Starting phenix.real_space_refine on Sun Feb 25 14:13:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aja_15475/02_2024/8aja_15475_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aja_15475/02_2024/8aja_15475.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/8aja_15475/02_2024/8aja_15475.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aja_15475/02_2024/8aja_15475.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aja_15475/02_2024/8aja_15475_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aja_15475/02_2024/8aja_15475_trim.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= -0.001 sd= 0.111 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: 5 Type Number sf(0) Gaussians S 132 5.16 5 C 16641 2.51 5 N 4320 2.21 5 O 5190 1.98 5 H 24870 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 100": "OE1" <-> "OE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 51153 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 16785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1090, 16785 Classifications: {'peptide': 1090} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 49, 'TRANS': 1040} Chain breaks: 1 Chain: "B" Number of atoms: 16785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1090, 16785 Classifications: {'peptide': 1090} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 49, 'TRANS': 1040} Chain breaks: 1 Chain: "C" Number of atoms: 16785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1090, 16785 Classifications: {'peptide': 1090} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 49, 'TRANS': 1040} Chain breaks: 1 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" 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: "U" 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: "V" 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: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 22.20, per 1000 atoms: 0.43 Number of scatterers: 51153 At special positions: 0 Unit cell: (132.09, 150.96, 174.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 O 5190 8.00 N 4320 7.00 C 16641 6.00 H 24870 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 140 " distance=2.03 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 164 " distance=2.04 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 293 " distance=2.02 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 353 " distance=2.03 Simple disulfide: pdb=" SG CYS A 371 " - pdb=" SG CYS A 424 " distance=2.04 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 499 " distance=2.03 Simple disulfide: pdb=" SG CYS A 512 " - pdb=" SG CYS A 564 " distance=2.03 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 623 " distance=2.04 Simple disulfide: pdb=" SG CYS A 636 " - pdb=" SG CYS A 645 " distance=2.04 Simple disulfide: pdb=" SG CYS A 708 " - pdb=" SG CYS A 730 " distance=2.04 Simple disulfide: pdb=" SG CYS A 713 " - pdb=" SG CYS A 719 " distance=2.04 Simple disulfide: pdb=" SG CYS A 810 " - pdb=" SG CYS A 821 " distance=2.04 Simple disulfide: pdb=" SG CYS A1002 " - pdb=" SG CYS A1013 " distance=2.03 Simple disulfide: pdb=" SG CYS A1052 " - pdb=" SG CYS A1096 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 140 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 164 " distance=2.04 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 293 " distance=2.02 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 353 " distance=2.03 Simple disulfide: pdb=" SG CYS B 371 " - pdb=" SG CYS B 424 " distance=2.04 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 499 " distance=2.03 Simple disulfide: pdb=" SG CYS B 512 " - pdb=" SG CYS B 564 " distance=2.03 Simple disulfide: pdb=" SG CYS B 591 " - pdb=" SG CYS B 623 " distance=2.04 Simple disulfide: pdb=" SG CYS B 636 " - pdb=" SG CYS B 645 " distance=2.03 Simple disulfide: pdb=" SG CYS B 708 " - pdb=" SG CYS B 730 " distance=2.04 Simple disulfide: pdb=" SG CYS B 713 " - pdb=" SG CYS B 719 " distance=2.04 Simple disulfide: pdb=" SG CYS B 810 " - pdb=" SG CYS B 821 " distance=2.04 Simple disulfide: pdb=" SG CYS B1002 " - pdb=" SG CYS B1013 " distance=2.03 Simple disulfide: pdb=" SG CYS B1052 " - pdb=" SG CYS B1096 " distance=2.04 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 140 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 293 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 353 " distance=2.03 Simple disulfide: pdb=" SG CYS C 371 " - pdb=" SG CYS C 424 " distance=2.04 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 499 " distance=2.03 Simple disulfide: pdb=" SG CYS C 512 " - pdb=" SG CYS C 564 " distance=2.03 Simple disulfide: pdb=" SG CYS C 591 " - pdb=" SG CYS C 623 " distance=2.04 Simple disulfide: pdb=" SG CYS C 636 " - pdb=" SG CYS C 645 " distance=2.03 Simple disulfide: pdb=" SG CYS C 708 " - pdb=" SG CYS C 730 " distance=2.03 Simple disulfide: pdb=" SG CYS C 713 " - pdb=" SG CYS C 719 " distance=2.04 Simple disulfide: pdb=" SG CYS C 810 " - pdb=" SG CYS C 821 " distance=2.04 Simple disulfide: pdb=" SG CYS C1002 " - pdb=" SG CYS C1013 " distance=2.03 Simple disulfide: pdb=" SG CYS C1052 " - pdb=" SG CYS C1096 " 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 L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A1104 " " NAG A1302 " - " ASN A 66 " " NAG A1303 " - " ASN A 126 " " NAG A1304 " - " ASN A 323 " " NAG A1305 " - " ASN A 590 " " NAG A1306 " - " ASN A 631 " " NAG A1307 " - " ASN A 679 " " NAG A1308 " - " ASN A1044 " " NAG A1309 " - " ASN A1068 " " NAG A1310 " - " ASN A 163 " " NAG A1311 " - " ASN A 274 " " NAG A1312 " - " ASN A 335 " " NAG A1313 " - " ASN A 362 " " NAG B1301 " - " ASN B1104 " " NAG B1302 " - " ASN B 66 " " NAG B1303 " - " ASN B 126 " " NAG B1304 " - " ASN B 323 " " NAG B1305 " - " ASN B 590 " " NAG B1306 " - " ASN B 631 " " NAG B1307 " - " ASN B 679 " " NAG B1308 " - " ASN B1044 " " NAG B1309 " - " ASN B1068 " " NAG B1310 " - " ASN B 163 " " NAG B1311 " - " ASN B 274 " " NAG B1312 " - " ASN B 335 " " NAG B1313 " - " ASN B 362 " " NAG C1301 " - " ASN C1104 " " NAG C1302 " - " ASN C 66 " " NAG C1303 " - " ASN C 126 " " NAG C1304 " - " ASN C 323 " " NAG C1305 " - " ASN C 590 " " NAG C1306 " - " ASN C 631 " " NAG C1307 " - " ASN C 679 " " NAG C1308 " - " ASN C1044 " " NAG C1309 " - " ASN C1068 " " NAG C1310 " - " ASN C 163 " " NAG C1311 " - " ASN C 274 " " NAG C1312 " - " ASN C 335 " " NAG C1313 " - " ASN C 362 " " NAG L 1 " - " ASN A 232 " " NAG M 1 " - " ASN A 687 " " NAG N 1 " - " ASN A 771 " " NAG P 1 " - " ASN B 232 " " NAG Q 1 " - " ASN B 687 " " NAG R 1 " - " ASN B 771 " " NAG T 1 " - " ASN C 232 " " NAG U 1 " - " ASN C 687 " " NAG V 1 " - " ASN C 771 " Time building additional restraints: 45.38 Conformation dependent library (CDL) restraints added in 6.3 seconds 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6168 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 51 sheets defined 27.5% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.88 Creating SS restraints... Processing helix chain 'A' and resid 76 through 79 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 329 through 335 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 375 through 381 removed outlier: 4.438A pdb=" N ILE A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 removed outlier: 4.216A pdb=" N ARG A 400 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 414 Processing helix chain 'A' and resid 476 through 479 Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 707 through 714 Processing helix chain 'A' and resid 716 through 724 Processing helix chain 'A' and resid 725 through 727 No H-bonds generated for 'chain 'A' and resid 725 through 727' Processing helix chain 'A' and resid 728 through 752 removed outlier: 3.623A pdb=" N ASP A 745 " --> pdb=" O ALA A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 775 No H-bonds generated for 'chain 'A' and resid 773 through 775' Processing helix chain 'A' and resid 786 through 796 removed outlier: 3.535A pdb=" N VAL A 796 " --> pdb=" O LEU A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 817 Processing helix chain 'A' and resid 818 through 826 Processing helix chain 'A' and resid 836 through 855 Processing helix chain 'A' and resid 856 through 861 removed outlier: 3.775A pdb=" N ALA A 860 " --> pdb=" O TRP A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 880 Processing helix chain 'A' and resid 882 through 888 removed outlier: 4.014A pdb=" N LEU A 886 " --> pdb=" O THR A 882 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR A 887 " --> pdb=" O GLN A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 911 Processing helix chain 'A' and resid 912 through 914 No H-bonds generated for 'chain 'A' and resid 912 through 914' Processing helix chain 'A' and resid 915 through 935 removed outlier: 4.072A pdb=" N VAL A 921 " --> pdb=" O LYS A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 938 No