Starting phenix.real_space_refine on Thu Mar 5 21:06:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y9s_33690/03_2026/7y9s_33690.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y9s_33690/03_2026/7y9s_33690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y9s_33690/03_2026/7y9s_33690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y9s_33690/03_2026/7y9s_33690.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y9s_33690/03_2026/7y9s_33690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y9s_33690/03_2026/7y9s_33690.map" } resolution = 3.0 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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16135 2.51 5 N 4139 2.21 5 O 4885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25273 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 8170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8170 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 53, 'TRANS': 987} Chain breaks: 8 Chain: "B" Number of atoms: 8191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8191 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 53, 'TRANS': 990} Chain breaks: 8 Chain: "C" Number of atoms: 8170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8170 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 53, 'TRANS': 987} Chain breaks: 8 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "P" 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: "Q" 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: "R" 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: "S" 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: 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 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.02, per 1000 atoms: 0.24 Number of scatterers: 25273 At special positions: 0 Unit cell: (138.75, 152.07, 203.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4885 8.00 N 4139 7.00 C 16135 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " 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=2.02 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=2.06 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 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 P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A 122 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 234 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 61 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN A 331 " " NAG I 1 " - " ASN B 343 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1074 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN B1134 " " NAG O 1 " - " ASN C 282 " " NAG P 1 " - " ASN C 717 " " NAG Q 1 " - " ASN C 801 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C1134 " Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 853.6 milliseconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5880 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 45 sheets defined 24.5% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.890A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 506 removed outlier: 4.051A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.945A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.656A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.537A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 806 removed outlier: 3.578A pdb=" N ILE A 805 " --> pdb=" O PHE A 802 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 806 " --> pdb=" O SER A 803 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 802 through 806' Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.034A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.200A 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 945 through 965 removed outlier: 3.656A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 4.065A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.076A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.625A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.871A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 407' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.608A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.050A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) 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 760 through 783 removed outlier: 3.570A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.558A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.539A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.384A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.583A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.675A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.226A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.575A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.847A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.540A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.565A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.722A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.528A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 937 removed outlier: 3.821A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.577A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) 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 removed outlier: 3.734A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.899A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.276A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.025A 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: 3.610A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.577A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 removed outlier: 6.695A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.061A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.120A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.568A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.643A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 31 removed outlier: 8.344A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.159A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.805A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 135 through 142 removed outlier: 7.615A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.996A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.098A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.720A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.548A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.119A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.470A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.692A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.240A 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: 3.600A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 140 through 141 removed outlier: 3.612A pdb=" N LEU C 141 " --> pdb=" O LEU C 242 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.544A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.224A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 715 through 728 removed outlier: 6.169A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.639A 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 Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1097 1014 hydrogen bonds defined for protein. 