Starting phenix.real_space_refine on Wed Jul 24 13:10:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyk_36724/07_2024/8jyk_36724.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyk_36724/07_2024/8jyk_36724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyk_36724/07_2024/8jyk_36724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyk_36724/07_2024/8jyk_36724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyk_36724/07_2024/8jyk_36724.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyk_36724/07_2024/8jyk_36724.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 111 5.16 5 C 16341 2.51 5 N 4203 2.21 5 O 4983 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 25638 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8294 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 57, 'TRANS': 1003} Chain breaks: 6 Chain: "B" 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: "C" 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: "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: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "E" Number of atoms: 8294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8294 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 57, 'TRANS': 1003} Chain breaks: 6 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: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "I" Number of atoms: 8294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8294 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 57, 'TRANS': 1003} Chain breaks: 6 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: "I" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 14.70, per 1000 atoms: 0.57 Number of scatterers: 25638 At special positions: 0 Unit cell: (137.685, 130.65, 164.82, 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 111 16.00 O 4983 8.00 N 4203 7.00 C 16341 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 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 A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.04 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.04 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.02 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E 840 " - pdb=" SG CYS E 851 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 166 " distance=2.04 Simple disulfide: pdb=" SG CYS I 291 " - pdb=" SG CYS I 301 " distance=2.03 Simple disulfide: pdb=" SG CYS I 336 " - pdb=" SG CYS I 361 " distance=2.03 Simple disulfide: pdb=" SG CYS I 379 " - pdb=" SG CYS I 432 " distance=2.03 Simple disulfide: pdb=" SG CYS I 391 " - pdb=" SG CYS I 525 " distance=2.04 Simple disulfide: pdb=" SG CYS I 480 " - pdb=" SG CYS I 488 " distance=2.03 Simple disulfide: pdb=" SG CYS I 538 " - pdb=" SG CYS I 590 " distance=2.04 Simple disulfide: pdb=" SG CYS I 617 " - pdb=" SG CYS I 649 " distance=2.03 Simple disulfide: pdb=" SG CYS I 662 " - pdb=" SG CYS I 671 " distance=2.03 Simple disulfide: pdb=" SG CYS I 738 " - pdb=" SG CYS I 760 " distance=2.03 Simple disulfide: pdb=" SG CYS I 743 " - pdb=" SG CYS I 749 " distance=2.03 Simple disulfide: pdb=" SG CYS I 840 " - pdb=" SG CYS I 851 " distance=2.03 Simple disulfide: pdb=" SG CYS I1032 " - pdb=" SG CYS I1043 " distance=2.03 Simple disulfide: pdb=" SG CYS I1082 " - pdb=" SG CYS I1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A1134 " " NAG A1312 " - " ASN A 616 " " NAG B 1 " - " ASN A 717 " " NAG C 1 " - " ASN A 801 " " NAG D 1 " - " ASN A1098 " " NAG E1301 " - " ASN E 61 " " NAG E1302 " - " ASN E 122 " " NAG E1303 " - " ASN E 165 " " NAG E1304 " - " ASN E 234 " " NAG E1305 " - " ASN E 282 " " NAG E1306 " - " ASN E 331 " " NAG E1307 " - " ASN E 343 " " NAG E1308 " - " ASN E 657 " " NAG E1309 " - " ASN E 709 " " NAG E1310 " - " ASN E1074 " " NAG E1311 " - " ASN E1134 " " NAG E1312 " - " ASN E 616 " " NAG F 1 " - " ASN E 717 " " NAG G 1 " - " ASN E 801 " " NAG H 1 " - " ASN E1098 " " NAG I1301 " - " ASN I 61 " " NAG I1302 " - " ASN I 122 " " NAG I1303 " - " ASN I 165 " " NAG I1304 " - " ASN I 234 " " NAG I1305 " - " ASN I 282 " " NAG I1306 " - " ASN I 331 " " NAG I1307 " - " ASN I 343 " " NAG I1308 " - " ASN I 657 " " NAG I1309 " - " ASN I 709 " " NAG I1310 " - " ASN I1074 " " NAG I1311 " - " ASN I1134 " " NAG I1312 " - " ASN I 616 " " NAG J 1 " - " ASN I 717 " " NAG K 1 " - " ASN I 801 " " NAG L 1 " - " ASN I1098 " Time building additional restraints: 9.73 Conformation dependent library (CDL) restraints added in 4.3 seconds 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5970 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 42 sheets defined 25.6% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.074A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 342' Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.752A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.680A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.822A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.747A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.563A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.588A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 