Starting phenix.real_space_refine on Fri Apr 12 12:08:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyk_36724/04_2024/8jyk_36724.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyk_36724/04_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_36724/04_2024/8jyk_36724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyk_36724/04_2024/8jyk_36724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyk_36724/04_2024/8jyk_36724.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyk_36724/04_2024/8jyk_36724.pdb" } 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-5288/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: 13.61, per 1000 atoms: 0.53 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: 9.47 Conformation dependent library (CDL) restraints added in 4.6 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: 3.19 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: 3.538A 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: 10.25 Time building geometry restraints manager: 10.37 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: 6563 1.47 - 1.59: 11398 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: 9223 120.36 - 127.19: 11036 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: 23696 3.28 - 3.82: 39247 3.82 - 4.36: 46280 4.36 - 4.90: 83760 Nonbonded interactions: 194853 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 194848 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: 5.400 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: 0.030 Extract box with map and model: 16.470 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 65.990 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.570 ------------------------------------------------------------------------------- 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= 0.280 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: 0.19 (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 : 2.747 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: 0.7325 (m-80) cc_final: 0.6933 (m-80) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 1.2357 time to fit residues: 244.6768 Evaluate side-chains 75 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 5.330 ------------------------------------------------------------------------------- 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: 5.9990 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: 0.0050 chunk 96 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 185 optimal weight: 1.9990 chunk 288 optimal weight: 0.0270 overall best weight: 0.8056 ------------------------------------------------------------------------------- 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: 0.8513 moved from start: 0.0639 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= 0.152 Angle : 0.507 9.659 35712 Z= 0.264 Chirality : 0.045 0.325 4206 Planarity : 0.004 0.053 4548 Dihedral : 7.059 57.839 4548 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % 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: 2.55 (0.21), residues: 696 sheet: 1.30 (0.18), residues: 762 loop : -1.25 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 436 HIS 0.002 0.001 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 : 2.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 849 LEU cc_start: 0.7875 (mt) cc_final: 0.7621 (mt) REVERT: E 52 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7941 (tm-30) REVERT: E 189 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8291 (tm) REVERT: E 239 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7491 (tp40) REVERT: I 319 ARG cc_start: 0.8585 (ttm110) cc_final: 0.8357 (ptm160) REVERT: I 427 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7830 (t0) outliers start: 18 outliers final: 8 residues processed: 103 average time/residue: 1.1253 time to fit residues: 138.7717 Evaluate side-chains 86 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 2.168 ------------------------------------------------------------------------------- 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 E residue 239 GLN Chi-restraints excluded: chain E residue 242 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: 0.9990 chunk 89 optimal weight: 2.9990 chunk 240 optimal weight: 0.9990 chunk 196 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 289 optimal weight: 0.8980 chunk 312 optimal weight: 0.2980 chunk 257 optimal weight: 8.9990 chunk 286 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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: 0.8539 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26229 Z= 0.168 Angle : 0.504 8.334 35712 Z= 0.265 Chirality : 0.045 0.300 4206 Planarity : 0.004 0.063 4548 Dihedral : 6.423 57.130 4548 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.05 % Allowed : 5.95 % Favored : 93.01 % 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: 0.49 (0.15), residues: 3141 helix: 2.52 (0.21), residues: 711 sheet: 1.33 (0.18), residues: 759 loop : -1.22 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 436 HIS 0.002 0.001 HIS A1064 PHE 0.024 0.001 PHE A 906 TYR 0.018 0.001 TYR E 170 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 115 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 86 time to evaluate : 3.043 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: A 849 LEU cc_start: 0.7915 (mt) cc_final: 0.7659 (mt) REVERT: E 52 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7928 (tm-30) REVERT: E 988 GLU cc_start: 0.8045 (mp0) cc_final: 0.7777 (mp0) REVERT: I 427 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7853 (t0) outliers start: 29 outliers final: 12 residues processed: 111 average time/residue: 1.3345 time to fit residues: 177.7686 Evaluate side-chains 87 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 3.017 ------------------------------------------------------------------------------- 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 130 VAL Chi-restraints excluded: chain E residue 641 ASN 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: 0.6980 chunk 290 optimal weight: 1.9990 chunk 307 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 275 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 613 GLN E 613 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 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 : 0.006 0.067 26229 Z= 0.410 Angle : 0.637 8.722 35712 Z= 0.339 Chirality : 0.050 0.273 4206 Planarity : 0.005 0.057 4548 Dihedral : 6.671 59.933 4548 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.41 % Allowed : 7.35 % Favored : 91.24 % 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: 0.12 (0.15), residues: 3141 helix: 2.23 (0.20), residues: 693 sheet: 1.20 (0.19), residues: 729 loop : -1.44 (0.13), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 886 HIS 0.005 0.001 HIS A1064 PHE 0.042 0.002 PHE I 906 TYR 0.021 0.002 TYR A1067 ARG 0.006 0.001 ARG A 319 *********************** 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 115 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 76 time to evaluate : 3.