2748 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.58 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7793 1.34 - 1.46: 6606 1.46 - 1.59: 11300 1.59 - 1.72: 0 1.72 - 1.85: 141 Bond restraints: 25840 Sorted by residual: bond pdb=" N THR B 376 " pdb=" CA THR B 376 " ideal model delta sigma weight residual 1.453 1.491 -0.038 1.27e-02 6.20e+03 8.83e+00 bond pdb=" CA SER A 366 " pdb=" CB SER A 366 " ideal model delta sigma weight residual 1.532 1.488 0.044 1.53e-02 4.27e+03 8.28e+00 bond pdb=" N ALA B 372 " pdb=" CA ALA B 372 " ideal model delta sigma weight residual 1.452 1.480 -0.028 1.11e-02 8.12e+03 6.27e+00 bond pdb=" C PHE A 374 " pdb=" N PHE A 375 " ideal model delta sigma weight residual 1.331 1.300 0.031 1.23e-02 6.61e+03 6.25e+00 bond pdb=" CA ALA B 372 " pdb=" CB ALA B 372 " ideal model delta sigma weight residual 1.536 1.505 0.031 1.25e-02 6.40e+03 6.13e+00 ... (remaining 25835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 34745 2.57 - 5.13: 366 5.13 - 7.70: 21 7.70 - 10.27: 2 10.27 - 12.84: 2 Bond angle restraints: 35136 Sorted by residual: angle pdb=" CA PHE B 375 " pdb=" CB PHE B 375 " pdb=" CG PHE B 375 " ideal model delta sigma weight residual 113.80 120.88 -7.08 1.00e+00 1.00e+00 5.02e+01 angle pdb=" N PRO A 373 " pdb=" CA PRO A 373 " pdb=" C PRO A 373 " ideal model delta sigma weight residual 112.47 99.63 12.84 2.06e+00 2.36e-01 3.88e+01 angle pdb=" CA THR B 376 " pdb=" C THR B 376 " pdb=" O THR B 376 " ideal model delta sigma weight residual 121.88 115.72 6.16 1.13e+00 7.83e-01 2.97e+01 angle pdb=" N PRO B 373 " pdb=" CA PRO B 373 " pdb=" C PRO B 373 " ideal model delta sigma weight residual 112.47 101.80 10.67 2.06e+00 2.36e-01 2.68e+01 angle pdb=" N SER A 366 " pdb=" CA SER A 366 " pdb=" C SER A 366 " ideal model delta sigma weight residual 113.41 107.86 5.55 1.22e+00 6.72e-01 2.07e+01 ... (remaining 35131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 14399 17.61 - 35.23: 1317 35.23 - 52.84: 307 52.84 - 70.46: 66 70.46 - 88.07: 23 Dihedral angle restraints: 16112 sinusoidal: 6995 harmonic: 9117 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 12.14 80.86 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 27.02 65.98 1 1.00e+01 1.00e-02 5.69e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 155.69 -62.69 1 1.00e+01 1.00e-02 5.20e+01 ... (remaining 16109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3278 0.054 - 0.108: 705 0.108 - 0.162: 138 0.162 - 0.216: 12 0.216 - 0.269: 5 Chirality restraints: 4138 Sorted by residual: chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA PRO A 373 " pdb=" N PRO A 373 " pdb=" C PRO A 373 " pdb=" CB PRO A 373 " both_signs ideal model delta sigma weight residual False 2.72 2.98 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 4135 not shown) Planarity restraints: 4501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 498 " 0.065 5.00e-02 4.00e+02 9.84e-02 1.55e+01 pdb=" N PRO C 499 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO C 499 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 499 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 498 " 0.064 5.00e-02 4.00e+02 9.71e-02 1.51e+01 pdb=" N PRO B 499 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO B 499 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 499 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 321 " -0.063 5.00e-02 4.00e+02 9.39e-02 1.41e+01 pdb=" N PRO A 322 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " -0.051 5.00e-02 4.00e+02 ... (remaining 4498 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1982 2.74 - 3.28: 23509 3.28 - 3.82: 37880 3.82 - 4.36: 42499 4.36 - 4.90: 78505 Nonbonded interactions: 184375 Sorted by model distance: nonbonded pdb=" OG1 THR B 716 " pdb=" O GLN B1071 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR B 912 " pdb=" OD1 ASN B 914 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.239 3.040 nonbonded pdb=" NE2 GLN C 804 " pdb=" OE1 GLN C 935 " model vdw 2.258 3.120 nonbonded pdb=" OD2 ASP A 40 " pdb=" NH1 ARG A 44 " model vdw 2.264 3.120 ... (remaining 184370 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 15 through 1306) selection = (chain 'B' and (resid 15 through 827 or resid 848 through 1306)) selection = (chain 'C' and resid 15 through 1306) } 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' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.930 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 25935 Z= 0.191 Angle : 0.672 16.387 35379 Z= 0.348 Chirality : 0.047 0.269 4138 Planarity : 0.005 0.098 4464 Dihedral : 14.215 88.070 10106 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.92 % Favored : 94.79 % Rotamer: Outliers : 0.26 % Allowed : 0.33 % Favored : 99.42 % 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: -0.13 (0.15), residues: 3072 helix: 2.02 (0.21), residues: 679 sheet: 1.05 (0.19), residues: 682 loop : -1.55 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1107 TYR 0.019 0.001 TYR C 351 PHE 0.020 0.001 PHE A 486 TRP 0.015 0.001 TRP A 886 HIS 0.002 0.000 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00381 (25840) covalent geometry : angle 0.64331 (35136) SS BOND : bond 0.00588 ( 42) SS BOND : angle 1.54281 ( 84) hydrogen bonds : bond 0.12452 ( 1014) hydrogen bonds : angle 5.76921 ( 2748) link_BETA1-4 : bond 0.00397 ( 16) link_BETA1-4 : angle 1.00582 ( 48) link_NAG-ASN : bond 0.00591 ( 37) link_NAG-ASN : angle 3.23757 ( 111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 527 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.7624 (t80) cc_final: 0.7277 (t80) REVERT: A 331 ASN cc_start: 0.6430 (m110) cc_final: 0.6039 (t0) REVERT: A 368 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8511 (mm) REVERT: A 558 LYS cc_start: 0.8001 (mmpt) cc_final: 0.7284 (mmpt) REVERT: A 571 ASP cc_start: 0.7813 (t70) cc_final: 0.7399 (t0) REVERT: A 586 ASP cc_start: 0.7679 (m-30) cc_final: 0.7443 (m-30) REVERT: A 955 ASN cc_start: 0.8343 (m-40) cc_final: 0.8135 (m110) REVERT: A 988 GLU cc_start: 0.7257 (tp30) cc_final: 0.6851 (tm-30) REVERT: A 1017 GLU cc_start: 0.7089 (tp30) cc_final: 0.6622 (tp30) REVERT: A 1084 ASP cc_start: 0.7290 (t0) cc_final: 0.6908 (OUTLIER) REVERT: B 81 ASN cc_start: 0.7917 (m110) cc_final: 0.7655 (m110) REVERT: B 349 SER cc_start: 0.8564 (p) cc_final: 0.8275 (p) REVERT: B 440 LYS cc_start: 0.8383 (ptmm) cc_final: 0.8116 (tmmm) REVERT: B 493 ARG cc_start: 0.7803 (mtp85) cc_final: 0.7551 (mmm-85) REVERT: B 534 VAL cc_start: 0.8372 (m) cc_final: 0.8129 (t) REVERT: B 654 GLU cc_start: 0.7842 (tt0) cc_final: 0.7589 (tt0) REVERT: B 752 LEU cc_start: 0.8175 (mt) cc_final: 0.7904 (mt) REVERT: B 776 LYS cc_start: 0.8437 (ttpp) cc_final: 0.8217 (ttmm) REVERT: B 780 GLU cc_start: 0.7716 (tt0) cc_final: 0.7494 (tp30) REVERT: B 814 LYS cc_start: 0.8323 (mmtm) cc_final: 0.8036 (mmtt) REVERT: B 817 PHE cc_start: 0.7760 (t80) cc_final: 0.7517 (t80) REVERT: B 921 LYS cc_start: 0.8044 (mtpp) cc_final: 0.7839 (mtpp) REVERT: B 1144 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7445 (tp30) REVERT: C 194 PHE cc_start: 0.8591 (m-10) cc_final: 0.8280 (m-80) REVERT: C 370 ASN cc_start: 0.7547 (p0) cc_final: 0.7255 (p0) REVERT: C 371 LEU cc_start: 0.8740 (mp) cc_final: 0.8536 (mt) REVERT: C 465 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6973 (tm-30) REVERT: C 478 LYS cc_start: 0.8814 (ptpp) cc_final: 0.8611 (ptpp) REVERT: C 493 ARG cc_start: 0.7836 (mmt-90) cc_final: 0.7632 (mmt-90) REVERT: C 556 ASN cc_start: 0.8383 (m-40) cc_final: 0.8147 (m-40) REVERT: C 577 ARG cc_start: 0.8473 (ttm-80) cc_final: 0.8259 (ttm-80) REVERT: C 603 ASN cc_start: 0.8344 (t0) cc_final: 0.8115 (t0) REVERT: C 751 ASN cc_start: 0.8328 (m110) cc_final: 0.7962 (m110) REVERT: C 754 LEU cc_start: 0.8445 (mt) cc_final: 0.8168 (mm) REVERT: C 790 LYS cc_start: 0.8166 (mttp) cc_final: 0.7953 (mttp) REVERT: C 935 GLN cc_start: 0.7848 (pt0) cc_final: 0.7596 (pt0) REVERT: C 1010 GLN cc_start: 0.8137 (mp10) cc_final: 0.7711 (mp10) REVERT: C 1038 LYS cc_start: 0.8362 (mmmt) cc_final: 0.8112 (mmmm) REVERT: C 1141 LEU cc_start: 0.8562 (tp) cc_final: 0.8286 (tm) outliers start: 