843 removed outlier: 4.271A pdb=" N ASP A 843 " --> pdb=" O ASP A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 855 removed outlier: 3.579A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.068A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.177A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.591A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.505A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.635A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 337 through 342 removed outlier: 4.073A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE E 342 " --> pdb=" O PHE E 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 337 through 342' Processing helix chain 'E' and resid 364 through 371 removed outlier: 3.752A pdb=" N VAL E 367 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 Processing helix chain 'E' and resid 403 through 410 removed outlier: 3.680A pdb=" N VAL E 407 " --> pdb=" O GLY E 404 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N SER E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 506 removed outlier: 3.822A pdb=" N GLN E 506 " --> pdb=" O VAL E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 744 Processing helix chain 'E' and resid 746 through 754 removed outlier: 3.747A pdb=" N SER E 750 " --> pdb=" O SER E 746 " (cutoff:3.500A) Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.563A pdb=" N GLN E 762 " --> pdb=" O SER E 758 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 826 removed outlier: 3.587A pdb=" N VAL E 826 " --> pdb=" O LEU E 822 " (cutoff:3.500A) Processing helix chain 'E' and resid 835 through 843 removed outlier: 4.271A pdb=" N ASP E 843 " --> pdb=" O ASP E 839 " (cutoff:3.500A) Processing helix chain 'E' and resid 848 through 855 removed outlier: 3.578A pdb=" N ALA E 852 " --> pdb=" O ASP E 848 " (cutoff:3.500A) Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 886 through 891 removed outlier: 4.067A pdb=" N GLY E 891 " --> pdb=" O PHE E 888 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 909 Processing helix chain 'E' and resid 912 through 918 removed outlier: 4.176A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 removed outlier: 3.591A pdb=" N ILE E 934 " --> pdb=" O ALA E 930 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN E 935 " --> pdb=" O ILE E 931 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP E 936 " --> pdb=" O GLY E 932 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR E 941 " --> pdb=" O SER E 937 " (cutoff:3.500A) Processing helix chain 'E' and resid 945 through 965 removed outlier: 3.505A pdb=" N GLN E 949 " --> pdb=" O LEU E 945 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL E 952 " --> pdb=" O LEU E 948 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.635A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN E 992 " --> pdb=" O GLU E 988 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG E 995 " --> pdb=" O VAL E 991 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU E 996 " --> pdb=" O GLN E 992 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL E1033 " --> pdb=" O MET E1029 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 304 Processing helix chain 'I' and resid 337 through 342 removed outlier: 4.073A pdb=" N VAL I 341 " --> pdb=" O PRO I 337 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE I 342 " --> pdb=" O PHE I 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 337 through 342' Processing helix chain 'I' and resid 364 through 371 removed outlier: 3.751A pdb=" N VAL I 367 " --> pdb=" O ASP I 364 " (cutoff:3.500A) Processing helix chain 'I' and resid 383 through 387 Processing helix chain 'I' and resid 403 through 410 removed outlier: 3.680A pdb=" N VAL I 407 " --> pdb=" O GLY I 404 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N SER I 408 " --> pdb=" O ASN I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 416 through 422 Processing helix chain 'I' and resid 502 through 506 removed outlier: 3.822A pdb=" N GLN I 506 " --> pdb=" O VAL I 503 " (cutoff:3.500A) Processing helix chain 'I' and resid 737 through 744 Processing helix chain 'I' and resid 746 through 754 removed outlier: 3.747A pdb=" N SER I 750 " --> pdb=" O SER I 746 " (cutoff:3.500A) Processing helix chain 'I' and resid 758 through 783 removed outlier: 3.563A pdb=" N GLN I 762 " --> pdb=" O SER I 758 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP I 775 " --> pdb=" O ALA I 771 " (cutoff:3.500A) Processing helix chain 'I' and resid 816 through 826 removed outlier: 3.588A pdb=" N VAL I 826 " --> pdb=" O LEU I 822 " (cutoff:3.500A) Processing helix chain 'I' and resid 835 through 843 removed outlier: 4.271A pdb=" N ASP I 843 " --> pdb=" O ASP I 839 " (cutoff:3.500A) Processing helix chain 'I' and resid 848 through 855 removed outlier: 3.578A pdb=" N ALA I 852 " --> pdb=" O ASP I 848 " (cutoff:3.500A) Processing helix chain 'I' and resid 866 through 885 Processing helix chain 'I' and resid 886 through 891 removed outlier: 4.067A pdb=" N GLY I 