Starting phenix.real_space_refine on Thu Mar 14 22:32:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejg_28181/03_2024/8ejg_28181.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejg_28181/03_2024/8ejg_28181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejg_28181/03_2024/8ejg_28181.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejg_28181/03_2024/8ejg_28181.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejg_28181/03_2024/8ejg_28181.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejg_28181/03_2024/8ejg_28181.pdb" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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 90 5.16 5 C 6174 2.51 5 N 1530 2.21 5 O 2172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 129": "OD1" <-> "OD2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 250": "OD1" <-> "OD2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 129": "OD1" <-> "OD2" Residue "B TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 250": "OD1" <-> "OD2" Residue "B TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 129": "OD1" <-> "OD2" Residue "C TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 250": "OD1" <-> "OD2" Residue "C TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9966 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1551 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain: "a" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1337 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "B" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1551 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain: "C" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1551 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain: "b" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1337 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "c" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1337 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BGC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BGC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BGC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 Time building chain proxies: 6.16, per 1000 atoms: 0.62 Number of scatterers: 9966 At special positions: 0 Unit cell: (101.2, 102.35, 104.65, 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 90 16.00 O 2172 8.00 N 1530 7.00 C 6174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 230 " distance=2.04 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 154 " distance=2.16 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 211 " distance=2.03 Simple disulfide: pdb=" SG CYS A 206 " - pdb=" SG CYS a 359 " distance=2.02 Simple disulfide: pdb=" SG CYS a 278 " - pdb=" SG CYS a 291 " distance=2.03 Simple disulfide: pdb=" SG CYS a 300 " - pdb=" SG CYS a 309 " distance=2.03 Simple disulfide: pdb=" SG CYS a 363 " - pdb=" SG CYS a 384 " distance=2.01 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 230 " distance=2.04 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 154 " distance=2.16 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 211 " distance=2.03 Simple disulfide: pdb=" SG CYS B 206 " - pdb=" SG CYS b 359 " distance=2.02 Simple disulfide: pdb=" SG CYS C 85 " - pdb=" SG CYS C 230 " distance=2.04 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 154 " distance=2.16 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 211 " distance=2.04 Simple disulfide: pdb=" SG CYS C 206 " - pdb=" SG CYS c 359 " distance=2.02 Simple disulfide: pdb=" SG CYS b 278 " - pdb=" SG CYS b 291 " distance=2.03 Simple disulfide: pdb=" SG CYS b 300 " - pdb=" SG CYS b 309 " distance=2.03 Simple disulfide: pdb=" SG CYS b 363 " - pdb=" SG CYS b 384 " distance=2.01 Simple disulfide: pdb=" SG CYS c 278 " - pdb=" SG CYS c 291 " distance=2.03 Simple disulfide: pdb=" SG CYS c 300 " - pdb=" SG CYS c 309 " distance=2.03 Simple disulfide: pdb=" SG CYS c 363 " - pdb=" SG CYS c 384 " distance=2.01 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 ALPHA1-2 " MAN K 4 " - " MAN K 5 " " MAN d 4 " - " MAN d 5 " " MAN f 4 " - " MAN f 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA K 3 " - " MAN K 4 " " MAN K 6 " - " MAN K 7 " " BMA M 3 " - " MAN M 4 " " BMA T 3 " - " MAN T 4 " " BMA d 3 " - " MAN d 4 " " MAN d 6 " - " MAN d 7 " " BMA