Starting phenix.real_space_refine on Mon Feb 19 18:09:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7q_31778/02_2024/7v7q_31778.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7q_31778/02_2024/7v7q_31778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7q_31778/02_2024/7v7q_31778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7q_31778/02_2024/7v7q_31778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7q_31778/02_2024/7v7q_31778.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7q_31778/02_2024/7v7q_31778.pdb" } resolution = 2.8 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= -0.002 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 16114 2.51 5 N 4129 2.21 5 O 5020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 652": "OE1" <-> "OE2" Residue "A GLU 1015": "OE1" <-> "OE2" Residue "B PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B TYR 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1073": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1090": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25371 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 8035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8035 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 53, 'TRANS': 975} Chain breaks: 7 Chain: "B" Number of atoms: 8077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8077 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 53, 'TRANS': 979} Chain breaks: 7 Chain: "C" Number of atoms: 8083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8083 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 54, 'TRANS': 979} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" 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: "X" 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: "Y" 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 13.08, per 1000 atoms: 0.52 Number of scatterers: 25371 At special positions: 0 Unit cell: (141.9, 145.2, 198, 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 108 16.00 O 5020 8.00 N 4129 7.00 C 16114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.04 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.02 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.04 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.02 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 164 " distance=2.04 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.04 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.04 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.02 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.04 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 D 1 " - " NAG D 2 " " 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 U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " 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-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 601 " " NAG A2003 " - " ASN A 655 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 232 " " NAG B2003 " - " ASN B 329 " " NAG B2004 " - " ASN B 601 " " NAG B2005 " - " ASN B 655 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 329 " " NAG C2003 " - " ASN C 601 " " NAG C2004 " - " ASN C 655 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 163 " " NAG F 1 " - " ASN A 232 " " NAG G 1 " - " ASN A 280 " " NAG H 1 " - " ASN A 329 " " NAG I 1 " - " ASN A 341 " " NAG J 1 " - " ASN A 614 " " NAG K 1 " - " ASN A 707 " " NAG L 1 " - " ASN A 715 " " NAG M 1 " - " ASN A 799 " " NAG N 1 " - " ASN A1072 " " NAG O 1 " - " ASN A1096 " " NAG P 1 " - " ASN A1132 " " NAG Q 1 " - " ASN B 122 " " NAG R 1 " - " ASN B 163 " " NAG S 1 " - " ASN B 280 " " NAG T 1 " - " ASN B 341 " " NAG U 1 " - " ASN B 614 " " NAG V 1 " - " ASN B 707 " " NAG W 1 " - " ASN B 715 " " NAG X 1 " - " ASN B 799 " " NAG Y 1 " - " ASN B1072 " " NAG Z 1 " - " ASN B1096 " " NAG a 1 " - " ASN B1132 " " NAG b 1 " - " ASN C 122 " " NAG c 1 " - " ASN C 163 " " NAG d 1 " - " ASN C 232 " " NAG e 1 " - " ASN C 280 " " NAG f 1 " - " ASN C 341 " " NAG g 1 " - " ASN C 614 " " NAG h 1 " - " ASN C 707 " " NAG i 1 " - " ASN C 715 " " NAG j 1 " - " ASN C 799 " " NAG k 1 " - " ASN C1072 " " NAG l 1 " - " ASN C1096 " " NAG m 1 " - " ASN C1132 " Time building additional restraints: 9.62 Conformation dependent library (CDL) restraints added in 4.0 seconds 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5802 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 47 sheets defined 25.3% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 347 through 351 removed outlier: 3.649A pdb=" N TRP A 351 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 369 Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 403 through 408 removed outlier: 4.232A pdb=" N ARG A 406 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 408 " --> pdb=" O VAL A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 735 through 741 Processing helix chain 'A' and resid 744 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 758 through 781 Processing helix chain 'A' and resid 814 through 824 Processing helix chain 'A' and resid 864 through 883 removed outlier: 3.591A pdb=" N GLY A 883 " --> pdb=" O THR A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 910 through 917 removed outlier: 4.076A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 939 Processing