891 " --> pdb=" O PHE I 888 " (cutoff:3.500A) Processing helix chain 'I' and resid 897 through 909 Processing helix chain 'I' and resid 912 through 918 removed outlier: 4.177A pdb=" N LEU I 916 " --> pdb=" O THR I 912 " (cutoff:3.500A) Processing helix chain 'I' and resid 919 through 941 removed outlier: 3.591A pdb=" N ILE I 934 " --> pdb=" O ALA I 930 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN I 935 " --> pdb=" O ILE I 931 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP I 936 " --> pdb=" O GLY I 932 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR I 941 " --> pdb=" O SER I 937 " (cutoff:3.500A) Processing helix chain 'I' and resid 945 through 965 removed outlier: 3.505A pdb=" N GLN I 949 " --> pdb=" O LEU I 945 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL I 951 " --> pdb=" O LYS I 947 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL I 952 " --> pdb=" O LEU I 948 " (cutoff:3.500A) Processing helix chain 'I' and resid 966 through 968 No H-bonds generated for 'chain 'I' and resid 966 through 968' Processing helix chain 'I' and resid 976 through 984 Processing helix chain 'I' and resid 985 through 1033 removed outlier: 4.635A pdb=" N VAL I 991 " --> pdb=" O PRO I 987 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN I 992 " --> pdb=" O GLU I 988 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG I 995 " --> pdb=" O VAL I 991 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU I 996 " --> pdb=" O GLN I 992 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL I1033 " --> pdb=" O MET I1029 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 23 through 30 removed outlier: 8.378A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.934A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 140 through 141 removed outlier: 3.721A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.245A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.538A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.523A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=10, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.030A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.879A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.600A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=14, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=15, first strand: chain 'E' and resid 23 through 30 removed outlier: 8.377A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N HIS E 207 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N ALA E 222 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'E' and resid 48 through 55 removed outlier: 3.934A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.722A pdb=" N LEU E 241 " --> pdb=" O GLY E 103 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA E 243 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE E 101 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASN E 121 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE E 106 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS E 129 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.245A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'E' and resid 325 through 328 removed outlier: 3.538A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=21, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.522A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL E 524 " --> pdb=" O PHE E 392 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'E' and resid 452 through 453 Processing sheet with id=23, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=24, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.030A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.878A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.600A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'E' and resid 1120 through 1121 Processing sheet with id=28, first strand: chain 'E' and resid 1094 through 1097 Processing sheet with id=29, first strand: chain 'I' and resid 23 through 30 removed outlier: 8.377A pdb=" N ASN I 61 " --> pdb=" O TYR I 269 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N TYR I 269 " --> pdb=" O ASN I 61 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE I 201 " --> pdb=" O ASP I 228 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP I 228 " --> pdb=" O PHE I 201 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE I 203 " --> pdb=" O LEU I 226 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N HIS I 207 " --> pdb=" O ALA I 222 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N ALA I 222 " --> pdb=" O HIS I 207 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL I 36 " --> pdb=" O LEU I 223 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'I' and resid 48 through 55 removed outlier: 3.934A pdb=" N ASP I 287 " --> pdb=" O LYS I 278 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'I' and resid 140 through 141 removed outlier: 3.721A pdb=" N LEU I 241 " --> pdb=" O GLY I 103 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLY I 103 " --> pdb=" O LEU I 241 