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.7149 (m) cc_final: 0.6774 (p) REVERT: A 988 GLU cc_start: 0.8042 (tp30) cc_final: 0.7657 (tp30) REVERT: E 52 GLN cc_start: 0.8335 (tm-30) cc_final: 0.8065 (tm-30) REVERT: E 988 GLU cc_start: 0.7712 (mp0) cc_final: 0.7360 (mp0) REVERT: I 427 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7840 (t0) REVERT: I 988 GLU cc_start: 0.8090 (tp30) cc_final: 0.7712 (tp30) outliers start: 39 outliers final: 21 residues processed: 111 average time/residue: 1.1444 time to fit residues: 154.1505 Evaluate side-chains 92 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 70 time to evaluate : 3.063 ------------------------------------------------------------------------------- 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 118 LEU 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 1100 THR 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 1134 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 228 optimal weight: 0.0470 chunk 126 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 212 optimal weight: 10.0000 chunk 0 optimal weight: 0.9980 chunk 156 optimal weight: 8.9990 chunk 275 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 493 GLN A 613 GLN E 613 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26229 Z= 0.153 Angle : 0.516 8.321 35712 Z= 0.271 Chirality : 0.045 0.292 4206 Planarity : 0.004 0.045 4548 Dihedral : 6.059 56.480 4548 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.94 % Allowed : 8.50 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3141 helix: 2.36 (0.20), residues: 699 sheet: 1.20 (0.18), residues: 747 loop : -1.35 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 886 HIS 0.003 0.001 HIS I 69 PHE 0.009 0.001 PHE A1121 TYR 0.016 0.001 TYR E 170 ARG 0.009 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 110 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 84 time to evaluate : 2.831 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: 0.8322 (tm-30) cc_final: 0.8080 (tm-30) REVERT: E 988 GLU cc_start: 0.7857 (mp0) cc_final: 0.7476 (mp0) REVERT: I 427 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7826 (t0) outliers start: 26 outliers final: 14 residues processed: 109 average time/residue: 1.2415 time to fit residues: 162.5733 Evaluate side-chains 89 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 2.969 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 60 optimal weight: 0.8980 chunk 180 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 307 optimal weight: 3.9990 chunk 255 optimal weight: 3.9990 chunk 142 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN E 69 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26229 Z= 0.238 Angle : 0.550 10.369 35712 Z= 0.289 Chirality : 0.046 0.271 4206 Planarity : 0.004 0.059 4548 Dihedral : 6.033 57.752 4548 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.26 % Allowed : 8.90 % 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: 0.23 (0.15), residues: 3141 helix: 2.43 (0.21), residues: 693 sheet: 1.18 (0.18), residues: 747 loop : -1.40 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 886 HIS 0.003 0.001 HIS A1064 PHE 0.019 0.001 PHE I 906 TYR 0.018 0.001 TYR I1067 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: 35 poor density : 79 time to evaluate : 3.036 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 988 GLU cc_start: 0.7810 (mp0) cc_final: 0.7388 (mp0) REVERT: I 427 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7840 (t0) outliers start: 35 outliers final: 22 residues processed: 110 average time/residue: 1.0845 time to fit residues: 147.0124 Evaluate side-chains 98 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 75 time to evaluate : 2.846 ------------------------------------------------------------------------------- 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 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 828 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 224 optimal weight: 0.7980 chunk 174 optimal weight: 1.9990 chunk 259 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 306 optimal weight: 1.9990 chunk 191 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 613 GLN I 69 HIS I1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26229 Z= 0.268 Angle : 0.570 10.913 35712 Z= 0.301 Chirality : 0.047 0.259 4206 Planarity : 0.004 0.060 4548 Dihedral : 6.059 58.217 4548 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.19 % Allowed : 9.19 % 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: 0.13 (0.15), residues: 3141 helix: 2.31 (0.20), residues: 693 sheet: 1.13 (0.18), residues: 747 loop : -1.45 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 886 HIS 0.004 0.001 HIS A1064 PHE 0.018 0.001 PHE A 906 TYR 0.018 0.001 TYR A1067 ARG 0.012 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 112 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 79 time to evaluate : 2.811 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: A 841 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7169 (pp) REVERT: E 988 GLU cc_start: 0.7774 (mp0) cc_final: 0.7362 (mp0) REVERT: I 427 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7824 (t0) outliers start: 33 outliers final: 21 residues processed: 109 average time/residue: 1.1291 time to fit residues: 150.5604 Evaluate side-chains 98 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 75 time to evaluate : 3.110 ------------------------------------------------------------------------------- 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 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 1100 THR 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 1134 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 59 optimal weight: 0.5980 chunk 194 optimal weight: 0.7980 