7 outliers final: 4 residues processed: 531 average time/residue: 0.6564 time to fit residues: 401.7147 Evaluate side-chains 485 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 481 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 676 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 196 ASN A 239 GLN A 360 ASN A 603 ASN A 777 ASN B 81 ASN B 370 ASN B 409 GLN C 52 GLN C 81 ASN C 99 ASN C 690 GLN C 907 ASN C 965 GLN C1002 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.139133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.111434 restraints weight = 38675.364| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.64 r_work: 0.3335 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25935 Z= 0.182 Angle : 0.654 15.901 35379 Z= 0.331 Chirality : 0.047 0.426 4138 Planarity : 0.005 0.079 4464 Dihedral : 7.330 82.700 4469 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.37 % Favored : 94.53 % Rotamer: Outliers : 1.21 % Allowed : 10.45 % Favored : 88.34 % 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: -0.20 (0.15), residues: 3072 helix: 1.90 (0.21), residues: 695 sheet: 1.06 (0.19), residues: 689 loop : -1.64 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 237 TYR 0.024 0.002 TYR C 453 PHE 0.024 0.002 PHE B 400 TRP 0.018 0.002 TRP A 436 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00430 (25840) covalent geometry : angle 0.62307 (35136) SS BOND : bond 0.00486 ( 42) SS BOND : angle 1.73980 ( 84) hydrogen bonds : bond 0.06282 ( 1014) hydrogen bonds : angle 5.12037 ( 2748) link_BETA1-4 : bond 0.00416 ( 16) link_BETA1-4 : angle 1.02558 ( 48) link_NAG-ASN : bond 0.00593 ( 37) link_NAG-ASN : angle 3.29879 ( 111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 512 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 TYR cc_start: 0.7832 (p90) cc_final: 0.7604 (p90) REVERT: A 436 TRP cc_start: 0.7768 (p90) cc_final: 0.7400 (p90) REVERT: A 529 LYS cc_start: 0.8458 (tmtt) cc_final: 0.8189 (tmtt) REVERT: A 558 LYS cc_start: 0.8170 (mmpt) cc_final: 0.7449 (mmpt) REVERT: A 571 ASP cc_start: 0.7869 (t70) cc_final: 0.7401 (t0) REVERT: A 988 GLU cc_start: 0.7486 (tp30) cc_final: 0.7020 (tm-30) REVERT: A 1084 ASP cc_start: 0.7671 (t0) cc_final: 0.7227 (t0) REVERT: B 129 LYS cc_start: 0.8097 (mttm) cc_final: 0.7818 (mttp) REVERT: B 132 GLU cc_start: 0.6110 (pm20) cc_final: 0.5589 (pm20) REVERT: B 324 GLU cc_start: 0.7874 (pm20) cc_final: 0.7607 (pm20) REVERT: B 402 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7867 (mp) REVERT: B 440 LYS cc_start: 0.8571 (ptmm) cc_final: 0.8356 (tmmm) REVERT: B 493 ARG cc_start: 0.8236 (mtp85) cc_final: 0.7955 (mmm-85) REVERT: B 534 VAL cc_start: 0.8342 (m) cc_final: 0.8142 (t) REVERT: B 583 GLU cc_start: 0.8363 (pt0) cc_final: 0.8126 (pt0) REVERT: B 752 LEU cc_start: 0.8185 (mt) cc_final: 0.7871 (mt) REVERT: B 768 THR cc_start: 0.8303 (m) cc_final: 0.8074 (p) REVERT: B 776 LYS cc_start: 0.8624 (ttpp) cc_final: 0.8418 (ttmm) REVERT: B 790 LYS cc_start: 0.8107 (mtmm) cc_final: 0.7848 (ptpp) REVERT: B 814 LYS cc_start: 0.8360 (mmtm) cc_final: 0.8061 (mmtt) REVERT: B 817 PHE cc_start: 0.7786 (t80) cc_final: 0.7560 (t80) REVERT: B 1144 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7717 (mm-30) REVERT: C 117 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7444 (mt) REVERT: C 194 PHE cc_start: 0.8692 (m-10) cc_final: 0.8397 (m-80) REVERT: C 370 ASN cc_start: 0.7826 (p0) cc_final: 0.7586 (p0) REVERT: C 371 LEU cc_start: 0.8800 (mp) cc_final: 0.8563 (mt) REVERT: C 405 ASP cc_start: 0.7952 (p0) cc_final: 0.7442 (p0) REVERT: C 474 GLN cc_start: 0.7705 (tm-30) cc_final: 0.7397 (tm-30) REVERT: C 478 LYS cc_start: 0.8820 (ptpp) cc_final: 0.8584 (ptpp) REVERT: C 751 ASN cc_start: 0.8426 (m110) cc_final: 0.8181 (m-40) REVERT: C 754 LEU cc_start: 0.8498 (mt) cc_final: 0.8236 (mm) REVERT: C 780 GLU cc_start: 0.8199 (tt0) cc_final: 0.7955 (tp30) REVERT: C 790 LYS cc_start: 0.8443 (mttp) cc_final: 0.8212 (mttp) REVERT: C 918 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7961 (mt-10) REVERT: C 950 ASP cc_start: 0.7504 (m-30) cc_final: 0.7277 (m-30) REVERT: C 1010 GLN cc_start: 0.8402 (mp10) cc_final: 0.8000 (mp10) REVERT: C 1038 LYS cc_start: 0.8526 (mmmt) cc_final: 0.8283 (mmmm) REVERT: C 1118 ASP cc_start: 0.8125 (m-30) cc_final: 0.7923 (m-30) REVERT: C 1141 LEU cc_start: 0.8521 (tp) cc_final: 0.8227 (tt) outliers start: 33 outliers final: 14 residues processed: 525 average time/residue: 0.7084 time to fit residues: 426.5978 Evaluate side-chains 509 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 493 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 129 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 5 optimal weight: 0.0870 chunk 81 optimal weight: 0.9980 chunk 262 optimal weight: 0.1980 chunk 175 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 309 optimal weight: 0.1980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 81 ASN A 239 GLN A 360 ASN A 777 ASN B 556 ASN B 703 ASN C 52 GLN C 66 HIS C 81 ASN C 317 ASN C 603 ASN C 675 GLN C 779 GLN C 804 GLN C 907 ASN C 935 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.140258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.112330 restraints weight = 38614.767| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.69 r_work: 0.3348 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25935 Z= 0.131 Angle : 0.611 15.028 35379 Z= 0.307 Chirality : 0.045 0.432 4138 Planarity : 0.005 0.067 4464 Dihedral : 6.717 57.053 4463 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.59 % Favored : 95.31 % Rotamer: Outliers : 1.83 % Allowed : 13.04 % Favored : 85.13 % 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: -0.14 (0.15), residues: 3072 helix: 1.84 (0.21), residues: 715 sheet: 1.10 (0.19), residues: 675 loop : -1.57 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1107 TYR 0.023 0.001 TYR C 453 PHE 0.023 0.001 PHE B 400 TRP 0.014 0.001 TRP A 436 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00294 (25840) covalent geometry : angle 0.58112 (35136) SS BOND : bond 0.00416 ( 42) SS BOND : angle 1.50575 ( 84) hydrogen bonds : bond 0.05616 ( 1014) hydrogen bonds : angle 4.95838 ( 2748) link_BETA1-4 : bond 0.00396 ( 16) link_BETA1-4 : angle 1.08428 ( 48) link_NAG-ASN : bond 0.00598 ( 37) link_NAG-ASN : angle 3.13787 ( 111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 492 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 TYR cc_start: 0.7876 (p90) cc_final: 0.7650 (p90) REVERT: A 436 TRP cc_start: 0.7851 (p90) cc_final: 0.7437 (p90) REVERT: A 529 LYS cc_start: 0.8467 (tmtt) cc_final: 0.8194 (tmtt) REVERT: A 537 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7513 (tttp) REVERT: A 558 LYS cc_start: 0.8185 (mmpt) cc_final: 0.7437 (mmpt) REVERT: A 571 ASP cc_start: 0.7886 (t70) cc_final: 0.7415 (t0) REVERT: A 752 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8527 (mt) REVERT: A 900 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7976 (mtp) REVERT: A 988 GLU cc_start: 0.7484 (tp30) cc_final: 0.7150 (tp30) REVERT: A 1084 ASP cc_start: 0.7686 (t0) cc_final: 0.7201 (t0) REVERT: B 440 LYS cc_start: 0.8595 (ptmm) cc_final: 0.8378 (tmmm) REVERT: B 493 ARG cc_start: 0.8236 (mtp85) cc_final: 0.7925 (mmm-85) REVERT: B 654 GLU cc_start: 0.8459 (tt0) cc_final: 0.8218 (tt0) REVERT: B 751 ASN cc_start: 0.8546 (m-40) cc_final: 0.7935 (m-40) REVERT: B 752 LEU cc_start: 0.8126 (mt) cc_final: 0.7773 (mt) REVERT: B 768 THR cc_start: 0.8159 (m) cc_final: 0.7913 (p) REVERT: B 776 LYS cc_start: 0.8628 (ttpp) cc_final: 0.8383 (ttmm) REVERT: B 780 GLU cc_start: 0.8315 (tt0) cc_final: 0.7909 (tp30) REVERT: B 814 LYS cc_start: 0.8348 (mmtm) cc_final: 0.8043 (mmtt) REVERT: B 817 PHE cc_start: 0.7747 (t80) cc_final: 0.7533 (t80) REVERT: B 960 ASN cc_start: 0.8735 (t0) cc_final: 0.8293 (t0) REVERT: B 1031 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7868 (mt-10) REVERT: B 1050 MET cc_start: 0.8433 (ptm) cc_final: 0.8218 (ptm) REVERT: B 1072 GLU cc_start: 0.8475 (pm20) cc_final: 0.8211 (pm20) REVERT: B 1144 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7683 (tp30) REVERT: C 117 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7572 (mt) REVERT: C 194 PHE cc_start: 0.8687 (m-10) cc_final: 0.8372 (m-80) REVERT: C 370 ASN cc_start: 0.7874 (p0) cc_final: 0.7641 (p0) REVERT: C 371 LEU cc_start: 0.8812 (mp) cc_final: 0.8555 (mt) REVERT: C 405 ASP cc_start: 0.7827 (p0) cc_final: 0.7508 (p0) REVERT: C 465 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7756 (pt0) REVERT: C 478 LYS cc_start: 0.8818 (ptpp) cc_final: 0.8573 (ptpp) REVERT: C 751 ASN cc_start: 0.8399 (m110) cc_final: 0.7967 (m110) REVERT: C 754 LEU cc_start: 0.8501 (mt) cc_final: 0.8242 (mm) REVERT: C 780 GLU cc_start: 0.8161 (tt0) cc_final: 0.7940 (tp30) REVERT: C 918 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7936 (mt-10) REVERT: C 950 ASP cc_start: 0.7525 (m-30) cc_final: 0.7258 (m-30) REVERT: C 1010 GLN cc_start: 0.8449 (mp10) cc_final: 0.8078 (mp10) REVERT: C 1038 LYS cc_start: 0.8528 (mmmt) cc_final: 0.8273 (mmmm) REVERT: C 1118 ASP cc_start: 0.8123 (m-30) cc_final: 0.7922 (m-30) REVERT: C 1141 LEU cc_start: 0.8490 (tp) cc_final: 0.8170 (tt) outliers start: 50 outliers final: 22 residues processed: 512 average time/residue: 0.6666 time to fit residues: 393.8753 Evaluate side-chains 512 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 484 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 219 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 chunk 293 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 311 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 232 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 81 ASN A 239 GLN A 360 ASN A 777 ASN B 703 ASN C 66 HIS C 81 ASN C 779 GLN C 824 ASN C 907 ASN C 935 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.138066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.110267 restraints weight = 38471.326| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.67 r_work: 0.3316 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 25935 Z= 0.194 Angle : 0.648 14.801 35379 Z= 0.328 Chirality : 0.047 0.432 4138 Planarity : 0.005 0.069 4464 Dihedral : 6.570 59.085 4463 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.66 % Favored : 94.24 % Rotamer: Outliers : 2.34 % Allowed : 14.25 % Favored : 83.41 % 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: 3072 helix: 1.75 (0.21), residues: 710 sheet: 0.94 (0.19), residues: 703 loop : -1.64 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1107 TYR 0.027 0.002 TYR C 453 PHE 0.022 0.002 PHE B 400 TRP 0.015 0.002 TRP C 436 HIS 0.004 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00461 (25840) covalent geometry : angle 0.61720 (35136) SS BOND : bond 0.00512 ( 42) SS BOND : angle 1.85915 ( 84) hydrogen bonds : bond 0.06630 ( 1014) hydrogen bonds : angle 5.00463 ( 2748) link_BETA1-4 : bond 0.00388 ( 16) link_BETA1-4 : angle 1.13382 ( 48) link_NAG-ASN : bond 0.00513 ( 37) link_NAG-ASN : angle 3.16881 ( 111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 507 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7656 (mp0) cc_final: 0.7331 (mm-30) REVERT: A 369 TYR cc_start: 0.7942 (p90) cc_final: 0.7695 (p90) REVERT: A 436 TRP cc_start: 0.7841 (p90) cc_final: 0.7588 (p90) REVERT: A 529 LYS cc_start: 0.8461 (tmtt) cc_final: 0.8212 (tmtt) REVERT: A 571 ASP cc_start: 0.7936 (t70) cc_final: 0.7450 (t0) REVERT: A 988 GLU cc_start: 0.7529 (tp30) cc_final: 0.7207 (tp30) REVERT: A 1084 ASP cc_start: 0.7740 (t0) cc_final: 0.7221 (t0) REVERT: B 81 ASN cc_start: 0.7829 (m-40) cc_final: 0.7519 (m-40) REVERT: B 132 GLU cc_start: 0.6439 (pm20) cc_final: 0.5794 (pm20) REVERT: B 241 LEU cc_start: 0.7930 (mt) cc_final: 0.7703 (mt) REVERT: B 242 LEU cc_start: 0.8311 (mm) cc_final: 0.8046 (mp) REVERT: B 440 LYS cc_start: 0.8602 (ptmm) cc_final: 0.8293 (tmmm) REVERT: B 493 ARG cc_start: 0.8247 (mtp85) cc_final: 0.7951 (mmm-85) REVERT: B 654 GLU cc_start: 0.8452 (tt0) cc_final: 0.8214 (tt0) REVERT: B 751 ASN cc_start: 0.8529 (m-40) cc_final: 0.7867 (m-40) REVERT: B 752 LEU cc_start: 0.8178 (mt) cc_final: 0.7810 (mt) REVERT: B 776 LYS cc_start: 0.8649 (ttpp) cc_final: 0.8405 (ttmm) REVERT: B 780 GLU cc_start: 0.8325 (tt0) cc_final: 0.7873 (tp30) REVERT: B 790 LYS cc_start: 0.8056 (mtmm) cc_final: 0.7836 (mtmm) REVERT: B 814 LYS cc_start: 0.8369 (mmtm) cc_final: 0.8078 (mmtt) REVERT: B 848 ASP cc_start: 0.6913 (t0) cc_final: 0.6631 (t0) REVERT: B 1050 MET cc_start: 0.8480 (ptm) cc_final: 0.8258 (ptm) REVERT: B 1072 GLU cc_start: 0.8387 (pm20) cc_final: 0.8167 (pm20) REVERT: B 1144 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7697 (tp30) REVERT: C 83 VAL cc_start: 0.8314 (t) cc_final: 0.8097 (p) REVERT: C 118 LEU cc_start: 0.8381 (mp) cc_final: 0.8033 (mp) REVERT: C 133 PHE cc_start: 0.6887 (m-80) cc_final: 0.6166 (m-80) REVERT: C 194 PHE cc_start: 0.8705 (m-10) cc_final: 0.8378 (m-80) REVERT: C 370 ASN cc_start: 0.7860 (p0) cc_final: 0.7616 (p0) REVERT: C 371 LEU cc_start: 0.8819 (mp) cc_final: 0.8554 (mt) REVERT: C 405 ASP cc_start: 0.7921 (p0) cc_final: 0.7623 (p0) REVERT: C 465 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7593 (pp20) REVERT: C 478 LYS cc_start: 0.8776 (ptpp) cc_final: 0.8539 (ptpp) REVERT: C 751 ASN cc_start: 0.8447 (m110) cc_final: 0.8184 (m-40) REVERT: C 754 LEU cc_start: 0.8517 (mt) cc_final: 0.8265 (mm) REVERT: C 780 GLU cc_start: 0.8211 (tt0) cc_final: 0.7928 (tp30) REVERT: C 918 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7959 (mt-10) REVERT: C 950 ASP cc_start: 0.7651 (m-30) cc_final: 0.7354 (m-30) REVERT: C 965 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8694 (mt0) REVERT: C 1010 GLN cc_start: 0.8486 (mp10) cc_final: 0.8092 (mp10) REVERT: C 1038 LYS cc_start: 0.8543 (mmmt) cc_final: 0.8290 (mmmm) REVERT: C 1073 LYS cc_start: 0.8427 (mtpt) cc_final: 0.8186 (mmmm) REVERT: C 1141 LEU cc_start: 0.8491 (tp) cc_final: 0.8238 (tt) outliers start: 64 outliers final: 40 residues processed: 539 average time/residue: 0.6290 time to fit residues: 392.2608 Evaluate side-chains 539 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 497 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 257 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 0.0370 chunk 132 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 chunk 277 optimal weight: 0.5980 chunk 83 optimal weight: 0.3980 chunk 157 optimal weight: 0.1980 chunk 147 optimal weight: 0.4980 chunk 208 optimal weight: 60.0000 chunk 103 optimal weight: 0.0060 overall best weight: 0.2274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 239 GLN A 360 ASN B 556 ASN B 703 ASN C 66 HIS C 81 ASN C 779 GLN C 824 ASN C 907 ASN C 935 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.140858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.113447 restraints weight = 38326.901| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.57 r_work: 0.3362 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 25935 Z= 0.114 Angle : 0.596 13.987 35379 Z= 0.299 Chirality : 0.045 0.421 4138 Planarity : 0.005 0.065 4464 Dihedral : 6.201 56.623 4463 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.26 % Favored : 95.64 % Rotamer: Outliers : 1.79 % Allowed : 16.08 % Favored : 82.13 % 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: -0.08 (0.15), residues: 3072 helix: 1.96 (0.21), residues: 