866 / 1.11 ( 102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: C residue: PRO 139 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.9042 (mt) cc_final: 0.8822 (mp) REVERT: A 125 ASN cc_start: 0.9208 (m-40) cc_final: 0.8980 (p0) REVERT: A 130 VAL cc_start: 0.7686 (p) cc_final: 0.7141 (p) REVERT: A 189 LEU cc_start: 0.8522 (mp) cc_final: 0.7902 (tp) REVERT: A 498 ARG cc_start: 0.8732 (ptp-110) cc_final: 0.8496 (pmm-80) REVERT: C 351 TYR cc_start: 0.8932 (p90) cc_final: 0.8618 (p90) REVERT: C 368 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8969 (mm) REVERT: C 512 VAL cc_start: 0.9186 (t) cc_final: 0.8976 (m) REVERT: C 904 TYR cc_start: 0.8674 (t80) cc_final: 0.8244 (t80) outliers start: 27 outliers final: 16 residues processed: 185 average time/residue: 0.4941 time to fit residues: 111.5869 Evaluate side-chains 143 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 139 PRO Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 858 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 762 GLN C1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.101644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.060126 restraints weight = 53556.462| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.90 r_work: 0.2754 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25486 Z= 0.165 Angle : 0.548 11.815 34767 Z= 0.279 Chirality : 0.044 0.234 4043 Planarity : 0.004 0.039 4387 Dihedral : 4.884 59.074 4284 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.16 % Favored : 95.80 % Rotamer: Outliers : 2.88 % Allowed : 16.53 % Favored : 80.60 % 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 are not related in a simple way. whole: 0.31 (0.15), residues: 3026 helix: 3.05 (0.19), residues: 694 sheet: -0.22 (0.19), residues: 618 loop : -0.87 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 983 TYR 0.019 0.001 TYR A1067 PHE 0.018 0.001 PHE A 939 TRP 0.016 0.001 TRP A 452 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (25401) covalent geometry : angle 0.53627 / 0.28 (34551) SS BOND : bond 0.00340 / 0.24 ( 39) SS BOND : angle 0.86794 / 0.62 ( 78) hydrogen bonds : bond 0.04470 / 2.87 ( 982) hydrogen bonds : angle 5.92600 / 4.06 ( 2829) link_BETA1-4 : bond 0.00313 / 0.19 ( 12) link_BETA1-4 : angle 1.38900 / 0.82 ( 36) link_NAG-ASN : bond 0.00292 / 0.19 ( 34) link_NAG-ASN : angle 1.90308 / 1.22 ( 102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 135 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: C residue: PRO 139 >>> skipping revert: symmetry clash REVERT: A 100 ILE cc_start: 0.8971 (mt) cc_final: 0.8743 (mp) REVERT: A 125 ASN cc_start: 0.9212 (m-40) cc_final: 0.8877 (m110) REVERT: A 498 ARG cc_start: 0.8865 (ptp-110) cc_final: 0.8461 (pmm-80) REVERT: A 869 MET cc_start: 0.9503 (mtt) cc_final: 0.9284 (mtt) REVERT: B 27 GLN cc_start: 0.6736 (OUTLIER) cc_final: 0.6467 (pt0) REVERT: B 223 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6521 (mt) REVERT: B 269 TYR cc_start: 0.8012 (m-80) cc_final: 0.7738 (m-80) REVERT: C 239 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.7176 (tm-30) REVERT: C 351 TYR cc_start: 0.8937 (p90) cc_final: 0.8540 (p90) REVERT: C 382 VAL cc_start: 0.8632 (t) cc_final: 0.8273 (p) outliers start: 79 outliers final: 38 residues processed: 203 average time/residue: 0.4241 time to fit residues: 107.7853 Evaluate side-chains 165 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 139 PRO Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 859 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 187 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 292 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 81 optimal weight: 0.0670 chunk 83 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 303 optimal weight: 3.9990 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.101777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.060587 restraints weight = 53579.591| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.91 r_work: 0.2719 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25486 Z= 0.156 Angle : 0.525 11.045 34767 Z= 0.266 Chirality : 0.044 0.232 4043 Planarity : 