f 3 " - " MAN f 4 " " MAN f 6 " - " MAN f 7 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " " BMA K 3 " - " MAN K 6 " " BMA M 3 " - " MAN M 5 " " BMA T 3 " - " MAN T 5 " " BMA d 3 " - " MAN d 6 " " BMA f 3 " - " MAN f 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BGC G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BGC P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BGC W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " NAG-ASN " NAG D 1 " - " ASN A 78 " " NAG E 1 " - " ASN A 88 " " NAG F 1 " - " ASN A 98 " " NAG G 1 " - " ASN A 108 " " NAG H 1 " - " ASN A 118 " " NAG I 1 " - " ASN A 166 " " NAG J 1 " - " ASN A 223 " " NAG K 1 " - " ASN a 364 " " NAG L 1 " - " ASN a 372 " " NAG M 1 " - " ASN B 78 " " NAG N 1 " - " ASN B 88 " " NAG O 1 " - " ASN B 98 " " NAG P 1 " - " ASN B 108 " " NAG Q 1 " - " ASN B 118 " " NAG R 1 " - " ASN B 166 " " NAG S 1 " - " ASN B 223 " " NAG T 1 " - " ASN C 78 " " NAG U 1 " - " ASN C 88 " " NAG V 1 " - " ASN C 98 " " NAG W 1 " - " ASN C 108 " " NAG X 1 " - " ASN C 118 " " NAG Y 1 " - " ASN C 166 " " NAG Z 1 " - " ASN C 223 " " NAG a 501 " - " ASN a 389 " " NAG a 502 " - " ASN a 394 " " NAG b 501 " - " ASN b 389 " " NAG b 502 " - " ASN b 394 " " NAG c 501 " - " ASN c 389 " " NAG c 502 " - " ASN c 394 " " NAG d 1 " - " ASN b 364 " " NAG e 1 " - " ASN b 372 " " NAG f 1 " - " ASN c 364 " " NAG g 1 " - " ASN c 372 " Time building additional restraints: 5.69 Conformation dependent library (CDL) restraints added in 1.7 seconds 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 9 sheets defined 41.0% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.680A pdb=" N THR A 76 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 126 Processing helix chain 'A' and resid 129 through 142 Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 197 through 201 Processing helix chain 'A' and resid 237 through 245 Processing helix chain 'a' and resid 263 through 269 Processing helix chain 'a' and resid 293 through 298 Processing helix chain 'a' and resid 299 through 302 Processing helix chain 'a' and resid 306 through 324 Processing helix chain 'a' and resid 335 through 340 Processing helix chain 'a' and resid 341 through 343 No H-bonds generated for 'chain 'a' and resid 341 through 343' Processing helix chain 'a' and resid 345 through 358 removed outlier: 3.649A pdb=" N ILE a 349 " --> pdb=" O ASN a 345 " (cutoff:3.500A) Processing helix chain 'a' and resid 398 through 421 Processing helix chain 'B' and resid 73 through 78 removed outlier: 3.682A pdb=" N THR B 76 " --> pdb=" O ASN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 126 Processing helix chain 'B' and resid 129 through 142 Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 197 through 201 Processing helix chain 'B' and resid 237 through 245 Processing helix chain 'C' and resid 73 through 78 removed outlier: 3.681A pdb=" N THR C 76 " --> pdb=" O ASN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 129 through 142 Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 197 through 201 Processing helix chain 'C' and resid 237 through 245 Processing helix chain 'b' and resid 263 through 269 Processing helix chain 'b' and resid 293 through 298 Processing helix chain 'b' and resid 299 through 302 Processing helix chain 'b' and resid 306 through 324 Processing helix chain 'b' and resid 335 through 340 Processing helix chain 'b' and resid 341 through 343 No H-bonds generated for 'chain 'b' and resid 341 through 343' Processing helix chain 'b' and resid 345 through 358 removed outlier: 3.648A pdb=" N ILE b 349 " --> pdb=" O ASN b 345 " (cutoff:3.500A) Processing helix chain 'b' and resid 398 through 421 Processing helix chain 'c' and resid 263 through 269 Processing helix chain 'c' and resid 293 through 298 Processing helix chain 'c' and resid 299 through 302 Processing helix chain 'c' and resid 306 through 324 Processing helix chain 'c' and resid 335 through 340 Processing helix chain 'c' and resid 341 through 343 No H-bonds generated for 'chain 'c' and resid 341 through 343' Processing helix chain 'c' and resid 345 through 358 removed outlier: 3.648A pdb=" N ILE c 349 " --> pdb=" O ASN c 345 " (cutoff:3.500A) Processing helix chain 'c' and resid 398 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61 