H-bonds generated for 'chain 'A' and resid 936 through 938' Processing helix chain 'A' and resid 946 through 954 Processing helix chain 'A' and resid 955 through 1003 removed outlier: 5.034A pdb=" N VAL A 961 " --> pdb=" O VAL A 957 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN A 962 " --> pdb=" O GLU A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1115 removed outlier: 3.593A pdb=" N LEU A1115 " --> pdb=" O GLN A1112 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 341 through 345 Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 375 through 381 removed outlier: 4.479A pdb=" N ILE B 380 " --> pdb=" O SER B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 removed outlier: 4.084A pdb=" N ARG B 400 " --> pdb=" O SER B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 414 Processing helix chain 'B' and resid 476 through 479 Processing helix chain 'B' and resid 593 through 598 Processing helix chain 'B' and resid 604 through 609 Processing helix chain 'B' and resid 610 through 612 No H-bonds generated for 'chain 'B' and resid 610 through 612' Processing helix chain 'B' and resid 707 through 714 Processing helix chain 'B' and resid 716 through 724 Processing helix chain 'B' and resid 725 through 727 No H-bonds generated for 'chain 'B' and resid 725 through 727' Processing helix chain 'B' and resid 728 through 753 removed outlier: 3.538A pdb=" N ASP B 745 " --> pdb=" O ALA B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 796 removed outlier: 3.533A pdb=" N VAL B 796 " --> pdb=" O LEU B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 817 removed outlier: 3.733A pdb=" N ARG B 817 " --> pdb=" O ILE B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 826 Processing helix chain 'B' and resid 836 through 855 Processing helix chain 'B' and resid 856 through 861 removed outlier: 3.881A pdb=" N ALA B 860 " --> pdb=" O TRP B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 879 Processing helix chain 'B' and resid 882 through 888 removed outlier: 4.072A pdb=" N LEU B 886 " --> pdb=" O THR B 882 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR B 887 " --> pdb=" O GLN B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 911 Processing helix chain 'B' and resid 912 through 914 No H-bonds generated for 'chain 'B' and resid 912 through 914' Processing helix chain 'B' and resid 915 through 935 removed outlier: 4.080A pdb=" N VAL B 921 " --> pdb=" O LYS B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 938 No H-bonds generated for 'chain 'B' and resid 936 through 938' Processing helix chain 'B' and resid 946 through 954 Processing helix chain 'B' and resid 955 through 1003 removed outlier: 5.052A pdb=" N VAL B 961 " --> pdb=" O VAL B 957 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN B 962 " --> pdb=" O GLU B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 1110 through 1115 removed outlier: 3.716A pdb=" N GLU B1114 " --> pdb=" O PRO B1110 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 329 through 335 Processing helix chain 'C' and resid 341 through 345 removed outlier: 3.507A pdb=" N TRP C 345 " --> pdb=" O VAL C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 363 removed outlier: 3.903A pdb=" N ASN C 362 " --> pdb=" O VAL C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 381 removed outlier: 4.410A pdb=" N ILE C 380 " --> pdb=" O SER C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.922A pdb=" N ARG C 400 " --> pdb=" O SER C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 414 Processing helix chain 'C' and resid 476 through 479 Processing helix chain 'C' and resid 593 through 598 Processing helix chain 'C' and resid 604 through 609 Processing helix chain 'C' and resid 610 through 612 No H-bonds generated for 'chain 'C' and resid 610 through 612' Processing helix chain 'C' and resid 707 through 714 Processing helix chain 'C' and resid 716 through 724 Processing helix chain 'C' and resid 725 through 727 No H-bonds generated for 'chain 'C' and resid 725 through 727' Processing helix chain 'C' and resid 728 through 753 removed outlier: 3.532A pdb=" N ASP C 745 " --> pdb=" O ALA C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 786 through 796 Processing helix chain 'C' and resid 813 through 817 removed outlier: 3.875A pdb=" N ARG C 817 " --> pdb=" O ILE C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 826 Processing helix chain 'C' and resid 836 through 855 Processing helix chain 'C' and resid 856 through 861 removed outlier: 3.799A pdb=" N ALA C 860 " --> pdb=" O TRP C 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 879 removed outlier: 3.515A pdb=" N TYR C 874 " --> pdb=" O MET C 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 889 removed outlier: 4.011A pdb=" N LEU C 886 " --> pdb=" O THR C 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 889 through 911 Processing helix chain 'C' and resid 912 through 914 No H-bonds generated for 'chain 'C' and resid 912 through 914' Processing helix chain 'C' and resid 915 through 936 removed outlier: 3.933A pdb=" N VAL C 921 " --> pdb=" O LYS C 917 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 936 " --> pdb=" O LEU C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 954 Processing helix chain 'C' and resid 955 through 1003 removed outlier: 5.111A pdb=" N VAL C 961 " --> pdb=" O VAL C 957 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN C 962 " --> pdb=" O GLU C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 1111 through 1115 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 removed outlier: 7.997A pdb=" N ASN A 66 " --> pdb=" O TYR A 261 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N TYR A 261 " --> pdb=" O ASN A 66 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS A 185 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU A 199 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS A 226 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A 201 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR A 205 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N VAL A 220 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL A 41 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 60 removed outlier: 3.853A pdb=" N ASP A 279 " --> pdb=" O LYS A 270 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 88 through 89 removed outlier: 13.981A pdb=" N PHE A 236 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 12.909A pdb=" N ASP A 141 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N VAL A 238 " --> pdb=" O ASP A 141 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET A 240 " --> pdb=" O PRO A 143 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N CYS A 140 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N THR A 159 " --> pdb=" O CYS A 140 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASP A 142 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL A 157 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N MET A 144 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N THR A 155 " --> pdb=" O MET A 144 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR A 146 " --> pdb=" O TYR A 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 88 through 89 removed outlier: 6.967A pdb=" N SER A 235 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE A 110 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ARG A 237 " --> pdb=" O TRP A 108 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TRP A 108 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 239 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ARG A 106 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR A 166 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 303 through 306 Processing sheet with id=AA7, first strand: chain 'A' and resid 317 through 320 removed outlier: 4.855A pdb=" N ASP A 548 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 346 through 350 removed outlier: 3.805A pdb=" N VAL A 387 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER A 386 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 353 through 354 removed outlier: 6.619A pdb=" N CYS A 353 " --> pdb=" O CYS A 499 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 436 through 441 Processing sheet with id=AB2, first strand: chain 'A' and resid 628 through 629 removed outlier: 6.193A pdb=" N GLU A 628 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N THR A 666 " --> pdb=" O GLU A 628 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE A 644 " --> pdb=" O ILE A 640 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 671 through 673 removed outlier: 6.999A pdb=" N ALA A 671 " --> pdb=" O MET B 758 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 681 through 698 removed outlier: 6.482A pdb=" N SER A 681 " --> pdb=" O THR A1046 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR A1046 " --> pdb=" O SER A 681 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA A 683 " --> pdb=" O ASN A1044 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN A1044 " --> pdb=" O ALA A 683 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU A1042 " --> pdb=" O PRO A 685 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N TYR A1037 " --> pdb=" O HIS A1018 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N HIS A1018 " --> pdb=" O TYR A1037 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 681 through 698 removed outlier: 6.482A pdb=" N SER A 681 " --> pdb=" O THR A1046 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR A1046 " --> pdb=" O SER A 681 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA A 683 " --> pdb=" O ASN A1044 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN A1044 " --> pdb=" O ALA A 683 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU A1042 " --> pdb=" O PRO A 685 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A1046 " --> pdb=" O SER A1067 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A1048 " --> pdb=" O PHE A1065 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE A1065 " --> pdb=" O ALA A1048 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 703 through 706 removed outlier: 4.163A pdb=" N LYS A 703 " --> pdb=" O LEU A 831 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 757 through 759 removed outlier: 3.760A pdb=" N ASN C 673 " --> pdb=" O MET A 758 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB9, first strand: chain 'A' and resid 1090 through 1095 removed outlier: 4.442A pdb=" N ALA A1057 " --> pdb=" O ALA A1093 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 33 through 35 removed outlier: 7.968A pdb=" N ASN B 66 " --> pdb=" O TYR B 261 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N TYR B 261 " --> pdb=" O ASN B 66 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS B 185 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU B 199 " --> pdb=" O LYS B 226 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS B 226 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B 201 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TYR B 205 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N VAL B 220 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL B 41 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.164A pdb=" N ILE B 80 " --> pdb=" O ALA B 75 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 52 through 60 removed outlier: 3.781A pdb=" N ASP B 279 " --> pdb=" O LYS B 270 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 88 through 89 removed outlier: 6.697A pdb=" N THR B 241 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 105 " --> pdb=" O THR B 241 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ARG B 106 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE B 130 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL B 169 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE B 132 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU B 167 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 134 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASN B 163 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N GLN B 138 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA B 161 " --> pdb=" O GLN B 138 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N CYS B 140 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N THR B 159 " --> pdb=" O CYS B 140 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP B 142 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL B 157 " --> pdb=" O ASP B 142 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N MET B 144 " --> pdb=" O THR B 155 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N THR B 155 " --> pdb=" O MET B 144 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR B 146 " --> pdb=" O TYR B 153 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 88 through 89 removed outlier: 12.955A pdb=" N PHE B 236 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 12.821A pdb=" N LEU B 139 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 12.767A pdb=" N VAL B 238 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N ASP B 141 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 9.762A pdb=" N MET B 240 " --> pdb=" O ASP B 141 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N MET B 242 " --> pdb=" O PRO B 143 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE B 145 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N SER B 244 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL B 147 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE B 130 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL B 169 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE B 132 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU B 167 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 134 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASN B 163 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N GLN B 138 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA B 161 " --> pdb=" O GLN B 138 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N CYS B 140 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N THR B 159 " --> pdb=" O CYS B 140 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP B 142 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL B 157 " --> pdb=" O ASP B 142 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N MET B 144 " --> pdb=" O THR B 155 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N THR B 155 " --> pdb=" O MET B 144 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR B 146 " --> pdb=" O TYR B 153 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 303 through 306 Processing sheet with id=AC7, first strand: chain 'B' and resid 317 through 320 removed outlier: 4.805A pdb=" N ASP B 548 " --> pdb=" O ILE B 561 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.941A pdb=" N VAL B 387 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER B 386 " --> pdb=" O GLU B 490 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 353 through 354 removed outlier: 6.650A pdb=" N CYS B 353 " --> pdb=" O CYS B 499 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 436 through 441 removed outlier: 3.611A pdb=" N TYR B 438 " --> pdb=" O TYR B 469 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 628 through 629 removed outlier: 6.215A pdb=" N GLU B 628 " --> pdb=" O ALA B 664 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N THR B 666 " --> pdb=" O GLU B 628 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE B 644 " --> pdb=" O ILE B 640 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 671 through 673 removed outlier: 6.896A pdb=" N ALA B 671 " --> pdb=" O MET C 758 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 681 through 698 removed outlier: 6.503A pdb=" N SER B 681 " --> pdb=" O THR B1046 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR B1046 " --> pdb=" O SER B 681 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA B 683 " --> pdb=" O ASN B1044 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN B1044 " --> pdb=" O ALA B 683 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLU B1042 " --> pdb=" O PRO B 685 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N TYR B1037 " --> pdb=" O HIS B1018 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N HIS B1018 " --> pdb=" O TYR B1037 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 681 through 698 removed outlier: 6.503A pdb=" N SER B 681 " --> pdb=" O THR B1046 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR B1046 " --> pdb=" O SER B 681 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA B 683 " --> pdb=" O ASN B1044 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN B1044 " --> pdb=" O ALA B 683 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLU B1042 " --> pdb=" O PRO B 685 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR B1046 " --> pdb=" O SER B1067 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B1048 " --> pdb=" O PHE B1065 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE B1065 " --> pdb=" O ALA B1048 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 703 through 706 removed outlier: 4.181A pdb=" N LYS B 703 " --> pdb=" O LEU B 831 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 766 through 767 Processing sheet with id=AD8, first strand: chain 'B' and resid 1090 through 1095 removed outlier: 5.500A pdb=" N VAL B1092 " --> pdb=" O PHE B1059 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE B1059 " --> pdb=" O VAL B1092 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY B1094 " --> pdb=" O ALA B1057 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 33 through 35 removed outlier: 7.967A pdb=" N ASN C 66 " --> pdb=" O TYR C 261 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N