Starting phenix.real_space_refine on Sat Dec 28 10:31:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aja_15475/12_2024/8aja_15475_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aja_15475/12_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/cci-nas-00/data/ceres_data/8aja_15475/12_2024/8aja_15475.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aja_15475/12_2024/8aja_15475.map" model { file = "/net/cci-nas-00/data/ceres_data/8aja_15475/12_2024/8aja_15475_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aja_15475/12_2024/8aja_15475_trim.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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. Time to flip 2 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 18.53, per 1000 atoms: 0.36 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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: 10.60 Conformation dependent library (CDL) restraints added in 3.3 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: 4.20 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: 22.76 Time building geometry restraints manager: 12.81 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: 0.00 - 1.49: 88765 1.49 - 2.98: 3694 2.98 - 4.47: 308 4.47 - 5.97: 43 5.97 - 7.46: 7 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 2.450 nonbonded pdb=" HH TYR C 726 " pdb=" OD1 ASP C 964 " model vdw 1.525 2.450 nonbonded pdb=" HG1 THR A 430 " pdb=" OD2 ASP A 434 " model vdw 1.542 2.450 nonbonded pdb=" HG1 THR A 573 " pdb=" O PRO A 574 " model vdw 1.544 2.450 nonbonded pdb=" O THR B 246 " pdb=" HG1 THR B 247 " model vdw 1.551 2.450 ... (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 Time spend for trying shortcut: 0.00 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: 0.010 Normalize map: mean=0, sd=1: 2.060 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: 0.700 Extract box with map and model: 1.600 Check model and map are aligned: 0.300 Set scattering table: 0.370 Process input model: 90.770 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.460 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 665 time to evaluate : 3.041 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: 2.1511 time to fit residues: 1690.3477 Evaluate side-chains 384 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 3.075 ------------------------------------------------------------------------------- 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: 0.5980 chunk 84 optimal weight: 0.9990 chunk 167 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 256 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 190 optimal weight: 0.6980 chunk 296 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 GLN B 160 ASN B 554 GLN B 587 GLN B 732 GLN B 774 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: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 26847 Z= 0.219 Angle : 0.645 15.199 36528 Z= 0.346 Chirality : 0.048 0.279 4332 Planarity : 0.005 0.065 4659 Dihedral : 8.140 59.598 4716 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.72 % Allowed : 10.32 % Favored : 87.96 % 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: 0.08 (0.14), residues: 3258 helix: 0.74 (0.19), residues: 741 sheet: 0.38 (0.17), residues: 822 loop : -0.35 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 856 HIS 0.005 0.001 HIS C 129 PHE 0.014 0.002 PHE A 868 TYR 0.021 0.002 TYR C 469 ARG 0.006 0.001 ARG B 320 *********************** 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 to be fit. rotamer outliers: 49 poor density : 410 time to evaluate : 3.102 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 138 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.6978 (tm-30) REVERT: A 240 MET cc_start: 0.8422 (mtp) cc_final: 0.8073 (mtm) REVERT: A 265 THR cc_start: 0.8152 (p) cc_final: 0.7759 (t) REVERT: A 268 MET cc_start: 0.8814 (ttp) cc_final: 0.8495 (ttm) REVERT: A 710 MET cc_start: 0.8532 (ttm) cc_final: 0.8254 (ttm) REVERT: A 999 MET cc_start: 0.9110 (tpp) cc_final: 0.8638 (tpp) REVERT: A 1042 GLU cc_start: 0.8131 (pm20) cc_final: 0.7849 (pm20) REVERT: A 1089 ASN cc_start: 0.6868 (m-40) cc_final: 0.6622 (m-40) REVERT: B 69 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7680 (ttt180) REVERT: B 151 GLN cc_start: 0.7680 (mt0) cc_final: 0.7098 (mt0) REVERT: B 185 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.7780 (mtpp) REVERT: B 242 MET cc_start: 0.8794 (mtm) cc_final: 0.8441 (mtt) REVERT: B 616 VAL cc_start: 0.8429 (m) cc_final: 0.8149 (m) REVERT: B 755 VAL cc_start: 0.7660 (m) cc_final: 0.7412 (t) REVERT: B 999 MET cc_start: 0.8942 (tpp) cc_final: 