Processing sheet with id=AA2, first strand: chain 'A' and resid 152 through 154 removed outlier: 6.854A pdb=" N HIS A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N THR A 86 " --> pdb=" O ARG A 234 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ARG A 234 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 387 through 388 Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 154 removed outlier: 6.854A pdb=" N HIS B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N THR B 86 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ARG B 234 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 60 through 61 Processing sheet with id=AA7, first strand: chain 'C' and resid 152 through 154 removed outlier: 6.854A pdb=" N HIS C 91 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N THR C 86 " --> pdb=" O ARG C 234 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ARG C 234 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 387 through 388 Processing sheet with id=AA9, first strand: chain 'c' and resid 387 through 388 378 hydrogen bonds defined for protein. 990 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: 2.67 Time building geometry restraints manager: 5.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 2577 1.33 - 1.47: 3187 1.47 - 1.60: 4251 1.60 - 1.74: 11 1.74 - 1.88: 132 Bond restraints: 10158 Sorted by residual: bond pdb=" NE1 TRP c 385 " pdb=" CE2 TRP c 385 " ideal model delta sigma weight residual 1.370 1.284 0.086 1.10e-02 8.26e+03 6.15e+01 bond pdb=" NE1 TRP a 385 " pdb=" CE2 TRP a 385 " ideal model delta sigma weight residual 1.370 1.284 0.086 1.10e-02 8.26e+03 6.15e+01 bond pdb=" NE1 TRP b 385 " pdb=" CE2 TRP b 385 " ideal model delta sigma weight residual 1.370 1.284 0.086 1.10e-02 8.26e+03 6.13e+01 bond pdb=" CB LEU A 59 " pdb=" CG LEU A 59 " ideal model delta sigma weight residual 1.530 1.668 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" CB LEU C 59 " pdb=" CG LEU C 59 " ideal model delta sigma weight residual 1.530 1.668 -0.138 2.00e-02 2.50e+03 4.75e+01 ... (remaining 10153 not shown) Histogram of bond angle deviations from ideal: 98.01 - 110.74: 4001 110.74 - 123.47: 9135 123.47 - 136.20: 616 136.20 - 148.92: 0 148.92 - 161.65: 3 Bond angle restraints: 13755 Sorted by residual: angle pdb=" C2 NAG b 502 " pdb=" N2 NAG b 502 " pdb=" C7 NAG b 502 " ideal model delta sigma weight residual 124.56 161.65 -37.09 3.00e+00 1.11e-01 1.53e+02 angle pdb=" C2 NAG c 502 " pdb=" N2 NAG c 502 " pdb=" C7 NAG c 502 " ideal model delta sigma weight residual 124.56 161.59 -37.03 3.00e+00 1.11e-01 1.52e+02 angle pdb=" C2 NAG a 502 " pdb=" N2 NAG a 502 " pdb=" C7 NAG a 502 " ideal model delta sigma weight residual 124.56 161.59 -37.03 3.00e+00 1.11e-01 1.52e+02 angle pdb=" CA PHE a 398 " pdb=" CB PHE a 398 " pdb=" CG PHE a 398 " ideal model delta sigma weight residual 113.80 122.30 -8.50 1.00e+00 1.00e+00 7.23e+01 angle pdb=" CA PHE b 398 " pdb=" CB PHE b 398 " pdb=" CG PHE b 398 " ideal model delta sigma weight residual 113.80 122.30 -8.50 1.00e+00 1.00e+00 7.22e+01 ... (remaining 13750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.44: 6813 21.44 - 42.88: 264 42.88 - 64.33: 79 64.33 - 85.77: 134 85.77 - 107.21: 84 Dihedral angle restraints: 7374 sinusoidal: 4200 harmonic: 3174 Sorted by residual: dihedral pdb=" C PHE a 398 " pdb=" N PHE a 398 " pdb=" CA PHE a 398 " pdb=" CB PHE a 398 " ideal model delta harmonic sigma weight residual -122.60 -111.92 -10.68 0 2.50e+00 1.60e-01 1.83e+01 dihedral pdb=" C PHE b 398 " pdb=" N PHE b 398 " pdb=" CA PHE b 398 " pdb=" CB PHE b 398 " ideal model delta harmonic sigma weight residual -122.60 -111.94 -10.66 0 2.50e+00 1.60e-01 1.82e+01 dihedral pdb=" C PHE c 398 " pdb=" N PHE c 398 " pdb=" CA PHE c 398 " pdb=" CB PHE c 398 " ideal model delta harmonic sigma weight residual -122.60 -111.95 -10.65 0 2.50e+00 1.60e-01 1.82e+01 ... (remaining 7371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1047 0.108 - 0.216: 410 0.216 - 0.325: 211 0.325 - 0.433: 100 0.433 - 0.541: 44 Chirality restraints: 1812 Sorted by residual: chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.61e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.59e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.58e+02 ... (remaining 1809 not