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA I 243 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE I 101 " --> pdb=" O ALA I 243 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ARG I 102 " --> pdb=" O ASN I 121 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASN I 121 " --> pdb=" O ARG I 102 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE I 106 " --> pdb=" O LEU I 117 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS I 129 " --> pdb=" O LEU I 118 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'I' and resid 311 through 319 removed outlier: 5.246A pdb=" N ILE I 312 " --> pdb=" O THR I 599 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR I 599 " --> pdb=" O ILE I 312 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N GLN I 314 " --> pdb=" O VAL I 597 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL I 597 " --> pdb=" O GLN I 314 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER I 316 " --> pdb=" O VAL I 595 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY I 594 " --> pdb=" O GLN I 613 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'I' and resid 325 through 328 removed outlier: 3.537A pdb=" N ALA I 575 " --> pdb=" O GLY I 566 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'I' and resid 354 through 358 Processing sheet with id=35, first strand: chain 'I' and resid 361 through 362 removed outlier: 6.523A pdb=" N CYS I 361 " --> pdb=" O CYS I 525 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL I 524 " --> pdb=" O PHE I 392 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'I' and resid 452 through 453 Processing sheet with id=37, first strand: chain 'I' and resid 473 through 474 Processing sheet with id=38, first strand: chain 'I' and resid 654 through 655 removed outlier: 6.029A pdb=" N GLU I 654 " --> pdb=" O ALA I 694 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR I 696 " --> pdb=" O GLU I 654 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'I' and resid 711 through 728 removed outlier: 6.878A pdb=" N SER I 711 " --> pdb=" O THR I1076 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR I1076 " --> pdb=" O SER I 711 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA I 713 " --> pdb=" O ASN I1074 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASN I1074 " --> pdb=" O ALA I 713 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLU I1072 " --> pdb=" O PRO I 715 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N TYR I1067 " --> pdb=" O HIS I1048 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS I1048 " --> pdb=" O TYR I1067 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'I' and resid 733 through 736 removed outlier: 4.600A pdb=" N LYS I 733 " --> pdb=" O LEU I 861 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'I' and resid 1120 through 1121 Processing sheet with id=42, first strand: chain 'I' and resid 1094 through 1097 996 hydrogen bonds defined for protein. 2664 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.95 Time building geometry restraints manager: 10.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8133 1.34 - 1.47: 6564 1.47 - 1.59: 11397 1.59 - 1.71: 0 1.71 - 1.83: 135 Bond restraints: 26229 Sorted by residual: bond pdb=" C1 NAG I1308 " pdb=" O5 NAG I1308 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.04e+00 bond pdb=" C1 NAG E1308 " pdb=" O5 NAG E1308 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.01e+00 bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.01e+00 bond pdb=" C1 NAG E1307 " pdb=" O5 NAG E1307 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.73e+00 bond pdb=" C1 NAG A1307 " pdb=" O5 NAG A1307 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.59e+00 ... (remaining 26224 not shown) Histogram of bond angle deviations from ideal: 99.88 - 106.71: 748 106.71 - 113.54: 14468 113.54 - 120.36: 9221 120.36 - 127.19: 11038 127.19 - 134.02: 237 Bond angle restraints: 35712 Sorted by residual: angle pdb=" N THR A 108 " pdb=" CA THR A 108 " pdb=" C THR A 108 " ideal model delta sigma weight residual 114.56 110.93 3.63 1.27e+00 6.20e-01 8.19e+00 angle pdb=" N THR I 108 " pdb=" CA THR I 108 " pdb=" C THR I 108 " ideal model delta sigma weight residual 114.56 110.93 3.63 1.27e+00 6.20e-01 8.15e+00 angle pdb=" N THR E 108 " pdb=" CA THR E 108 " pdb=" C THR E 108 " ideal model delta sigma weight residual 114.56 110.94 3.62 1.27e+00 6.20e-01 8.11e+00 angle pdb=" C PHE I 342 " pdb=" N ASN I 343 " pdb=" CA ASN I 343 " ideal model delta sigma weight residual 121.54 126.89 -5.35 1.91e+00 2.74e-01 7.85e+00 angle pdb=" CA LEU E 118 " pdb=" CB LEU E 118 " pdb=" CG LEU E 118 " ideal model delta sigma weight residual 116.30 126.09 -9.79 3.50e+00 8.16e-02 7.82e+00 ... (remaining 35707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.37: 14688 16.37 - 32.74: 1204 32.74 - 49.11: 305 49.11 - 65.48: 99 65.48 - 81.85: 42 Dihedral angle restraints: 16338 sinusoidal: 7062 harmonic: 9276 Sorted by residual: dihedral pdb=" CB CYS I1082 " pdb=" SG CYS I1082 " pdb=" SG CYS I1126 " pdb=" CB