0.8729 (tpp) REVERT: C 141 ASP cc_start: 0.7279 (m-30) cc_final: 0.6905 (t0) REVERT: C 237 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7610 (ptt180) REVERT: C 324 ILE cc_start: 0.6230 (pt) cc_final: 0.5815 (tp) REVERT: C 804 MET cc_start: 0.6218 (mtm) cc_final: 0.5969 (tmt) outliers start: 49 outliers final: 18 residues processed: 438 average time/residue: 2.1642 time to fit residues: 1122.6860 Evaluate side-chains 372 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 350 time to evaluate : 3.148 ------------------------------------------------------------------------------- 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 308 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 693 THR 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 693 THR Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 980 GLN Chi-restraints excluded: chain C residue 138 GLN 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 446 THR Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 693 THR 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: 0.7980 chunk 81 optimal weight: 1.9990 chunk 297 optimal weight: 2.9990 chunk 321 optimal weight: 0.7980 chunk 264 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 238 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 285 GLN A 721 ASN A 774 GLN ** A 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 GLN B 160 ASN B 905 GLN C 103 ASN C 326 ASN ** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 26847 Z= 0.245 Angle : 0.597 12.723 36528 Z= 0.321 Chirality : 0.046 0.257 4332 Planarity : 0.004 0.066 4659 Dihedral : 7.598 59.675 4716 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.21 % Allowed : 11.19 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.18 (0.14), residues: 3258 helix: 1.12 (0.19), residues: 723 sheet: 0.28 (0.17), residues: 861 loop : -0.34 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 856 HIS 0.004 0.001 HIS B 200 PHE 0.014 0.001 PHE A 868 TYR 0.019 0.002 TYR C 469 ARG 0.006 0.000 ARG C 82 *********************** 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 440 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 377 time to evaluate : 3.109 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: 0.7723 (OUTLIER) cc_final: 0.7107 (tm-30) REVERT: A 265 THR cc_start: 0.8184 (p) cc_final: 0.7769 (t) REVERT: A 924 GLN cc_start: 0.8035 (mt0) cc_final: 0.7817 (mt0) REVERT: A 999 MET cc_start: 0.9126 (tpp) cc_final: 0.8709 (tpp) REVERT: A 1042 GLU cc_start: 0.8143 (pm20) cc_final: 0.7795 (pm20) REVERT: A 1089 ASN cc_start: 0.6914 (m-40) cc_final: 0.6677 (m-40) REVERT: B 57 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: B 69 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7801 (ttt180) REVERT: B 151 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7220 (mt0) REVERT: B 167 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7929 (tp30) REVERT: B 242 MET cc_start: 0.8804 (mtm) cc_final: 0.8496 (mtt) REVERT: B 616 VAL cc_start: 0.8420 (m) cc_final: 0.8143 (m) REVERT: B 710 MET cc_start: 0.8592 (ttm) cc_final: 0.8287 (ttm) REVERT: B 755 VAL cc_start: 0.7664 (m) cc_final: 0.7408 (t) REVERT: C 141 ASP cc_start: 0.7332 (m-30) cc_final: 0.6932 (t0) REVERT: C 272 ASN cc_start: 0.6839 (t0) cc_final: 0.6215 (t0) REVERT: C 296 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7935 (mttm) REVERT: C 422 THR cc_start: 0.8816 (t) cc_final: 0.8387 (m) REVERT: C 715 ASP cc_start: 0.6227 (t0) cc_final: 0.5935 (t0) REVERT: C 804 MET cc_start: 0.6181 (mtm) cc_final: 0.5981 (tmt) REVERT: C 870 MET cc_start: 0.8800 (mtp) cc_final: 0.8519 (ttm) REVERT: C 917 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8481 (mtmm) outliers start: 63 outliers final: 36 residues processed: 415 average time/residue: 2.2853 time to fit residues: 1112.9032 Evaluate side-chains 387 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 344 time to evaluate : 3.100 ------------------------------------------------------------------------------- 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 172 SER Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 396 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 1020 MET Chi-restraints excluded: chain A residue 1103 ILE 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 167 GLU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 397 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 527 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 971 LEU Chi-restraints excluded: chain B residue 980 GLN Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 212 ARG Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 