Starting phenix.real_space_refine on Tue Mar 19 20:19:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7u_31782/03_2024/7v7u_31782.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7u_31782/03_2024/7v7u_31782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7u_31782/03_2024/7v7u_31782.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7u_31782/03_2024/7v7u_31782.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7u_31782/03_2024/7v7u_31782.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7u_31782/03_2024/7v7u_31782.pdb" } resolution = 3.0 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= 0.056 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 16055 2.51 5 N 4115 2.21 5 O 5005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 652": "OE1" <-> "OE2" Residue "A PHE 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25283 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8016 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 53, 'TRANS': 973} 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: 8028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8028 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 53, 'TRANS': 974} 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: "A" 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 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: 13.16, per 1000 atoms: 0.52 Number of scatterers: 25283 At special positions: 0 Unit cell: (139.7, 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 5005 8.00 N 4115 7.00 C 16055 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, 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=2.04 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 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=2.03 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=2.03 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=2.03 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-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 341 " " NAG A2003 " - " ASN A 601 " " NAG A2004 " - " 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 341 " " 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 614 " " NAG J 1 " - " ASN A 707 " " NAG K 1 " - " ASN A 715 " " NAG L 1 " - " ASN A 799 " " NAG M 1 " - " ASN A1072 " " NAG N 1 " - " ASN A1096 " " NAG O 1 " - " ASN A1132 " " NAG P 1 " - " ASN B 122 " " NAG Q 1 " - " ASN B 163 " " NAG R 1 " - " ASN B 280 " " NAG S 1 " - " ASN B 341 " " NAG T 1 " - " ASN B 614 " " NAG U 1 " - " ASN B 707 " " NAG V 1 " - " ASN B 715 " " NAG W 1 " - " ASN B 799 " " NAG X 1 " - " ASN B1072 " " NAG Y 1 " - " ASN B1096 " " NAG Z 1 " - " ASN B1132 " " NAG a 1 " - " ASN C 122 " " NAG b 1 " - " ASN C 163 " " NAG c 1 " - " ASN C 232 " " NAG d 1 " - " ASN C 280 " " NAG e 1 " - " ASN C 329 " " NAG f 1 " - " ASN C 614 " " NAG g 1 " - " ASN C 707 " " NAG h 1 " - " ASN C 715 " " NAG i 1 " - " ASN C 799 " " NAG j 1 " - " ASN C1072 " " NAG k 1 " - " ASN C1096 " " NAG l 1 " - " ASN C1132 " Time building additional restraints: 10.96 Conformation dependent library (CDL) restraints added in 4.4 seconds 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5786 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 43 sheets defined 24.7% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.37 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 363 through 369 Processing helix chain 'A' and resid 382 through 387 removed outlier: 3.892A pdb=" N ASN A 386 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 removed outlier: 3.838A pdb=" N VAL A 405 " --> pdb=" O GLY A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 436 through 441 removed outlier: 3.539A pdb=" N SER A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 742 Processing helix chain 'A' and resid 744 through 753 removed outlier: 4.068A pdb=" N GLN A 753 " --> pdb=" O ASN A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 781 removed outlier: 3.928A pdb=" N LEU A 761 " --> pdb=" O PHE A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 Processing helix chain 'A' and resid 864 through 883 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: 4.265A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 939 removed outlier: 3.598A pdb=" N LEU A 936 " --> pdb=" O ILE A 932 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 937 " --> pdb=" O GLN A 933 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER A 938 " --> pdb=" O ASP A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 963 Processing helix chain 'A' and resid 974 through 982 removed outlier: 3.692A pdb=" N LEU A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.024A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1143 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: 4.109A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.902A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 436 through 441 Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 736 through 741 Processing helix chain 'B' and resid 744 through 752 Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.716A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.557A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.556A pdb=" N GLY B 883 " --> pdb=" O THR B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 889 removed outlier: 4.005A 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 916 removed outlier: 3.593A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU B 916 " --> pdb=" O ASN B 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 911 through 916' Processing helix chain 'B' and resid 917 through 939 Processing helix chain 'B' and resid 943 through 963 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: 3.732A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.408A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1144 removed outlier: 3.680A 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 363 through 369 Processing helix chain 'C' and resid 381 through 387 removed outlier: 3.641A pdb=" N LEU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN C 386 " --> pdb=" O THR C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 735 through 741 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 758 through 781 removed outlier: 3.514A pdb=" N ASN C 762 " --> pdb=" O CYS C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 824 removed outlier: 3.531A pdb=" N VAL C 824 " --> pdb=" O LEU C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.635A 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 910 through 917 removed outlier: 4.265A pdb=" N LEU C 914 " --> pdb=" O THR C 910 " (cutoff:3.500A) 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 982 removed outlier: 3.609A pdb=" N ILE C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU C 982 " --> pdb=" O ILE C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 1031 removed outlier: 4.529A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C1031 " --> pdb=" O MET C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1144 removed outlier: 3.558A pdb=" N ASP C1144 " --> pdb=" O GLN C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 7.847A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 7.035A 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: 5.985A pdb=" N PHE A 43 " --> pdb=" O ARG C 565 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.687A 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: 4.032A 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: 7.093A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.468A pdb=" N VAL A 126 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 10.177A pdb=" N GLU A 167 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.383A pdb=" N ILE A 128 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N THR A 165 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL A 130 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ASN A 163 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLU A 132 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ALA A 161 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.391A 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: 3.548A pdb=" N THR A 313 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL A 593 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASN A 315 " --> pdb=" O GLY A 591 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLY A 591 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 4.669A 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: 3.754A pdb=" N ASN A 540 " --> pdb=" O ILE A 324 " (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 450 through 452 Processing sheet with id=AA9, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AB1, first strand: chain 'A' and resid 571 through 574 removed outlier: 6.662A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N PHE A 563 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.046A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 709 through 711 Processing sheet with id=AB4, first strand: chain 'A' and resid 715 through 726 removed outlier: 3.508A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.569A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1118 through 1120 Processing sheet with id=AB7, first strand: chain 'A' and resid 1092 through 1095 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.331A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.480A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.375A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.005A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.547A pdb=" N LEU B 84 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ARG B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N PHE B 106 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN B 237 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N TRP B 104 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU B 239 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.442A pdb=" N VAL B 126 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N GLU B 167 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.038A pdb=" N ILE B 128 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N