shown) Planarity restraints: 1629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 98 " -0.038 2.00e-02 2.50e+03 4.19e-02 2.19e+01 pdb=" CG ASN C 98 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN C 98 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C 98 " 0.067 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 98 " -0.038 2.00e-02 2.50e+03 4.19e-02 2.19e+01 pdb=" CG ASN A 98 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN A 98 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 98 " 0.068 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 98 " -0.038 2.00e-02 2.50e+03 4.18e-02 2.18e+01 pdb=" CG ASN B 98 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN B 98 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 98 " 0.067 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.050 2.00e-02 2.50e+03 ... (remaining 1626 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 303 2.66 - 3.22: 9737 3.22 - 3.78: 15061 3.78 - 4.34: 21516 4.34 - 4.90: 33333 Nonbonded interactions: 79950 Sorted by model distance: nonbonded pdb=" NH1 ARG a 378 " pdb=" O THR a 379 " model vdw 2.106 2.520 nonbonded pdb=" NH1 ARG b 378 " pdb=" O THR b 379 " model vdw 2.107 2.520 nonbonded pdb=" NH1 ARG c 378 " pdb=" O THR c 379 " model vdw 2.109 2.520 nonbonded pdb=" N HIS c 397 " pdb=" O HIS c 397 " model vdw 2.286 2.496 nonbonded pdb=" N HIS a 397 " pdb=" O HIS a 397 " model vdw 2.286 2.496 ... (remaining 79945 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'T' } ncs_group { reference = (chain 'E' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) } ncs_group { reference = chain 'F' selection = chain 'O' selection = chain 'V' } ncs_group { reference = chain 'K' selection = chain 'd' selection = chain 'f' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.300 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 31.190 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.090 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 : 0.025 0.138 10158 Z= 1.570 Angle : 1.944 37.092 13755 Z= 1.146 Chirality : 0.172 0.541 1812 Planarity : 0.009 0.051 1596 Dihedral : 20.946 107.210 5271 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.29 % 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: -1.09 (0.24), residues: 1071 helix: -1.09 (0.22), residues: 423 sheet: 1.26 (0.50), residues: 102 loop : -0.71 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.007 TRP A 226 HIS 0.008 0.002 HIS B 91 PHE 0.024 0.006 PHE b 261 TYR 0.055 0.008 TYR A 240 ARG 0.008 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 305 ASP cc_start: 0.6570 (p0) cc_final: 0.6359 (p0) REVERT: a 330 GLN cc_start: 0.7109 (mp10) cc_final: 0.6559 (pp30) REVERT: b 305 ASP cc_start: 0.6440 (p0) cc_final: 0.6091 (p0) REVERT: c 305 ASP cc_start: 0.6753 (p0) cc_final: 0.6429 (p0) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.2770 time to fit residues: 116.4663 Evaluate side-chains 180 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 222 GLN a 304 HIS ** a 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 341 ASN ** a 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS C 91 HIS b 304 HIS b 330 GLN b 404 GLN c 304 HIS c 341 ASN c 347 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10158 Z= 0.278 Angle : 0.961 12.222 13755 Z= 0.450 Chirality : 0.056 0.388 1812 Planarity : 0.005 0.039 1596 Dihedral : 17.362 84.889 3228 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.35 % Favored : 93.09 % Rotamer: Outliers : 2.17 % Allowed : 12.53 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -0.78 (0.25), residues: 1071 helix: -0.37 (0.25), residues: 426 sheet: 1.57 (0.50), residues: 120 loop : -1.11 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP c 263 HIS 0.007 0.002 HIS B 123 PHE 0.025 0.002 PHE b 261 TYR 0.022 0.002 TYR c 277 ARG 0.005 0.001 ARG c 378 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 211 time to evaluate : 1.137 Fit side-chains revert: symmetry clash REVERT: A 178 HIS cc_start: 0.7553 (p90) cc_final: 0.7336 (p90) REVERT: a 305 ASP cc_start: 0.6828 (p0) cc_final: 0.6595 (p0) REVERT: a 331 MET cc_start: 0.6593 (tmm) cc_final: 0.6236 (tmm) REVERT: b 305 ASP cc_start: 0.6717 (p0) cc_final: 0.6426 (p0) REVERT: c 305 ASP cc_start: 0.6909 (p0) cc_final: 0.6575 (p0) outliers start: 21 outliers