Starting phenix.real_space_refine on Wed Feb 21 07:58:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnd_32039/02_2024/7vnd_32039.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnd_32039/02_2024/7vnd_32039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnd_32039/02_2024/7vnd_32039.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnd_32039/02_2024/7vnd_32039.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnd_32039/02_2024/7vnd_32039.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnd_32039/02_2024/7vnd_32039.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2442 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 17563 2.51 5 N 4549 2.21 5 O 5394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B ASP 614": "OD1" <-> "OD2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27632 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 8372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8372 Classifications: {'peptide': 1070} Link IDs: {'PTRANS': 53, 'TRANS': 1016} Chain breaks: 4 Chain: "A" Number of atoms: 8372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8372 Classifications: {'peptide': 1070} Link IDs: {'PTRANS': 53, 'TRANS': 1016} Chain breaks: 4 Chain: "C" Number of atoms: 8372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8372 Classifications: {'peptide': 1070} Link IDs: {'CIS': 1, 'PTRANS': 53, 'TRANS': 1015} Chain breaks: 4 Chain: "V" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 111} Chain: "D" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 111} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 14.46, per 1000 atoms: 0.52 Number of scatterers: 27632 At special positions: 0 Unit cell: (187.59, 172.38, 164.268, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 5394 8.00 N 4549 7.00 C 17563 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 149 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 122 " " NAG A1306 " - " ASN A 616 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 616 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 149 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 801 " " NAG C1305 " - " ASN C 122 " " NAG C1306 " - " ASN C 234 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 616 " " NAG E 1 " - " ASN B 234 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN B 801 " " NAG H 1 " - " ASN B1098 " " NAG I 1 " - " ASN A 234 " " NAG J 1 " - " ASN A 282 " " NAG K 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN A 717 " " NAG O 1 " - " ASN A 801 " " NAG P 1 " - " ASN C 282 " " NAG R 1 " - " ASN C1074 " " NAG T 1 " - " ASN C 331 " Time building additional restraints: 10.67 Conformation dependent library (CDL) restraints added in 4.8 seconds 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6422 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 54 sheets defined 22.1% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.23 Creating SS restraints... Processing helix chain 'B' and resid 155 through 159 removed outlier: 4.075A pdb=" N ARG B 158 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.546A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.192A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.149A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.608A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.691A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 753 " --> pdb=" O CYS B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 761 through 783 removed outlier: 3.811A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 4.106A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.739A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 869 Processing helix chain 'B' and resid 870 through 882 removed outlier: 3.994A pdb=" N ALA B 879 " --> pdb=" O SER B 875 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.664A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.704A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 940 removed outlier: 4.208A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.601A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 977 through 984 removed outlier: 3.945A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.763A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B1008 " --> pdb=" O LEU B1004 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA B1025 " --> pdb=" O SER B1021 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B1026 " --> pdb=" O ALA B1022 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1146 removed outlier: 3.527A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.518A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.566A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 762 through 782 removed outlier: 3.508A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 818 through 825 Processing helix chain 'A' and resid 866 through 884 removed outlier: 4.057A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 891 removed outlier: 3.980A pdb=" N PHE A 888 " --> pdb=" O GLY A 885 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 4.376A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.537A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.826A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.573A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 