TYR C 261 " --> pdb=" O ASN C 66 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS C 185 " --> pdb=" O ILE C 208 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU C 199 " --> pdb=" O LYS C 226 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS C 226 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL C 201 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR C 205 " --> pdb=" O VAL C 220 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N VAL C 220 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL C 41 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 33 through 35 removed outlier: 6.232A pdb=" N ILE C 80 " --> pdb=" O ALA C 75 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 52 through 60 removed outlier: 3.712A pdb=" N ASP C 279 " --> pdb=" O LYS C 270 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 88 through 89 removed outlier: 6.920A pdb=" N THR C 241 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE C 105 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ARG C 106 " --> pdb=" O ASN C 125 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR C 166 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ASN C 136 " --> pdb=" O CYS C 164 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N CYS C 164 " --> pdb=" O ASN C 136 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N GLN C 138 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ARG C 162 " --> pdb=" O GLN C 138 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N CYS C 140 " --> pdb=" O ASN C 160 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N ASN C 160 " --> pdb=" O CYS C 140 " (cutoff:3.500A) removed outlier: 10.249A pdb=" N ASP C 142 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N TYR C 158 " --> pdb=" O ASP C 142 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS C 154 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N SER C 148 " --> pdb=" O HIS C 152 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N HIS C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 88 through 89 removed outlier: 13.878A pdb=" N PHE C 236 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 12.881A pdb=" N ASP C 141 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 9.503A pdb=" N VAL C 238 " --> pdb=" O ASP C 141 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET C 240 " --> pdb=" O PRO C 143 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR C 166 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ASN C 136 " --> pdb=" O CYS C 164 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N CYS C 164 " --> pdb=" O ASN C 136 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N GLN C 138 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ARG C 162 " --> pdb=" O GLN C 138 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N CYS C 140 " --> pdb=" O ASN C 160 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N ASN C 160 " --> pdb=" O CYS C 140 " (cutoff:3.500A) removed outlier: 10.249A pdb=" N ASP C 142 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N TYR C 158 " --> pdb=" O ASP C 142 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS C 154 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N SER C 148 " --> pdb=" O HIS C 152 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N HIS C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 303 through 306 Processing sheet with id=AE6, first strand: chain 'C' and resid 317 through 320 removed outlier: 4.871A pdb=" N ASP C 548 " --> pdb=" O ILE C 561 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 346 through 350 removed outlier: 3.826A pdb=" N VAL C 387 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER C 386 " --> pdb=" O GLU C 490 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 353 through 354 removed outlier: 6.648A pdb=" N CYS C 353 " --> pdb=" O CYS C 499 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 436 through 441 Processing sheet with id=AF1, first strand: chain 'C' and resid 628 through 629 removed outlier: 6.169A pdb=" N GLU C 628 " --> pdb=" O ALA C 664 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N THR C 666 " --> pdb=" O GLU C 628 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE C 644 " --> pdb=" O ILE C 640 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 681 through 698 removed outlier: 6.598A pdb=" N SER C 681 " --> pdb=" O THR C1046 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR C1046 " --> pdb=" O SER C 681 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA C 683 " --> pdb=" O ASN C1044 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN C1044 " --> pdb=" O ALA C 683 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLU C1042 " --> pdb=" O PRO C 685 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR C1037 " --> pdb=" O HIS C1018 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N HIS C1018 " --> pdb=" O TYR C1037 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 681 through 698 removed outlier: 6.598A pdb=" N SER C 681 " --> pdb=" O THR C1046 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR C1046 " --> pdb=" O SER C 681 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA C 683 " --> pdb=" O ASN C1044 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN C1044 " --> pdb=" O ALA C 683 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLU C1042 " --> pdb=" O PRO C 685 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR C1046 " --> pdb=" O SER C1067 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA C1048 " --> pdb=" O PHE C1065 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE C1065 " --> pdb=" O ALA C1048 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 703 through 706 removed outlier: 4.115A pdb=" N LYS C 703 " --> pdb=" O LEU C 831 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 766 through 767 Processing sheet with id=AF6, first strand: chain 'C' and resid 1090 through 1095 removed outlier: 4.598A pdb=" N ALA C1057 " --> pdb=" O ALA C1093 " (cutoff:3.500A) 1185 hydrogen bonds defined for protein. 3195 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: 26.97 Time building geometry restraints manager: 46.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 24870 1.03 - 1.23: 1262 1.23 - 1.43: 10268 1.43 - 1.63: 15137 1.63 - 1.83: 180 Bond restraints: 51717 Sorted by residual: bond pdb=" N THR B 19 " pdb=" H1 THR B 19 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" N THR C 19 " pdb=" H1 THR C 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N THR A 19 " pdb=" H1 THR A 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C1 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 51712 not shown) Histogram of bond angle deviations from ideal: 98.31 - 105.48: 567 105.48 - 112.64: 58409 112.64 - 119.81: 13934 119.81 - 126.97: 19658 126.97 - 134.14: 249 Bond angle restraints: 92817 Sorted by residual: angle pdb=" N ASN A 362 " pdb=" CA ASN A 362 " pdb=" CB ASN A 362 " ideal model delta sigma weight residual 110.39 103.82 6.57 1.66e+00 3.63e-01 1.56e+01 angle pdb=" N ASN B 362 " pdb=" CA ASN B 362 " pdb=" CB ASN B 362 " ideal model delta sigma weight residual 110.32 103.97 6.35 1.70e+00 3.46e-01 1.39e+01 angle pdb=" N ASN C 362 " pdb=" CA ASN C 362 " pdb=" CB ASN C 362 " ideal model delta sigma weight residual 110.39 104.67 5.72 1.66e+00 3.63e-01 1.19e+01 angle pdb=" N SER C 37 " pdb=" CA SER C 37 " pdb=" C SER C 37 " ideal model delta sigma weight residual 108.63 113.94 -5.31 1.60e+00 3.91e-01 1.10e+01 angle pdb=" N SER C 178 " pdb=" CA SER C 178 " pdb=" C SER C 178 " ideal model delta sigma weight residual 110.70 115.65 -4.95 1.55e+00 4.16e-01 1.02e+01 ... (remaining 92812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 23459 17.91 - 35.82: 1358 35.82 - 53.73: 414 53.73 - 71.64: 379 71.64 - 89.55: 21 Dihedral angle restraints: 25631 sinusoidal: 14240 harmonic: 11391 Sorted by residual: dihedral pdb=" CA TYR A 586 " pdb=" C TYR A 586 " pdb=" N GLN A 587 " pdb=" CA GLN A 587 " ideal model delta harmonic sigma weight residual 180.00 -149.23 -30.77 0 5.00e+00 4.00e-02 3.79e+01 dihedral pdb=" CA THR A 573 " pdb=" C THR A 573 " pdb=" N PRO A 574 " pdb=" CA PRO A 574 " ideal model delta harmonic sigma weight residual 180.00 150.92 29.08 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA THR A 99 " pdb=" C THR A 99 " pdb=" N GLU A 100 " pdb=" CA GLU A 100 " ideal model delta harmonic sigma weight residual -180.00 -150.93 -29.07 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 25628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3653 0.073 - 0.147: 639 0.147 - 0.220: 31 0.220 - 0.293: 7 0.293 - 0.367: 2 Chirality restraints: 4332 Sorted by residual: chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 590 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" C1 NAG C1313 " pdb=" ND2 ASN C 362 " pdb=" C2 NAG