final: 10 residues processed: 227 average time/residue: 0.2322 time to fit residues: 71.9424 Evaluate side-chains 183 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 173 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain a residue 341 ASN Chi-restraints excluded: chain a residue 375 SER Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 375 SER Chi-restraints excluded: chain c residue 375 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 422 GLN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 341 ASN b 404 GLN b 422 GLN c 422 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10158 Z= 0.225 Angle : 0.844 11.806 13755 Z= 0.390 Chirality : 0.052 0.389 1812 Planarity : 0.005 0.057 1596 Dihedral : 13.702 73.622 3228 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.84 % Favored : 91.69 % Rotamer: Outliers : 3.31 % Allowed : 13.35 % Favored : 83.33 % 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: -0.74 (0.25), residues: 1071 helix: 0.10 (0.26), residues: 414 sheet: 2.11 (0.52), residues: 102 loop : -1.49 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP a 263 HIS 0.006 0.001 HIS B 92 PHE 0.016 0.002 PHE c 261 TYR 0.013 0.001 TYR A 149 ARG 0.006 0.001 ARG c 421 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 191 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 HIS cc_start: 0.7648 (p90) cc_final: 0.7393 (p90) REVERT: a 331 MET cc_start: 0.6717 (tmm) cc_final: 0.6153 (tmm) REVERT: B 249 ARG cc_start: 0.7414 (ttm-80) cc_final: 0.6935 (mtm-85) REVERT: C 191 MET cc_start: 0.8253 (mmm) cc_final: 0.8002 (tpt) REVERT: b 305 ASP cc_start: 0.6926 (p0) cc_final: 0.6673 (p0) REVERT: c 305 ASP cc_start: 0.6995 (p0) cc_final: 0.6673 (p0) outliers start: 32 outliers final: 15 residues processed: 212 average time/residue: 0.2379 time to fit residues: 68.8618 Evaluate side-chains 177 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 162 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 375 SER Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 288 GLU Chi-restraints excluded: chain b residue 375 SER Chi-restraints excluded: chain c residue 322 ILE Chi-restraints excluded: chain c residue 375 SER Chi-restraints excluded: chain c residue 398 PHE Chi-restraints excluded: chain c residue 420 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS C 246 GLN ** b 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 10158 Z= 0.354 Angle : 0.853 11.736 13755 Z= 0.399 Chirality : 0.053 0.352 1812 Planarity : 0.004 0.055 1596 Dihedral : 11.425 67.526 3228 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.24 % Favored : 90.48 % Rotamer: Outliers : 3.83 % Allowed : 14.80 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.79 (0.25), residues: 1071 helix: 0.09 (0.26), residues: 414 sheet: 2.10 (0.51), residues: 96 loop : -1.52 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP b 385 HIS 0.006 0.002 HIS B 123 PHE 0.018 0.002 PHE b 398 TYR 0.014 0.002 TYR A 216 ARG 0.006 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 180 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 305 ASP cc_start: 0.7548 (p0) cc_final: 0.7303 (p0) REVERT: a 331 MET cc_start: 0.7005 (tmm) cc_final: 0.6654 (tmm) REVERT: c 331 MET cc_start: 0.7068 (mmp) cc_final: 0.6826 (mmp) outliers start: 37 outliers final: 23 residues processed: 200 average time/residue: 0.2474 time to fit residues: 66.7758 Evaluate side-chains 192 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 169 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 375 SER Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 323 GLN Chi-restraints excluded: chain b residue 348 LEU Chi-restraints excluded: chain b residue 375 SER Chi-restraints excluded: chain b residue 398 PHE Chi-restraints excluded: chain c residue 295 THR Chi-restraints excluded: chain c residue 322 ILE Chi-restraints excluded: chain c residue 375 SER Chi-restraints excluded: chain c residue 398 PHE Chi-restraints excluded: chain c residue 420 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 1 optimal weight: 0.0050 chunk 75 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 HIS C 140 HIS C 178 HIS ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10158 Z= 0.237 Angle : 0.786 11.609 13755 Z= 0.367 Chirality : 0.049 0.353 1812 Planarity : 