958 " --> pdb=" O GLN A 954 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.741A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.684A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN A1010 " --> pdb=" O THR A1006 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A1018 " --> pdb=" O ARG A1014 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.785A pdb=" N ALA C 352 " --> pdb=" O SER C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.032A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.617A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.730A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 removed outlier: 4.099A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.742A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 773 removed outlier: 3.513A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 783 removed outlier: 3.725A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 removed outlier: 4.133A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 882 removed outlier: 3.980A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.722A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 899 No H-bonds generated for 'chain 'C' and resid 897 through 899' Processing helix chain 'C' and resid 900 through 909 removed outlier: 3.719A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.662A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.641A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 964 removed outlier: 3.976A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN C 957 " --> pdb=" O ASN C 953 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 968 removed outlier: 3.937A pdb=" N SER C 968 " --> pdb=" O GLN C 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 965 through 968' Processing helix chain 'C' and resid 977 through 982 removed outlier: 3.652A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.338A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.760A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'V' and resid 60 through 64 removed outlier: 3.839A pdb=" N LYS V 64 " --> pdb=" O PRO V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 86 through 90 Processing helix chain 'V' and resid 98 through 102 removed outlier: 4.056A pdb=" N GLY V 102 " --> pdb=" O TRP V 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 removed outlier: 4.112A pdb=" N TYR D 30 " --> pdb=" O PHE D 27 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP D 31 " --> pdb=" O SER D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 removed outlier: 3.896A pdb=" N LYS D 64 " --> pdb=" O PRO D 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 99 through 102 removed outlier: 4.202A pdb=" N GLY D 102 " --> pdb=" O TRP D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 99 through 102' Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.595A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 55 Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 92 removed outlier: 3.600A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 168 through 172 removed outlier: 3.775A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 311 through 317 removed outlier: 7.041A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 355 removed outlier: 3.985A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'B' and resid 542 through 543 removed outlier: 3.852A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 584 through 586 removed outlier: 3.605A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.982A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 701 through 702 removed outlier: 7.142A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 711 through 719 removed outlier: 6.490A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 722 through 728 removed outlier: 4.550A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.486A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AC1, first strand: chain 'B' and resid 1086 through 1090 removed outlier: 4.512A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AC3, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.990A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 42 through 44 removed outlier: 6.267A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.610A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AC7, first strand: chain 'A' and resid 225 through 229 removed outlier: 6.998A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 101 through 104 removed outlier: 6.466A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.543A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 132 through 133 removed outlier: 3.851A pdb=" N GLU A 132 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.337A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 326 through 328 removed outlier: 3.643A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 376 through 379 removed outlier: 3.646A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.299A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AD7, first strand: chain 'A' and resid 720 through 722 Processing sheet with id=AD8, first strand: chain 'A' and