296 LYS Chi-restraints excluded: chain C residue 386 SER 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 293 optimal weight: 0.6980 chunk 223 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 chunk 316 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 905 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: 0.8003 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 26847 Z= 0.327 Angle : 0.635 11.593 36528 Z= 0.338 Chirality : 0.048 0.281 4332 Planarity : 0.005 0.072 4659 Dihedral : 7.454 59.372 4716 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.60 % Allowed : 11.86 % Favored : 85.54 % 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: 1.02 (0.19), residues: 720 sheet: 0.33 (0.17), residues: 882 loop : -0.53 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 156 HIS 0.007 0.002 HIS B 200 PHE 0.017 0.002 PHE A 868 TYR 0.025 0.002 TYR C 469 ARG 0.007 0.001 ARG C 237 *********************** 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 455 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 381 time to evaluate : 3.161 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: 0.7859 (OUTLIER) cc_final: 0.7213 (tm-30) REVERT: A 758 MET cc_start: 0.8958 (mmm) cc_final: 0.8236 (mmm) REVERT: A 804 MET cc_start: 0.4686 (tpt) cc_final: 0.4361 (tpt) REVERT: A 999 MET cc_start: 0.9105 (tpp) cc_final: 0.8746 (tpp) REVERT: B 27 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8217 (m) REVERT: B 57 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.7607 (tm-30) REVERT: B 69 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7734 (ttt180) REVERT: B 133 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8439 (tttp) REVERT: B 151 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7411 (mt0) REVERT: B 242 MET cc_start: 0.8773 (mtm) cc_final: 0.8416 (mtt) REVERT: B 616 VAL cc_start: 0.8546 (m) cc_final: 0.8281 (m) REVERT: B 710 MET cc_start: 0.8633 (ttm) cc_final: 0.8196 (ttm) REVERT: B 755 VAL cc_start: 0.7682 (m) cc_final: 0.7385 (t) REVERT: B 872 MET cc_start: 0.8593 (mmt) cc_final: 0.8232 (tpp) REVERT: B 955 ASP cc_start: 0.7083 (OUTLIER) cc_final: 0.6880 (p0) REVERT: B 972 GLN cc_start: 0.7715 (tp40) cc_final: 0.7475 (mm-40) REVERT: C 31 MET cc_start: 0.8589 (mtp) cc_final: 0.8353 (mtm) REVERT: C 115 ASP cc_start: 0.8696 (p0) cc_final: 0.8372 (p0) REVERT: C 185 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8167 (mtpp) REVERT: C 272 ASN cc_start: 0.7124 (t0) cc_final: 0.6580 (t0) REVERT: C 422 THR cc_start: 0.8859 (t) cc_final: 0.8418 (m) REVERT: C 715 ASP cc_start: 0.6225 (t0) cc_final: 0.6013 (t0) REVERT: C 804 MET cc_start: 0.6266 (mtm) cc_final: 0.6062 (tmt) REVERT: C 805 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.6877 (mptm) outliers start: 74 outliers final: 39 residues processed: 422 average time/residue: 2.3301 time to fit residues: 1150.0239 Evaluate side-chains 393 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 345 time to evaluate : 3.102 ------------------------------------------------------------------------------- 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 172 SER Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 396 SER 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 565 SER Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 141 ASP 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 523 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 955 ASP Chi-restraints excluded: chain B residue 980 GLN Chi-restraints excluded: chain B residue 1096 CYS Chi-restraints excluded: chain C residue 67 VAL 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 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 694 THR Chi-restraints excluded: chain C residue 805 LYS 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: 0.7980 chunk 179 optimal weight: 1.9990 chunk 4 optimal weight: 0.0770 chunk 235 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 269 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 283 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN A 721 ASN ** A 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 GLN B 826 ASN B 905 GLN C 326 ASN ** C 774 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: 0.7993 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26847 Z= 0.231 Angle : 0.564 7.548 36528 Z= 0.302 Chirality : 0.046 0.268 4332 Planarity : 0.004 0.052 4659 Dihedral : 7.021 59.135 4716 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.18 % Allowed : 12.67 % Favored : 85.16 % 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: 0.07 (0.14), residues: 3258 helix: 1.11 (0.20), residues: 723 sheet: 0.26 (0.17), residues: 870 loop : -0.49 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 856 HIS 0.006 0.001 HIS B 200 PHE 0.015 0.001 PHE A 868 TYR 0.019 0.002 TYR A 469 ARG 0.006 0.000 ARG C1077 *********************** 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 437 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 375 time to evaluate : 3.