CYS I1126 " ideal model delta sinusoidal sigma weight residual -86.00 -144.55 58.55 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -144.52 58.52 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" CB CYS E1082 " pdb=" SG CYS E1082 " pdb=" SG CYS E1126 " pdb=" CB CYS E1126 " ideal model delta sinusoidal sigma weight residual -86.00 -144.50 58.50 1 1.00e+01 1.00e-02 4.58e+01 ... (remaining 16335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3632 0.069 - 0.138: 562 0.138 - 0.206: 9 0.206 - 0.275: 0 0.275 - 0.344: 3 Chirality restraints: 4206 Sorted by residual: chirality pdb=" C1 NAG A1309 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1309 " pdb=" O5 NAG A1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" C1 NAG E1309 " pdb=" ND2 ASN E 709 " pdb=" C2 NAG E1309 " pdb=" O5 NAG E1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" C1 NAG I1309 " pdb=" ND2 ASN I 709 " pdb=" C2 NAG I1309 " pdb=" O5 NAG I1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 4203 not shown) Planarity restraints: 4593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 208 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.05e+00 pdb=" N PRO A 209 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 209 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 209 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 208 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.05e+00 pdb=" N PRO I 209 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO I 209 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 209 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 208 " 0.028 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO E 209 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 209 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 209 " 0.024 5.00e-02 4.00e+02 ... (remaining 4590 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1870 2.74 - 3.28: 23697 3.28 - 3.82: 39246 3.82 - 4.36: 46280 4.36 - 4.90: 83759 Nonbonded interactions: 194852 Sorted by model distance: nonbonded pdb=" NZ LYS I 811 " pdb=" OG SER I 813 " model vdw 2.202 2.520 nonbonded pdb=" NZ LYS E 811 " pdb=" OG SER E 813 " model vdw 2.202 2.520 nonbonded pdb=" NZ LYS A 811 " pdb=" OG SER A 813 " model vdw 2.202 2.520 nonbonded pdb=" O THR E 393 " pdb=" OG1 THR E 523 " model vdw 2.205 2.440 nonbonded pdb=" O THR I 393 " pdb=" OG1 THR I 523 " model vdw 2.205 2.440 ... (remaining 194847 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.180 Set scattering table: 0.200 Process input model: 70.660 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26229 Z= 0.207 Angle : 0.546 9.789 35712 Z= 0.281 Chirality : 0.046 0.344 4206 Planarity : 0.004 0.044 4548 Dihedral : 13.582 81.848 10242 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 3141 helix: 2.09 (0.21), residues: 723 sheet: 1.07 (0.18), residues: 729 loop : -1.26 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 436 HIS 0.002 0.000 HIS I1064 PHE 0.016 0.001 PHE I 906 TYR 0.015 0.001 TYR E1067 ARG 0.002 0.000 ARG E 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 849 LEU cc_start: 0.7835 (mt) cc_final: 0.7584 (mt) REVERT: E 52 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7945 (tm-30) REVERT: E 489 TYR cc_start: 0.7326 (m-80) cc_final: 0.6936 (m-80) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 1.1947 time to fit residues: 237.1728 Evaluate side-chains 75 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.0980 chunk 241 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 249 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 185 optimal weight: 1.9990 chunk 288 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.0628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26229 Z= 0.147 Angle : 0.503 9.769 35712 Z= 0.262 Chirality : 0.045 0.327 4206 Planarity : 0.004 0.053 4548 Dihedral : 7.037 57.774 4548 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.65 % Allowed : 4.83 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.15), residues: 3141 helix: 2.50 (0.21), residues: 708 sheet: 1.30 (0.18), residues: 762 loop : -1.25 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 436 HIS 0.002 0.000 HIS A 66 PHE 0.016 0.001 PHE A 168 TYR 0.021 0.001 TYR I 170 ARG 0.007 0.000 ARG I 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 849 LEU cc_start: 0.7871 (mt) cc_final: 0.7617 (mt) REVERT: E 52 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7939 (tm-30) REVERT: E 189 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8290 (tm) REVERT: I 319 ARG cc_start: 0.8583 (ttm110) cc_final: 0.8356 (ptm160) REVERT: I 427 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7831 (t0) outliers start: 18 outliers final: 7 residues processed: 103 average time/residue: 1.1884 time to fit residues: 147.1904 Evaluate side-chains 83 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 427 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 240 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 289 optimal weight: 0.8980 chunk 312 optimal weight: 0.8980 chunk 257 optimal weight: 5.9990 chunk 286 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 232 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26229 Z= 0.247 Angle : 0.551 8.087 35712 Z= 0.292 Chirality : 0.046 0.289 4206 Planarity : 0.004 0.067 4548 Dihedral : 6.610 58.237 4548 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.08 % Allowed : 6.13 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 3141 helix: 2.49 (0.21), residues: 693 sheet: 1.26 (0.18), residues: 756 loop : -1.32 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 436 HIS 0.004 0.001 HIS A1064 PHE 0.033 0.001 PHE A 906 TYR 0.019 0.001 TYR A1067 ARG 0.008 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 84 time to evaluate : 3.