resid 725 through 728 removed outlier: 3.608A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AE1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.808A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.579A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 49 through 55 Processing sheet with id=AE5, first strand: chain 'C' and resid 92 through 94 removed outlier: 3.659A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 101 through 104 removed outlier: 6.176A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N LEU C 141 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N LEU C 242 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL C 143 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU C 244 " --> pdb=" O VAL C 143 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 126 through 133 removed outlier: 8.055A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 311 through 317 removed outlier: 6.890A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.607A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.133A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.575A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.575A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF5, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id=AF6, first strand: chain 'V' and resid 19 through 22 removed outlier: 3.644A pdb=" N ASP V 72 " --> pdb=" O THR V 77 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR V 79 " --> pdb=" O SER V 70 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER V 70 " --> pdb=" O TYR V 79 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN V 81 " --> pdb=" O THR V 68 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR V 68 " --> pdb=" O GLN V 81 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 35 through 39 Processing sheet with id=AF8, first strand: chain 'D' and resid 22 through 23 removed outlier: 4.743A pdb=" N CYS D 22 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU D 78 " --> pdb=" O CYS D 22 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR D 68 " --> pdb=" O GLN D 81 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 57 through 59 removed outlier: 5.130A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TRP D 36 " --> pdb=" O GLY D 49 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER D 35 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL D 96 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN D 39 " --> pdb=" O MET D 92 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N MET D 92 " --> pdb=" O GLN D 39 " (cutoff:3.500A) 742 hydrogen bonds defined for protein. 1974 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.44 Time building geometry restraints manager: 11.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4477 1.31 - 1.44: 7786 1.44 - 1.57: 15831 1.57 - 1.70: 1 1.70 - 1.83: 164 Bond restraints: 28259 Sorted by residual: bond pdb=" C7 NAG C1302 " pdb=" N2 NAG C1302 " ideal model delta sigma weight residual 1.346 1.487 -0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C7 NAG J 1 " pdb=" N2 NAG J 1 " ideal model delta sigma weight residual 1.346 1.483 -0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" C7 NAG S 2 " pdb=" N2 NAG S 2 " ideal model delta sigma weight residual 1.346 1.483 -0.137 2.00e-02 2.50e+03 4.66e+01 bond pdb=" C7 NAG K 2 " pdb=" N2 NAG K 2 " ideal model delta sigma weight residual 1.346 1.482 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C7 NAG R 2 " pdb=" N2 NAG R 2 " ideal model delta sigma weight residual 1.346 1.482 -0.136 2.00e-02 2.50e+03 4.61e+01 ... (remaining 28254 not shown) Histogram of bond angle deviations from ideal: 99.23 - 106.20: 602 106.20 - 113.18: 15451 113.18 - 120.16: 9579 120.16 - 127.13: 12576 127.13 - 134.11: 244 Bond angle restraints: 38452 Sorted by residual: angle pdb=" CA CYS C 336 " pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " ideal model delta sigma weight residual 114.40 122.10 -7.70 2.30e+00 1.89e-01 1.12e+01 angle pdb=" C GLN C 613 " pdb=" N ASP C 614 " pdb=" CA ASP C 614 " ideal model delta sigma weight residual 121.54 127.76 -6.22 1.91e+00 2.74e-01 1.06e+01 angle pdb=" C8 NAG J 1 " pdb=" C7 NAG J 1 " pdb=" N2 NAG J 1 " ideal model delta sigma weight residual 115.06 124.62 -9.56 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C8 NAG R 2 " pdb=" C7 NAG R 2 " pdb=" N2 NAG R 2 " ideal model delta sigma weight residual 115.06 124.54 -9.48 3.00e+00 1.11e-01 9.99e+00 angle pdb=" C8 NAG K 2 " pdb=" C7 NAG K 2 " pdb=" N2 NAG K 2 " ideal model delta sigma weight residual 115.06 124.40 -9.34 3.00e+00 1.11e-01 9.69e+00 ... (remaining 38447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.11: 16158 24.11 - 48.21: 967 48.21 - 72.32: 166 72.32 - 96.43: 79 96.43 - 120.54: 57 Dihedral angle restraints: 17427 sinusoidal: 7423 harmonic: 10004 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -174.99 88.99 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 95 " pdb=" CB CYS D 95 " ideal model delta sinusoidal sigma weight residual 93.00 166.23 -73.23 1 1.00e+01 1.00e-02 6.83e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -14.31 -71.69 1 1.00e+01 1.00e-02 6.58e+01 ... (remaining 