0.003 0.039 4387 Dihedral : 4.753 58.749 4269 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.06 % Favored : 95.90 % Rotamer: Outliers : 2.99 % Allowed : 16.27 % Favored : 80.75 % 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 are not related in a simple way. whole: 0.32 (0.15), residues: 3026 helix: 3.04 (0.19), residues: 694 sheet: -0.19 (0.19), residues: 627 loop : -0.87 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 983 TYR 0.019 0.001 TYR B1067 PHE 0.015 0.001 PHE A 898 TRP 0.018 0.001 TRP A 452 HIS 0.003 0.000 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (25401) covalent geometry : angle 0.51344 / 0.26 (34551) SS BOND : bond 0.00320 / 0.22 ( 39) SS BOND : angle 0.77298 / 0.56 ( 78) hydrogen bonds : bond 0.04281 / 2.74 ( 982) hydrogen bonds : angle 5.65632 / 3.86 ( 2829) link_BETA1-4 : bond 0.00284 / 0.18 ( 12) link_BETA1-4 : angle 1.35021 / 0.79 ( 36) link_NAG-ASN : bond 0.00267 / 0.18 ( 34) link_NAG-ASN : angle 1.88642 / 1.20 ( 102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 134 time to evaluate : 0.891 Fit side-chains revert: symmetry clash Corrupt residue: chain: C residue: PRO 139 >>> skipping revert: symmetry clash REVERT: A 498 ARG cc_start: 0.8873 (ptp-110) cc_final: 0.8494 (pmm-80) REVERT: A 636 TYR cc_start: 0.8697 (t80) cc_final: 0.8289 (t80) REVERT: A 820 ASP cc_start: 0.9032 (OUTLIER) cc_final: 0.8815 (m-30) REVERT: B 223 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6579 (mt) REVERT: C 189 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8211 (tt) REVERT: C 239 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7245 (tm-30) REVERT: C 351 TYR cc_start: 0.8971 (p90) cc_final: 0.8547 (p90) REVERT: C 586 ASP cc_start: 0.8272 (m-30) cc_final: 0.8065 (m-30) REVERT: C 1145 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7556 (tt) outliers start: 82 outliers final: 37 residues processed: 205 average time/residue: 0.3773 time to fit residues: 96.3111 Evaluate side-chains 164 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 139 PRO Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 30 optimal weight: 6.9990 chunk 284 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 chunk 225 optimal weight: 0.5980 chunk 128 optimal weight: 6.9990 chunk 235 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 300 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 360 ASN C 762 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.101842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.060712 restraints weight = 53502.983| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.88 r_work: 0.2755 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25486 Z= 0.149 Angle : 0.522 11.466 34767 Z= 0.263 Chirality : 0.044 0.233 4043 Planarity : 0.003 0.040 4387 Dihedral : 4.715 59.691 4267 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.23 % Favored : 95.74 % Rotamer: Outliers : 3.14 % Allowed : 16.71 % Favored : 80.15 % 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 are not related in a simple way. whole: 0.32 (0.15), residues: 3026 helix: 3.04 (0.19), residues: 694 sheet: -0.17 (0.19), residues: 640 loop : -0.88 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 457 TYR 0.019 0.001 TYR B1067 PHE 0.018 0.001 PHE A 338 TRP 0.018 0.001 TRP A 452 HIS 0.002 0.000 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (25401) covalent geometry : angle 0.51068 / 0.26 (34551) SS BOND : bond 0.00305 / 0.21 ( 39) SS BOND : angle 0.73367 / 0.53 ( 78) hydrogen bonds : bond 0.04113 / 2.63 ( 982) hydrogen bonds : angle 5.53886 / 3.78 ( 2829) link_BETA1-4 : bond 0.00308 / 0.19 ( 12) link_BETA1-4 : angle 1.32715 / 0.77 ( 36) link_NAG-ASN : bond 0.00262 / 0.17 ( 34) link_NAG-ASN : angle 1.85844 / 1.19 ( 102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 130 time to evaluate : 0.932 Fit side-chains revert: symmetry clash Corrupt residue: chain: C residue: PRO 139 >>> skipping revert: symmetry clash REVERT: A 498 ARG cc_start: 0.8884 (ptp-110) cc_final: 0.8506 (pmm-80) REVERT: A 636 TYR cc_start: 0.8659 (t80) cc_final: 0.8248 (t80) REVERT: A 820 ASP cc_start: 0.9017 (OUTLIER) cc_final: 0.8802 (m-30) REVERT: B 223 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6538 (mt) REVERT: B 821 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8668 (mp) REVERT: C 131 CYS cc_start: 0.6250 (OUTLIER) cc_final: 0.5729 (m) REVERT: C 189 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8205 (tt) REVERT: C 239 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.7216 (tm-30) REVERT: C 269 TYR cc_start: 0.8542 (m-80) cc_final: 0.8334 (m-80) REVERT: C 351 TYR cc_start: 0.8967 (p90) cc_final: 0.8552 (p90) REVERT: C 1145 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7541 (tt) outliers start: 86 outliers final: 43 residues processed: 204 average time/residue: 0.3377 time to fit residues: 87.8607 Evaluate side-chains 172 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 122 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 139 PRO Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 281 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 235 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 chunk 300 optimal weight: 3.9990 chunk 132 optimal weight: 50.0000 chunk 278 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN C 339 HIS C 360 ASN C 762 GLN C1113 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.100823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.059531 restraints weight = 53529.088| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.88 r_work: 0.2729 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25486 Z= 0.225 Angle : 0.554 11.495 34767 Z= 0.280 Chirality : 0.045 0.241 4043 Planarity : 0.004 0.041 4387 Dihedral : 4.735 56.229 4265 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.46 % Favored : 95.51 % Rotamer: Outliers : 3.43 % Allowed : 16.41 % Favored : 80.15 % 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 are not related in a simple way. whole: 0.28 (0.15), residues: 3026 helix: 2.95 (0.19), residues: 699 sheet: -0.21 (0.20), residues: 623 loop : -0.88 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 457 TYR 0.019 0.001 TYR A1067 PHE 0.019 0.001 PHE A 371 TRP 0.029 0.002 TRP C 436 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.23 (25401) covalent geometry : angle 0.54257 / 0.28 (34551) SS BOND : bond 0.00430 / 0.31 ( 39) SS BOND : angle 0.80573 / 0.58 ( 78) hydrogen bonds : bond 0.04473 / 2.87 ( 982) hydrogen bonds : angle 5.57361 / 3.81 ( 2829) link_BETA1-4 : bond 0.00238 / 0.15 ( 12) link_BETA1-4 : angle 1.35250 / 0.79 ( 36) link_NAG-ASN : bond 0.00302 / 0.21 ( 34) link_NAG-ASN : angle 1.98431 / 1.26 ( 102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 125 time to evaluate : 1.141 Fit side-chains revert: symmetry clash Corrupt residue: chain: C residue: PRO 139 >>> skipping revert: symmetry clash REVERT: A 188 ASN cc_start: 0.8301 (OUTLIER) cc_final: 0.7771 (p0) REVERT: A 498 ARG cc_start: 0.8868 (ptp-110) cc_final: 0.8510 (pmm-80) REVERT: A 636 TYR cc_start: 0.8662 (t80) cc_final: 0.8254 (t80) REVERT: A 820 ASP cc_start: 0.9067 (OUTLIER) cc_final: 0.8833 (m-30) REVERT: B 223 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6571 (mt) REVERT: C 131 CYS cc_start: 0.6312 (OUTLIER) cc_final: 0.5787 (m) REVERT: C 189 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8309 (tt) REVERT: C 304 LYS cc_start: 0.9517 (OUTLIER) cc_final: 0.9134 (mtmm) REVERT: C 351 TYR cc_start: 0.8974 (p90) cc_final: 0.8565 (p90) REVERT: C 1145 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7573 (tt) outliers start: 94 outliers final: 50 residues processed: 207 average time/residue: 0.4250 time to fit residues: 110.1728 Evaluate side-chains 172 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 115 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 139 PRO Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 304 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 262 optimal weight: 3.9990 chunk 269 optimal weight: 0.8980 chunk 300 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 292 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B1005 GLN C 360 ASN C 613 GLN C 762 GLN C1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.101757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.061091 