703 sheet: 1.06 (0.19), residues: 689 loop : -1.53 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 403 TYR 0.021 0.001 TYR C 351 PHE 0.021 0.001 PHE A 377 TRP 0.012 0.001 TRP A 436 HIS 0.004 0.000 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00244 (25840) covalent geometry : angle 0.56874 (35136) SS BOND : bond 0.00421 ( 42) SS BOND : angle 1.38784 ( 84) hydrogen bonds : bond 0.05100 ( 1014) hydrogen bonds : angle 4.84645 ( 2748) link_BETA1-4 : bond 0.00445 ( 16) link_BETA1-4 : angle 1.10287 ( 48) link_NAG-ASN : bond 0.00581 ( 37) link_NAG-ASN : angle 2.96595 ( 111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 496 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7514 (mp0) cc_final: 0.7153 (mm-30) REVERT: A 302 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8259 (t) REVERT: A 355 ARG cc_start: 0.7797 (mmm-85) cc_final: 0.7584 (mmm-85) REVERT: A 369 TYR cc_start: 0.7935 (p90) cc_final: 0.7623 (p90) REVERT: A 436 TRP cc_start: 0.7843 (p90) cc_final: 0.7524 (p90) REVERT: A 529 LYS cc_start: 0.8446 (tmtt) cc_final: 0.8211 (tmtt) REVERT: A 571 ASP cc_start: 0.7947 (t70) cc_final: 0.7450 (t0) REVERT: A 900 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7983 (mtp) REVERT: A 988 GLU cc_start: 0.7479 (tp30) cc_final: 0.7148 (tp30) REVERT: A 1084 ASP cc_start: 0.7740 (t0) cc_final: 0.7203 (t0) REVERT: B 132 GLU cc_start: 0.6103 (pm20) cc_final: 0.5074 (pm20) REVERT: B 440 LYS cc_start: 0.8587 (ptmm) cc_final: 0.8292 (tmmm) REVERT: B 493 ARG cc_start: 0.8192 (mtp85) cc_final: 0.7875 (mmm-85) REVERT: B 508 TYR cc_start: 0.8300 (m-10) cc_final: 0.8075 (m-10) REVERT: B 588 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8317 (p) REVERT: B 654 GLU cc_start: 0.8436 (tt0) cc_final: 0.8204 (tt0) REVERT: B 702 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7286 (tp30) REVERT: B 751 ASN cc_start: 0.8434 (m-40) cc_final: 0.7821 (m-40) REVERT: B 752 LEU cc_start: 0.8055 (mt) cc_final: 0.7699 (mt) REVERT: B 776 LYS cc_start: 0.8645 (ttpp) cc_final: 0.8409 (ttmm) REVERT: B 780 GLU cc_start: 0.8289 (tt0) cc_final: 0.7914 (tp30) REVERT: B 814 LYS cc_start: 0.8357 (mmtm) cc_final: 0.8062 (mmtt) REVERT: B 817 PHE cc_start: 0.7789 (t80) cc_final: 0.7589 (t80) REVERT: B 960 ASN cc_start: 0.8711 (t0) cc_final: 0.8296 (t0) REVERT: B 1050 MET cc_start: 0.8401 (ptm) cc_final: 0.8095 (ptm) REVERT: B 1144 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7668 (tp30) REVERT: C 118 LEU cc_start: 0.8320 (mp) cc_final: 0.8008 (mp) REVERT: C 133 PHE cc_start: 0.6797 (m-80) cc_final: 0.6008 (m-80) REVERT: C 194 PHE cc_start: 0.8665 (m-10) cc_final: 0.8370 (m-80) REVERT: C 370 ASN cc_start: 0.7907 (p0) cc_final: 0.7666 (p0) REVERT: C 371 LEU cc_start: 0.8795 (mp) cc_final: 0.8515 (mt) REVERT: C 405 ASP cc_start: 0.7845 (p0) cc_final: 0.7557 (p0) REVERT: C 465 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7574 (pp20) REVERT: C 478 LYS cc_start: 0.8785 (ptpp) cc_final: 0.8562 (ptpp) REVERT: C 751 ASN cc_start: 0.8420 (m110) cc_final: 0.8050 (m110) REVERT: C 754 LEU cc_start: 0.8495 (mt) cc_final: 0.8245 (mm) REVERT: C 822 LEU cc_start: 0.8034 (mt) cc_final: 0.7813 (mp) REVERT: C 1010 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8071 (mp10) REVERT: C 1014 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8261 (mtm180) REVERT: C 1038 LYS cc_start: 0.8517 (mmmt) cc_final: 0.8266 (mmmm) REVERT: C 1141 LEU cc_start: 0.8502 (tp) cc_final: 0.8194 (tt) outliers start: 49 outliers final: 20 residues processed: 520 average time/residue: 0.6784 time to fit residues: 406.2692 Evaluate side-chains 510 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 484 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 260 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 250 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 294 optimal weight: 1.9990 chunk 306 optimal weight: 0.0770 chunk 199 optimal weight: 0.4980 chunk 225 optimal weight: 0.0770 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 81 ASN A 239 GLN A 360 ASN A 777 ASN B 703 ASN C 81 ASN C 603 ASN C 779 GLN C 824 ASN C 907 ASN C 935 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.140665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.112911 restraints weight = 38444.534| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.68 r_work: 0.3350 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25935 Z= 0.133 Angle : 0.609 13.580 35379 Z= 0.306 Chirality : 0.046 0.512 4138 Planarity : 0.005 0.070 4464 Dihedral : 6.098 56.667 4462 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.85 % Favored : 95.05 % Rotamer: Outliers : 2.05 % Allowed : 16.48 % Favored : 81.48 % 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: -0.08 (0.15), residues: 3072 helix: 1.94 (0.21), residues: 704 sheet: 1.03 (0.19), residues: 701 loop : -1.52 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 577 TYR 0.027 0.001 TYR C 453 PHE 0.024 0.001 PHE C 456 TRP 0.011 0.001 TRP C 436 HIS 0.003 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00304 (25840) covalent geometry : angle 0.57913 (35136) SS BOND : bond 0.00421 ( 42) SS BOND : angle 1.50789 ( 84) hydrogen bonds : bond 0.05400 ( 1014) hydrogen bonds : angle 4.82258 ( 2748) link_BETA1-4 : bond 0.00380 ( 16) link_BETA1-4 : angle 1.08376 ( 48) link_NAG-ASN : bond 0.00533 ( 37) link_NAG-ASN : angle 3.14735 ( 111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 491 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7540 (mp0) cc_final: 0.7288 (mm-30) REVERT: A 302 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8312 (t) REVERT: A 356 LYS cc_start: 0.8524 (mmmm) cc_final: 0.8289 (mmmm) REVERT: A 369 TYR cc_start: 0.7974 (p90) cc_final: 0.7668 (p90) REVERT: A 436 TRP cc_start: 0.7862 (p90) cc_final: 0.7598 (p90) REVERT: A 529 LYS cc_start: 0.8418 (tmtt) cc_final: 0.8190 (tmtt) REVERT: A 537 LYS cc_start: 0.7636 (tttp) cc_final: 0.7418 (ttpp) REVERT: A 571 ASP cc_start: 0.7968 (t70) cc_final: 0.7439 (t0) REVERT: A 702 GLU cc_start: 0.7030 (tp30) cc_final: 0.6804 (tp30) REVERT: A 988 GLU cc_start: 0.7453 (tp30) cc_final: 0.7087 (tp30) REVERT: A 1084 ASP cc_start: 0.7755 (t0) cc_final: 0.7213 (t0) REVERT: B 81 ASN cc_start: 0.7744 (m-40) cc_final: 0.7441 (m-40) REVERT: B 132 GLU cc_start: 0.6156 (pm20) cc_final: 0.5505 (pm20) REVERT: B 242 LEU cc_start: 0.8394 (mm) cc_final: 0.8027 (mp) REVERT: B 324 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7542 (pm20) REVERT: B 440 LYS cc_start: 0.8602 (ptmm) cc_final: 0.8300 (tmmm) REVERT: B 493 ARG cc_start: 0.8329 (mtp85) cc_final: 0.7987 (mmm-85) REVERT: B 588 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8296 (p) REVERT: B 654 GLU cc_start: 0.8449 (tt0) cc_final: 0.8212 (tt0) REVERT: B 702 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7317 (tp30) REVERT: B 748 GLU cc_start: 0.7765 (mp0) cc_final: 0.7541 (mp0) REVERT: B 751 ASN cc_start: 0.8467 (m-40) cc_final: 0.7845 (m-40) REVERT: B 752 LEU cc_start: 0.8115 (mt) cc_final: 0.7747 (mt) REVERT: B 776 LYS cc_start: 0.8625 (ttpp) cc_final: 0.8374 (ttmm) REVERT: B 780 GLU cc_start: 0.8301 (tt0) cc_final: 0.7897 (tp30) REVERT: B 790 LYS cc_start: 0.8049 (mtmm) cc_final: 0.7778 (mtmm) REVERT: B 814 LYS cc_start: 0.8353 (mmtm) cc_final: 0.8051 (mmtt) REVERT: B 848 ASP cc_start: 0.6912 (t0) cc_final: 0.6608 (t0) REVERT: B 960 ASN cc_start: 0.8683 (t0) cc_final: 0.8273 (t0) REVERT: B 1050 MET cc_start: 0.8389 (ptm) cc_final: 0.8122 (ptm) REVERT: B 1144 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7673 (tp30) REVERT: C 118 LEU cc_start: 0.8354 (mp) cc_final: 0.8010 (mp) REVERT: C 133 PHE cc_start: 0.7010 (m-80) cc_final: 0.6289 (m-80) REVERT: C 194 PHE cc_start: 0.8689 (m-10) cc_final: 0.8390 (m-80) REVERT: C 226 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7675 (tm) REVERT: C 370 ASN cc_start: 0.7898 (p0) cc_final: 0.7656 (p0) REVERT: C 371 LEU cc_start: 0.8793 (mp) cc_final: 0.8494 (mt) REVERT: C 405 ASP cc_start: 0.7869 (p0) cc_final: 0.7615 (p0) REVERT: C 465 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7656 (pp20) REVERT: C 478 LYS cc_start: 0.8759 (ptpp) cc_final: 0.8513 (ptpp) REVERT: C 751 ASN cc_start: 0.8417 (m110) cc_final: 0.8022 (m110) REVERT: C 754 LEU cc_start: 0.8483 (mt) cc_final: 0.8230 (mm) REVERT: C 950 ASP cc_start: 0.7528 (m-30) cc_final: 0.7233 (m-30) REVERT: C 1010 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8104 (mp10) REVERT: C 1038 LYS cc_start: 0.8549 (mmmt) cc_final: 0.8283 (mmmm) REVERT: C 1111 GLU cc_start: 0.8325 (tt0) cc_final: 0.8002 (mt-10) outliers start: 56 outliers final: 27 residues processed: 519 average time/residue: 0.6612 time to fit residues: 395.5260 Evaluate side-chains 509 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 476 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 226 optimal weight: 2.9990 chunk 230 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 307 optimal weight: 0.1980 chunk 165 optimal weight: 0.9990 chunk 309 optimal weight: 0.6980 chunk 188 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 199 optimal weight: 0.5980 chunk 193 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 239 GLN A 360 ASN A 777 ASN A 960 ASN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN C 81 ASN C 779 GLN C 804 GLN C 824 ASN C 907 ASN C 935 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.139849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.112326 restraints weight = 38239.746| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.64 r_work: 0.3347 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25935 Z= 0.153 Angle : 0.636 13.561 35379 Z= 0.317 Chirality : 0.047 0.511 4138 Planarity : 0.005 0.072 4464 Dihedral : 6.136 57.247 4462 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.98 % Favored : 94.92 % Rotamer: Outliers : 1.94 % Allowed : 17.57 % Favored : 80.49 % 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: -0.08 (0.15), residues: 3072 helix: 1.91 (0.21), residues: 704 sheet: 1.03 (0.19), residues: 697 loop : -1.50 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 577 TYR 0.028 0.001 TYR C 351 PHE 0.016 0.001 PHE B 400 TRP 0.013 0.001 TRP C 436 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00356 (25840) covalent geometry : angle 0.60853 (35136) SS BOND : bond 0.00429 ( 42) SS BOND : angle 1.63842 ( 84) hydrogen bonds : bond 0.05724 ( 1014) hydrogen bonds : angle 4.86621 ( 2748) link_BETA1-4 : bond 0.00383 ( 16) link_BETA1-4 : angle 1.11591 ( 48) link_NAG-ASN : bond 0.00503 ( 37) link_NAG-ASN : angle 3.02450 ( 111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 487 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7535 (mp0) cc_final: 0.7305 (mm-30) REVERT: A 302 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8315 (t) REVERT: A 369 TYR cc_start: 0.7992 (p90) cc_final: 0.7681 (p90) REVERT: A 436 TRP cc_start: 0.7848 (p90) cc_final: 0.7611 (p90) REVERT: A 529 LYS cc_start: 0.8457 (tmtt) cc_final: 0.8224 (tmtt) REVERT: A 537 LYS cc_start: 0.7718 (tttp) cc_final: 0.7440 (ttpp) REVERT: A 571 ASP cc_start: 0.7965 (t70) cc_final: 0.7437 (t0) REVERT: A 988 GLU cc_start: 0.7479 (tp30) cc_final: 0.7107 (tp30) REVERT: A 1084 ASP cc_start: 0.7752 (t0) cc_final: 0.7237 (t0) REVERT: B 81 ASN cc_start: 0.7869 (m-40) cc_final: 0.7606 (m-40) REVERT: B 132 GLU cc_start: 0.6171 (pm20) cc_final: 0.5492 (pm20) REVERT: B 196 ASN cc_start: 0.8897 (t0) cc_final: 0.8642 (t0) REVERT: B 242 LEU cc_start: 0.8395 (mm) cc_final: 0.8017 (mp) REVERT: B 324 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7547 (pm20) REVERT: B 440 LYS cc_start: 0.8608 (ptmm) cc_final: 0.8329 (tmmm) REVERT: B 493 ARG cc_start: 0.8303 (mtp85) cc_final: 0.7982 (mmm-85) REVERT: B 588 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8335 (p) REVERT: B 654 GLU cc_start: 0.8418 (tt0) cc_final: 0.8180 (tt0) REVERT: B 702 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7423 (tp30) REVERT: B 748 GLU cc_start: 0.7803 (mp0) cc_final: 0.7500 (pm20) REVERT: B 751 ASN cc_start: 0.8432 (m-40) cc_final: 0.7834 (m-40) REVERT: B 752 LEU cc_start: 0.8107 (mt) cc_final: 0.7771 (mt) REVERT: B 776 LYS cc_start: 0.8604 (ttpp) cc_final: 0.8355 (ttmm) REVERT: B 780 GLU cc_start: 0.8300 (tt0) cc_final: 0.7876 (tp30) REVERT: B 814 LYS cc_start: 0.8363 (mmtm) cc_final: 0.8064 (mmtt) REVERT: B 848 ASP cc_start: 0.6966 (t0) cc_final: 0.6648 (t0) REVERT: B 960 ASN cc_start: 0.8729 (t0) cc_final: 0.8321 (t0) REVERT: B 1050 MET cc_start: 0.8390 (ptm) cc_final: 0.8152 (ptm) REVERT: B 1144 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7649 (tp30) REVERT: C 110 LEU cc_start: 0.7684 (mp) cc_final: 0.7446 (mm) REVERT: C 118 LEU cc_start: 0.8401 (mp) cc_final: 0.8112 (mp) REVERT: C 194 PHE cc_start: 0.8683 (m-10) cc_final: 0.8350 (m-80) REVERT: C 226 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7673 (tm) REVERT: C 371 LEU cc_start: 0.8798 (mp) cc_final: 0.8568 (mt) REVERT: C 405 ASP cc_start: 0.7869 (p0) cc_final: 0.7597 (p0) REVERT: C 465 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7596 (pp20) REVERT: C 478 LYS cc_start: 0.8671 (ptpp) cc_final: 0.8424 (ptpp) REVERT: C 754 LEU cc_start: 0.8487 (mt) cc_final: 0.8234 (mm) REVERT: C 790 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7814 (mmtp) REVERT: C 950 ASP cc_start: 0.7543 (m-30) cc_final: 0.7244 (m-30) REVERT: C 1010 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8105 (mp10) REVERT: C 1014 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8208 (mtm180) REVERT: C 1038 LYS cc_start: 0.8535 (mmmt) cc_final: 0.8273 (mmmm) outliers start: 53 outliers final: 29 residues processed: 515 average time/residue: 0.6275 time to fit residues: 373.6058 Evaluate side-chains 521 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 484 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 163 optimal weight: 1.9990 chunk 208 optimal weight: 50.0000 chunk 213 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 253 optimal weight: 0.0770 chunk 221 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 191 optimal weight: 0.6980 chunk 277 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 293 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 81 ASN A 239 GLN A 360 ASN A 777 ASN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN C 52 GLN C 81 ASN C 751 ASN C 779 GLN C 804 GLN C 824 ASN C 907 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.139666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.112427 restraints weight = 38528.536| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.56 r_work: 0.3341 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25935 Z= 0.151 Angle : 0.641 13.372 35379 Z= 0.321 Chirality : 0.048 0.826 4138 Planarity : 0.005 0.074 4464 Dihedral : 6.176 58.115 4462 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.08 % Favored : 94.79 % Rotamer: Outliers : 1.83 % Allowed : 18.23 % Favored : 79.94 % 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: -0.09 (0.15), residues: 3072 helix: 1.90 (0.21), residues: 704 sheet: 0.98 (0.19), residues: 699 loop : -1.48 (0.14), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 237 TYR 0.028 0.001 TYR C 351 PHE 0.026 0.001 PHE C 456 TRP 0.013 0.001 TRP C 436 HIS 0.002 0.000 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00350 (25840) covalent geometry : angle 0.61095 (35136) SS BOND : bond 0.00436 ( 42) SS BOND : angle 1.65926 ( 84) hydrogen