helix chain 'A' and resid 943 through 963 Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 974 through 982 removed outlier: 3.690A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 3.597A pdb=" N ALA A 987 " --> pdb=" O ASP A 983 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A1031 " --> pdb=" O MET A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1144 removed outlier: 3.705A pdb=" N ASP A1144 " --> pdb=" O GLN A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.000A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 removed outlier: 3.632A pdb=" N LEU B 385 " --> pdb=" O PRO B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 4.724A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 408 " --> pdb=" O VAL B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 436 through 441 removed outlier: 3.623A pdb=" N SER B 441 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 744 through 752 Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.832A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.683A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.644A pdb=" N GLY B 883 " --> pdb=" O THR B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 889 removed outlier: 3.985A pdb=" N GLY B 889 " --> pdb=" O PHE B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 911 through 917 removed outlier: 3.639A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 916 " --> pdb=" O ASN B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 938 Processing helix chain 'B' and resid 943 through 963 removed outlier: 3.526A pdb=" N GLN B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 974 through 980 removed outlier: 3.628A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.324A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1144 removed outlier: 3.874A pdb=" N ASP B1144 " --> pdb=" O GLN B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.831A pdb=" N SER C 369 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 388 removed outlier: 3.733A pdb=" N LEU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN C 386 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C 388 " --> pdb=" O LEU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 removed outlier: 4.083A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 436 through 441 Processing helix chain 'C' and resid 631 through 636 removed outlier: 3.820A pdb=" N THR C 636 " --> pdb=" O VAL C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 744 through 752 Processing helix chain 'C' and resid 753 through 755 No H-bonds generated for 'chain 'C' and resid 753 through 755' Processing helix chain 'C' and resid 756 through 781 removed outlier: 3.653A pdb=" N GLN C 760 " --> pdb=" O SER C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 822 Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.643A pdb=" N GLY C 883 " --> pdb=" O THR C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 911 through 917 removed outlier: 4.048A pdb=" N TYR C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU C 916 " --> pdb=" O ASN C 912 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN C 917 " --> pdb=" O VAL C 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 911 through 917' Processing helix chain 'C' and resid 917 through 939 Processing helix chain 'C' and resid 943 through 963 Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 980 Processing helix chain 'C' and resid 983 through 1031 removed outlier: 4.265A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C1031 " --> pdb=" O MET C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1144 removed outlier: 3.631A pdb=" N ASP C1144 " --> pdb=" O GLN C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.995A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.359A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.265A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL A 36 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.548A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASP C 572 " --> pdb=" O ILE C 585 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.129A pdb=" N ASP A 285 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.082A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.352A pdb=" N VAL A 126 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 10.110A pdb=" N GLU A 167 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.159A pdb=" N ILE A 128 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N THR A 165 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N VAL A 130 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASN A 163 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU A 132 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA A 161 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLN A 134 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 317 removed outlier: 3.501A pdb=" N THR A 313 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL A 593 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ASN A 315 " --> pdb=" O GLY A 591 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY A 591 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 324 removed outlier: 3.601A pdb=" N VAL A 574 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASP A 572 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N