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 52 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7945 (tm-30) REVERT: E 985 ASP cc_start: 0.7647 (p0) cc_final: 0.7273 (p0) REVERT: E 988 GLU cc_start: 0.8108 (mp0) cc_final: 0.7700 (mp0) REVERT: I 319 ARG cc_start: 0.8509 (ttm110) cc_final: 0.8296 (ptm160) REVERT: I 427 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7873 (t0) outliers start: 30 outliers final: 12 residues processed: 108 average time/residue: 1.2072 time to fit residues: 155.7827 Evaluate side-chains 87 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 2.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 1134 ASN Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 635 VAL Chi-restraints excluded: chain I residue 1134 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 6.9990 chunk 217 optimal weight: 7.9990 chunk 150 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 194 optimal weight: 0.7980 chunk 290 optimal weight: 0.0570 chunk 307 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 275 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 overall best weight: 2.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 613 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 26229 Z= 0.316 Angle : 0.591 8.625 35712 Z= 0.313 Chirality : 0.048 0.281 4206 Planarity : 0.004 0.068 4548 Dihedral : 6.488 58.780 4548 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.30 % Allowed : 7.75 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 3141 helix: 2.30 (0.21), residues: 693 sheet: 1.20 (0.19), residues: 732 loop : -1.40 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 886 HIS 0.004 0.001 HIS A1064 PHE 0.035 0.002 PHE I 906 TYR 0.019 0.001 TYR I 170 ARG 0.009 0.000 ARG E 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 80 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.7117 (m) cc_final: 0.6777 (p) REVERT: A 988 GLU cc_start: 0.8004 (tp30) cc_final: 0.7660 (tp30) REVERT: E 52 GLN cc_start: 0.8322 (tm-30) cc_final: 0.8058 (tm-30) REVERT: E 189 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8342 (tm) REVERT: E 988 GLU cc_start: 0.7801 (mp0) cc_final: 0.7379 (mp0) REVERT: I 319 ARG cc_start: 0.8503 (ttm110) cc_final: 0.8286 (ptm160) REVERT: I 427 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7837 (t0) outliers start: 36 outliers final: 20 residues processed: 113 average time/residue: 1.1189 time to fit residues: 153.2228 Evaluate side-chains 96 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 74 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 635 VAL Chi-restraints excluded: chain E residue 1134 ASN Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 415 THR Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 635 VAL Chi-restraints excluded: chain I residue 1092 GLU Chi-restraints excluded: chain I residue 1134 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 7.9990 chunk 174 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 228 optimal weight: 0.0010 chunk 126 optimal weight: 0.9980 chunk 262 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 chunk 0 optimal weight: 0.9980 chunk 156 optimal weight: 8.9990 chunk 275 optimal weight: 0.7980 chunk 77 optimal weight: 0.2980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 613 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26229 Z= 0.141 Angle : 0.506 9.448 35712 Z= 0.265 Chirality : 0.044 0.290 4206 Planarity : 0.004 0.044 4548 Dihedral : 5.959 56.247 4548 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.94 % Allowed : 8.68 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3141 helix: 2.44 (0.20), residues: 696 sheet: 1.20 (0.18), residues: 753 loop : -1.33 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 886 HIS 0.003 0.000 HIS A 69 PHE 0.010 0.001 PHE I 168 TYR 0.015 0.001 TYR A1067 ARG 0.008 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 82 time to evaluate : 2.