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7507 (m-30) cc_final: 0.7216 (m-30) REVERT: A 138 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: A 177 VAL cc_start: 0.7160 (OUTLIER) cc_final: 0.6953 (t) REVERT: A 758 MET cc_start: 0.8943 (mmm) cc_final: 0.8238 (mmm) REVERT: B 69 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7599 (ttt180) REVERT: B 151 GLN cc_start: 0.7901 (mt0) cc_final: 0.7480 (mm-40) REVERT: B 159 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7779 (p) REVERT: B 242 MET cc_start: 0.8716 (mtm) cc_final: 0.8369 (mtt) REVERT: B 710 MET cc_start: 0.8621 (ttm) cc_final: 0.8284 (ttm) REVERT: B 755 VAL cc_start: 0.7639 (m) cc_final: 0.7326 (t) REVERT: B 804 MET cc_start: 0.6149 (tpt) cc_final: 0.5594 (tpt) REVERT: B 872 MET cc_start: 0.8585 (mmt) cc_final: 0.8134 (tpp) REVERT: B 955 ASP cc_start: 0.7140 (OUTLIER) cc_final: 0.6832 (p0) REVERT: B 972 GLN cc_start: 0.7744 (tp40) cc_final: 0.7440 (mm110) REVERT: C 115 ASP cc_start: 0.8553 (p0) cc_final: 0.8295 (p0) REVERT: C 185 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8193 (mtpp) REVERT: C 422 THR cc_start: 0.8841 (t) cc_final: 0.8386 (m) REVERT: C 735 ARG cc_start: 0.7987 (ttm110) cc_final: 0.7720 (mtm110) REVERT: C 891 LYS cc_start: 0.7966 (mtmp) cc_final: 0.7643 (mmpt) outliers start: 62 outliers final: 35 residues processed: 408 average time/residue: 2.3588 time to fit residues: 1129.0952 Evaluate side-chains 390 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 349 time to evaluate : 3.113 ------------------------------------------------------------------------------- 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 177 VAL 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 749 GLN 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 94 ILE Chi-restraints excluded: chain B residue 159 THR 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 523 THR Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 937 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 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 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 694 THR Chi-restraints excluded: chain C residue 788 ILE 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: 1.9990 chunk 62 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 316 optimal weight: 0.5980 chunk 262 optimal weight: 0.0060 chunk 146 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 166 optimal weight: 0.0980 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN A 326 ASN A 587 GLN A 721 ASN ** A 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 ASN B 272 ASN B 871 GLN C 326 ASN C 774 GLN C 905 GLN C 980 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4463 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= 0.171 Angle : 0.526 5.962 36528 Z= 0.281 Chirality : 0.045 0.251 4332 Planarity : 0.004 0.051 4659 Dihedral : 6.516 59.983 4716 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.79 % Allowed : 13.79 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.26 (0.20), residues: 726 sheet: 0.23 (0.17), residues: 849 loop : -0.51 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 607 HIS 0.003 0.001 HIS C 599 PHE 0.012 0.001 PHE A 868 TYR 0.016 0.001 TYR A 469 ARG 0.006 0.000 ARG C1077 *********************** 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 420 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 369 time to evaluate : 3.119 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: A 138 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7190 (tm-30) REVERT: A 735 ARG cc_start: 0.8005 (ttm110) cc_final: 0.7772 (ttm110) REVERT: A 886 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8034 (tp) REVERT: A 999 MET cc_start: 0.9032 (tpp) cc_final: 0.8770 (tpp) REVERT: B 69 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7681 (ttt180) REVERT: B 151 GLN cc_start: 0.7881 (mt0) cc_final: 0.7505 (mm-40) REVERT: B 185 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8077 (mtpp) REVERT: B 212 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7122 (mtp85) REVERT: B 242 MET cc_start: 0.8690 (mtm) cc_final: 0.8369 (mtt) REVERT: B 710 MET cc_start: 0.8586 (ttm) cc_final: 0.8103 (ttm) REVERT: B 755 VAL cc_start: 0.7676 (m) cc_final: 0.7404 (t) REVERT: B 760 LYS cc_start: 0.7962 (pttp) cc_final: 0.7469 (mtmm) REVERT: B 804 MET cc_start: 0.6280 (tpt) cc_final: 0.5684 (tpt) REVERT: B 872 MET cc_start: 0.8604 (mmt) cc_final: 0.8175 (tpp) REVERT: B 972 GLN cc_start: 0.7650 (tp40) cc_final: 0.7379 (mm110) REVERT: C 115 ASP cc_start: 0.8522 (p0) cc_final: 0.8273 (p0) REVERT: C 185 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8089 (mtpp) REVERT: C 332 LYS cc_start: 0.8212 (ttpp) cc_final: 0.7956 (tttp) REVERT: C 422 THR cc_start: 0.8822 (t) cc_final: 0.8354 (m) REVERT: C 715 ASP cc_start: 0.5782 (t0) cc_final: 0.5522 (t0) REVERT: C 972 GLN cc_start: 0.7468 (tp-100) cc_final: 0.7228 (tp-100) outliers start: 51 outliers final: 30 residues processed: 396 average time/residue: 2.3794 time to fit residues: 1101.1832 Evaluate side-chains 378 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 342 time to evaluate : 3.077 ------------------------------------------------------------------------------- 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 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 886 LEU 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 212 ARG 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 674 SER Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 937 SER 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 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 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 1089 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 305 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 180 optimal weight: 2.9990 chunk 231 optimal weight: 0.0870 chunk 179 optimal weight: 0.8980 chunk 266 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 315 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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 A 774 GLN ** A 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 ASN B 160 ASN B 272 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 ASN C 774 GLN C 980 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 26847 Z= 0.201 Angle : 0.528 11.727 36528 Z= 0.281 Chirality : 0.045 0.253 4332 Planarity : 0.004 0.047 4659 Dihedral : 6.334 59.459 4716 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.93 % Allowed : 14.21 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.36 (0.20), residues: 726 sheet: 0.25 (0.17), residues: 837 loop : -0.53 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 607 HIS 0.003 0.001 HIS C 599 PHE 0.013 0.001 PHE A 868 TYR 0.017 0.001 TYR A 469 ARG 0.007 0.000 ARG C1077 *********************** 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 405 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 350 time to evaluate : 3.107 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 46 ASP cc_start: 0.7355 (m-30) cc_final: 0.7021 (m-30) REVERT: A 50 SER cc_start: 0.8904 (OUTLIER) cc_final: 0.8623 (t) REVERT: A 138 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7187 (tm-30) REVERT: A 240 MET cc_start: 0.9119 (mtm) cc_final: 0.8678 (mtt) REVERT: A 265 THR cc_start: 0.8138 (p) cc_final: 0.7681 (t) REVERT: A 732 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: A 758 MET cc_start: 0.8917 (mmm) cc_final: 0.8303 (mmm) REVERT: A 790 ASP cc_start: 0.7748 (m-30) cc_final: 0.7502 (m-30) REVERT: A 886 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8099 (tp) REVERT: A 999 MET cc_start: 0.9015 (tpp) cc_final: 0.8800 (tpp) REVERT: B 69 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7584 (ttt180) REVERT: B 151 GLN cc_start: 0.7893 (mt0) cc_final: 0.7654 (mm-40) REVERT: B 185 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8109 (mtpp) REVERT: B 229 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6841 (mt) REVERT: B 242 MET cc_start: 0.8675 (mtm) cc_final: 0.8351 (mtt) REVERT: B 324 ILE cc_start: 0.7621 (OUTLIER) cc_final: 0.7055 (pt) REVERT: B 710 MET cc_start: 0.8591 (ttm) cc_final: 0.8244 (ttm) REVERT: B 755 VAL cc_start: 0.7685 (m) cc_final: 0.7416 (t) REVERT: B 760 LYS cc_start: 0.7953 (pttp) cc_final: 0.7489 (mtmm) REVERT: B 872 MET cc_start: 0.8601 (mmt) cc_final: 0.8175 (tpp) REVERT: B 972 GLN cc_start: 0.7574 (tp40) cc_final: 0.7295 (mm110) REVERT: C 115 ASP cc_start: 0.8520 (p0) cc_final: 0.8260 (p0) REVERT: C 185 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8071 (mtpp) REVERT: C 332 LYS cc_start: 0.8192 (ttpp) cc_final: 0.7933 (tttp) REVERT: C 422 THR cc_start: 0.8836 (t) cc_final: 0.8344 (m) REVERT: C 715 ASP cc_start: 0.5776 (t0) cc_final: 0.5520 (t0) REVERT: C 760 LYS cc_start: 0.8005 (ptmm) cc_final: 0.7558 (mttt) REVERT: C 891 LYS cc_start: 