PHE A 563 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 360 removed outlier: 6.948A pdb=" N CYS A 359 " --> pdb=" O CYS A 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AB1, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AB2, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.050A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 699 through 701 Processing sheet with id=AB4, first strand: chain 'A' and resid 709 through 711 Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 726 removed outlier: 3.613A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.547A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 785 through 787 Processing sheet with id=AB8, first strand: chain 'A' and resid 1118 through 1120 Processing sheet with id=AB9, first strand: chain 'A' and resid 1092 through 1095 Processing sheet with id=AC1, first strand: chain 'B' and resid 26 through 30 removed outlier: 7.946A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN B 186 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.193A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.239A pdb=" N ARG B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N PHE B 106 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLN B 237 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TRP B 104 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU B 239 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.290A pdb=" N VAL B 126 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N GLU B 167 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.158A pdb=" N ILE B 128 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N THR B 165 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL B 130 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ASN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU B 132 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ALA B 161 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.540A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 326 removed outlier: 5.434A pdb=" N ASP B 572 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLY B 564 " --> pdb=" O ASP B 572 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AC7, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.180A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 450 through 452 Processing sheet with id=AC9, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AD1, first strand: chain 'B' and resid 652 through 653 removed outlier: 6.052A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 700 through 701 Processing sheet with id=AD3, first strand: chain 'B' and resid 713 through 726 removed outlier: 6.026A pdb=" N GLU B1070 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.475A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1118 through 1123 removed outlier: 5.035A pdb=" N ALA B1085 " --> pdb=" O SER B1121 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1092 through 1095 removed outlier: 5.082A pdb=" N GLN B1104 " --> pdb=" O GLU B1109 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLU B1109 " --> pdb=" O GLN B1104 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.051A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.922A pdb=" N VAL C 36 " --> pdb=" O LEU C 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.057A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.207A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 309 through 317 removed outlier: 5.556A pdb=" N ILE C 310 " --> pdb=" O THR C 597 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N THR C 597 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLN C 312 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL C 595 " --> pdb=" O GLN C 312 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER C 314 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AE4, first strand: chain 'C' and resid 359 through 360 removed outlier: 6.778A pdb=" N CYS C 359 " --> pdb=" O CYS C 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE6, first strand: chain 'C' and resid 471 through 472 removed outlier: 3.508A pdb=" N TYR C 487 " --> pdb=" O TYR C 471 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 652 through 653 removed outlier: 5.830A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 709 through 726 removed outlier: 6.779A pdb=" N SER C 709 " --> pdb=" O THR C1074 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR C1074 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA C 711 " --> pdb=" O ASN C1072 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN C1072 " --> pdb=" O ALA C 711 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLU C1070 " --> pdb=" O PRO C 713 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.574A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1118 through 1120 Processing sheet with id=AF2, first strand: chain 'C' and resid 1092 through 1095 989 hydrogen bonds defined for protein. 2703 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: 11.70 Time building geometry restraints manager: 10.