THR B 165 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL B 130 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ASN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLU B 132 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA B 161 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 309 through 317 removed outlier: 6.951A pdb=" N VAL B 593 " --> pdb=" O THR B 313 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASN B 315 " --> pdb=" O GLY B 591 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY B 591 " --> pdb=" O ASN B 315 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 326 removed outlier: 5.408A pdb=" N ASP B 572 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE B 563 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AC5, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.378A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 450 through 452 Processing sheet with id=AC7, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AC8, first strand: chain 'B' and resid 652 through 653 removed outlier: 5.846A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 699 through 701 removed outlier: 7.110A pdb=" N ALA B 699 " --> pdb=" O ILE C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 715 through 726 removed outlier: 5.999A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.540A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1118 through 1123 removed outlier: 4.991A pdb=" N ALA B1085 " --> pdb=" O SER B1121 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1092 through 1095 removed outlier: 5.106A pdb=" N GLN B1104 " --> pdb=" O GLU B1109 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLU B1109 " --> pdb=" O GLN B1104 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 26 through 30 removed outlier: 7.908A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N HIS C 205 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N LEU C 221 " --> pdb=" O HIS C 205 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL C 36 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.018A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.229A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 309 through 317 removed outlier: 6.967A pdb=" N VAL C 593 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ASN C 315 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY C 591 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AE1, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE2, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AE3, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.181A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 709 through 711 removed outlier: 3.669A pdb=" N THR C1074 " --> pdb=" O SER C1095 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 715 through 726 removed outlier: 3.564A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 731 through 733 removed outlier: 4.545A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1118 through 1120 1000 hydrogen bonds defined for protein. 2730 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.77 Time building geometry restraints manager: 11.81 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: 7964 1.34 - 1.46: 6252 1.46 - 1.58: 11482 1.58 - 1.70: 0 1.70 - 1.83: 132 Bond restraints: 25830 Sorted by residual: bond pdb=" C1 NAG X 1 " pdb=" O5 NAG X 1 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C1 NAG j 1 " pdb=" O5 NAG j 1 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.38e+00 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.87e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.71e+00 bond pdb=" C1 NAG a 1 " pdb=" O5 NAG a 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.01e+00 ... (remaining 25825 not shown) Histogram of bond angle deviations from ideal: 98.41 - 106.54: 672 106.54 - 114.66: 15749 114.66 - 122.79: 16028 122.79 - 130.91: 2638 130.91 - 139.04: 60 Bond angle restraints: 35147 Sorted by residual: angle pdb=" C LEU A 982 " pdb=" N ASP A 983 " pdb=" CA ASP A 983 " ideal model delta sigma weight residual 120.67 139.04 -18.37 1.34e+00 5.57e-01 1.88e+02 angle pdb=" N ILE A 466 " pdb=" CA ILE A 466 " pdb=" C ILE A 466 " ideal model delta sigma weight residual 112.43 109.12 3.31 9.20e-01 1.18e+00 1.30e+01 angle pdb=" N PRO B 984 " pdb=" CA PRO B 984 " pdb=" C PRO B 984 " ideal model delta sigma weight residual 110.70 114.63 -3.93 1.22e+00 6.72e-01 1.04e+01 angle pdb=" N PRO A 984 " pdb=" CA PRO A 984 " pdb=" C PRO A 984 " ideal model delta sigma weight residual 110.70 114.24 -3.54 1.22e+00 6.72e-01 8.40e+00 angle pdb=" C GLY B 646 " pdb=" N CYS B 647 " pdb=" CA CYS B 647 " ideal model delta sigma weight residual 121.75 117.44 4.31 1.73e+00 3.34e-01 6.19e+00 ... (remaining 35142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.04: 15219 21.04 - 42.07: 1023 42.07 - 63.11: 188 63.11 - 84.15: 37 84.15 - 105.19: 17 Dihedral angle restraints: 16484 sinusoidal: 7497 harmonic: 8987 Sorted by residual: dihedral pdb=" CB CYS A 736 " pdb=" SG CYS A 736 " pdb=" SG CYS A 758 " pdb=" CB CYS A 758 " ideal