bonds : bond 0.05707 ( 1014) hydrogen bonds : angle 4.85806 ( 2748) link_BETA1-4 : bond 0.00383 ( 16) link_BETA1-4 : angle 1.12459 ( 48) link_NAG-ASN : bond 0.00699 ( 37) link_NAG-ASN : angle 3.21796 ( 111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 484 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8281 (t) REVERT: A 369 TYR cc_start: 0.8015 (p90) cc_final: 0.7708 (p90) REVERT: A 529 LYS cc_start: 0.8442 (tmtt) cc_final: 0.8202 (tmtt) REVERT: A 537 LYS cc_start: 0.7717 (tttp) cc_final: 0.7453 (ttpp) REVERT: A 571 ASP cc_start: 0.7987 (t70) cc_final: 0.7459 (t0) REVERT: A 988 GLU cc_start: 0.7492 (tp30) cc_final: 0.7113 (tp30) REVERT: A 1084 ASP cc_start: 0.7761 (t0) cc_final: 0.7244 (t0) REVERT: B 81 ASN cc_start: 0.7876 (m-40) cc_final: 0.7628 (m-40) REVERT: B 132 GLU cc_start: 0.6166 (pm20) cc_final: 0.5172 (pm20) REVERT: B 196 ASN cc_start: 0.8895 (t0) cc_final: 0.8643 (t0) REVERT: B 242 LEU cc_start: 0.8302 (mm) cc_final: 0.7937 (mp) REVERT: B 324 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7611 (pm20) REVERT: B 440 LYS cc_start: 0.8602 (ptmm) cc_final: 0.8328 (tmmm) REVERT: B 493 ARG cc_start: 0.8300 (mtp85) cc_final: 0.7960 (mmm-85) REVERT: B 588 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8358 (p) REVERT: B 654 GLU cc_start: 0.8429 (tt0) cc_final: 0.8189 (tt0) REVERT: B 748 GLU cc_start: 0.7801 (mp0) cc_final: 0.7543 (pm20) REVERT: B 751 ASN cc_start: 0.8437 (m-40) cc_final: 0.7831 (m-40) REVERT: B 752 LEU cc_start: 0.8087 (mt) cc_final: 0.7750 (mt) REVERT: B 776 LYS cc_start: 0.8621 (ttpp) cc_final: 0.8380 (ttmm) REVERT: B 780 GLU cc_start: 0.8315 (tt0) cc_final: 0.7895 (tp30) REVERT: B 814 LYS cc_start: 0.8360 (mmtm) cc_final: 0.8061 (mmtt) REVERT: B 848 ASP cc_start: 0.6995 (t0) cc_final: 0.6676 (t0) REVERT: B 960 ASN cc_start: 0.8752 (t0) cc_final: 0.8334 (t0) REVERT: B 1050 MET cc_start: 0.8369 (ptm) cc_final: 0.8076 (ptm) REVERT: B 1138 TYR cc_start: 0.8399 (t80) cc_final: 0.7967 (t80) REVERT: B 1144 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7670 (tp30) REVERT: C 110 LEU cc_start: 0.7708 (mp) cc_final: 0.7492 (mm) REVERT: C 118 LEU cc_start: 0.8285 (mp) cc_final: 0.8043 (mp) REVERT: C 133 PHE cc_start: 0.7253 (m-80) cc_final: 0.6999 (m-80) REVERT: C 194 PHE cc_start: 0.8675 (m-10) cc_final: 0.8345 (m-80) REVERT: C 226 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7682 (tm) REVERT: C 371 LEU cc_start: 0.8790 (mp) cc_final: 0.8556 (mt) REVERT: C 405 ASP cc_start: 0.7792 (p0) cc_final: 0.7559 (p0) REVERT: C 465 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7577 (pp20) REVERT: C 478 LYS cc_start: 0.8647 (ptpp) cc_final: 0.8413 (ptpp) REVERT: C 754 LEU cc_start: 0.8489 (mt) cc_final: 0.8244 (mm) REVERT: C 790 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8113 (mmtp) REVERT: C 950 ASP cc_start: 0.7541 (m-30) cc_final: 0.7244 (m-30) REVERT: C 1010 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8090 (mp10) REVERT: C 1014 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8201 (mtm180) REVERT: C 1038 LYS cc_start: 0.8548 (mmmt) cc_final: 0.8289 (mmmm) REVERT: C 1072 GLU cc_start: 0.8148 (pm20) cc_final: 0.7827 (pm20) REVERT: C 1141 LEU cc_start: 0.8470 (tp) cc_final: 0.8264 (tt) outliers start: 50 outliers final: 32 residues processed: 512 average time/residue: 0.6246 time to fit residues: 369.5770 Evaluate side-chains 519 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 479 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 301 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 279 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 121 optimal weight: 0.2980 chunk 139 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 239 GLN A 360 ASN A 603 ASN A 777 ASN B 703 ASN B 804 GLN C 52 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 779 GLN C 824 ASN C 907 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.136894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.109461 restraints weight = 38587.669| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.57 r_work: 0.3308 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 25935 Z= 0.217 Angle : 0.694 13.861 35379 Z= 0.350 Chirality : 0.050 0.818 4138 Planarity : 0.005 0.076 4464 Dihedral : 6.388 59.300 4462 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.63 % Favored : 94.24 % Rotamer: Outliers : 2.08 % Allowed : 18.38 % Favored : 79.54 % 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: -0.22 (0.15), residues: 3072 helix: 1.80 (0.21), residues: 698 sheet: 0.86 (0.19), residues: 705 loop : -1.55 (0.14), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 237 TYR 0.026 0.002 TYR C 453 PHE 0.016 0.002 PHE A 238 TRP 0.036 0.002 TRP A 436 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00517 (25840) covalent geometry : angle 0.66316 (35136) SS BOND : bond 0.00502 ( 42) SS BOND : angle 1.99057 ( 84) hydrogen bonds : bond 0.06782 ( 1014) hydrogen bonds : angle 4.99819 ( 2748) link_BETA1-4 : bond 0.00388 ( 16) link_BETA1-4 : angle 1.17198 ( 48) link_NAG-ASN : bond 0.00696 ( 37) link_NAG-ASN : angle 3.26838 ( 111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 504 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8334 (t) REVERT: A 331 ASN cc_start: 0.6755 (m110) cc_final: 0.6444 (t0) REVERT: A 369 TYR cc_start: 0.8066 (p90) cc_final: 0.7709 (p90) REVERT: A 529 LYS cc_start: 0.8443 (tmtt) cc_final: 0.8222 (tmtt) REVERT: A 537 LYS cc_start: 0.7994 (tttp) cc_final: 0.7708 (ttpp) REVERT: A 571 ASP cc_start: 0.8045 (t70) cc_final: 0.7523 (t0) REVERT: A 988 GLU cc_start: 0.7560 (tp30) cc_final: 0.7185 (tp30) REVERT: A 1045 LYS cc_start: 0.8253 (tppp) cc_final: 0.7772 (tppp) REVERT: A 1084 ASP cc_start: 0.7807 (t0) cc_final: 0.7374 (t0) REVERT: B 81 ASN cc_start: 0.7983 (m-40) cc_final: 0.7727 (m-40) REVERT: B 169 GLU cc_start: 0.8199 (tp30) cc_final: 0.7996 (tp30) REVERT: B 196 ASN cc_start: 0.8912 (t0) cc_final: 0.8657 (t0) REVERT: B 242 LEU cc_start: 0.8342 (mm) cc_final: 0.8029 (mp) REVERT: B 324 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7545 (pm20) REVERT: B 378 LYS cc_start: 0.7790 (mmmm) cc_final: 0.7528 (mmmm) REVERT: B 440 LYS cc_start: 0.8621 (ptmm) cc_final: 0.8331 (tmmm) REVERT: B 467 ASP cc_start: 0.8409 (p0) cc_final: 0.8122 (p0) REVERT: B 493 ARG cc_start: 0.8294 (mtp85) cc_final: 0.7958 (mmm-85) REVERT: B 556 ASN cc_start: 0.8194 (m110) cc_final: 0.7993 (m110) REVERT: B 583 GLU cc_start: 0.8413 (pt0) cc_final: 0.8190 (pt0) REVERT: B 588 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8404 (p) REVERT: B 702 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7682 (tt0) REVERT: B 751 ASN cc_start: 0.8467 (m-40) cc_final: 0.7898 (m-40) REVERT: B 752 LEU cc_start: 0.8129 (mt) cc_final: 0.7788 (mt) REVERT: B 776 LYS cc_start: 0.8664 (ttpp) cc_final: 0.8463 (ttmm) REVERT: B 918 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7581 (mt-10) REVERT: B 1050 MET cc_start: 0.8442 (ptm) cc_final: 0.8165 (ptm) REVERT: B 1138 TYR cc_start: 0.8422 (t80) cc_final: 0.7965 (t80) REVERT: C 95 ILE cc_start: 0.7778 (mm) cc_final: 0.7431 (tp) REVERT: C 110 LEU cc_start: 0.7760 (mp) cc_final: 0.7550 (mm) REVERT: C 112 SER cc_start: 0.6767 (p) cc_final: 0.6370 (m) REVERT: C 194 PHE cc_start: 0.8694 (m-10) cc_final: 0.8371 (m-80) REVERT: C 371 LEU cc_start: 0.8823 (mp) cc_final: 0.8576 (mt) REVERT: C 405 ASP cc_start: 0.7817 (p0) cc_final: 0.7593 (p0) REVERT: C 465 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7664 (pp20) REVERT: C 478 LYS cc_start: 0.8629 (ptpp) cc_final: 0.8388 (ptpp) REVERT: C 754 LEU cc_start: 0.8524 (mt) cc_final: 0.8284 (mm) REVERT: C 790 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8159 (mmtp) REVERT: C 945 