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8002 1.34 - 1.46: 6372 1.46 - 1.58: 11416 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 25922 Sorted by residual: bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.58e+00 bond pdb=" C1 NAG b 1 " pdb=" O5 NAG b 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.09e+00 bond pdb=" C1 NAG k 1 " pdb=" O5 NAG k 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.69e+00 bond pdb=" C1 NAG B2003 " pdb=" O5 NAG B2003 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.49e+00 ... (remaining 25917 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.85: 775 106.85 - 113.63: 14544 113.63 - 120.42: 9140 120.42 - 127.21: 10614 127.21 - 134.00: 200 Bond angle restraints: 35273 Sorted by residual: angle pdb=" N PRO A 984 " pdb=" CA PRO A 984 " pdb=" C PRO A 984 " ideal model delta sigma weight residual 110.70 114.57 -3.87 1.22e+00 6.72e-01 1.01e+01 angle pdb=" N PRO B 984 " pdb=" CA PRO B 984 " pdb=" C PRO B 984 " ideal model delta sigma weight residual 110.70 114.48 -3.78 1.22e+00 6.72e-01 9.59e+00 angle pdb=" N PRO A 559 " pdb=" CA PRO A 559 " pdb=" C PRO A 559 " ideal model delta sigma weight residual 112.47 118.58 -6.11 2.06e+00 2.36e-01 8.81e+00 angle pdb=" C CYS C 660 " pdb=" N ASP C 661 " pdb=" CA ASP C 661 " ideal model delta sigma weight residual 121.54 127.09 -5.55 1.91e+00 2.74e-01 8.44e+00 angle pdb=" C VAL C 779 " pdb=" N PHE C 780 " pdb=" CA PHE C 780 " ideal model delta sigma weight residual 122.53 117.21 5.32 1.92e+00 2.71e-01 7.68e+00 ... (remaining 35268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 15333 21.50 - 43.00: 997 43.00 - 64.50: 163 64.50 - 86.01: 46 86.01 - 107.51: 7 Dihedral angle restraints: 16546 sinusoidal: 7534 harmonic: 9012 Sorted by residual: dihedral pdb=" CB CYS A 389 " pdb=" SG CYS A 389 " pdb=" SG CYS A 523 " pdb=" CB CYS A 523 " ideal model delta sinusoidal sigma weight residual -86.00 -9.18 -76.82 1 1.00e+01 1.00e-02 7.41e+01 dihedral pdb=" CB CYS A1080 " pdb=" SG CYS A1080 " pdb=" SG CYS A1124 " pdb=" CB CYS A1124 " ideal model delta sinusoidal sigma weight residual -86.00 -9.92 -76.08 1 1.00e+01 1.00e-02 7.29e+01 dihedral pdb=" CB CYS A 536 " pdb=" SG CYS A 536 " pdb=" SG CYS A 588 " pdb=" CB CYS A 588 " ideal model delta sinusoidal sigma weight residual -86.00 -10.02 -75.98 1 1.00e+01 1.00e-02 7.27e+01 ... (remaining 16543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3259 0.050 - 0.099: 768 0.099 - 0.149: 206 0.149 - 0.199: 15 0.199 - 0.248: 2 Chirality restraints: 4250 Sorted by residual: chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN C 163 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B 163 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA PRO A 559 " pdb=" N PRO A 559 " pdb=" C PRO A 559 " pdb=" CB PRO A 559 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.72e-01 ... (remaining 4247 not shown) Planarity restraints: 4504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A1137 " -0.047 5.00e-02 4.00e+02 7.23e-02 8.35e+00 pdb=" N PRO A1138 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A1138 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A1138 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 983 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO A 984 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 984 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 984 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 558 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A 559 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 559 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 559 " -0.025 5.00e-02 4.00e+02 ... (remaining 4501 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 691 2.70 - 3.25: 24245 3.25 - 3.80: 37902 3.80 - 4.35: 47221 4.35 - 4.90: 81838 Nonbonded interactions: 191897 Sorted by model distance: nonbonded pdb=" OH TYR C 754 " pdb=" OD1 ASP C 992 " model vdw 2.148 2.440 nonbonded pdb=" O ASP A 403 " pdb=" NH1 ARG A 406 " model vdw 2.156 2.520 nonbonded pdb=" OG SER A 347 " pdb=" O ARG A 450 " model vdw 2.164 2.440 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.193 2.440 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.196 2.440 ... (remaining 191892 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' and (resid 14 through 619 or resid 633 through 825 or resid 853 throu \ gh 1144 or resid 2001 through 2003)) selection = (chain 'C' and (resid 14 through 619 or resid 633 through 825 or resid 853 throu \ gh 1144 or resid 2001 through 2003)) } ncs_group { reference = chain 'D' selection = 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' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.880 Check model and map are aligned: 0.350 Set scattering table: 0.220 Process input model: 69.610 Find NCS groups from input model: 2.130 Set up NCS constraints: 0.480 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:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 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 : 0.004 0.049 25922 Z= 0.245 Angle : 0.585 8.068 35273 Z= 0.288 Chirality : 0.046 0.248 4250 Planarity : 0.004 0.072 4456 Dihedral : 13.999 107.507 10627 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.94 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 3048 helix: 1.99 (0.21), residues: 663 sheet: 0.60 (0.19), residues: 721 loop : -1.10 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 884 HIS 0.002 0.000 HIS B1086 PHE 0.025 0.001 PHE A 904 TYR 0.016 0.001 TYR C1065 ARG 0.003 0.000 ARG A 903 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 2709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 2.965 Fit side-chains REVERT: A 367 TYR cc_start: 0.8201 (t80) cc_final: 0.7735 (t80) REVERT: C 133 PHE cc_start: 0.8596 (m-80) cc_final: 0.8279 (m-80) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 1.6313 time to fit residues: 130.3463 Evaluate side-chains 52 residues out of total 2709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 0.3980 chunk 233 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 157 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 241 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 146 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 279 optimal weight: 6.