restraints weight = 53549.518| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.03 r_work: 0.2728 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25486 Z= 0.132 Angle : 0.521 11.914 34767 Z= 0.262 Chirality : 0.043 0.238 4043 Planarity : 0.003 0.041 4387 Dihedral : 4.634 56.290 4265 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.84 % Rotamer: Outliers : 2.51 % Allowed : 17.45 % Favored : 80.04 % 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 are not related in a simple way. whole: 0.30 (0.15), residues: 3026 helix: 2.98 (0.19), residues: 700 sheet: -0.15 (0.19), residues: 636 loop : -0.89 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 457 TYR 0.018 0.001 TYR B1067 PHE 0.019 0.001 PHE A 939 TRP 0.021 0.001 TRP B 436 HIS 0.002 0.000 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (25401) covalent geometry : angle 0.50951 / 0.26 (34551) SS BOND : bond 0.00252 / 0.18 ( 39) SS BOND : angle 0.90502 / 0.76 ( 78) hydrogen bonds : bond 0.03973 / 2.53 ( 982) hydrogen bonds : angle 5.42508 / 3.70 ( 2829) link_BETA1-4 : bond 0.00330 / 0.20 ( 12) link_BETA1-4 : angle 1.29595 / 0.75 ( 36) link_NAG-ASN : bond 0.00250 / 0.16 ( 34) link_NAG-ASN : angle 1.83994 / 1.18 ( 102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 132 time to evaluate : 0.920 Fit side-chains revert: symmetry clash Corrupt residue: chain: C residue: PRO 139 >>> skipping revert: symmetry clash REVERT: A 188 ASN cc_start: 0.8307 (OUTLIER) cc_final: 0.7778 (p0) REVERT: A 380 TYR cc_start: 0.9172 (m-80) cc_final: 0.8637 (m-80) REVERT: A 498 ARG cc_start: 0.8862 (ptp-110) cc_final: 0.8490 (pmm-80) REVERT: A 636 TYR cc_start: 0.8707 (t80) cc_final: 0.8301 (t80) REVERT: A 820 ASP cc_start: 0.9036 (OUTLIER) cc_final: 0.8803 (m-30) REVERT: B 223 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6538 (mt) REVERT: B 269 TYR cc_start: 0.8048 (m-80) cc_final: 0.7679 (m-80) REVERT: C 131 CYS cc_start: 0.6290 (OUTLIER) cc_final: 0.5765 (m) REVERT: C 189 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8297 (tt) REVERT: C 351 TYR cc_start: 0.8996 (p90) cc_final: 0.8564 (p90) REVERT: C 1145 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7571 (tt) outliers start: 69 outliers final: 39 residues processed: 192 average time/residue: 0.4069 time to fit residues: 97.6900 Evaluate side-chains 167 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 122 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 139 PRO Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 280 optimal weight: 2.9990 chunk 211 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.100742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.059414 restraints weight = 53518.625| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.93 r_work: 0.2688 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9081 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25486 Z= 0.216 Angle : 0.563 11.972 34767 Z= 0.284 Chirality : 0.045 0.237 4043 Planarity : 0.004 0.043 4387 Dihedral : 4.725 56.294 4265 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.36 % Favored : 95.60 % Rotamer: Outliers : 2.84 % Allowed : 17.30 % Favored : 79.86 % 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 are not related in a simple way. whole: 0.26 (0.15), residues: 3026 helix: 2.93 (0.19), residues: 699 sheet: -0.19 (0.20), residues: 624 loop : -0.90 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 983 TYR 0.019 0.001 TYR A1067 PHE 0.022 0.001 PHE A 375 TRP 0.023 0.002 TRP A 452 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.22 (25401) covalent geometry : angle 0.54987 / 0.28 (34551) SS BOND : bond 0.00422 / 0.30 ( 39) SS BOND : angle 1.10903 / 0.87 ( 78) hydrogen bonds : bond 0.04458 / 2.85 ( 982) hydrogen bonds : angle 5.50739 / 3.75 ( 2829) link_BETA1-4 : bond 0.00241 / 0.15 ( 12) link_BETA1-4 : angle 1.34755 / 0.78 ( 36) link_NAG-ASN : bond 0.00303 / 0.21 ( 34) link_NAG-ASN : angle 1.98780 / 1.26 ( 102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 125 time to evaluate : 0.928 Fit side-chains revert: symmetry clash Corrupt residue: chain: C residue: PRO 139 >>> skipping revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8822 (m-10) cc_final: 0.8616 (m-10) REVERT: A 102 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7352 (mmt-90) REVERT: A 188 ASN cc_start: 0.8350 (OUTLIER) cc_final: 0.7816 (p0) REVERT: A 380 TYR cc_start: 0.9209 (m-80) cc_final: 0.8640 (m-80) REVERT: A 498 ARG cc_start: 0.8861 (ptp-110) cc_final: 0.8497 (pmm-80) REVERT: A 636 TYR cc_start: 0.8683 (t80) cc_final: 0.8286 (t80) REVERT: A 820 ASP cc_start: 0.9086 (OUTLIER) cc_final: 0.8857 (m-30) REVERT: B 223 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6583 (mt) REVERT: B 229 LEU cc_start: 0.7446 (tm) cc_final: 0.7241 (pp) REVERT: B 1002 GLN cc_start: 0.9296 (tp40) cc_final: 0.8919 (tt0) REVERT: C 131 CYS cc_start: 0.6353 (OUTLIER) cc_final: 0.5804 (m) REVERT: C 304 LYS cc_start: 0.9540 (OUTLIER) cc_final: 0.9160 (mtmm) REVERT: C 351 TYR cc_start: 0.8997 (p90) cc_final: 0.8578 (p90) REVERT: C 1107 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8381 (mtt90) REVERT: C 1145 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7614 (tt) outliers start: 78 outliers final: 44 residues processed: 193 average time/residue: 0.4436 time to fit residues: 106.2853 Evaluate side-chains 172 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 120 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 139 PRO Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 0.4980 chunk 172 optimal weight: 0.7980 chunk 185 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 174 optimal weight: 9.9990 chunk 208 optimal weight: 0.9990 chunk 144 optimal weight: 7.9990 chunk 224 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.102164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.061182 restraints weight = 53398.067| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.93 r_work: 0.2769 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25486 Z= 0.116 Angle : 0.521 12.684 34767 Z= 0.262 Chirality : 0.043 0.244 4043 Planarity : 0.003 0.043 4387 Dihedral : 4.497 56.298 4261 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.90 % Favored : 96.03 % Rotamer: Outliers : 1.99 % Allowed : 18.33 % Favored : 79.68 % 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 are not related in a simple way. whole: 0.30 (0.15), residues: 3026 helix: 2.99 (0.19), residues: 700 sheet: -0.15 (0.20), residues: 633 loop : -0.91 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 983 TYR 0.018 0.001 TYR B1067 PHE 0.023 0.001 PHE A 939 TRP 0.024 0.001 TRP A 452 HIS 0.002 0.000 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (25401) covalent geometry : angle 0.51016 / 0.26 (34551) SS BOND : bond 0.00238 / 0.16 ( 39) SS BOND : angle 0.89771 / 0.68 ( 78) hydrogen bonds : bond 0.03781 / 2.41 ( 982) hydrogen bonds : angle 5.32909 / 3.62 ( 2829) link_BETA1-4 : bond 0.00363 / 0.22 ( 12) link_BETA1-4 : angle 1.27579 / 0.74 ( 36) link_NAG-ASN : bond 0.00256 / 0.16 ( 34) link_NAG-ASN : angle 1.78433 / 1.14 ( 102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 128 time to evaluate : 0.975 Fit side-chains revert: symmetry clash Corrupt residue: chain: C residue: PRO 139 >>> skipping revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8835 (m-10) cc_final: 0.8602 (m-10) REVERT: A 380 TYR cc_start: 0.9180 (m-80) cc_final: 0.8678 (m-80) REVERT: A 498 ARG cc_start: 0.8886 (ptp-110) cc_final: 0.8500 (pmm-80) REVERT: A 636 TYR cc_start: 0.8707 (t80) cc_final: 0.8289 (t80) REVERT: B 115 GLN cc_start: 0.6309 (OUTLIER) cc_final: 0.6040 (tm-30) REVERT: B 223 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.6505 (mt) REVERT: B 269 TYR cc_start: 0.8016 (m-80) cc_final: 0.7692 (m-80) REVERT: B 1002 GLN cc_start: 0.9253 (tp40) cc_final: 0.8885 (tt0) REVERT: C 59 PHE cc_start: 0.8564 (m-80) cc_final: 0.8354 (m-80) REVERT: C 131 CYS cc_start: 0.6269 (OUTLIER) cc_final: 0.5741 (m) REVERT: C 351 TYR cc_start: 0.9011 (p90) cc_final: 0.8562 (p90) REVERT: C 748 GLU cc_start: 0.9084 (mp0) cc_final: 0.8864 (pm20) REVERT: C 1107 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8444 (mtt90) REVERT: C 1145 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7611 (tt) outliers start: 