chunk 208 optimal weight: 0.5980 chunk 151 optimal weight: 0.2980 chunk 28 optimal weight: 0.9980 chunk 240 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8548 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26229 Z= 0.142 Angle : 0.508 12.054 35712 Z= 0.266 Chirality : 0.044 0.269 4206 Planarity : 0.004 0.045 4548 Dihedral : 5.670 56.379 4548 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.19 % Allowed : 9.37 % Favored : 89.44 % 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: 0.30 (0.15), residues: 3141 helix: 2.44 (0.20), residues: 696 sheet: 1.19 (0.18), residues: 753 loop : -1.33 (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 0.011 0.001 PHE I 168 TYR 0.017 0.001 TYR I 170 ARG 0.012 0.000 ARG A 237 *********************** 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 117 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 84 time to evaluate : 2.794 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: 0.7390 (OUTLIER) cc_final: 0.7190 (pp) REVERT: I 21 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6982 (pp) REVERT: I 210 ILE cc_start: 0.6719 (OUTLIER) cc_final: 0.6437 (pp) REVERT: I 427 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7809 (t0) outliers start: 33 outliers final: 20 residues processed: 112 average time/residue: 1.1405 time to fit residues: 155.2644 Evaluate side-chains 102 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 78 time to evaluate : 2.742 ------------------------------------------------------------------------------- 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 1100 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 5.9990 chunk 293 optimal weight: 0.7980 chunk 267 optimal weight: 2.9990 chunk 285 optimal weight: 0.4980 chunk 171 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 224 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 258 optimal weight: 0.8980 chunk 270 optimal weight: 0.6980 chunk 284 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.8548 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26229 Z= 0.151 Angle : 0.506 13.684 35712 Z= 0.264 Chirality : 0.044 0.258 4206 Planarity : 0.004 0.045 4548 Dihedral : 5.581 56.936 4548 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.12 % Allowed : 9.62 % Favored : 89.26 % 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: 0.37 (0.15), residues: 3141 helix: 2.50 (0.20), residues: 696 sheet: 1.26 (0.18), residues: 753 loop : -1.31 (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 69 PHE 0.012 0.001 PHE I 168 TYR 0.017 0.001 TYR A1067 ARG 0.009 0.000 ARG A 319 *********************** 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 117 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 86 time to evaluate : 3.657 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 237 ARG cc_start: 0.7402 (mtm110) cc_final: 0.7052 (mtp-110) REVERT: A 841 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7189 (pp) REVERT: A 985 ASP cc_start: 0.7743 (p0) cc_final: 0.7309 (p0) REVERT: A 988 GLU cc_start: 0.7750 (mp0) cc_final: 0.7424 (mp0) REVERT: I 21 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6975 (pp) REVERT: I 210 ILE cc_start: 0.6942 (OUTLIER) cc_final: 0.6667 (pp) outliers start: 31 outliers final: 20 residues processed: 113 average time/residue: 1.2140 time to fit residues: 166.3366 Evaluate side-chains 103 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 2.941 ------------------------------------------------------------------------------- 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 635 VAL Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 1100 THR 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 187 optimal weight: 0.5980 chunk 302 optimal weight: 0.5980 chunk 184 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 209 optimal weight: 0.8980 chunk 316 optimal weight: 0.8980 chunk 291 optimal weight: 1.9990 chunk 252 optimal weight: 0.0050 chunk 26 optimal weight: 0.9990 chunk 194 optimal weight: 0.1980 chunk 154 optimal weight: 5.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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: 0.8516 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26229 Z= 0.129 Angle : 0.495 14.410 35712 Z= 0.254 Chirality : 0.044 0.259 4206 Planarity : 0.004 0.046 4548 Dihedral : 5.384 56.522 4548 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.76 % Allowed : 10.02 % 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: 2.57 (0.21), residues: 696 sheet: 1.35 (0.18), residues: 756 loop : -1.25 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 436 HIS 0.005 0.000 HIS A 69 PHE 0.007 0.001 PHE I1121 TYR 0.016 0.001 TYR E1067 ARG 0.021 0.000 ARG A 319 ********************** 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 102 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 2.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7487 (mtm110) cc_final: 0.6993 (mtp-110) REVERT: A 988 GLU cc_start: 0.7736 (mp0) cc_final: 0.7488 (mp0) REVERT: E 988 GLU cc_start: 0.8042 (mp0) cc_final: 0.7592 (mp0) REVERT: I 21 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.7000 (pp) REVERT: I 210 ILE cc_start: 0.6793 (OUTLIER) cc_final: 0.6511 (pp) outliers start: 21 outliers final: 17 residues processed: 101 average time/residue: 1.1107 time to fit residues: 137.1931 Evaluate side-chains 97 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 705 VAL 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 1100 THR 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: 0.8980 chunk 232 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 252 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 259 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.106035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.071743 restraints weight = 50955.046| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.96 r_work: 0.2976 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26229 Z= 0.155 Angle : 0.511 13.625 35712 Z= 0.263 Chirality : 0.044 0.240 4206 Planarity : 0.004 0.082 4548 Dihedral : 5.406 57.239 4548 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.79 % Allowed : 10.05 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 0.001 HIS A1064 PHE 0.018 0.001 PHE I 168 TYR 0.017 0.001 TYR A1067 ARG 0.019 0.000 ARG A 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5930.55 seconds wall clock time: 113 minutes 24.40 seconds (6804.40 seconds total)