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 604 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.0502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25922 Z= 0.219 Angle : 0.545 17.687 35273 Z= 0.275 Chirality : 0.044 0.225 4250 Planarity : 0.004 0.053 4456 Dihedral : 8.238 90.321 5084 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.51 % Rotamer: Outliers : 0.26 % Allowed : 5.98 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 3048 helix: 2.15 (0.21), residues: 676 sheet: 0.62 (0.19), residues: 727 loop : -1.08 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 884 HIS 0.004 0.001 HIS B1086 PHE 0.020 0.001 PHE A 904 TYR 0.017 0.001 TYR C1065 ARG 0.005 0.000 ARG B 406 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 2709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 2.863 Fit side-chains revert: symmetry clash REVERT: A 367 TYR cc_start: 0.8194 (t80) cc_final: 0.7720 (t80) REVERT: A 898 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8267 (mtm) REVERT: B 1027 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8143 (tpp) outliers start: 7 outliers final: 4 residues processed: 57 average time/residue: 1.4742 time to fit residues: 101.0109 Evaluate side-chains 55 residues out of total 2709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 2.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain B residue 1027 MET Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 387 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 232 optimal weight: 8.9990 chunk 190 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 280 optimal weight: 0.0020 chunk 302 optimal weight: 3.9990 chunk 249 optimal weight: 3.9990 chunk 277 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 224 optimal weight: 9.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25922 Z= 0.264 Angle : 0.557 23.801 35273 Z= 0.278 Chirality : 0.044 0.231 4250 Planarity : 0.004 0.050 4456 Dihedral : 7.544 81.391 5084 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.53 % Favored : 95.37 % Rotamer: Outliers : 0.81 % Allowed : 9.38 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 3048 helix: 2.21 (0.21), residues: 669 sheet: 0.58 (0.19), residues: 731 loop : -1.11 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 884 HIS 0.003 0.001 HIS A1086 PHE 0.024 0.001 PHE A 904 TYR 0.018 0.001 TYR C1065 ARG 0.008 0.000 ARG A 401 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 51 time to evaluate : 3.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 367 TYR cc_start: 0.8182 (t80) cc_final: 0.7717 (t80) REVERT: A 569 ASP cc_start: 0.8264 (m-30) cc_final: 0.8037 (p0) REVERT: A 898 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8309 (mtm) outliers start: 22 outliers final: 7 residues processed: 69 average time/residue: 1.2088 time to fit residues: 102.9816 Evaluate side-chains 58 residues out of total 2709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 387 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 1.9990 chunk 210 optimal weight: 8.9990 chunk 145 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 133 optimal weight: 7.9990 chunk 188 optimal weight: 0.6980 chunk 281 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 chunk 266 optimal weight: 0.0870 chunk 80 optimal weight: 2.9990 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25922 Z= 0.257 Angle : 0.559 26.122 35273 Z= 0.278 Chirality : 0.044 0.250 4250 Planarity : 0.004 0.065 4456 Dihedral : 7.044 74.473 5084 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.69 % Favored : 95.21 % Rotamer: Outliers : 1.18 % Allowed : 11.18 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 3048 helix: 2.20 (0.21), residues: 669 sheet: 0.59 (0.19), residues: 729 loop : -1.11 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 884 HIS 0.003 0.001 HIS A1086 PHE 0.019 0.001 PHE A 904 TYR 0.018 0.001 TYR C1065 ARG 0.003 0.000 ARG A1037 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 52 time to evaluate : 2.