C1313 " pdb=" O5 NAG C1313 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 323 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 4329 not shown) Planarity restraints: 7824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 444 " 0.406 9.50e-02 1.11e+02 1.45e-01 8.02e+01 pdb=" NE ARG C 444 " 0.035 2.00e-02 2.50e+03 pdb=" CZ ARG C 444 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG C 444 " -0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG C 444 " -0.103 2.00e-02 2.50e+03 pdb="HH11 ARG C 444 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG C 444 " 0.017 2.00e-02 2.50e+03 pdb="HH21 ARG C 444 " -0.006 2.00e-02 2.50e+03 pdb="HH22 ARG C 444 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 320 " -0.545 9.50e-02 1.11e+02 1.82e-01 3.96e+01 pdb=" NE ARG C 320 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 320 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 320 " -0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG C 320 " 0.017 2.00e-02 2.50e+03 pdb="HH11 ARG C 320 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG C 320 " 0.028 2.00e-02 2.50e+03 pdb="HH21 ARG C 320 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 320 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 82 " -0.200 9.50e-02 1.11e+02 7.35e-02 2.58e+01 pdb=" NE ARG C 82 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG C 82 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG C 82 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG C 82 " 0.059 2.00e-02 2.50e+03 pdb="HH11 ARG C 82 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG C 82 " -0.009 2.00e-02 2.50e+03 pdb="HH21 ARG C 82 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG C 82 " -0.059 2.00e-02 2.50e+03 ... (remaining 7821 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 1134 2.10 - 2.72: 87604 2.72 - 3.35: 147419 3.35 - 3.97: 196224 3.97 - 4.60: 306880 Nonbonded interactions: 739261 Sorted by model distance: nonbonded pdb=" HH TYR B 726 " pdb=" OD1 ASP B 964 " model vdw 1.472 1.850 nonbonded pdb=" HH TYR C 726 " pdb=" OD1 ASP C 964 " model vdw 1.525 1.850 nonbonded pdb=" HG1 THR A 430 " pdb=" OD2 ASP A 434 " model vdw 1.542 1.850 nonbonded pdb=" HG1 THR A 573 " pdb=" O PRO A 574 " model vdw 1.544 1.850 nonbonded pdb=" O THR B 246 " pdb=" HG1 THR B 247 " model vdw 1.551 1.850 ... (remaining 739256 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 'B' selection = chain 'C' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' } 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=0.00 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: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.820 Extract box with map and model: 15.000 Check model and map are aligned: 0.760 Set scattering table: 0.490 Process input model: 173.000 Find NCS groups from input model: 2.380 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 208.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 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 : 0.006 0.077 26847 Z= 0.395 Angle : 0.798 7.457 36528 Z= 0.446 Chirality : 0.053 0.367 4332 Planarity : 0.010 0.223 4659 Dihedral : 12.808 89.547 10545 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.14), residues: 3258 helix: -0.68 (0.17), residues: 759 sheet: 0.70 (0.17), residues: 819 loop : -0.57 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.006 TRP C 607 HIS 0.009 0.003 HIS B 152 PHE 0.024 0.003 PHE C 321 TYR 0.036 0.005 TYR B 887 ARG 0.036 0.004 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 665 time to evaluate : 4.257 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8249 (mtp) cc_final: 0.7818 (mtm) REVERT: A 265 THR cc_start: 0.8076 (p) cc_final: 0.7845 (t) REVERT: A 268 MET cc_start: 0.8696 (ttp) cc_final: 0.8300 (ttm) REVERT: A 710 MET cc_start: 0.8527 (ttm) cc_final: 0.8232 (ttm) REVERT: A 715 ASP cc_start: 0.5835 (t0) cc_final: 0.5599 (t70) REVERT: A 743 GLU cc_start: 0.8062 (tt0) cc_final: 0.7520 (tt0) REVERT: B 27 THR cc_start: 0.8320 (p) cc_final: 0.8048 (m) REVERT: B 242 MET cc_start: 0.8684 (mtm) cc_final: 0.8318 (mtt) REVERT: B 248 SER cc_start: 0.7620 (t) cc_final: 0.7364 (p) REVERT: B 755 VAL cc_start: 0.7653 (m) cc_final: 0.7363 (t) REVERT: B 999 MET cc_start: 0.9029 (tpp) cc_final: 0.8817 (tpp) REVERT: C 268 MET cc_start: 0.9009 (ttp) cc_final: 0.8399 (ttp) REVERT: C 324 ILE cc_start: 0.6347 (pt) cc_final: 0.5864 (tp) REVERT: C 734 ASN cc_start: 0.8332 (m110) cc_final: 0.7809 (m-40) REVERT: C 1008 LYS cc_start: 0.7660 (mmtp) cc_final: 0.7459 (mmtt) outliers start: 0 outliers final: 0 residues processed: 665 average time/residue: 2.7033 time to fit residues: 2118.0498 Evaluate side-chains 384 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 4.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 137 optimal weight: 0.0970 chunk 84 optimal weight: 0.9990 chunk 167 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 256 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 296 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN A 433 GLN A 717 GLN A 732 GLN A 734 ASN A 980 GLN B 160 ASN B 554 GLN B 587 GLN B 732 GLN B 871 GLN B 927 GLN B 993 ASN C 30 ASN C 306 GLN C 326 ASN C 587 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C 980 GLN C 993 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 26847 Z= 0.233 Angle : 0.636 14.876 36528 Z= 0.342 Chirality : 0.047 0.279 4332 Planarity : 0.005 0.066 4659 Dihedral : 8.226 59.888 4716 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.04 % Allowed : 10.00 % Favored : 87.96 % 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: 0.11 (0.14), residues: 3258 helix: 0.74 (0.19), residues: 744 sheet: 0.51 (0.17), residues: 828 loop : -0.39 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 856 HIS 0.005 0.001 HIS C 129 PHE 0.015 0.002 PHE A 868 TYR 0.025 0.002 TYR C 469 ARG 0.006 0.001 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 401 time to evaluate : 3.876 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7895 (tm-30) REVERT: A 138 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.6929 (tm-30) REVERT: A 240 MET cc_start: 0.8457 (mtp) cc_final: 0.7980 (mtm) REVERT: A 265 THR cc_start: 0.8170 (p) cc_final: 0.7802 (t) REVERT: A 710 MET cc_start: 0.8527 (ttm) cc_final: 0.8226 (ttm) REVERT: A 743 GLU cc_start: 0.7828 (tt0) cc_final: 0.7627 (tt0) REVERT: A 883 GLN cc_start: 0.7482 (tt0) cc_final: 0.7282 (tt0) REVERT: A 999 MET cc_start: 0.9110 (tpp) cc_final: 0.8564 (tpp) REVERT: A 1042 GLU cc_start: 0.8114 (pm20) cc_final: 0.7854 (pm20) REVERT: B 69 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7675 (ttt180) REVERT: B 151 GLN cc_start: 0.7698 (mt0) cc_final: 0.7122 (mt0) REVERT: B 185 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.7820 (mtpp) REVERT: B 242 MET cc_start: 0.8800 (mtm) cc_final: 0.8409 (mtt) REVERT: B 248 SER cc_start: 0.7664 (t) cc_final: 0.7395 (p) REVERT: B 616 VAL cc_start: 0.8508 (m) cc_final: 0.8220 (m) REVERT: B 755 VAL cc_start: 0.7609 (m) cc_final: 0.7353 (t) REVERT: C 141 ASP cc_start: 0.7368 (m-30) cc_final: 0.6956 (t0) REVERT: C 237 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7716 (ptt180) REVERT: C 272 ASN cc_start: 0.6941 (t0) cc_final: 0.6709 (t0) REVERT: C 324 ILE cc_start: 0.6257 (pt) cc_final: 0.5778 (tp) REVERT: C 804 MET cc_start: 0.6307 (mtm) cc_final: 0.6092 (tmt) REVERT: C 870 MET cc_start: 0.8766 (mtp) cc_final: 0.8402 (ttm) outliers start: 58 outliers final: 29 residues processed: 437 average time/residue: 2.7801 time to fit residues: 1429.8936 Evaluate side-chains 380 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 346 time to evaluate : 3.