model delta sinusoidal sigma weight residual 93.00 3.62 89.38 1 1.00e+01 1.00e-02 9.50e+01 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 2.95 -88.95 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CB CYS C 389 " pdb=" SG CYS C 389 " pdb=" SG CYS C 523 " pdb=" CB CYS C 523 " ideal model delta sinusoidal sigma weight residual 93.00 9.21 83.79 1 1.00e+01 1.00e-02 8.56e+01 ... (remaining 16481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3558 0.065 - 0.131: 628 0.131 - 0.196: 45 0.196 - 0.262: 2 0.262 - 0.327: 1 Chirality restraints: 4234 Sorted by residual: chirality pdb=" C1 NAG B2001 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B2001 " pdb=" O5 NAG B2001 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN B 707 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB THR A 95 " pdb=" CA THR A 95 " pdb=" OG1 THR A 95 " pdb=" CG2 THR A 95 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 4231 not shown) Planarity restraints: 4492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1072 " 0.032 2.00e-02 2.50e+03 2.98e-02 1.11e+01 pdb=" CG ASN B1072 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN B1072 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B1072 " -0.031 2.00e-02 2.50e+03 pdb=" C1 NAG X 1 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 904 " 0.019 2.00e-02 2.50e+03 1.81e-02 5.72e+00 pdb=" CG PHE B 904 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE B 904 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 904 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 904 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 904 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 904 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 984 " 0.034 5.00e-02 4.00e+02 5.03e-02 4.06e+00 pdb=" N PRO A 985 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 985 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 985 " 0.028 5.00e-02 4.00e+02 ... (remaining 4489 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 2021 2.74 - 3.28: 24777 3.28 - 3.82: 39888 3.82 - 4.36: 45242 4.36 - 4.90: 80554 Nonbonded interactions: 192482 Sorted by model distance: nonbonded pdb=" OG1 THR A 124 " pdb=" OD1 ASN A 125 " model vdw 2.194 2.440 nonbonded pdb=" OG SER A 638 " pdb=" OD1 ASN A 639 " model vdw 2.203 2.440 nonbonded pdb=" OG1 THR B 616 " pdb=" OE1 GLU B 617 " model vdw 2.212 2.440 nonbonded pdb=" O ASN C 437 " pdb=" OG SER C 441 " model vdw 2.241 2.440 nonbonded pdb=" O SER C 965 " pdb=" OG SER C 965 " model vdw 2.248 2.440 ... (remaining 192477 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 635 through 825 or resid 853 throu \ gh 1144 or resid 2001 through 2004)) selection = (chain 'C' and (resid 14 through 619 or resid 635 through 1144 or resid 2001 thr \ ough 2004)) } 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' } 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: 3.510 Set stop_for_unknowns flag: 0.010 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: 13.330 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 69.100 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.440 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.005 0.063 25830 Z= 0.350 Angle : 0.645 18.371 35147 Z= 0.324 Chirality : 0.048 0.327 4234 Planarity : 0.003 0.050 4444 Dihedral : 13.996 105.187 10578 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.80 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 3040 helix: 2.25 (0.21), residues: 655 sheet: 0.67 (0.19), residues: 716 loop : -0.98 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 884 HIS 0.003 0.001 HIS B1062 PHE 0.042 0.001 PHE B 904 TYR 0.021 0.001 TYR A 871 ARG 0.004 0.000 ARG B1037 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 2.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.7592 (mpt-90) cc_final: 0.7360 (mmt90) REVERT: A 569 ASP cc_start: 0.7963 (m-30) cc_final: 0.7139 (t0) REVERT: B 118 LEU cc_start: 0.7678 (tt) cc_final: 0.7376 (tt) REVERT: B 955 GLN cc_start: 0.8379 (tm-30) cc_final: 0.8137 (tm-30) REVERT: B 1048 MET cc_start: 0.8057 (ptm) cc_final: 0.7734 (ptm) REVERT: C 375 PHE cc_start: 0.8181 (t80) cc_final: 0.7849 (t80) REVERT: C 434 TRP cc_start: 0.7422 (p-90) cc_final: 0.7193 (p90) outliers start: 0 outliers final: 2 residues processed: 207 average time/residue: 1.2759 time to fit residues: 309.7997 Evaluate side-chains 106 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 2.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain C residue 992 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 259 optimal weight: 1.9990 chunk 232 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 240 optimal weight: 20.0000 chunk 93 optimal weight: 0.6980 chunk 146 optimal weight: 8.9990 chunk 179 optimal weight: 0.9980 chunk 278 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 237 GLN A 540 ASN B 496 GLN C 899 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25830 Z= 0.198 Angle : 0.578 9.363 35147 Z= 0.289 Chirality : 0.046 0.355 4234 Planarity : 0.004 0.054 4444 Dihedral : 8.280 90.497 5057 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.78 % Favored : 96.15 % Rotamer: Outliers : 0.81 % Allowed : 7.44 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.15), residues: 3040 helix: 2.26 (0.21), residues: 683 sheet: 0.76 (0.19), residues: 719 loop : -1.00 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 434 HIS 0.003 0.001 HIS B1086 PHE 0.026 0.001 PHE A 757 TYR 0.021 0.001 TYR A 168 ARG 0.007 0.000 ARG B 450 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 3.