0.004 0.041 1596 Dihedral : 10.540 63.963 3228 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.15 % Favored : 90.57 % Rotamer: Outliers : 3.42 % Allowed : 15.73 % Favored : 80.85 % 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: -0.67 (0.26), residues: 1071 helix: 0.30 (0.26), residues: 414 sheet: 1.94 (0.52), residues: 96 loop : -1.50 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 263 HIS 0.009 0.001 HIS C 178 PHE 0.016 0.002 PHE b 398 TYR 0.013 0.001 TYR C 65 ARG 0.009 0.001 ARG b 421 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 180 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 303 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7517 (ttpp) REVERT: a 331 MET cc_start: 0.6927 (tmm) cc_final: 0.6600 (tmm) REVERT: C 191 MET cc_start: 0.8220 (mmm) cc_final: 0.8011 (tpt) outliers start: 33 outliers final: 22 residues processed: 203 average time/residue: 0.2339 time to fit residues: 64.4806 Evaluate side-chains 190 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 167 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 303 LYS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 375 SER Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 323 GLN Chi-restraints excluded: chain b residue 332 SER Chi-restraints excluded: chain b residue 375 SER Chi-restraints excluded: chain b residue 398 PHE Chi-restraints excluded: chain c residue 295 THR Chi-restraints excluded: chain c residue 322 ILE Chi-restraints excluded: chain c residue 344 ILE Chi-restraints excluded: chain c residue 375 SER Chi-restraints excluded: chain c residue 398 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.0980 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 10158 Z= 0.318 Angle : 0.815 11.566 13755 Z= 0.383 Chirality : 0.051 0.348 1812 Planarity : 0.004 0.039 1596 Dihedral : 9.984 61.762 3228 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.43 % Favored : 90.29 % Rotamer: Outliers : 4.24 % Allowed : 16.25 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.26), residues: 1071 helix: 0.25 (0.26), residues: 417 sheet: 1.53 (0.51), residues: 96 loop : -1.59 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 263 HIS 0.007 0.002 HIS C 169 PHE 0.016 0.002 PHE b 398 TYR 0.012 0.002 TYR C 65 ARG 0.012 0.001 ARG c 421 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 178 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 303 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7565 (ttpp) REVERT: a 331 MET cc_start: 0.7176 (tmm) cc_final: 0.6825 (tmm) REVERT: C 150 GLU cc_start: 0.8040 (pm20) cc_final: 0.7484 (tm-30) outliers start: 41 outliers final: 29 residues processed: 202 average time/residue: 0.2324 time to fit residues: 64.0172 Evaluate side-chains 196 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 166 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 303 LYS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 375 SER Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain a residue 420 ASP Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 323 GLN Chi-restraints excluded: chain b residue 332 SER Chi-restraints excluded: chain b residue 348 LEU Chi-restraints excluded: chain b residue 375 SER Chi-restraints excluded: chain b residue 398 PHE Chi-restraints excluded: chain c residue 295 THR Chi-restraints excluded: chain c residue 304 HIS Chi-restraints excluded: chain c residue 322 ILE Chi-restraints excluded: chain c residue 375 SER Chi-restraints excluded: chain c residue 398 PHE Chi-restraints excluded: chain c residue 420 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 0.0040 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 46 optimal weight: 30.0000 chunk 62 optimal weight: 3.