17424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 4108 0.093 - 0.187: 356 0.187 - 0.280: 7 0.280 - 0.373: 5 0.373 - 0.466: 4 Chirality restraints: 4480 Sorted by residual: chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.44e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 149 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.05e+00 ... (remaining 4477 not shown) Planarity restraints: 4947 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 383 " 0.067 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO C 384 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO C 384 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 384 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 271 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO B 272 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO A 987 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.031 5.00e-02 4.00e+02 ... (remaining 4944 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1015 2.72 - 3.26: 27098 3.26 - 3.81: 41338 3.81 - 4.35: 53029 4.35 - 4.90: 88766 Nonbonded interactions: 211246 Sorted by model distance: nonbonded pdb=" O GLN C 580 " pdb=" O3 NAG T 1 " model vdw 2.170 2.440 nonbonded pdb=" OE2 GLU C 281 " pdb=" O3 NAG P 1 " model vdw 2.184 2.440 nonbonded pdb=" OG1 THR A1076 " pdb=" OG SER A1097 " model vdw 2.185 2.440 nonbonded pdb=" O SER B 937 " pdb=" OG1 THR B 941 " model vdw 2.186 2.440 nonbonded pdb=" OH TYR A 369 " pdb=" O PRO A 384 " model vdw 2.201 2.440 ... (remaining 211241 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 14 through 1146 or resid 1301 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'V' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.010 Extract box with map and model: 5.360 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 71.020 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 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 : 0.009 0.141 28259 Z= 0.578 Angle : 0.751 9.564 38452 Z= 0.345 Chirality : 0.051 0.466 4480 Planarity : 0.004 0.099 4914 Dihedral : 18.080 120.535 10930 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -2.53 (0.14), residues: 3408 helix: -1.63 (0.20), residues: 615 sheet: -0.22 (0.22), residues: 578 loop : -2.24 (0.13), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 886 HIS 0.005 0.001 HIS A 69 PHE 0.024 0.001 PHE C 106 TYR 0.020 0.001 TYR A1067 ARG 0.009 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 2.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7773 (m-80) cc_final: 0.7492 (m-80) REVERT: C 106 PHE cc_start: 0.7661 (m-80) cc_final: 0.7424 (m-80) REVERT: C 457 ARG cc_start: 0.2105 (mtt180) cc_final: 0.1740 (mmm160) REVERT: C 645 THR cc_start: 0.8719 (p) cc_final: 0.8515 (p) REVERT: C 1081 ILE cc_start: 0.9231 (mm) cc_final: 0.8946 (mm) REVERT: V 82 MET cc_start: 0.3986 (mmt) cc_final: 0.2097 (ptt) REVERT: D 92 MET cc_start: 0.0667 (pmm) cc_final: 0.0426 (pmm) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.4017 time to fit residues: 176.9390 Evaluate side-chains 210 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 1.9990 chunk 259 optimal weight: 30.0000 chunk 144 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 175 optimal weight: 0.6980 chunk 138 optimal weight: 50.0000 chunk 268 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 chunk 311 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B1054 GLN ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28259 Z= 0.260 Angle : 0.691 10.631 38452 Z= 0.332 Chirality : 0.051 0.471 4480 Planarity : 0.004 0.055 4914 Dihedral : 15.102 114.572 4792 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.73 % Allowed : 6.20 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -2.34 (0.14), residues: 3408 helix: -1.14 (0.20), residues: 652 sheet: -0.32 (0.21), residues: 628 loop : -2.20 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 436 HIS 0.004 0.001 HIS A1058 PHE 0.037 0.002 PHE C 643 TYR 0.029 0.002 TYR C 741 ARG 0.005 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 222 time to evaluate : 3.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 457 ARG cc_start: 0.2104 (mtt180) cc_final: 0.1734 (mmm160) REVERT: C 1081 ILE cc_start: 0.9266 (mm) cc_final: 0.8981 (mm) REVERT: V 82 MET cc_start: 0.4066 (mmt) cc_final: 0.2090 (ptt) outliers start: 22 outliers final: 15 residues processed: 236 average time/residue: 0.3638 time to fit residues: 141.2391 Evaluate side-chains 217 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 202 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 981 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 173 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 259 optimal weight: 30.0000 chunk 212 optimal weight: 0.0970 chunk 85 optimal weight: 3.9990 chunk 312 optimal weight: 4.9990 chunk 337 optimal weight: 30.0000 chunk 277 optimal weight: 10.0000 chunk 309 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 250 optimal weight: 30.0000 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 28259 Z= 0.299 Angle : 0.686 11.156 38452 Z= 0.329 Chirality : 0.051 0.475 4480 Planarity : 0.004 0.050 4914 Dihedral : 13.488 115.772 4792 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 