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.7566 (mpt-90) cc_final: 0.7351 (mmt90) REVERT: A 227 LEU cc_start: 0.7911 (mm) cc_final: 0.7685 (mt) REVERT: A 569 ASP cc_start: 0.8014 (m-30) cc_final: 0.7291 (t0) REVERT: B 53 ASP cc_start: 0.7161 (t0) cc_final: 0.6938 (t0) REVERT: B 955 GLN cc_start: 0.8371 (tm-30) cc_final: 0.8039 (tp-100) REVERT: B 1048 MET cc_start: 0.8000 (ptm) cc_final: 0.7686 (ptm) REVERT: C 375 PHE cc_start: 0.8080 (t80) cc_final: 0.7785 (t80) REVERT: C 434 TRP cc_start: 0.7473 (p-90) cc_final: 0.7221 (p90) outliers start: 22 outliers final: 8 residues processed: 141 average time/residue: 0.9852 time to fit residues: 170.5565 Evaluate side-chains 109 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 101 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 154 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 232 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 279 optimal weight: 0.9980 chunk 301 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 276 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 224 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 854 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 GLN B 948 ASN B 952 GLN C 115 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 25830 Z= 0.225 Angle : 0.568 9.808 35147 Z= 0.283 Chirality : 0.046 0.360 4234 Planarity : 0.004 0.054 4444 Dihedral : 7.671 85.564 5053 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.05 % Favored : 95.89 % Rotamer: Outliers : 1.22 % Allowed : 10.26 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3040 helix: 2.26 (0.21), residues: 678 sheet: 0.72 (0.19), residues: 710 loop : -1.00 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 884 HIS 0.003 0.001 HIS A 66 PHE 0.019 0.001 PHE C 390 TYR 0.021 0.001 TYR A1065 ARG 0.005 0.000 ARG B 450 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 117 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 THR cc_start: 0.9268 (OUTLIER) cc_final: 0.8954 (p) REVERT: A 188 ARG cc_start: 0.7579 (mpt-90) cc_final: 0.7352 (mmt90) REVERT: A 569 ASP cc_start: 0.8114 (m-30) cc_final: 0.7254 (t0) REVERT: B 53 ASP cc_start: 0.7222 (t0) cc_final: 0.6871 (t70) REVERT: B 774 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8616 (ttpp) REVERT: B 955 GLN cc_start: 0.8415 (tm-30) cc_final: 0.8056 (tp-100) REVERT: B 1048 MET cc_start: 0.7943 (ptm) cc_final: 0.7698 (ptm) REVERT: C 434 TRP cc_start: 0.7457 (p-90) cc_final: 0.7199 (p90) outliers start: 33 outliers final: 16 residues processed: 145 average time/residue: 1.0027 time to fit residues: 178.8554 Evaluate side-chains 125 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 774 LYS Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 275 optimal weight: 0.8980 chunk 209 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 280 optimal weight: 2.9990 chunk 296 optimal weight: 2.9990 chunk 146 optimal weight: 0.3980 chunk 265 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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** ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 25830 Z= 0.356 Angle : 0.632 11.949 35147 Z= 0.316 Chirality : 0.048 0.375 4234 Planarity : 0.004 0.051 4444 Dihedral : 7.285 76.833 5053 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.67 % Favored : 95.26 % Rotamer: Outliers : 1.81 % Allowed : 12.51 % Favored : 85.67 % 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: 3040 helix: 2.11 (0.20), residues: 683 sheet: 0.57 (0.19), residues: 714 loop : -1.17 (0.14), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 884 HIS 0.004 0.001 HIS A1086 PHE 0.024 0.002 PHE B 904 TYR 0.027 0.001 TYR A1065 ARG 0.008 0.000 ARG A1037 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 114 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7483 (t60) cc_final: 0.6481 (t60) REVERT: A 124 THR cc_start: 0.9346 (OUTLIER) cc_final: 0.8988 (p) REVERT: A 188 ARG cc_start: 0.7681 (mpt-90) cc_final: 0.7262 (mmt90) REVERT: A 227 LEU cc_start: 0.8035 (mm) cc_final: 0.7833 (mt) REVERT: A 569 ASP cc_start: 0.8279 (m-30) cc_final: 0.7394 (t0) REVERT: A 976 ASN cc_start: 0.8944 (m-40) cc_final: 0.8557 (t0) REVERT: B 53 ASP cc_start: 0.7286 (t0) cc_final: 0.6920 (t70) REVERT: B 118 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7136 (tt) REVERT: B 774 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8645 (ttpp) REVERT: B 955 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8194 (tm-30) REVERT: B 1037 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8873 (mtp180) REVERT: B 1048 MET cc_start: 0.8093 (ptm) cc_final: 0.7827 (ptm) REVERT: C 434 TRP