LEU cc_start: 0.8170 (mt) cc_final: 0.7958 (mm) REVERT: C 950 ASP cc_start: 0.7661 (m-30) cc_final: 0.7352 (m-30) REVERT: C 1010 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8074 (mp10) REVERT: C 1014 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8208 (mtm180) REVERT: C 1038 LYS cc_start: 0.8537 (mmmt) cc_final: 0.8290 (mmmm) REVERT: C 1072 GLU cc_start: 0.8184 (pm20) cc_final: 0.7950 (pm20) REVERT: C 1073 LYS cc_start: 0.8413 (mtpt) cc_final: 0.8158 (mtpm) REVERT: C 1141 LEU cc_start: 0.8549 (tp) cc_final: 0.8248 (tm) outliers start: 57 outliers final: 34 residues processed: 534 average time/residue: 0.6760 time to fit residues: 415.7949 Evaluate side-chains 533 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 491 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 0.0470 chunk 287 optimal weight: 0.4980 chunk 259 optimal weight: 0.7980 chunk 290 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 269 optimal weight: 3.9990 chunk 221 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 176 optimal weight: 0.5980 chunk 265 optimal weight: 0.6980 chunk 153 optimal weight: 0.7980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 81 ASN A 239 GLN A 360 ASN A 658 ASN B 703 ASN B 804 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.139668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.112249 restraints weight = 38403.245| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.61 r_work: 0.3348 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25935 Z= 0.141 Angle : 0.662 13.293 35379 Z= 0.332 Chirality : 0.048 0.767 4138 Planarity : 0.005 0.074 4464 Dihedral : 6.278 59.606 4462 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.79 % Favored : 95.12 % Rotamer: Outliers : 1.53 % Allowed : 19.40 % Favored : 79.06 % 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: -0.13 (0.15), residues: 3072 helix: 1.89 (0.21), residues: 698 sheet: 0.99 (0.19), residues: 696 loop : -1.52 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 237 TYR 0.029 0.001 TYR C 351 PHE 0.031 0.001 PHE C 456 TRP 0.024 0.001 TRP A 436 HIS 0.002 0.000 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00319 (25840) covalent geometry : angle 0.63370 (35136) SS BOND : bond 0.00431 ( 42) SS BOND : angle 1.65658 ( 84) hydrogen bonds : bond 0.05712 ( 1014) hydrogen bonds : angle 4.90774 ( 2748) link_BETA1-4 : bond 0.00394 ( 16) link_BETA1-4 : angle 1.17287 ( 48) link_NAG-ASN : bond 0.00694 ( 37) link_NAG-ASN : angle 3.12367 ( 111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 490 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8692 (mttt) cc_final: 0.8416 (mttt) REVERT: A 109 THR cc_start: 0.8594 (m) cc_final: 0.8363 (p) REVERT: A 302 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8276 (t) REVERT: A 331 ASN cc_start: 0.6626 (m110) cc_final: 0.6094 (t0) REVERT: A 369 TYR cc_start: 0.8007 (p90) cc_final: 0.7660 (p90) REVERT: A 529 LYS cc_start: 0.8436 (tmtt) cc_final: 0.8210 (tmtt) REVERT: A 537 LYS cc_start: 0.7860 (tttp) cc_final: 0.7611 (ttpp) REVERT: A 571 ASP cc_start: 0.7975 (t70) cc_final: 0.7454 (t0) REVERT: A 979 ASP cc_start: 0.7845 (p0) cc_final: 0.7505 (p0) REVERT: A 988 GLU cc_start: 0.7507 (tp30) cc_final: 0.7158 (tp30) REVERT: A 1084 ASP cc_start: 0.7800 (t0) cc_final: 0.7371 (t0) REVERT: B 81 ASN cc_start: 0.7976 (m-40) cc_final: 0.7705 (m-40) REVERT: B 132 GLU cc_start: 0.6134 (pm20) cc_final: 0.5627 (pm20) REVERT: B 196 ASN cc_start: 0.8888 (t0) cc_final: 0.8635 (t0) REVERT: B 220 PHE cc_start: 0.8690 (t80) cc_final: 0.8280 (t80) REVERT: B 242 LEU cc_start: 0.8325 (mm) cc_final: 0.7968 (mp) REVERT: B 324 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7625 (pm20) REVERT: B 440 LYS cc_start: 0.8580 (ptmm) cc_final: 0.8301 (tmmm) REVERT: B 467 ASP cc_start: 0.8380 (p0) cc_final: 0.8137 (p0) REVERT: B 493 ARG cc_start: 0.8271 (mtp85) cc_final: 0.7929 (mmm-85) REVERT: B 588 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8369 (p) REVERT: B 702 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7672 (tt0) REVERT: B 751 ASN cc_start: 0.8442 (m-40) cc_final: 0.7814 (m-40) REVERT: B 752 LEU cc_start: 0.8144 (mt) cc_final: 0.7789 (mt) REVERT: B 776 LYS cc_start: 0.8632 (ttpp) cc_final: 0.8393 (ttmm) REVERT: B 780 GLU cc_start: 0.8319 (tt0) cc_final: 0.7915 (tp30) REVERT: B 848 ASP cc_start: 0.7056 (t0) cc_final: 0.6719 (t0) REVERT: B 1050 MET cc_start: 0.8389 (ptm) cc_final: 0.8111 (ptm) REVERT: B 1138 TYR cc_start: 0.8460 (t80) cc_final: 0.8057 (t80) REVERT: B 1144 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7680 (tp30) REVERT: C 95 ILE cc_start: 0.7686 (mm) cc_final: 0.7391 (tp) REVERT: C 110 LEU cc_start: 0.7740 (mp) cc_final: 0.7532 (mm) REVERT: C 112 SER cc_start: 0.6828 (p) cc_final: 0.6446 (m) REVERT: C 194 PHE cc_start: 0.8677 (m-10) cc_final: 0.8348 (m-80) REVERT: C 371 LEU cc_start: 0.8807 (mp) cc_final: 0.8574 (mt) REVERT: C 465 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7581 (pp20) REVERT: C 478 LYS cc_start: 0.8624 (ptpp) cc_final: 0.8389 (ptpp) REVERT: C 754 LEU cc_start: 0.8512 (mt) cc_final: 0.8279 (mm) REVERT: C 790 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8041 (mmtp) REVERT: C 950 ASP cc_start: 0.7562 (m-30) cc_final: 0.7281 (m-30) REVERT: C 1010 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8117 (mp10) REVERT: C 1014 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8185 (mtm180) REVERT: C 1038 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8264 (mmmm) REVERT: C 1141 LEU cc_start: 0.8492 (tp) cc_final: 0.8199 (tt) outliers start: 42 outliers final: 29 residues processed: 515 average time/residue: 0.6603 time to fit residues: 392.0011 Evaluate side-chains 511 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 474 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 33 optimal weight: 2.9990 chunk 249 optimal weight: 0.9990 chunk 252 optimal weight: 1.9990 chunk 283 optimal weight: 0.0370 chunk 58 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 193 optimal weight: 0.7980 chunk 267 optimal weight: 1.9990 chunk 238 optimal weight: 0.9990 overall best weight: 0.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 239 GLN A 360 ASN A 751 ASN A 777 ASN B 703 ASN C 30 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 779 GLN C 804 GLN C 824 ASN C 907 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.138831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.111354 restraints weight = 38362.041| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.63 r_work: 0.3321 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25935 Z= 0.173 Angle : 0.677 13.352 35379 Z= 0.340 Chirality : 0.048 0.724 4138 Planarity : 0.005 0.074 4464 Dihedral : 6.277 57.766 4462 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.47 % Favored : 94.43 % Rotamer: Outliers : 1.53 % Allowed : 19.69 % Favored : 78.77 % 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: -0.17 (0.15), residues: 3072 helix: 1.83 (0.21), residues: 698 sheet: 1.00 (0.19), residues: 694 loop : -1.55 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1107 TYR 0.029 0.002 TYR C 351 PHE 0.021 0.001 PHE A 592 TRP 0.023 0.002 TRP A 436 HIS 0.003 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00409 (25840) covalent geometry : angle 0.64948 (35136) SS BOND : bond 0.00454 ( 42) SS BOND : angle 1.76731 ( 84) hydrogen bonds : bond 0.06054 ( 1014) hydrogen bonds : angle 4.92539 ( 2748) link_BETA1-4 : bond 0.00381 ( 16) link_BETA1-4 : angle 1.15783 ( 48) link_NAG-ASN : bond 0.00656 ( 37) link_NAG-ASN : angle 3.12423 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10625.95 seconds wall clock time: 181 minutes 3.61 seconds (10863.61 seconds total)