1.40 % Allowed : 10.14 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -2.29 (0.14), residues: 3408 helix: -0.82 (0.20), residues: 659 sheet: -0.40 (0.21), residues: 614 loop : -2.22 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 886 HIS 0.006 0.001 HIS A1058 PHE 0.028 0.002 PHE C 643 TYR 0.034 0.002 TYR A1067 ARG 0.007 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 213 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1010 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.8051 (tp40) REVERT: A 957 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8443 (tm-30) REVERT: C 457 ARG cc_start: 0.2279 (mtt180) cc_final: 0.1873 (mmm160) REVERT: V 82 MET cc_start: 0.3945 (mmt) cc_final: 0.1909 (ptt) REVERT: D 34 MET cc_start: 0.4927 (tpp) cc_final: 0.2573 (ttm) outliers start: 42 outliers final: 28 residues processed: 242 average time/residue: 0.3527 time to fit residues: 143.1320 Evaluate side-chains 224 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 195 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 741 TYR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain V residue 113 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 308 optimal weight: 1.9990 chunk 234 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 chunk 313 optimal weight: 4.9990 chunk 331 optimal weight: 8.9990 chunk 163 optimal weight: 5.9990 chunk 296 optimal weight: 0.3980 chunk 89 optimal weight: 8.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 439 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 955 ASN V 110 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 28259 Z= 0.314 Angle : 0.685 11.144 38452 Z= 0.330 Chirality : 0.052 0.479 4480 Planarity : 0.004 0.077 4914 Dihedral : 12.409 117.718 4792 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 2.30 % Allowed : 12.10 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -2.32 (0.14), residues: 3408 helix: -0.63 (0.21), residues: 656 sheet: -0.60 (0.21), residues: 634 loop : -2.26 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 886 HIS 0.005 0.001 HIS A1058 PHE 0.018 0.002 PHE C 92 TYR 0.038 0.002 TYR A1067 ARG 0.010 0.000 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 207 time to evaluate : 3.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 457 ARG cc_start: 0.2286 (mtt180) cc_final: 0.1809 (mmm160) REVERT: V 82 MET cc_start: 0.3951 (mmt) cc_final: 0.1965 (ptt) REVERT: D 34 MET cc_start: 0.4862 (tpp) cc_final: 0.2588 (ttm) outliers start: 69 outliers final: 38 residues processed: 261 average time/residue: 0.3635 time to fit residues: 160.0229 Evaluate side-chains 235 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 197 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 741 TYR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain V residue 113 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 276 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 246 optimal weight: 0.0770 chunk 136 optimal weight: 7.9990 chunk 282 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 169 optimal weight: 6.9990 chunk 297 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28259 Z= 0.191 Angle : 0.632 11.208 38452 Z= 0.302 Chirality : 0.050 0.518 4480 Planarity : 0.004 0.066 4914 Dihedral : 11.687 117.724 4792 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 1.87 % Allowed : 13.40 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -2.12 (0.14), residues: 3408 helix: -0.30 (0.21), residues: 656 sheet: -0.50 (0.21), residues: 638 loop : -2.18 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 886 HIS 0.004 0.001 HIS C 49 PHE 0.029 0.001 PHE B 238 TYR 0.018 0.001 TYR C 37 ARG 0.012 0.000 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 220 time to evaluate : 3.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 VAL cc_start: 0.4856 (OUTLIER) cc_final: 0.4529 (m) REVERT: B 1010 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.8021 (tp40) REVERT: A 208 THR cc_start: 0.7704 (p) cc_final: 0.7495 (t) REVERT: A 737 ASP cc_start: 0.8267 (t0) cc_final: 0.7919 (t0) REVERT: A 902 MET cc_start: 0.9113 (mmm) cc_final: 0.8886 (tpt) REVERT: C 457 ARG cc_start: 0.2236 (mtt180) cc_final: 0.1750 (mmm160) REVERT: V 82 MET cc_start: 0.3928 (mmt) cc_final: 0.1921 (ptt) REVERT: D 34 MET cc_start: 0.4355 (tpp) cc_final: 0.2487 (ttm) outliers start: 56 outliers final: 35 residues processed: 263 average time/residue: 0.3776 time to fit residues: 166.8345 Evaluate side-chains 241 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 204 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 741 TYR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 96 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 111 optimal weight: 5.9990 chunk 298 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 331 optimal weight: 20.0000 chunk 275 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS C 49 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 717 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 28259 Z= 0.446 Angle : 0.762 11.728 38452 Z= 0.370 Chirality : 0.054 0.444 4480 Planarity : 0.005 0.084 4914 Dihedral : 11.522 121.947 4792 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 2.97 % Allowed : 13.80 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -2.46 (0.14), residues: 3408 helix: -0.67 (0.20), residues: 660 sheet: -0.78 (0.20), residues: 635 loop : -2.35 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 886 HIS 0.008 0.002 HIS B 146 PHE 0.040 0.002 PHE B 238 TYR 0.055 0.002 TYR C1067 ARG 0.011 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 198 time to evaluate : 3.