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 367 TYR cc_start: 0.8184 (t80) cc_final: 0.7732 (t80) REVERT: A 569 ASP cc_start: 0.8294 (m-30) cc_final: 0.8076 (p0) REVERT: A 898 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8282 (mtm) outliers start: 32 outliers final: 18 residues processed: 80 average time/residue: 1.0526 time to fit residues: 104.4384 Evaluate side-chains 67 residues out of total 2709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 48 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 669 CYS Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 977 ASP Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1128 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 221 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 254 optimal weight: 0.3980 chunk 205 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 152 optimal weight: 7.9990 chunk 267 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25922 Z= 0.158 Angle : 0.531 25.801 35273 Z= 0.261 Chirality : 0.043 0.229 4250 Planarity : 0.004 0.062 4456 Dihedral : 6.560 67.797 5084 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.07 % Favored : 95.83 % Rotamer: Outliers : 1.59 % Allowed : 11.70 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3048 helix: 2.34 (0.21), residues: 665 sheet: 0.71 (0.19), residues: 723 loop : -1.04 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 434 HIS 0.002 0.000 HIS B1086 PHE 0.018 0.001 PHE A 390 TYR 0.016 0.001 TYR C1065 ARG 0.002 0.000 ARG B 406 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 52 time to evaluate : 2.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 367 TYR cc_start: 0.8183 (t80) cc_final: 0.7737 (t80) REVERT: A 898 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8212 (mtm) outliers start: 43 outliers final: 15 residues processed: 90 average time/residue: 1.0184 time to fit residues: 114.4659 Evaluate side-chains 68 residues out of total 2709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 52 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 669 CYS Chi-restraints excluded: chain C residue 703 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 1.9990 chunk 268 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 298 optimal weight: 4.9990 chunk 247 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 156 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 963 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 25922 Z= 0.379 Angle : 0.626 28.202 35273 Z= 0.310 Chirality : 0.046 0.237 4250 Planarity : 0.004 0.062 4456 Dihedral : 6.544 60.871 5084 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.25 % Favored : 94.65 % Rotamer: Outliers : 1.73 % Allowed : 12.81 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 3048 helix: 2.24 (0.21), residues: 661 sheet: 0.48 (0.19), residues: 715 loop : -1.14 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 884 HIS 0.004 0.001 HIS A1086 PHE 0.025 0.002 PHE A 904 TYR 0.021 0.001 TYR C1065 ARG 0.005 0.000 ARG A1037 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 48 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 367 TYR cc_start: 0.8222 (t80) cc_final: 0.7797 (t80) REVERT: A 898 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8196 (mtp) REVERT: A 982 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9232 (pp) REVERT: C 1134 THR cc_start: 0.9287 (OUTLIER) cc_final: 0.9045 (p) outliers start: 47 outliers final: 20 residues processed: 91 average time/residue: 0.9206 time to fit residues: 105.7256 Evaluate side-chains 68 residues out of total 2709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 45 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1134 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 169 optimal weight: 0.7980 chunk 217 optimal weight: 20.0000 chunk 168 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 296 optimal weight: 0.9980 chunk 185 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25922 Z= 0.215 Angle : 0.563 27.685 35273 Z= 0.277 Chirality : 0.044 0.241 4250 Planarity : 0.004 0.061 4456 Dihedral : 6.189 57.449 5084 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.20 % Favored : 95.70 % Rotamer: Outliers : 1.55 % Allowed : 13.44 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 3048 helix: 2.30 (0.21), residues: 664 sheet: 0.60 (0.19), residues: 733 loop : -1.08 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 884 HIS 0.003 0.001 HIS B1086 PHE 0.029 0.001 PHE A 390 TYR 0.017 0.001 TYR C1065 ARG 0.004 0.000 ARG C1037 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 48 time to evaluate : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 367 TYR cc_start: 0.8213 (t80) cc_final: 0.7780 (t80) REVERT: A 569 ASP cc_start: 0.8291 (m-30) cc_final: 0.8065 (p0) REVERT: A 898 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8246 (mtm) REVERT: A 982 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9232 (pp) outliers start: 42 outliers final: 23 residues processed: 86 average time/residue: 1.0134 time to fit residues: 109.2132 Evaluate side-chains 72 residues out of total 2709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 47 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1128 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 233 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25922 Z= 0.231 Angle : 0.565 27.674 35273 Z= 0.277 Chirality : 0.044 0.256 4250 Planarity : 0.004 0.062 4456 Dihedral : 5.978 56.592 5084 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.82 % Favored : 95.08 % Rotamer: Outliers : 1.26 % Allowed : 14.06 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 3048 helix: 2.33 (0.21), residues: 665 sheet: 0.57 (0.19), residues: 713 loop : -1.07 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 884 HIS 0.002 0.001 HIS B1086 PHE 0.022 0.001 PHE A 390 TYR 0.018 0.001 TYR C1065 ARG 0.003 0.000 ARG A1037 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 48 