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 52 GLN cc_start: 0.8313 (tm-30) cc_final: 0.8076 (tm-30) REVERT: E 189 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8378 (tm) REVERT: E 988 GLU cc_start: 0.7881 (mp0) cc_final: 0.7469 (mp0) REVERT: I 427 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7806 (t0) outliers start: 26 outliers final: 14 residues processed: 108 average time/residue: 1.1932 time to fit residues: 154.4181 Evaluate side-chains 89 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 1134 ASN Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 1134 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 180 optimal weight: 0.0010 chunk 75 optimal weight: 0.0870 chunk 307 optimal weight: 3.9990 chunk 255 optimal weight: 4.9990 chunk 142 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 101 optimal weight: 0.0060 chunk 161 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26229 Z= 0.149 Angle : 0.502 10.548 35712 Z= 0.262 Chirality : 0.044 0.279 4206 Planarity : 0.004 0.058 4548 Dihedral : 5.719 56.893 4548 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.15 % Allowed : 9.01 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 3141 helix: 2.54 (0.21), residues: 696 sheet: 1.27 (0.18), residues: 753 loop : -1.29 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 886 HIS 0.002 0.001 HIS A 69 PHE 0.011 0.001 PHE I 168 TYR 0.017 0.001 TYR A1067 ARG 0.017 0.000 ARG E 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 82 time to evaluate : 2.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 189 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8375 (tm) REVERT: E 988 GLU cc_start: 0.7920 (mp0) cc_final: 0.7472 (mp0) REVERT: I 427 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7783 (t0) outliers start: 32 outliers final: 19 residues processed: 110 average time/residue: 1.1045 time to fit residues: 148.4219 Evaluate side-chains 96 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 75 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 635 VAL Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 1134 ASN Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 635 VAL Chi-restraints excluded: chain I residue 705 VAL Chi-restraints excluded: chain I residue 1134 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 174 optimal weight: 0.5980 chunk 259 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 306 optimal weight: 0.8980 chunk 191 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN A 613 GLN E 69 HIS E 613 GLN I 69 HIS I1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26229 Z= 0.283 Angle : 0.575 12.773 35712 Z= 0.303 Chirality : 0.047 0.250 4206 Planarity : 0.004 0.054 4548 Dihedral : 5.974 58.596 4548 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.26 % Allowed : 9.12 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 3141 helix: 2.40 (0.21), residues: 693 sheet: 1.25 (0.19), residues: 729 loop : -1.39 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 886 HIS 0.004 0.001 HIS I 66 PHE 0.020 0.001 PHE A 906 TYR 0.019 0.001 TYR I1067 ARG 0.013 0.000 ARG E 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 82 time to evaluate : 3.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 841 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7143 (pp) REVERT: A 985 ASP cc_start: 0.7878 (p0) cc_final: 0.7672 (p0) REVERT: A 988 GLU cc_start: 0.7782 (mp0) cc_final: 0.7385 (mp0) REVERT: E 988 GLU cc_start: 0.7871 (mp0) cc_final: 0.7400 (mp0) REVERT: I 427 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7788 (t0) outliers start: 35 outliers final: 21 residues processed: 114 average time/residue: 1.0109 time to fit residues: 142.9593 Evaluate side-chains 100 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 77 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 635 VAL Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 1134 ASN Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 635 VAL Chi-restraints excluded: chain I residue 705 VAL Chi-restraints excluded: chain I residue 1092 GLU Chi-restraints excluded: chain I residue 1134 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 chunk 208 optimal weight: 0.5980 chunk 151 optimal weight: 0.0370 chunk 28 optimal weight: 0.4980 chunk 240 optimal weight: 9.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN E 613 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 26229 Z= 0.142 Angle : 0.506 12.675 35712 Z= 0.263 Chirality : 0.044 0.268 4206 Planarity : 0.004 0.046 4548 Dihedral : 5.602 56.247 4548 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.01 % Allowed : 9.48 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.15), residues: 3141 helix: 2.47 (0.20), residues: 696 sheet: 1.24 (0.18), residues: 753 loop : -1.30 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 886 HIS 0.002 0.000 HIS A 69 PHE 0.009 0.001 PHE I 168 TYR 0.016 0.001 TYR I 170 ARG 0.010 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 82 time to evaluate : 2.