0.7873 (mtmp) cc_final: 0.7563 (mmpt) outliers start: 55 outliers final: 34 residues processed: 379 average time/residue: 2.4347 time to fit residues: 1079.3850 Evaluate side-chains 377 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 334 time to evaluate : 3.109 ------------------------------------------------------------------------------- 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 146 THR Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 306 GLN 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 732 GLN Chi-restraints excluded: chain A residue 749 GLN Chi-restraints excluded: chain A residue 886 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 229 LEU 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 674 SER Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 937 SER 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 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 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 544 SER Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 694 THR 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: 3.9990 chunk 188 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 286 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 ASN B 272 ASN 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 26847 Z= 0.283 Angle : 0.569 14.745 36528 Z= 0.303 Chirality : 0.046 0.269 4332 Planarity : 0.004 0.047 4659 Dihedral : 6.435 58.959 4716 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.00 % Allowed : 14.42 % Favored : 83.58 % 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: 0.08 (0.14), residues: 3258 helix: 1.26 (0.20), residues: 729 sheet: 0.28 (0.17), residues: 840 loop : -0.56 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 607 HIS 0.005 0.001 HIS C 599 PHE 0.014 0.001 PHE A 868 TYR 0.018 0.002 TYR C 469 ARG 0.008 0.000 ARG C1077 *********************** 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 402 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 345 time to evaluate : 3.368 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 46 ASP cc_start: 0.7363 (m-30) cc_final: 0.7050 (m-30) REVERT: A 50 SER cc_start: 0.8936 (OUTLIER) cc_final: 0.8652 (t) REVERT: A 138 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7215 (tm-30) REVERT: A 240 MET cc_start: 0.9105 (mtm) cc_final: 0.8730 (mtt) REVERT: A 758 MET cc_start: 0.8899 (mmm) cc_final: 0.8241 (mmm) REVERT: A 886 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8146 (tp) REVERT: A 999 MET cc_start: 0.9019 (tpp) cc_final: 0.8787 (tpp) REVERT: B 69 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7650 (ttt180) REVERT: B 151 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7715 (mm-40) REVERT: B 159 THR cc_start: 0.8070 (OUTLIER) cc_final: 0.7825 (p) REVERT: B 212 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7116 (mtp85) REVERT: B 229 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6954 (mt) REVERT: B 242 MET cc_start: 0.8670 (mtm) cc_final: 0.8317 (mtt) REVERT: B 324 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7059 (pt) REVERT: B 710 MET cc_start: 0.8617 (ttm) cc_final: 0.8263 (ttm) REVERT: B 755 VAL cc_start: 0.7640 (m) cc_final: 0.7356 (t) REVERT: B 760 LYS cc_start: 0.7978 (pttp) cc_final: 0.7511 (mtmm) REVERT: B 872 MET cc_start: 0.8613 (mmt) cc_final: 0.8180 (tpp) REVERT: B 972 GLN cc_start: 0.7606 (tp40) cc_final: 0.7323 (mm110) REVERT: C 115 ASP cc_start: 0.8518 (p0) cc_final: 0.8259 (p0) REVERT: C 185 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8072 (mtpp) REVERT: C 332 LYS cc_start: 0.8198 (ttpp) cc_final: 0.7925 (tttp) REVERT: C 422 THR cc_start: 0.8812 (t) cc_final: 0.8333 (m) REVERT: C 715 ASP cc_start: 0.5869 (t0) cc_final: 0.5591 (t0) REVERT: C 760 LYS cc_start: 0.8044 (ptmm) cc_final: 0.7588 (mttt) REVERT: C 972 GLN cc_start: 0.7557 (tp-100) cc_final: 0.7347 (tp-100) outliers start: 57 outliers final: 39 residues processed: 374 average time/residue: 2.4368 time to fit residues: 1080.6455 Evaluate side-chains 387 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 338 time to evaluate : 3.094 ------------------------------------------------------------------------------- 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 306 GLN Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 386 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 689 SER Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 749 GLN Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 886 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 151 GLN Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 229 LEU 