55 outliers final: 33 residues processed: 175 average time/residue: 0.4160 time to fit residues: 90.6058 Evaluate side-chains 162 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 139 PRO Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 24 optimal weight: 0.7980 chunk 168 optimal weight: 0.4980 chunk 199 optimal weight: 0.1980 chunk 78 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 241 optimal weight: 20.0000 chunk 152 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.102091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.061171 restraints weight = 53476.271| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.89 r_work: 0.2769 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25486 Z= 0.125 Angle : 0.526 12.664 34767 Z= 0.266 Chirality : 0.043 0.237 4043 Planarity : 0.003 0.044 4387 Dihedral : 4.498 57.093 4261 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.97 % Favored : 95.97 % Rotamer: Outliers : 1.77 % Allowed : 18.74 % Favored : 79.49 % 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 are not related in a simple way. whole: 0.32 (0.15), residues: 3026 helix: 3.02 (0.19), residues: 700 sheet: -0.13 (0.20), residues: 633 loop : -0.90 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 983 TYR 0.018 0.001 TYR B1067 PHE 0.025 0.001 PHE A 371 TRP 0.024 0.001 TRP B 436 HIS 0.002 0.000 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (25401) covalent geometry : angle 0.51578 / 0.26 (34551) SS BOND : bond 0.00255 / 0.17 ( 39) SS BOND : angle 0.77192 / 0.60 ( 78) hydrogen bonds : bond 0.03796 / 2.42 ( 982) hydrogen bonds : angle 5.27281 / 3.58 ( 2829) link_BETA1-4 : bond 0.00328 / 0.20 ( 12) link_BETA1-4 : angle 1.29089 / 0.74 ( 36) link_NAG-ASN : bond 0.00229 / 0.15 ( 34) link_NAG-ASN : angle 1.77526 / 1.13 ( 102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 122 time to evaluate : 1.156 Fit side-chains revert: symmetry clash Corrupt residue: chain: C residue: PRO 139 >>> skipping revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8843 (m-10) cc_final: 0.8625 (m-10) REVERT: A 380 TYR cc_start: 0.9166 (m-80) cc_final: 0.8679 (m-80) REVERT: A 498 ARG cc_start: 0.8896 (ptp-110) cc_final: 0.8511 (pmm-80) REVERT: A 636 TYR cc_start: 0.8695 (t80) cc_final: 0.8277 (t80) REVERT: B 223 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6502 (mt) REVERT: B 269 TYR cc_start: 0.7961 (m-80) cc_final: 0.7633 (m-80) REVERT: B 1002 GLN cc_start: 0.9252 (tp40) cc_final: 0.8888 (tt0) REVERT: C 59 PHE cc_start: 0.8577 (m-80) cc_final: 0.8375 (m-80) REVERT: C 131 CYS cc_start: 0.6254 (OUTLIER) cc_final: 0.5724 (m) REVERT: C 351 TYR cc_start: 0.9004 (p90) cc_final: 0.8543 (p90) REVERT: C 748 GLU cc_start: 0.9089 (mp0) cc_final: 0.8863 (pm20) REVERT: C 1107 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8440 (mtt90) REVERT: C 1145 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7610 (tt) outliers start: 49 outliers final: 34 residues processed: 166 average time/residue: 0.4728 time to fit residues: 97.0364 Evaluate side-chains 157 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 119 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 139 PRO Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 251 optimal weight: 2.9990 chunk 272 optimal weight: 0.8980 chunk 137 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 189 optimal weight: 0.8980 chunk 249 optimal weight: 0.8980 chunk 162 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 245 optimal weight: 20.0000 chunk 286 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.102226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.060931 restraints weight = 53393.305| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.92 r_work: 0.2778 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25486 Z= 0.118 Angle : 0.522 12.734 34767 Z= 0.263 Chirality : 0.043 0.236 4043 Planarity : 0.003 0.046 4387 Dihedral : 4.438 59.201 4261 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.87 % Favored : 96.07 % Rotamer: Outliers : 1.66 % Allowed : 18.92 % Favored : 79.42 % 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 are not related in a simple