cc_start: 0.7384 (p-90) cc_final: 0.7136 (p90) REVERT: C 527 LYS cc_start: 0.8587 (mmmt) cc_final: 0.7812 (mmtt) outliers start: 49 outliers final: 27 residues processed: 157 average time/residue: 0.9277 time to fit residues: 180.3871 Evaluate side-chains 131 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 100 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 584 ASP Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 774 LYS Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 247 optimal weight: 0.1980 chunk 168 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 220 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 205 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 151 optimal weight: 4.9990 chunk 266 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 81 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 GLN ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 GLN ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 25830 Z= 0.283 Angle : 0.597 11.225 35147 Z= 0.298 Chirality : 0.047 0.372 4234 Planarity : 0.004 0.048 4444 Dihedral : 6.864 69.588 5053 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.57 % Favored : 95.36 % Rotamer: Outliers : 2.33 % Allowed : 13.81 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 3040 helix: 2.16 (0.20), residues: 680 sheet: 0.59 (0.19), residues: 716 loop : -1.18 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 884 HIS 0.003 0.001 HIS C1086 PHE 0.023 0.001 PHE A 133 TYR 0.022 0.001 TYR A1065 ARG 0.004 0.000 ARG B 450 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 111 time to evaluate : 2.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7875 (OUTLIER) cc_final: 0.7510 (p0) REVERT: A 124 THR cc_start: 0.9275 (OUTLIER) cc_final: 0.8934 (p) REVERT: A 188 ARG cc_start: 0.7682 (mpt-90) cc_final: 0.7345 (mmt90) REVERT: A 227 LEU cc_start: 0.8005 (mm) cc_final: 0.7784 (mt) REVERT: A 569 ASP cc_start: 0.8360 (m-30) cc_final: 0.7394 (t0) REVERT: A 976 ASN cc_start: 0.8932 (m-40) cc_final: 0.8641 (t0) REVERT: B 53 ASP cc_start: 0.7285 (t0) cc_final: 0.6914 (t70) REVERT: B 538 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.8135 (p0) REVERT: B 774 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8667 (ttpp) REVERT: B 955 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8060 (tp-100) REVERT: B 1048 MET cc_start: 0.8029 (ptm) cc_final: 0.7829 (ptm) REVERT: C 434 TRP cc_start: 0.7380 (p-90) cc_final: 0.7134 (p90) outliers start: 63 outliers final: 29 residues processed: 166 average time/residue: 0.9345 time to fit residues: 193.2214 Evaluate side-chains 139 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 106 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 584 ASP Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 774 LYS Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 1104 GLN Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 99 optimal weight: 1.9990 chunk 267 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 174 optimal weight: 0.0980 chunk 73 optimal weight: 4.9990 chunk 297 optimal weight: 2.9990 chunk 246 optimal weight: 0.4980 chunk 137 optimal weight: 2.9990 chunk 24 optimal weight: 0.0370 chunk 98 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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** B 760 GLN ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 25830 Z= 0.156 Angle : 0.553 10.757 35147 Z= 0.274 Chirality : 0.045 0.362 4234 Planarity : 0.004 0.049 4444 Dihedral : 6.381 62.521 5053 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.05 % Favored : 95.89 % Rotamer: Outliers : 1.63 % Allowed : 14.81 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 3040 helix: 2.28 (0.21), residues: 681 sheet: 0.67 (0.19), residues: 716 loop : -1.07 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 64 HIS 0.003 0.000 HIS A 66 PHE 0.018 0.001 PHE C 133 TYR 0.015 0.001 TYR B1065 ARG 0.016 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 119 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 THR cc_start: 0.9350 (OUTLIER) cc_final: 0.9019 (p) REVERT: A 188 ARG cc_start: 0.7671 (mpt-90) cc_final: 0.7174 (mmt90) REVERT: A 227 LEU cc_start: 0.8012 (mm) cc_final: 0.7777 (mt) REVERT: A 569 ASP cc_start: 0.8295 (m-30) cc_final: 0.7395 (t0) REVERT: A 976 ASN cc_start: 0.8923 (m-40) cc_final: 0.8633 (t0) REVERT: B 538 ASN cc_start: 0.8350 (OUTLIER) cc_final: 0.8142 (p0) REVERT: B 955 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8003 (tp-100) REVERT: B 1037 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8738 (mtp180) REVERT: C 64 TRP cc_start: 0.7585 (t60) cc_final: 0.6993 (t60) REVERT: C 434 TRP cc_start: 0.7372 (p-90) cc_final: 0.7127 (p90) outliers start: 44 outliers final: 27 residues processed: 158 average time/residue: 0.9581 time to fit residues: 188.8074 Evaluate side-chains 138 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 108 time to evaluate : 3.