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 952 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 952 SER Chi-restraints excluded: chain B residue 980 GLN Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 212 ARG Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 952 SER Chi-restraints excluded: chain C residue 1089 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 165 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 297 optimal weight: 2.9990 chunk 321 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 chunk 238 optimal weight: 0.3980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 ASN A 721 ASN A 774 GLN ** A 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 GLN B 160 ASN B 774 GLN B 905 GLN C 103 ASN C 326 ASN C 587 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 871 GLN ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 980 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 26847 Z= 0.281 Angle : 0.603 7.578 36528 Z= 0.324 Chirality : 0.047 0.270 4332 Planarity : 0.004 0.072 4659 Dihedral : 7.735 59.811 4716 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.53 % Allowed : 10.91 % Favored : 86.56 % 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: 0.16 (0.14), residues: 3258 helix: 1.03 (0.20), residues: 723 sheet: 0.44 (0.17), residues: 852 loop : -0.44 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 856 HIS 0.005 0.001 HIS B 200 PHE 0.015 0.002 PHE A 868 TYR 0.022 0.002 TYR C 469 ARG 0.003 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 385 time to evaluate : 4.249 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: symmetry clash REVERT: A 138 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7070 (tm-30) REVERT: A 265 THR cc_start: 0.8207 (p) cc_final: 0.7802 (t) REVERT: A 577 ASN cc_start: 0.7654 (t0) cc_final: 0.7438 (t0) REVERT: A 999 MET cc_start: 0.9108 (tpp) cc_final: 0.8746 (tpp) REVERT: A 1042 GLU cc_start: 0.8197 (pm20) cc_final: 0.7895 (pm20) REVERT: B 27 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8191 (m) REVERT: B 57 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.7466 (tm-30) REVERT: B 69 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7730 (ttt180) REVERT: B 151 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7243 (mt0) REVERT: B 242 MET cc_start: 0.8845 (mtm) cc_final: 0.8477 (mtt) REVERT: B 248 SER cc_start: 0.7716 (t) cc_final: 0.7415 (p) REVERT: B 616 VAL cc_start: 0.8523 (m) cc_final: 0.8234 (m) REVERT: B 755 VAL cc_start: 0.7670 (m) cc_final: 0.7398 (t) REVERT: C 141 ASP cc_start: 0.7465 (m-30) cc_final: 0.7057 (t0) REVERT: C 185 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8074 (mtpp) REVERT: C 237 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7884 (ptt180) REVERT: C 272 ASN cc_start: 0.7025 (t0) cc_final: 0.6521 (t0) REVERT: C 296 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.8001 (mttm) REVERT: C 422 THR cc_start: 0.8858 (t) cc_final: 0.8413 (m) REVERT: C 870 MET cc_start: 0.8973 (mtp) cc_final: 0.8587 (mtp) REVERT: C 917 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8488 (mtmm) outliers start: 72 outliers final: 43 residues processed: 426 average time/residue: 2.7643 time to fit residues: 1383.4356 Evaluate side-chains 396 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 344 time to evaluate : 4.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 952 SER Chi-restraints excluded: chain B residue 980 GLN Chi-restraints excluded: chain B residue 1096 CYS Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 212 ARG Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 296 LYS Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 474 ASN Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 917 LYS Chi-restraints excluded: chain C residue 952 SER Chi-restraints excluded: chain C residue 1089 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 293 optimal weight: 0.0470 chunk 223 optimal weight: 2.9990 chunk 154 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 199 optimal weight: 2.9990 chunk 298 optimal weight: 0.0040 chunk 316 optimal weight: 0.0770 chunk 155 optimal weight: 0.7980 chunk 282 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN A 587 GLN ** A 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 GLN C 326 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 980 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 26847 Z= 0.140 Angle : 0.522 10.186 36528 Z= 0.278 Chirality : 0.045 0.243 4332 Planarity : 0.003 0.039 4659 Dihedral : 6.999 59.828 4716 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.58 % Allowed : 12.53 % Favored : 85.89 % 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: 0.24 (0.14), residues: 3258 helix: 1.32 (0.20), residues: 723 sheet: 0.23 (0.17), residues: 858 loop : -0.32 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 156 HIS 0.003 0.001 HIS A 599 PHE 0.010 0.001 PHE A 868 TYR 0.015 0.001 TYR A 469 ARG 0.003 0.000 ARG B 400 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 374 time to evaluate : 4.095 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 138 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7053 (tm-30) REVERT: A 265 THR cc_start: 0.8154 (p) cc_final: 0.7745 (t) REVERT: A 999 MET cc_start: 0.9069 (tpp) cc_final: 0.8745 (tpp) REVERT: B 27 THR cc_start: 0.8450 (OUTLIER) cc_final: 0.8228 (m) REVERT: B 69 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7582 (ttt180) REVERT: B 151 GLN cc_start: 0.7810 (mt0) cc_final: 0.7283 (mt0) REVERT: B 185 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8013 (mtpp) REVERT: B 242 MET cc_start: 0.8784 (mtm) cc_final: 0.8447 (mtt) REVERT: B 248 SER cc_start: 0.7567 (t) cc_final: 0.7316 (p) REVERT: B 710 MET cc_start: 0.8532 (ttp) cc_final: 0.8158 (ttm) REVERT: B 755 VAL cc_start: 0.7514 (m) cc_final: 0.7280 (t) REVERT: B 872 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8147 (tpp) REVERT: C 237 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7756 (ptt180) REVERT: C 422 THR cc_start: 0.8860 (t) cc_final: 0.8401 (m) outliers start: 45 outliers final: 25 residues processed: 397 average time/residue: 2.8066 time to fit residues: 1306.3062 Evaluate side-chains 379 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 348 time to evaluate : 3.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 872 MET Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 952 SER Chi-restraints excluded: chain B residue 980 GLN Chi-restraints excluded: chain B residue 1096 CYS Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 212 ARG Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 474 ASN Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 952 SER Chi-restraints excluded: chain C residue 1089 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 263 optimal weight: 0.0770 chunk 179 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 269 optimal weight: 0.9990 chunk 218 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 283 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 ASN ** A 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 GLN B 160 ASN C 326 ASN C 774 GLN C 905 GLN C 980 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 26847 Z= 0.227 Angle : 0.547 8.933 36528 Z= 0.292 Chirality : 0.045 0.251 4332 Planarity : 0.004 0.049 4659 Dihedral : 6.846 59.792 4716 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.07 % Allowed : 12.81 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.28 (0.14), residues: 3258 helix: 1.36 (0.20), residues: 723 sheet: 0.27 (0.17), residues: 858 loop : -0.31 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 607 HIS 0.004 0.001 HIS B 599 PHE 0.014 0.001 PHE C 787 TYR 0.019 0.002 TYR C 469 ARG 0.006 0.000 ARG A1009 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 362 time to evaluate : 3.611 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: symmetry clash REVERT: A 138 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7119 (tm-30) REVERT: A 790 ASP cc_start: 0.7754 (m-30) cc_final: 0.7502 (m-30) REVERT: A 999 MET cc_start: 0.9038 (tpp) cc_final: 0.8801 (tpp) REVERT: B 69 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7625 (ttt180) REVERT: B 151 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7399 (mt0) REVERT: B 242 MET cc_start: 0.8794 (mtm) cc_final: 0.8439 (mtt) REVERT: B 248 SER cc_start: 0.7723 (t) cc_final: 0.7433 (p) REVERT: B 370 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8250 (ttmt) REVERT: B 710 MET cc_start: 0.8563 (ttp) cc_final: 0.8191 (ttm) REVERT: B 755 VAL cc_start: 0.7603 (m) cc_final: 0.7347 (t) REVERT: B 804 MET cc_start: 0.6220 (tpt) cc_final: 0.5537 (tpt) REVERT: B 872 MET cc_start: 0.8560 (mmt) cc_final: 0.8165 (tpp) REVERT: C 185 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8052 (mtpp) REVERT: C 237 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7893 (ptt180) REVERT: C 332 LYS cc_start: 0.8199 (ttpp) cc_final: 0.7951 (tttp) REVERT: C 422 THR cc_start: 0.8840 (t) cc_final: 0.8369 (m) REVERT: C 735 ARG cc_start: 0.7918 (ttm110) cc_final: 0.7682 (mtm110) outliers start: 59 outliers final: 37 residues processed: 390 average time/residue: 2.9253 time to fit residues: 1333.4471 Evaluate side-chains 390 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 347 time to evaluate : 4.