way. whole: 0.34 (0.15), residues: 3026 helix: 3.03 (0.19), residues: 701 sheet: -0.07 (0.20), residues: 623 loop : -0.90 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 983 TYR 0.018 0.001 TYR B1067 PHE 0.030 0.001 PHE A 939 TRP 0.024 0.001 TRP A 452 HIS 0.003 0.000 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (25401) covalent geometry : angle 0.51228 / 0.26 (34551) SS BOND : bond 0.00239 / 0.16 ( 39) SS BOND : angle 0.74270 / 0.57 ( 78) hydrogen bonds : bond 0.03676 / 2.34 ( 982) hydrogen bonds : angle 5.20083 / 3.53 ( 2829) link_BETA1-4 : bond 0.00347 / 0.21 ( 12) link_BETA1-4 : angle 1.26585 / 0.73 ( 36) link_NAG-ASN : bond 0.00230 / 0.15 ( 34) link_NAG-ASN : angle 1.72582 / 1.10 ( 102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 131 time to evaluate : 0.932 Fit side-chains revert: symmetry clash Corrupt residue: chain: C residue: PRO 139 >>> skipping revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8863 (m-10) cc_final: 0.8653 (m-10) REVERT: A 380 TYR cc_start: 0.9172 (m-80) cc_final: 0.8737 (m-80) REVERT: A 498 ARG cc_start: 0.8906 (ptp-110) cc_final: 0.8494 (pmm-80) REVERT: A 636 TYR cc_start: 0.8676 (t80) cc_final: 0.8262 (t80) REVERT: A 820 ASP cc_start: 0.8994 (OUTLIER) cc_final: 0.8761 (m-30) REVERT: B 223 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6504 (mt) REVERT: B 229 LEU cc_start: 0.7694 (tm) cc_final: 0.7249 (pp) REVERT: B 269 TYR cc_start: 0.7917 (m-80) cc_final: 0.7577 (m-80) REVERT: B 1002 GLN cc_start: 0.9229 (tp40) cc_final: 0.8884 (tt0) REVERT: C 32 PHE cc_start: 0.9028 (m-80) cc_final: 0.8490 (m-10) REVERT: C 59 PHE cc_start: 0.8576 (m-80) cc_final: 0.8343 (m-80) REVERT: C 131 CYS cc_start: 0.6210 (OUTLIER) cc_final: 0.5682 (m) REVERT: C 351 TYR cc_start: 0.8991 (p90) cc_final: 0.8509 (p90) REVERT: C 360 ASN cc_start: 0.9402 (m-40) cc_final: 0.9148 (m-40) REVERT: C 904 TYR cc_start: 0.8754 (t80) cc_final: 0.8345 (t80) REVERT: C 1107 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8441 (mtt90) REVERT: C 1145 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7614 (tt) outliers start: 46 outliers final: 37 residues processed: 172 average time/residue: 0.3918 time to fit residues: 83.7704 Evaluate side-chains 165 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 123 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 139 PRO Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 230 optimal weight: 20.0000 chunk 213 optimal weight: 8.9990 chunk 195 optimal weight: 0.9990 chunk 231 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 49 optimal weight: 0.0980 chunk 43 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN C 115 GLN C 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.102535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.061744 restraints weight = 53296.734| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.89 r_work: 0.2783 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25486 Z= 0.114 Angle : 0.525 12.612 34767 Z= 0.264 Chirality : 0.043 0.234 4043 Planarity : 0.003 0.047 4387 Dihedral : 4.397 59.792 4261 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.73 % Favored : 96.20 % Rotamer: Outliers : 1.73 % Allowed : 18.92 % Favored : 79.34 % 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 are not related in a simple way. whole: 0.37 (0.15), residues: 3026 helix: 3.04 (0.19), residues: 702 sheet: -0.05 (0.20), residues: 616 loop : -0.88 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 983 TYR 0.018 0.001 TYR B1067 PHE 0.025 0.001 PHE A 371 TRP 0.023 0.001 TRP B 436 HIS 0.001 0.000 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (25401) covalent geometry : angle 0.51568 / 0.26 (34551) SS BOND : bond 0.00233 / 0.15 ( 39) SS BOND : angle 0.72612 / 0.56 ( 78) hydrogen bonds : bond 0.03643 / 2.32 ( 982) hydrogen bonds : angle 5.16769 / 3.51 ( 2829) link_BETA1-4 : bond 0.00348 / 0.21 ( 12) link_BETA1-4 : angle 1.26846 / 0.73 ( 36) link_NAG-ASN : bond 0.00226 / 0.15 ( 34) link_NAG-ASN : angle 1.70171 / 1.09 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11125.12 seconds wall clock time: 189 minutes 43.58 seconds (11383.58 seconds total)