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 286 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 250 optimal weight: 0.4980 chunk 165 optimal weight: 0.7980 chunk 295 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 GLN ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25830 Z= 0.235 Angle : 0.576 10.395 35147 Z= 0.286 Chirality : 0.046 0.364 4234 Planarity : 0.004 0.049 4444 Dihedral : 6.172 57.246 5053 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.28 % Favored : 95.66 % Rotamer: Outliers : 2.11 % Allowed : 15.07 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.15), residues: 3040 helix: 2.24 (0.21), residues: 687 sheet: 0.65 (0.19), residues: 715 loop : -1.10 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 351 HIS 0.003 0.001 HIS A1086 PHE 0.025 0.001 PHE A 757 TYR 0.021 0.001 TYR A1065 ARG 0.005 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 111 time to evaluate : 2.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8027 (OUTLIER) cc_final: 0.7698 (p0) REVERT: A 124 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.8934 (p) REVERT: A 188 ARG cc_start: 0.7688 (mpt-90) cc_final: 0.7341 (mmt90) REVERT: A 569 ASP cc_start: 0.8327 (m-30) cc_final: 0.7408 (t0) REVERT: B 53 ASP cc_start: 0.7208 (t70) cc_final: 0.6899 (t70) REVERT: B 538 ASN cc_start: 0.8360 (OUTLIER) cc_final: 0.8144 (p0) REVERT: B 774 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8541 (ttpp) REVERT: B 955 GLN cc_start: 0.8432 (tm-30) cc_final: 0.8014 (tp-100) REVERT: B 1037 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8891 (mtp180) REVERT: C 64 TRP cc_start: 0.7620 (t60) cc_final: 0.7052 (t60) REVERT: C 434 TRP cc_start: 0.7366 (p-90) cc_final: 0.7120 (p90) REVERT: C 876 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8687 (tt) outliers start: 57 outliers final: 37 residues processed: 162 average time/residue: 0.8963 time to fit residues: 182.9455 Evaluate side-chains 145 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 102 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 584 ASP Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 774 LYS Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1104 GLN Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 183 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 176 optimal weight: 0.0670 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 232 optimal weight: 8.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25830 Z= 0.173 Angle : 0.557 10.487 35147 Z= 0.275 Chirality : 0.045 0.359 4234 Planarity : 0.004 0.051 4444 Dihedral : 5.874 56.872 5053 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.98 % Favored : 95.95 % Rotamer: Outliers : 1.78 % Allowed : 15.77 % Favored : 82.45 % 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: 3040 helix: 2.26 (0.21), residues: 688 sheet: 0.71 (0.19), residues: 709 loop : -1.03 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 351 HIS 0.003 0.001 HIS B1086 PHE 0.016 0.001 PHE C 390 TYR 0.030 0.001 TYR C 168 ARG 0.004 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 114 time to evaluate : 3.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7744 (OUTLIER) cc_final: 0.7109 (p0) REVERT: A 124 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.8934 (p) REVERT: A 188 ARG cc_start: 0.7681 (mpt-90) cc_final: 0.7180 (mmt90) REVERT: A 569 ASP cc_start: 0.8289 (m-30) cc_final: 0.7434 (t0) REVERT: B 53 ASP cc_start: 0.7198 (t70) cc_final: 0.6891 (t70) REVERT: B 774 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8628 (ttpm) REVERT: B 955 GLN cc_start: 0.8431 (tm-30) cc_final: 0.7997 (tp-100) REVERT: B 1037 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8731 (mtp180) REVERT: C 64 TRP cc_start: 0.7551 (t60) cc_final: 0.7011 (t60) REVERT: C 434 TRP cc_start: 0.7361 (p-90) cc_final: 0.7103 (p90) REVERT: C 876 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8643 (tt) outliers start: 48 outliers final: 37 residues processed: 160 average time/residue: 0.8301 time to fit residues: 168.2151 Evaluate side-chains 144 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 102 time to evaluate : 2.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 584 ASP Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 740 ILE Chi-restraints excluded: chain B residue 774 LYS Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 269 optimal weight: 5.9990 chunk 283 optimal weight: 1.9990 chunk 258 optimal weight: 2.9990 chunk 275 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 216 optimal weight: 0.4980 chunk 84 optimal weight: 0.9980 chunk 249 optimal weight: 20.0000 chunk 260 optimal weight: 0.9990 chunk 274 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 81 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 GLN ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25830 Z= 0.185 Angle : 0.560 9.729 35147 Z= 0.276 Chirality : 0.045 0.358 4234 Planarity : 0.004 0.050 4444 Dihedral : 5.756 56.904 5053 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.21 % Favored : 95.72 % Rotamer: Outliers : 1.81 % Allowed : 16.22 % Favored : 81.97 % 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: 0.27 (0.15), residues: 3040 helix: 2.27 (0.20), residues: 690 sheet: 0.72 (0.19), residues: 709 