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 674 SER Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 980 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 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 544 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 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: 0.9990 chunk 293 optimal weight: 0.6980 chunk 176 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 265 optimal weight: 0.4980 chunk 277 optimal weight: 1.9990 chunk 292 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 ASN B 272 ASN B 306 GLN C 326 ASN ** 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: 0.7978 moved from start: 0.4697 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= 0.214 Angle : 0.544 13.980 36528 Z= 0.290 Chirality : 0.045 0.260 4332 Planarity : 0.004 0.052 4659 Dihedral : 6.318 59.786 4716 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.86 % Allowed : 14.67 % Favored : 83.47 % 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: 0.10 (0.14), residues: 3258 helix: 1.29 (0.20), residues: 729 sheet: 0.28 (0.17), residues: 840 loop : -0.55 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 607 HIS 0.003 0.001 HIS C 599 PHE 0.013 0.001 PHE A 868 TYR 0.016 0.001 TYR B1037 ARG 0.007 0.000 ARG C1077 *********************** 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 402 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 349 time to evaluate : 3.207 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 46 ASP cc_start: 0.7351 (m-30) cc_final: 0.7043 (m-30) REVERT: A 50 SER cc_start: 0.8924 (OUTLIER) cc_final: 0.8654 (t) REVERT: A 138 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7183 (tm-30) REVERT: A 240 MET cc_start: 0.9103 (mtm) cc_final: 0.8740 (mtt) REVERT: A 265 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7670 (t) REVERT: A 758 MET cc_start: 0.8879 (mmm) cc_final: 0.8228 (mmm) REVERT: A 886 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8153 (tp) REVERT: A 999 MET cc_start: 0.9025 (tpp) cc_final: 0.8805 (tpp) REVERT: B 69 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7651 (ttt180) REVERT: B 151 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7432 (mm110) REVERT: B 185 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8109 (mtpp) REVERT: B 212 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7089 (mtp85) REVERT: B 229 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6983 (mt) REVERT: B 242 MET cc_start: 0.8656 (mtm) cc_final: 0.8301 (mtt) REVERT: B 324 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7015 (pt) REVERT: B 710 MET cc_start: 0.8586 (ttm) cc_final: 0.8233 (ttm) REVERT: B 755 VAL cc_start: 0.7634 (m) cc_final: 0.7355 (t) REVERT: B 760 LYS cc_start: 0.7963 (pttp) cc_final: 0.7532 (mtmm) REVERT: B 872 MET cc_start: 0.8616 (mmt) cc_final: 0.8189 (tpp) REVERT: B 972 GLN cc_start: 0.7569 (tp40) cc_final: 0.7352 (mm110) REVERT: C 31 MET cc_start: 0.8554 (mtp) cc_final: 0.8313 (mtm) REVERT: C 115 ASP cc_start: 0.8510 (p0) cc_final: 0.8243 (p0) REVERT: C 185 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8080 (mtpp) REVERT: C 332 LYS cc_start: 0.8223 (ttpp) cc_final: 0.7952 (tttp) REVERT: C 422 THR cc_start: 0.8840 (t) cc_final: 0.8348 (m) REVERT: C 715 ASP cc_start: 0.5806 (t0) cc_final: 0.5545 (t0) REVERT: C 760 LYS cc_start: 0.8024 (ptmm) cc_final: 0.7597 (mttt) outliers start: 53 outliers final: 36 residues processed: 376 average time/residue: 2.3359 time to fit residues: 1030.8218 Evaluate side-chains 389 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 342 time to evaluate : 3.162 ------------------------------------------------------------------------------- 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 308 SER Chi-restraints excluded: chain A residue 386 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 689 SER Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 886 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 229 LEU 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 674 SER Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 980 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 488 SER Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 694 THR 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: 2.9990 chunk 189 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 325 optimal weight: 0.3980 chunk 299 optimal weight: 0.8980 chunk 259 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 200 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 GLN A1095 ASN B 272 ASN B 306 GLN C 326 ASN C 826 ASN C 980 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 