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 367 TYR cc_start: 0.8215 (t80) cc_final: 0.7778 (t80) REVERT: A 898 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8270 (mtm) REVERT: A 982 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9227 (pp) REVERT: B 738 MET cc_start: 0.8652 (mmm) cc_final: 0.8423 (ttm) outliers start: 34 outliers final: 23 residues processed: 80 average time/residue: 0.9834 time to fit residues: 98.3859 Evaluate side-chains 73 residues out of total 2709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 48 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 669 CYS Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1128 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 2.9990 chunk 284 optimal weight: 0.9980 chunk 259 optimal weight: 1.9990 chunk 276 optimal weight: 0.0980 chunk 166 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 217 optimal weight: 30.0000 chunk 84 optimal weight: 2.9990 chunk 249 optimal weight: 0.9990 chunk 261 optimal weight: 9.9990 chunk 275 optimal weight: 0.0870 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25922 Z= 0.160 Angle : 0.542 26.807 35273 Z= 0.266 Chirality : 0.044 0.275 4250 Planarity : 0.004 0.062 4456 Dihedral : 5.710 56.739 5084 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.10 % Favored : 95.80 % Rotamer: Outliers : 1.14 % Allowed : 14.36 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.15), residues: 3048 helix: 2.42 (0.21), residues: 667 sheet: 0.68 (0.19), residues: 740 loop : -1.00 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 434 HIS 0.002 0.001 HIS B1086 PHE 0.020 0.001 PHE A 390 TYR 0.016 0.001 TYR C1065 ARG 0.002 0.000 ARG B 406 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 51 time to evaluate : 2.890 Fit side-chains revert: symmetry clash REVERT: A 367 TYR cc_start: 0.8208 (t80) cc_final: 0.7762 (t80) REVERT: A 982 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9200 (pp) REVERT: B 738 MET cc_start: 0.8589 (mmm) cc_final: 0.8384 (ttm) REVERT: C 1134 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.9051 (p) outliers start: 31 outliers final: 18 residues processed: 79 average time/residue: 1.0182 time to fit residues: 100.7367 Evaluate side-chains 67 residues out of total 2709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 47 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 669 CYS Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1134 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 2.9990 chunk 292 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 203 optimal weight: 1.9990 chunk 306 optimal weight: 0.3980 chunk 282 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25922 Z= 0.249 Angle : 0.574 27.485 35273 Z= 0.282 Chirality : 0.044 0.284 4250 Planarity : 0.004 0.062 4456 Dihedral : 5.726 56.170 5084 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.92 % Favored : 94.98 % Rotamer: Outliers : 0.96 % Allowed : 14.77 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 3048 helix: 2.38 (0.21), residues: 666 sheet: 0.62 (0.19), residues: 712 loop : -1.04 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 884 HIS 0.002 0.001 HIS B1086 PHE 0.020 0.001 PHE A 390 TYR 0.019 0.001 TYR C1065 ARG 0.003 0.000 ARG A1037 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 46 time to evaluate : 2.858 Fit side-chains revert: symmetry clash REVERT: A 367 TYR cc_start: 0.8225 (t80) cc_final: 0.7778 (t80) REVERT: A 982 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9180 (pp) REVERT: B 454 PHE cc_start: 0.8272 (m-80) cc_final: 0.8043 (m-80) REVERT: B 738 MET cc_start: 0.8661 (mmm) cc_final: 0.8439 (ttm) REVERT: C 1134 THR cc_start: 0.9278 (OUTLIER) cc_final: 0.9056 (p) outliers start: 26 outliers final: 22 residues processed: 71 average time/residue: 1.0760 time to fit residues: 95.0062 Evaluate side-chains 67 residues out of total 2709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 43 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 669 CYS Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1134 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 0.9980 chunk 260 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 225 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 244 optimal weight: 0.7980 chunk 102 optimal weight: 20.0000 chunk 251 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 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 = 0.3597 r_free = 0.3597 target = 0.073469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.046241 restraints weight = 87835.298| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 4.07 r_work: 0.2722 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25922 Z= 0.164 Angle : 0.542 27.199 35273 Z= 0.265 Chirality : 0.044 0.291 4250 Planarity : 0.004 0.062 4456 Dihedral : 5.563 56.590 5084 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 1.03 % Allowed : 14.80 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 3048 helix: 2.43 (0.21), residues: 667 sheet: 0.70 (0.19), residues: 738 loop : -1.00 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 434 HIS 0.003 0.001 HIS B1086 PHE 0.018 0.001 PHE A 390 TYR 0.016 0.001 TYR C1065 ARG 0.002 0.000 ARG B 406 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5037.88 seconds wall clock time: 93 minutes 23.96 seconds (5603.96 seconds total)