loop : -1.04 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.003 0.001 HIS A1086 PHE 0.025 0.001 PHE A 757 TYR 0.023 0.001 TYR C 168 ARG 0.003 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 104 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.8922 (p) REVERT: A 188 ARG cc_start: 0.7679 (mpt-90) cc_final: 0.7152 (mmt90) REVERT: A 569 ASP cc_start: 0.8297 (m-30) cc_final: 0.7437 (t0) REVERT: B 53 ASP cc_start: 0.7247 (t70) cc_final: 0.6931 (t70) REVERT: B 774 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8626 (ttpm) REVERT: B 955 GLN cc_start: 0.8435 (tm-30) cc_final: 0.7994 (tp-100) REVERT: B 1037 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8770 (mtp180) REVERT: C 64 TRP cc_start: 0.7572 (t60) cc_final: 0.7038 (t60) REVERT: C 434 TRP cc_start: 0.7362 (p-90) cc_final: 0.7102 (p90) REVERT: C 876 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8649 (tt) outliers start: 49 outliers final: 37 residues processed: 150 average time/residue: 0.8824 time to fit residues: 167.0466 Evaluate side-chains 143 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 102 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 584 ASP Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 740 ILE Chi-restraints excluded: chain B residue 774 LYS Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 181 optimal weight: 1.9990 chunk 291 optimal weight: 0.5980 chunk 177 optimal weight: 0.0370 chunk 138 optimal weight: 6.9990 chunk 202 optimal weight: 0.0870 chunk 305 optimal weight: 3.9990 chunk 281 optimal weight: 0.6980 chunk 243 optimal weight: 30.0000 chunk 25 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 149 optimal weight: 0.1980 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25830 Z= 0.147 Angle : 0.546 9.760 35147 Z= 0.268 Chirality : 0.044 0.349 4234 Planarity : 0.004 0.052 4444 Dihedral : 5.404 56.551 5053 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.75 % Favored : 96.18 % Rotamer: Outliers : 1.55 % Allowed : 16.55 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 3040 helix: 2.33 (0.21), residues: 687 sheet: 0.81 (0.19), residues: 697 loop : -0.96 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.003 0.000 HIS A 66 PHE 0.015 0.001 PHE A 133 TYR 0.020 0.001 TYR C 168 ARG 0.004 0.000 ARG B 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 126 time to evaluate : 3.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 THR cc_start: 0.9321 (OUTLIER) cc_final: 0.8979 (p) REVERT: A 188 ARG cc_start: 0.7706 (mpt-90) cc_final: 0.7219 (mmt90) REVERT: A 227 LEU cc_start: 0.8014 (mm) cc_final: 0.7781 (mt) REVERT: A 569 ASP cc_start: 0.8236 (m-30) cc_final: 0.7431 (t0) REVERT: B 53 ASP cc_start: 0.7255 (t70) cc_final: 0.6926 (t70) REVERT: B 774 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8587 (ttpm) REVERT: B 955 GLN cc_start: 0.8414 (tm-30) cc_final: 0.7970 (tp-100) REVERT: C 64 TRP cc_start: 0.7550 (t60) cc_final: 0.7010 (t60) REVERT: C 434 TRP cc_start: 0.7389 (p-90) cc_final: 0.7120 (p90) REVERT: C 876 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8643 (tt) outliers start: 42 outliers final: 32 residues processed: 166 average time/residue: 0.9515 time to fit residues: 195.0977 Evaluate side-chains 143 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 108 time to evaluate : 3.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 740 ILE Chi-restraints excluded: chain B residue 774 LYS Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 193 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 74 optimal weight: 0.0270 chunk 224 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 67 optimal weight: 0.7980 chunk 243 optimal weight: 30.0000 chunk 102 optimal weight: 20.0000 chunk 250 optimal weight: 9.9990 chunk 30 optimal weight: 50.0000 chunk 44 optimal weight: 40.0000 overall best weight: 2.9644 ------------------------------------------------------------------------------- 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** B 760 GLN B 772 GLN ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 653 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.138455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.080423 restraints weight = 44479.524| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.20 r_work: 0.2982 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 25830 Z= 0.496 Angle : 0.696 14.583 35147 Z= 0.347 Chirality : 0.051 0.371 4234 Planarity : 0.004 0.049 4444 Dihedral : 5.933 58.214 5053 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.64 % Favored : 95.30 % Rotamer: Outliers : 1.85 % Allowed : 16.77 % Favored : 81.38 % 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: -0.03 (0.15), residues: 3040 helix: 1.98 (0.20), residues: 690 sheet: 0.54 (0.19), residues: 687 loop : -1.19 (0.14), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 884 HIS 0.006 0.001 HIS B1046 PHE 0.028 0.002 PHE B1119 TYR 0.032 0.002 TYR A1065 ARG 0.010 0.001 ARG A1037 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5794.77 seconds wall clock time: 105 minutes 2.83 seconds (6302.83 seconds total)