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 952 SER Chi-restraints excluded: chain B residue 980 GLN Chi-restraints excluded: chain B residue 1096 CYS Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 212 ARG Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 474 ASN Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 952 SER Chi-restraints excluded: chain C residue 1089 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 106 optimal weight: 3.9990 chunk 284 optimal weight: 3.9990 chunk 62 optimal weight: 0.1980 chunk 185 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 316 optimal weight: 0.7980 chunk 262 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 GLN B 160 ASN C 326 ASN ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 980 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 26847 Z= 0.241 Angle : 0.551 7.250 36528 Z= 0.293 Chirality : 0.046 0.271 4332 Planarity : 0.004 0.056 4659 Dihedral : 6.670 59.652 4716 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.21 % Allowed : 13.23 % Favored : 84.56 % 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: 0.24 (0.14), residues: 3258 helix: 1.35 (0.20), residues: 723 sheet: 0.27 (0.17), residues: 858 loop : -0.36 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 607 HIS 0.007 0.001 HIS B 200 PHE 0.014 0.001 PHE A 868 TYR 0.021 0.002 TYR C 469 ARG 0.004 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 364 time to evaluate : 3.973 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: symmetry clash REVERT: A 50 SER cc_start: 0.8978 (OUTLIER) cc_final: 0.8639 (t) REVERT: A 138 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7186 (tm-30) REVERT: A 735 ARG cc_start: 0.8048 (ttm110) cc_final: 0.7789 (ttm110) REVERT: A 790 ASP cc_start: 0.7772 (m-30) cc_final: 0.7501 (m-30) REVERT: A 886 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8219 (tp) REVERT: A 999 MET cc_start: 0.9044 (tpp) cc_final: 0.8791 (tpp) REVERT: B 69 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7645 (ttt180) REVERT: B 151 GLN cc_start: 0.7904 (mt0) cc_final: 0.7530 (mm-40) REVERT: B 242 MET cc_start: 0.8739 (mtm) cc_final: 0.8321 (mtt) REVERT: B 248 SER cc_start: 0.7659 (t) cc_final: 0.7380 (p) REVERT: B 370 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8227 (ttmt) REVERT: B 710 MET cc_start: 0.8600 (ttp) cc_final: 0.8216 (ttm) REVERT: B 755 VAL cc_start: 0.7708 (m) cc_final: 0.7411 (t) REVERT: B 760 LYS cc_start: 0.7893 (pttp) cc_final: 0.7422 (mtmm) REVERT: B 804 MET cc_start: 0.6202 (tpt) cc_final: 0.5641 (tpt) REVERT: B 872 MET cc_start: 0.8598 (mmt) cc_final: 0.8182 (tpp) REVERT: B 955 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.6800 (p0) REVERT: C 185 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8173 (mtpp) REVERT: C 332 LYS cc_start: 0.8195 (ttpp) cc_final: 0.7939 (tttp) REVERT: C 422 THR cc_start: 0.8802 (t) cc_final: 0.8338 (m) REVERT: C 760 LYS cc_start: 0.7927 (ptmm) cc_final: 0.7502 (mttt) REVERT: C 905 GLN cc_start: 0.7994 (tt0) cc_final: 0.7485 (tt0) outliers start: 63 outliers final: 40 residues processed: 398 average time/residue: 2.8672 time to fit residues: 1331.7023 Evaluate side-chains 389 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 342 time to evaluate : 3.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 749 GLN Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 952 SER Chi-restraints excluded: chain B residue 955 ASP Chi-restraints excluded: chain B residue 980 GLN Chi-restraints excluded: chain B residue 1096 CYS Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 212 ARG Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 474 ASN Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 952 SER Chi-restraints excluded: chain C residue 1089 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 305 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 231 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 266 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 315 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 871 GLN A 892 GLN A1095 ASN B 160 ASN B 732 GLN C 326 ASN ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 975 GLN C 980 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 26847 Z= 0.392 Angle : 0.643 9.977 36528 Z= 0.341 Chirality : 0.049 0.307 4332 Planarity : 0.005 0.060 4659 Dihedral : 6.988 57.577 4716 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.81 % Allowed : 13.40 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.09 (0.14), residues: 3258 helix: 1.07 (0.20), residues: 726 sheet: 0.36 (0.17), residues: 864 loop : -0.50 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 607 HIS 0.008 0.002 HIS C 599 PHE 0.017 0.002 PHE A 868 TYR 0.026 0.002 TYR C 469 ARG 0.007 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 361 time to evaluate : 3.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7337 (m-30) cc_final: 0.7098 (m-30) REVERT: A 50 SER cc_start: 0.9022 (OUTLIER) cc_final: 0.8621 (t) REVERT: A 138 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7203 (tm-30) REVERT: A 240 MET cc_start: 0.9186 (mtm) cc_final: 0.8725 (mtt) REVERT: A 273 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7670 (pt0) REVERT: A 735 ARG cc_start: 0.8159 (ttm110) cc_final: 0.7921 (ttm110) REVERT: A 758 MET cc_start: 0.8887 (mmm) cc_final: 0.8320 (mmm) REVERT: A 886 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8227 (tp) REVERT: B 69 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7607 (ttt180) REVERT: B 151 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7422 (mm110) REVERT: B 159 THR cc_start: 0.8053 (OUTLIER) cc_final: 0.7827 (p) REVERT: B 242 MET cc_start: 0.8771 (mtm) cc_final: 0.8379 (mtt) REVERT: B 587 GLN cc_start: 0.8308 (mp10) cc_final: 0.8030 (mp10) REVERT: B 710 MET cc_start: 0.8652 (ttp) cc_final: 0.8391 (ttm) REVERT: B 755 VAL cc_start: 0.7773 (m) cc_final: 0.7425 (t) REVERT: B 760 LYS cc_start: 0.8003 (pttp) cc_final: 0.7528 (mtmm) REVERT: B 804 MET cc_start: 0.6158 (tpt) cc_final: 0.5602 (tpt) REVERT: B 955 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.7023 (p0) REVERT: C 185 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8146 (mtpp) REVERT: C 332 LYS cc_start: 0.8224 (ttpp) cc_final: 0.7940 (tttp) REVERT: C 422 THR cc_start: 0.8853 (t) cc_final: 0.8407 (m) REVERT: C 760 LYS cc_start: 0.8005 (ptmm) cc_final: 0.7606 (mttt) REVERT: C 886 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7589 (tp) outliers start: 80 outliers final: 46 residues processed: 408 average time/residue: 2.7980 time to fit residues: 1337.0859 Evaluate side-chains 410 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 354 time to evaluate : 3.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 952 SER Chi-restraints excluded: chain B residue 955 ASP Chi-restraints excluded: chain B residue 980 GLN Chi-restraints excluded: chain B residue 1056 LYS Chi-restraints excluded: chain B residue 1096 CYS Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 212 ARG Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 474 ASN Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain C residue 952 SER Chi-restraints excluded: chain C residue 1089 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 194 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 247 optimal weight: 0.9990 chunk 286 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 306 GLN A 587 GLN ** A1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 ASN B 160 ASN B 587 GLN ** B 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 975 GLN C 980 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.134 26847 Z= 0.329 Angle : 0.606 14.889 36528 Z= 0.322 Chirality : 0.047 0.297 4332 Planarity : 0.004 0.056 4659 Dihedral : 6.857 59.915 4716 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.74 % Allowed : 14.00 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.05 (0.14), residues: 3258 helix: 1.03 (0.20), residues: 726 sheet: 0.35 (0.17), residues: 867 loop : -0.54 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 607 HIS 0.006 0.001 HIS C 599 PHE 0.016 0.002 PHE A 868 TYR 0.023 0.002 TYR C 469 ARG 0.004 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 360 time to evaluate : 3.133 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: symmetry clash REVERT: A 50 SER cc_start: 0.9001 (OUTLIER) cc_final: 0.8642 (t) REVERT: A 138 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: A 234 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8870 (p) REVERT: A 240 MET cc_start: 0.9135 (mtm) cc_final: 0.8706 (mtt) REVERT: A 735 ARG cc_start: 0.8131 (ttm110) cc_final: 0.7918 (mtm110) REVERT: A 758 MET cc_start: 0.8877 (mmm) cc_final: 0.8294 (mmm) REVERT: A 886 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8189 (tp) REVERT: B 151 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7589 (mm-40) REVERT: B 212 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7214 (mtp85) REVERT: B 242 MET cc_start: 0.8746 (mtm) cc_final: 0.8290 (mtt) REVERT: B 263 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8236 (mttp) REVERT: B 710 MET cc_start: 0.8623 (ttp) cc_final: 0.8353 (ttm) REVERT: B 755 VAL cc_start: 0.7781 (m) cc_final: 0.7442 (t) REVERT: B 760 LYS cc_start: 0.8015 (pttp) cc_final: 0.7573 (mtmm) REVERT: C 185 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8119 (mtpp) REVERT: C 332 LYS cc_start: 0.8200 (ttpp) cc_final: 0.7936 (tttp) REVERT: C 422 THR cc_start: 0.8830 (t) cc_final: 0.8378 (m) REVERT: C 760 LYS cc_start: 0.7995 (ptmm) cc_final: 0.7643 (mttt) REVERT: C 886 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7706 (tp) REVERT: C 905 GLN cc_start: 0.8063 (tt0) cc_final: 0.7686 (tt0) outliers start: 78 outliers final: 53 residues processed: 403 average time/residue: 2.7407 time to fit residues: 1293.0056 Evaluate side-chains 416 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 354 time to evaluate : 4.