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10158 Z= 0.271 Angle : 0.799 11.461 13755 Z= 0.375 Chirality : 0.050 0.348 1812 Planarity : 0.004 0.039 1596 Dihedral : 9.591 59.109 3228 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.06 % Favored : 90.66 % Rotamer: Outliers : 3.62 % Allowed : 17.60 % Favored : 78.78 % 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: -0.80 (0.26), residues: 1071 helix: 0.41 (0.27), residues: 417 sheet: 0.96 (0.51), residues: 114 loop : -1.67 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 263 HIS 0.005 0.001 HIS A 123 PHE 0.015 0.001 PHE b 398 TYR 0.018 0.001 TYR C 65 ARG 0.007 0.001 ARG B 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 182 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: a 303 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7627 (ttpp) REVERT: a 331 MET cc_start: 0.7169 (tmm) cc_final: 0.6837 (tmm) REVERT: C 150 GLU cc_start: 0.7975 (pm20) cc_final: 0.7334 (tm-30) outliers start: 35 outliers final: 28 residues processed: 199 average time/residue: 0.2431 time to fit residues: 65.6866 Evaluate side-chains 199 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 170 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 303 LYS Chi-restraints excluded: chain a residue 304 HIS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 332 SER Chi-restraints excluded: chain a residue 375 SER Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 323 GLN Chi-restraints excluded: chain b residue 332 SER Chi-restraints excluded: chain b residue 348 LEU Chi-restraints excluded: chain b residue 375 SER Chi-restraints excluded: chain b residue 398 PHE Chi-restraints excluded: chain c residue 295 THR Chi-restraints excluded: chain c residue 304 HIS Chi-restraints excluded: chain c residue 322 ILE Chi-restraints excluded: chain c residue 344 ILE Chi-restraints excluded: chain c residue 375 SER Chi-restraints excluded: chain c residue 398 PHE Chi-restraints excluded: chain c residue 420 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 HIS ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10158 Z= 0.210 Angle : 0.781 11.344 13755 Z= 0.366 Chirality : 0.049 0.345 1812 Planarity : 0.004 0.055 1596 Dihedral : 9.193 55.860 3228 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.59 % Favored : 91.13 % Rotamer: Outliers : 3.52 % Allowed : 17.81 % Favored : 78.67 % 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: -0.76 (0.26), residues: 1071 helix: 0.55 (0.27), residues: 417 sheet: 1.36 (0.53), residues: 96 loop : -1.75 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 263 HIS 0.004 0.001 HIS A 123 PHE 0.016 0.001 PHE b 398 TYR 0.017 0.001 TYR C 65 ARG 0.007 0.001 ARG B 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 178 time to evaluate : 1.021 Fit side-chains REVERT: a 303 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7565 (ttpp) REVERT: a 331 MET cc_start: 0.7128 (tmm) cc_final: 0.6871 (tmm) REVERT: C 150 GLU cc_start: 0.7926 (pm20) cc_final: 0.7300 (tm-30) REVERT: c 326 LYS cc_start: 0.7641 (tppt) cc_final: 0.7234 (tppt) outliers start: 34 outliers final: 25 residues processed: 198 average time/residue: 0.2444 time to fit residues: 65.8156 Evaluate side-chains 191 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 165 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 303 LYS Chi-restraints excluded: chain a residue 304 HIS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 341 ASN Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain a residue 375 SER Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 323 GLN Chi-restraints excluded: chain b residue 332 SER Chi-restraints excluded: chain b residue 348 LEU Chi-restraints excluded: chain b residue 375 SER Chi-restraints excluded: chain b residue 398 PHE Chi-restraints excluded: chain c residue 295 THR Chi-restraints excluded: chain c residue 304 HIS Chi-restraints excluded: chain c residue 344 ILE Chi-restraints excluded: chain c residue 375 SER Chi-restraints excluded: chain c residue 398 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 10158 Z= 0.226 Angle : 0.822 15.383 13755 Z= 0.389 Chirality : 0.050 0.340 1812 Planarity : 0.004 0.040 1596 Dihedral : 8.912 53.334 3228 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.03 % Favored : 91.69 % Rotamer: Outliers : 2.80 % Allowed : 18.63 % Favored : 78.57 % 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: -0.78 (0.26), residues: 1071 helix: 0.55 (0.26), residues: 417 sheet: 1.40 (0.53), residues: 96 loop : -1.79 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 263 HIS 0.004 0.001 HIS A 123 PHE 0.030 0.002 PHE C 116 TYR 0.019 0.001 TYR B 65 ARG 0.008 0.001 ARG a 421 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 174 time to evaluate : 1.167 Fit side-chains revert: symmetry clash REVERT: a 303 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7573 (ttpp) REVERT: a 331 MET cc_start: 0.7008 (tmm) cc_final: 0.6751 (tmm) REVERT: B 150 GLU cc_start: 0.7830 (pm20) cc_final: 0.7491 (tm-30) REVERT: C 150 GLU cc_start: 0.7905 (pm20) cc_final: 0.7287 (tm-30) REVERT: b 316 ASP cc_start: 0.8167 (t70) cc_final: 0.7926 (t0) outliers start: 27 outliers final: 22 residues processed: 191 average time/residue: 0.2359 time to fit residues: 61.5015 Evaluate side-chains 189 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 166 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 303 LYS Chi-restraints excluded: chain a residue 304 HIS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 341 ASN Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain a residue 375 SER Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain b residue 323 GLN Chi-restraints excluded: chain b residue 348 LEU Chi-restraints excluded: chain b residue 375 SER Chi-restraints excluded: chain c residue 295 THR Chi-restraints excluded: chain c residue 304 HIS Chi-restraints excluded: chain c residue 332 SER Chi-restraints excluded: chain c residue 344 ILE Chi-restraints excluded: chain c residue 375 SER Chi-restraints excluded: chain c residue 398 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 404 GLN ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 373 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.5636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.121 10158 Z= 0.432 Angle : 0.924 20.503 13755 Z= 0.437 Chirality : 0.053 0.347 1812 Planarity : 0.005 0.040 1596 Dihedral : 9.169 55.733 3228 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.71 % Favored : 89.92 % Rotamer: Outliers : 3.00 % Allowed : 18.84 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.25), residues: 1071 helix: 0.29 (0.26), residues: 414 sheet: 0.43 (0.51), residues: 114 loop : -1.91 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 385 HIS 0.006 0.002 HIS b 397 PHE 0.017 0.002 PHE c 398 TYR 0.023 0.002 TYR B 65 ARG 0.010 0.001 ARG A 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 1.075 Fit side-chains REVERT: A 59 LEU cc_start: 0.6513 (tt) cc_final: 0.6050 (tt) REVERT: B 150 GLU cc_start: 0.8068 (pm20) cc_final: 0.7594 (tm-30) REVERT: C 150 GLU cc_start: 0.8022 (pm20) cc_final: 0.7380 (tm-30) REVERT: c 398 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.5948 (m-80) outliers start: 29 outliers final: 22 residues processed: 180 average time/residue: 0.2394 time to fit residues: 58.8341 Evaluate side-chains 184 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 304 HIS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 341 ASN Chi-restraints excluded: chain a residue 375 SER Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 323 GLN Chi-restraints excluded: chain b residue 348 LEU Chi-restraints excluded: chain b residue 375 SER Chi-restraints excluded: chain b residue 398 PHE Chi-restraints excluded: chain b residue 420 ASP Chi-restraints excluded: chain c residue 295 THR Chi-restraints excluded: chain c residue 304 HIS Chi-restraints excluded: chain c residue 332 SER Chi-restraints excluded: chain c residue 398 PHE Chi-restraints excluded: chain c residue 400 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 83 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.087876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.061725 restraints weight = 28591.533| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 4.46 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.5746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 10158 Z= 0.244 Angle : 0.864 18.690 13755 Z= 0.404 Chirality : 0.050 0.340 1812 Planarity : 0.004 0.042 1596 Dihedral : 8.749 52.933 3228 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.31 % Favored : 91.32 % Rotamer: Outliers : 2.07 % Allowed : 19.57 % Favored : 78.36 % 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: -0.99 (0.26), residues: 1071 helix: 0.49 (0.26), residues: 414 sheet: 0.48 (0.51), residues: 114 loop : -1.90 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP c 263 HIS 0.005 0.001 HIS c 373 PHE 0.014 0.001 PHE b 398 TYR 0.019 0.001 TYR B 65 ARG 0.008 0.001 ARG A 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2186.97 seconds wall clock time: 40 minutes 39.78 seconds (2439.78 seconds total)