26847 Z= 0.228 Angle : 0.549 13.800 36528 Z= 0.292 Chirality : 0.045 0.266 4332 Planarity : 0.004 0.057 4659 Dihedral : 6.280 57.600 4716 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.75 % Allowed : 14.70 % Favored : 83.54 % 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: 0.10 (0.14), residues: 3258 helix: 1.32 (0.20), residues: 726 sheet: 0.30 (0.17), residues: 840 loop : -0.57 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 607 HIS 0.004 0.001 HIS A 200 PHE 0.013 0.001 PHE A 868 TYR 0.017 0.001 TYR C 469 ARG 0.008 0.000 ARG C1077 ********************** 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 398 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 348 time to evaluate : 3.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7351 (m-30) cc_final: 0.7060 (m-30) REVERT: A 50 SER cc_start: 0.8929 (OUTLIER) cc_final: 0.8661 (t) REVERT: A 138 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7187 (tm-30) REVERT: A 240 MET cc_start: 0.9110 (mtm) cc_final: 0.8755 (mtt) REVERT: A 265 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7908 (t) REVERT: A 758 MET cc_start: 0.8908 (mmm) cc_final: 0.8258 (mmm) REVERT: A 886 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8161 (tp) REVERT: A 999 MET cc_start: 0.9027 (tpp) cc_final: 0.8805 (tpp) REVERT: B 69 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7615 (ttt180) REVERT: B 151 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7512 (mm-40) REVERT: B 185 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8101 (mtpp) REVERT: B 212 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7025 (mtp85) REVERT: B 229 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6974 (mt) REVERT: B 242 MET cc_start: 0.8655 (mtm) cc_final: 0.8319 (mtt) REVERT: B 301 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7206 (mm-30) REVERT: B 324 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.7054 (pt) REVERT: B 755 VAL cc_start: 0.7655 (m) cc_final: 0.7372 (t) REVERT: B 760 LYS cc_start: 0.7968 (pttp) cc_final: 0.7553 (mtmm) REVERT: B 872 MET cc_start: 0.8615 (mmt) cc_final: 0.8198 (tpp) REVERT: C 31 MET cc_start: 0.8558 (mtp) cc_final: 0.8319 (mtm) REVERT: C 115 ASP cc_start: 0.8506 (p0) cc_final: 0.8239 (p0) REVERT: C 185 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8104 (mtpp) REVERT: C 422 THR cc_start: 0.8840 (t) cc_final: 0.8342 (m) REVERT: C 715 ASP cc_start: 0.5905 (t0) cc_final: 0.5653 (t0) REVERT: C 760 LYS cc_start: 0.8040 (ptmm) cc_final: 0.7625 (mttt) outliers start: 50 outliers final: 33 residues processed: 375 average time/residue: 2.3867 time to fit residues: 1049.4406 Evaluate side-chains 385 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 341 time to evaluate : 3.132 ------------------------------------------------------------------------------- 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 386 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 689 SER Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 886 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 229 LEU 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 674 SER Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 980 GLN Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 348 THR 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 544 SER Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 694 THR 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: 4.9990 chunk 108 optimal weight: 2.9990 chunk 266 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 A 883 GLN A1095 ASN B 272 ASN B 306 GLN B 587 GLN C 326 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 980 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.125343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.105603 restraints weight = 72160.339| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.39 r_work: 0.2970 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 26847 Z= 0.315 Angle : 0.606 14.239 36528 Z= 0.322 Chirality : 0.047 0.292 4332 Planarity : 0.004 0.058 4659 Dihedral : 6.606 59.424 4716 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.86 % Allowed : 14.67 % Favored : 83.47 % 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: 0.03 (0.14), residues: 3258 helix: 1.15 (0.20), residues: 726 sheet: 0.32 (0.17), residues: 834 loop : -0.60 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 607 HIS 0.006 0.001 HIS C 599 PHE 0.016 0.002 PHE A 868 TYR 0.021 0.002 TYR C 469 ARG 0.009 0.001 ARG C1077 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16624.66 seconds wall clock time: 285 minutes 0.39 seconds (17100.39 seconds total)