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 749 GLN Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 532 ARG Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 952 SER Chi-restraints excluded: chain B residue 980 GLN Chi-restraints excluded: chain B residue 1096 CYS Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 212 ARG Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 474 ASN Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain C residue 952 SER Chi-restraints excluded: chain C residue 960 GLU Chi-restraints excluded: chain C residue 1084 ILE Chi-restraints excluded: chain C residue 1089 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 301 optimal weight: 3.9990 chunk 275 optimal weight: 0.7980 chunk 293 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 230 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 265 optimal weight: 0.7980 chunk 277 optimal weight: 2.9990 chunk 292 optimal weight: 0.8980 chunk 192 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 ASN B 160 ASN B 774 GLN B 905 GLN ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 980 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 26847 Z= 0.200 Angle : 0.537 12.492 36528 Z= 0.286 Chirality : 0.045 0.268 4332 Planarity : 0.004 0.046 4659 Dihedral : 6.419 58.158 4716 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.14 % Allowed : 14.74 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.14), residues: 3258 helix: 1.25 (0.20), residues: 726 sheet: 0.27 (0.17), residues: 858 loop : -0.50 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 607 HIS 0.003 0.001 HIS B 200 PHE 0.012 0.001 PHE A 868 TYR 0.016 0.001 TYR C 257 ARG 0.003 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 369 time to evaluate : 3.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8980 (OUTLIER) cc_final: 0.8672 (t) REVERT: A 138 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7182 (tm-30) REVERT: A 234 THR cc_start: 0.9056 (m) cc_final: 0.8852 (p) REVERT: A 240 MET cc_start: 0.9137 (mtm) cc_final: 0.8745 (mtt) REVERT: A 265 THR cc_start: 0.8153 (p) cc_final: 0.7699 (t) REVERT: A 273 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7650 (pt0) REVERT: B 69 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7669 (ttt180) REVERT: B 151 GLN cc_start: 0.7943 (mt0) cc_final: 0.7598 (mm110) REVERT: B 212 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7075 (mtp85) REVERT: B 242 MET cc_start: 0.8701 (mtm) cc_final: 0.8395 (mtt) REVERT: B 324 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7093 (pt) REVERT: B 532 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.6855 (mmm160) REVERT: B 710 MET cc_start: 0.8574 (ttp) cc_final: 0.8173 (ttm) REVERT: B 755 VAL cc_start: 0.7694 (m) cc_final: 0.7381 (t) REVERT: B 760 LYS cc_start: 0.7982 (pttp) cc_final: 0.7617 (mtmm) REVERT: B 872 MET cc_start: 0.8657 (mmt) cc_final: 0.8147 (tpp) REVERT: C 185 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8027 (mtpp) REVERT: C 332 LYS cc_start: 0.8150 (ttpp) cc_final: 0.7885 (tttp) REVERT: C 422 THR cc_start: 0.8809 (t) cc_final: 0.8341 (m) REVERT: C 760 LYS cc_start: 0.7946 (ptmm) cc_final: 0.7608 (mttt) REVERT: C 905 GLN cc_start: 0.8010 (tt0) cc_final: 0.7660 (tt0) outliers start: 61 outliers final: 42 residues processed: 400 average time/residue: 2.3594 time to fit residues: 1102.3664 Evaluate side-chains 405 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 355 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 749 GLN Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 532 ARG Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 952 SER Chi-restraints excluded: chain B residue 980 GLN Chi-restraints excluded: chain B residue 1096 CYS Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 212 ARG Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 474 ASN Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 952 SER Chi-restraints excluded: chain C residue 960 GLU Chi-restraints excluded: chain C residue 965 ARG Chi-restraints excluded: chain C residue 1084 ILE Chi-restraints excluded: chain C residue 1089 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 310 optimal weight: 0.6980 chunk 189 optimal weight: 0.9980 chunk 147 optimal weight: 0.1980 chunk 215 optimal weight: 2.9990 chunk 325 optimal weight: 0.5980 chunk 299 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 200 optimal weight: 0.5980 chunk 159 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1089 ASN A1095 ASN B 160 ASN ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 980 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 26847 Z= 0.189 Angle : 0.530 13.430 36528 Z= 0.281 Chirality : 0.045 0.260 4332 Planarity : 0.004 0.045 4659 Dihedral : 6.161 58.865 4716 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.96 % Allowed : 15.19 % Favored : 82.84 % 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: 0.16 (0.14), residues: 3258 helix: 1.35 (0.20), residues: 726 sheet: 0.22 (0.17), residues: 837 loop : -0.45 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 607 HIS 0.003 0.001 HIS C 599 PHE 0.011 0.001 PHE A 868 TYR 0.015 0.001 TYR C 257 ARG 0.003 0.000 ARG C 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 371 time to evaluate : 3.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7200 (tm-30) REVERT: A 234 THR cc_start: 0.9058 (m) cc_final: 0.8846 (p) REVERT: A 240 MET cc_start: 0.9128 (mtm) cc_final: 0.8735 (mtt) REVERT: A 265 THR cc_start: 0.8135 (p) cc_final: 0.7926 (t) REVERT: A 758 MET cc_start: 0.8893 (mmm) cc_final: 0.8276 (mmm) REVERT: A 790 ASP cc_start: 0.7726 (m-30) cc_final: 0.7483 (m-30) REVERT: A 999 MET cc_start: 0.9026 (tpp) cc_final: 0.8795 (tpp) REVERT: B 69 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7605 (ttt180) REVERT: B 151 GLN cc_start: 0.7874 (mt0) cc_final: 0.7551 (mm110) REVERT: B 212 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7041 (mtp85) REVERT: B 242 MET cc_start: 0.8694 (mtm) cc_final: 0.8397 (mtt) REVERT: B 301 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7217 (mm-30) REVERT: B 324 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.7124 (pt) REVERT: B 532 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6856 (mmm160) REVERT: B 710 MET cc_start: 0.8564 (ttp) cc_final: 0.8160 (ttm) REVERT: B 755 VAL cc_start: 0.7663 (m) cc_final: 0.7363 (t) REVERT: B 760 LYS cc_start: 0.7992 (pttp) cc_final: 0.7631 (mtmm) REVERT: B 872 MET cc_start: 0.8661 (mmt) cc_final: 0.8157 (tpp) REVERT: C 332 LYS cc_start: 0.8145 (ttpp) cc_final: 0.7870 (tttp) REVERT: C 422 THR cc_start: 0.8855 (t) cc_final: 0.8364 (m) REVERT: C 760 LYS cc_start: 0.7913 (ptmm) cc_final: 0.7597 (mttt) REVERT: C 905 GLN cc_start: 0.8024 (tt0) cc_final: 0.7651 (tt0) outliers start: 56 outliers final: 41 residues processed: 399 average time/residue: 2.3684 time to fit residues: 1106.6192 Evaluate side-chains 401 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 355 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 749 GLN Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 532 ARG Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 952 SER Chi-restraints excluded: chain B residue 980 GLN Chi-restraints excluded: chain B residue 1096 CYS Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 952 SER Chi-restraints excluded: chain C residue 960 GLU Chi-restraints excluded: chain C residue 1084 ILE Chi-restraints excluded: chain C residue 1089 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 266 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 64 ASN A 285 GLN A1095 ASN B 160 ASN B 732 GLN ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 975 GLN C 980 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.125346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.105631 restraints weight = 72276.150| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.41 r_work: 0.2974 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 26847 Z= 0.317 Angle : 0.595 15.111 36528 Z= 0.315 Chirality : 0.047 0.375 4332 Planarity : 0.004 0.055 4659 Dihedral : 6.398 59.260 4716 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.11 % Allowed : 15.09 % Favored : 82.81 % 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 (0.14), residues: 3258 helix: 1.25 (0.20), residues: 726 sheet: 0.26 (0.17), residues: 831 loop : -0.46 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 607 HIS 0.006 0.001 HIS B 200 PHE 0.014 0.002 PHE A 868 TYR 0.021 0.002 TYR C 469 ARG 0.004 0.001 ARG A1009 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19547.42 seconds wall clock time: 339 minutes 55.46 seconds (20395.46 seconds total)