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 841 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7216 (pp) REVERT: A 988 GLU cc_start: 0.7768 (mp0) cc_final: 0.7457 (mp0) REVERT: I 21 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6953 (pp) REVERT: I 210 ILE cc_start: 0.6954 (OUTLIER) cc_final: 0.6663 (pp) outliers start: 28 outliers final: 19 residues processed: 108 average time/residue: 1.0568 time to fit residues: 140.0485 Evaluate side-chains 101 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 1134 ASN Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 635 VAL Chi-restraints excluded: chain I residue 705 VAL Chi-restraints excluded: chain I residue 1134 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 3.9990 chunk 293 optimal weight: 0.9980 chunk 267 optimal weight: 4.9990 chunk 285 optimal weight: 0.6980 chunk 171 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 224 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 258 optimal weight: 0.9990 chunk 270 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26229 Z= 0.223 Angle : 0.541 12.328 35712 Z= 0.283 Chirality : 0.046 0.243 4206 Planarity : 0.004 0.055 4548 Dihedral : 5.710 57.778 4548 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.12 % Allowed : 9.55 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3141 helix: 2.51 (0.21), residues: 693 sheet: 1.21 (0.18), residues: 753 loop : -1.36 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 886 HIS 0.003 0.001 HIS A 66 PHE 0.013 0.001 PHE A 906 TYR 0.018 0.001 TYR I1067 ARG 0.013 0.000 ARG E 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 82 time to evaluate : 2.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 841 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7216 (pp) REVERT: A 988 GLU cc_start: 0.7840 (mp0) cc_final: 0.7554 (mp0) REVERT: E 988 GLU cc_start: 0.7948 (mp0) cc_final: 0.7475 (mp0) REVERT: I 21 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.7080 (pp) REVERT: I 210 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6650 (pp) outliers start: 31 outliers final: 20 residues processed: 111 average time/residue: 1.0556 time to fit residues: 144.2899 Evaluate side-chains 99 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 76 time to evaluate : 2.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 1134 ASN Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 635 VAL Chi-restraints excluded: chain I residue 705 VAL Chi-restraints excluded: chain I residue 1134 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 0.6980 chunk 302 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 316 optimal weight: 0.7980 chunk 291 optimal weight: 3.9990 chunk 252 optimal weight: 0.0040 chunk 26 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 154 optimal weight: 0.7980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26229 Z= 0.140 Angle : 0.502 12.758 35712 Z= 0.260 Chirality : 0.044 0.257 4206 Planarity : 0.004 0.055 4548 Dihedral : 5.483 56.540 4548 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.86 % Allowed : 9.84 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 3141 helix: 2.51 (0.21), residues: 696 sheet: 1.27 (0.18), residues: 753 loop : -1.27 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 886 HIS 0.002 0.000 HIS E 66 PHE 0.011 0.001 PHE A 168 TYR 0.016 0.001 TYR E1067 ARG 0.014 0.000 ARG E 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 81 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 841 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7256 (pp) REVERT: A 988 GLU cc_start: 0.7904 (mp0) cc_final: 0.7649 (mp0) REVERT: E 988 GLU cc_start: 0.8054 (mp0) cc_final: 0.7581 (mp0) REVERT: I 21 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6982 (pp) REVERT: I 210 ILE cc_start: 0.6899 (OUTLIER) cc_final: 0.6600 (pp) outliers start: 24 outliers final: 18 residues processed: 102 average time/residue: 1.0681 time to fit residues: 133.6176 Evaluate side-chains 100 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 79 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 635 VAL Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 1134 ASN Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 635 VAL Chi-restraints excluded: chain I residue 705 VAL Chi-restraints excluded: chain I residue 1134 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 1.9990 chunk 268 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 232 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 70 optimal weight: 0.2980 chunk 252 optimal weight: 0.0970 chunk 105 optimal weight: 0.7980 chunk 259 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.106447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.072279 restraints weight = 50976.391| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.97 r_work: 0.2987 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26229 Z= 0.139 Angle : 0.494 13.747 35712 Z= 0.256 Chirality : 0.044 0.242 4206 Planarity : 0.004 0.057 4548 Dihedral : 5.377 56.954 4548 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.83 % Allowed : 9.95 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.15), residues: 3141 helix: 2.60 (0.21), residues: 696 sheet: 1.33 (0.18), residues: 753 loop : -1.25 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 886 HIS 0.002 0.000 HIS A 66 PHE 0.021 0.001 PHE I 168 TYR 0.017 0.001 TYR E1067 ARG 0.019 0.000 ARG A 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5818.73 seconds wall clock time: 104 minutes 10.07 seconds (6250.07 seconds total)