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 318 PHE cc_start: 0.6371 (m-10) cc_final: 0.6038 (m-10) REVERT: B 1146 ASP cc_start: 0.6213 (OUTLIER) cc_final: 0.5960 (m-30) REVERT: A 737 ASP cc_start: 0.8364 (t0) cc_final: 0.8031 (t0) REVERT: A 902 MET cc_start: 0.9179 (mmm) cc_final: 0.8801 (tpt) REVERT: C 100 ILE cc_start: 0.7456 (pt) cc_final: 0.7183 (pt) REVERT: V 82 MET cc_start: 0.3955 (mmt) cc_final: 0.3657 (mmt) REVERT: D 34 MET cc_start: 0.4475 (tpp) cc_final: 0.2210 (ttm) outliers start: 89 outliers final: 62 residues processed: 271 average time/residue: 0.3385 time to fit residues: 156.5078 Evaluate side-chains 250 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 187 time to evaluate : 3.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain V residue 113 LEU Chi-restraints excluded: chain D residue 96 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 319 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 189 optimal weight: 0.8980 chunk 242 optimal weight: 0.6980 chunk 187 optimal weight: 0.9980 chunk 279 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 330 optimal weight: 40.0000 chunk 206 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 152 optimal weight: 40.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28259 Z= 0.176 Angle : 0.630 11.916 38452 Z= 0.304 Chirality : 0.050 0.506 4480 Planarity : 0.004 0.048 4914 Dihedral : 10.645 119.107 4792 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.00 % Allowed : 14.80 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -2.10 (0.14), residues: 3408 helix: -0.15 (0.21), residues: 648 sheet: -0.58 (0.20), residues: 645 loop : -2.19 (0.13), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 886 HIS 0.002 0.001 HIS B 69 PHE 0.033 0.001 PHE B 238 TYR 0.014 0.001 TYR B 204 ARG 0.007 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 201 time to evaluate : 2.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 PHE cc_start: 0.6527 (t80) cc_final: 0.6273 (t80) REVERT: B 1010 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8027 (tp40) REVERT: A 737 ASP cc_start: 0.8332 (t0) cc_final: 0.8009 (t0) REVERT: A 817 PHE cc_start: 0.6751 (OUTLIER) cc_final: 0.6430 (m-80) REVERT: A 902 MET cc_start: 0.9116 (mmm) cc_final: 0.8876 (tpt) REVERT: D 34 MET cc_start: 0.4281 (tpp) cc_final: 0.2287 (ttm) outliers start: 60 outliers final: 42 residues processed: 253 average time/residue: 0.3432 time to fit residues: 146.9356 Evaluate side-chains 228 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 184 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1067 TYR Chi-restraints excluded: chain D residue 96 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 204 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 197 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 210 optimal weight: 6.9990 chunk 225 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 259 optimal weight: 30.0000 chunk 300 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 717 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 28259 Z= 0.393 Angle : 0.713 9.984 38452 Z= 0.348 Chirality : 0.052 0.466 4480 Planarity : 0.004 0.058 4914 Dihedral : 10.546 121.585 4792 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 2.80 % Allowed : 14.87 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -2.36 (0.14), residues: 3408 helix: -0.42 (0.21), residues: 653 sheet: -0.80 (0.20), residues: 646 loop : -2.32 (0.13), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 886 HIS 0.006 0.001 HIS A1058 PHE 0.043 0.002 PHE B 238 TYR 0.027 0.002 TYR C1067 ARG 0.009 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 187 time to evaluate : 2.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 318 PHE cc_start: 0.6369 (m-10) cc_final: 0.5986 (m-10) REVERT: B 333 THR cc_start: 0.4332 (OUTLIER) cc_final: 0.4116 (m) REVERT: B 1010 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8125 (tp40) REVERT: A 737 ASP cc_start: 0.8406 (t0) cc_final: 0.8122 (t0) REVERT: A 817 PHE cc_start: 0.6831 (OUTLIER) cc_final: 0.6470 (m-80) REVERT: A 902 MET cc_start: 0.9167 (mmm) cc_final: 0.8807 (tpt) REVERT: A 983 ARG cc_start: 0.7774 (ptt90) cc_final: 0.7447 (ptp90) REVERT: D 34 MET cc_start: 0.4449 (tpp) cc_final: 0.2380 (ttm) outliers start: 84 outliers final: 68 residues processed: 260 average time/residue: 0.3409 time to fit residues: 151.7916 Evaluate side-chains 248 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 177 time to evaluate : 2.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1067 TYR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain V residue 113 LEU Chi-restraints excluded: chain D residue 96 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 316 optimal weight: 2.9990 chunk 288 optimal weight: 2.9990 chunk 308 optimal weight: 1.9990 chunk 185 optimal weight: 0.5980 chunk 134 optimal weight: 0.9980 chunk 241 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 278 optimal weight: 2.9990 chunk 291 optimal weight: 7.9990 chunk 306 optimal weight: 1.9990 chunk 202 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28259 Z= 0.179 Angle : 0.619 9.661 38452 Z= 0.301 Chirality : 0.049 0.527 4480 Planarity : 0.004 0.047 4914 Dihedral : 9.964 119.327 4792 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.00 % Allowed : 15.84 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -2.07 (0.14), residues: 3408 helix: -0.00 (0.22), residues: 645 sheet: -0.60 (0.20), residues: 635 loop : -2.18 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 886 HIS 0.003 0.001 HIS B 69 PHE 0.038 0.001 PHE B 238 TYR 0.022 0.001 TYR B 160 ARG 0.009 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 190 time to evaluate : 2.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 509 ARG cc_start: 0.5530 (OUTLIER) cc_final: 0.4616 (mpt180) REVERT: B 1010 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.8033 (tp40) REVERT: A 737 ASP cc_start: 0.8328 (t0) cc_final: 0.7999 (t0) REVERT: A 817 PHE cc_start: 0.6783 (OUTLIER) cc_final: 0.6482 (m-80) REVERT: A 902 MET cc_start: 0.9097 (mmm) cc_final: 0.8841 (tpt) REVERT: C 457 ARG cc_start: 0.2698 (mtt180) cc_final: 0.2335 (mmm160) REVERT: D 34 MET cc_start: 0.4477 (tpp) cc_final: 0.2410 (ttm) outliers start: 60 outliers final: 50 residues processed: 244 average time/residue: 0.3463 time to fit residues: 143.3740 Evaluate side-chains 239 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 186 time to evaluate : 3.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1067 TYR Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 325 optimal weight: 9.9990 chunk 198 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 226 optimal weight: 7.9990 chunk 341 optimal weight: 0.0980 chunk 314 optimal weight: 0.6980 chunk 272 optimal weight: 0.0010 chunk 28 optimal weight: 10.0000 chunk 210 optimal weight: 0.0010 chunk 166 optimal weight: 3.9990 chunk 216 optimal weight: 7.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28259 Z= 0.175 Angle : 0.600 9.648 38452 Z= 0.292 Chirality : 0.049 0.537 4480 Planarity : 0.004 0.046 4914 Dihedral : 9.361 118.260 4792 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 1.90 % Allowed : 15.97 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -1.87 (0.14), residues: 3408 helix: 0.23 (0.22), residues: 649 sheet: -0.41 (0.21), residues: 621 loop : -2.10 (0.13), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 886 HIS 0.003 0.001 HIS B 69 PHE 0.032 0.001 PHE B 238 TYR 0.017 0.001 TYR B 160 ARG 0.009 0.000 ARG C 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 207 time to evaluate : 3.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 PHE cc_start: 0.6415 (t80) cc_final: 0.6194 (t80) REVERT: B 333 THR cc_start: 0.4420 (OUTLIER) cc_final: 0.4202 (m) REVERT: B 509 ARG cc_start: 0.5537 (OUTLIER) cc_final: 0.4527 (mpt180) REVERT: B 1010 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.8024 (tp40) REVERT: A 737 ASP cc_start: 0.8281 (t0) cc_final: 0.7965 (t0) REVERT: A 817 PHE cc_start: 0.6782 (OUTLIER) cc_final: 0.6516 (m-80) REVERT: A 902 MET cc_start: 0.9083 (mmm) cc_final: 0.8868 (tpt) REVERT: A 983 ARG cc_start: 0.7739 (ptp90) cc_final: 0.7399 (ptt-90) REVERT: A 994 ASP cc_start: 0.7200 (OUTLIER) cc_final: 0.6932 (m-30) REVERT: C 1081 ILE cc_start: 0.9195 (mm) cc_final: 0.8938 (mm) REVERT: D 34 MET cc_start: 0.4406 (tpp) cc_final: 0.2585 (ttm) outliers start: 57 outliers final: 48 residues processed: 256 average time/residue: 0.3591 time to fit residues: 154.5019 Evaluate side-chains 247 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 194 time to evaluate : 2.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1067 TYR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 250 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 272 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 279 optimal weight: 0.5980 chunk 34 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 239 optimal weight: 7.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.169762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.129458 restraints weight = 46219.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.122206 restraints weight = 65456.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.119666 restraints weight = 43608.709| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28259 Z= 0.260 Angle : 0.642 9.670 38452 Z= 0.312 Chirality : 0.050 0.501 4480 Planarity : 0.004 0.049 4914 Dihedral : 9.306 119.436 4792 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 2.20 % Allowed : 15.97 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -1.93 (0.14), residues: 3408 helix: 0.08 (0.22), residues: 649 sheet: -0.43 (0.20), residues: 640 loop : -2.11 (0.13), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 104 HIS 0.004 0.001 HIS B 69 PHE 0.037 0.001 PHE B 238 TYR 0.023 0.001 TYR B 904 ARG 0.009 0.001 ARG C 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4500.92 seconds wall clock time: 84 minutes 16.42 seconds (5056.42 seconds total)