Starting phenix.real_space_refine on Fri Jan 19 00:52:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejg_28181/01_2024/8ejg_28181.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejg_28181/01_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_28181/01_2024/8ejg_28181.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejg_28181/01_2024/8ejg_28181.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejg_28181/01_2024/8ejg_28181.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejg_28181/01_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-1.21-5211/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: 9 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: 9 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: 9 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: 9 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: 9 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: 9 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: 5.56, per 1000 atoms: 0.56 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: 5.80 Conformation dependent library (CDL) restraints added in 1.5 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: 0.98 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: 2.62 Time building geometry restraints manager: 6.01 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: 6471 21.44 - 42.88: 264 42.88 - 64.33: 79 64.33 - 85.77: 134 85.77 - 107.21: 84 Dihedral angle restraints: 7032 sinusoidal: 3858 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 7029 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: 0.490 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: 0.010 Extract box with map and model: 2.230 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 30.470 Find NCS groups from input model: 0.620 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: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.720 ------------------------------------------------------------------------------- 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 : 21.613 107.210 4929 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 : 1.080 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: 0.2787 time to fit residues: 117.3854 Evaluate side-chains 180 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS C 91 HIS b 304 HIS b 404 GLN c 304 HIS c 341 ASN c 347 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10158 Z= 0.281 Angle : 0.954 12.268 13755 Z= 0.451 Chirality : 0.055 0.388 1812 Planarity : 0.005 0.037 1596 Dihedral : 18.640 85.527 2886 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.26 % Favored : 93.18 % Rotamer: Outliers : 2.07 % Allowed : 12.63 % 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: -0.75 (0.25), residues: 1071 helix: -0.34 (0.25), residues: 426 sheet: 1.58 (0.50), residues: 120 loop : -1.10 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP c 263 HIS 0.006 0.002 HIS A 178 PHE 0.023 0.002 PHE b 261 TYR 0.021 0.002 TYR c 277 ARG 0.006 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 229 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 209 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 305 ASP cc_start: 0.6805 (p0) cc_final: 0.6572 (p0) REVERT: a 331 MET cc_start: 0.6652 (tmm) cc_final: 0.6168 (tmm) REVERT: b 305 ASP cc_start: 0.6684 (p0) cc_final: 0.6389 (p0) REVERT: c 305 ASP cc_start: 0.6886 (p0) cc_final: 0.6552 (p0) REVERT: c 331 MET cc_start: 0.6757 (mmp) cc_final: 0.6538 (mmp) outliers start: 20 outliers final: 12 residues processed: 225 average time/residue: 0.2392 time to fit residues: 73.2435 Evaluate side-chains 181 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 169 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 394 ASN 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 Chi-restraints excluded: chain c residue 394 ASN 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: 0.6980 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 76 optimal weight: 0.0770 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 341 ASN a 422 GLN B 178 HIS ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 341 ASN ** b 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 422 GLN c 422 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10158 Z= 0.236 Angle : 0.846 11.811 13755 Z= 0.391 Chirality : 0.052 0.389 1812 Planarity : 0.005 0.065 1596 Dihedral : 14.240 72.368 2886 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.66 % Favored : 91.78 % Rotamer: Outliers : 3.00 % Allowed : 13.77 % Favored : 83.23 % 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: -0.73 (0.25), residues: 1071 helix: 0.07 (0.26), residues: 414 sheet: 2.45 (0.52), residues: 96 loop : -1.49 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP a 263 HIS 0.007 0.001 HIS A 123 PHE 0.016 0.002 PHE b 398 TYR 0.014 0.001 TYR A 149 ARG 0.007 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 219 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 190 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: a 331 MET cc_start: 0.6685 (tmm) cc_final: 0.6186 (tmm) REVERT: C 191 MET cc_start: 0.8250 (mmm) cc_final: 0.7989 (tpt) REVERT: b 305 ASP cc_start: 0.6958 (p0) cc_final: 0.6707 (p0) REVERT: c 305 ASP cc_start: 0.7022 (p0) cc_final: 0.6695 (p0) outliers start: 29 outliers final: 15 residues processed: 211 average time/residue: 0.2385 time to fit residues: 68.7947 Evaluate side-chains 174 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 159 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 49 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS a 341 ASN ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** 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: 0.8096 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10158 Z= 0.350 Angle : 0.840 11.738 13755 Z= 0.391 Chirality : 0.052 0.403 1812 Planarity : 0.004 0.041 1596 Dihedral : 11.966 68.031 2886 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.52 % Favored : 90.20 % Rotamer: Outliers : 3.83 % Allowed : 15.53 % Favored : 80.64 % 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 (0.25), residues: 1071 helix: 0.09 (0.26), residues: 414 sheet: 2.14 (0.52), residues: 96 loop : -1.51 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP a 263 HIS 0.007 0.002 HIS A 123 PHE 0.018 0.002 PHE b 398 TYR 0.013 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 216 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 179 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 331 MET cc_start: 0.7010 (tmm) cc_final: 0.6573 (tmm) REVERT: C 213 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7537 (mmp) REVERT: c 331 MET cc_start: 0.6917 (mmp) cc_final: 0.6614 (mmp) outliers start: 37 outliers final: 25 residues processed: 200 average time/residue: 0.2416 time to fit residues: 65.8645 Evaluate side-chains 191 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 165 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 178 HIS 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 341 ASN 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 211 CYS Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain b residue 347 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 394 ASN 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: 1.9990 chunk 1 optimal weight: 0.1980 chunk 75 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- 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** A 178 HIS B 178 HIS ** C 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10158 Z= 0.257 Angle : 0.788 11.605 13755 Z= 0.368 Chirality : 0.050 0.349 1812 Planarity : 0.004 0.042 1596 Dihedral : 10.974 64.545 2886 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.24 % Favored : 90.48 % Rotamer: Outliers : 4.04 % Allowed : 15.53 % Favored : 80.43 % 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: -0.65 (0.26), residues: 1071 helix: 0.30 (0.27), residues: 414 sheet: 1.88 (0.51), residues: 96 loop : -1.46 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 263 HIS 0.014 0.002 HIS A 178 PHE 0.016 0.002 PHE b 398 TYR 0.015 0.001 TYR B 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 214 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 175 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 331 MET cc_start: 0.6971 (tmm) cc_final: 0.6536 (tmm) REVERT: C 191 MET cc_start: 0.8225 (mmm) cc_final: 0.8019 (tpt) outliers start: 39 outliers final: 26 residues processed: 198 average time/residue: 0.2348 time to fit residues: 63.6267 Evaluate side-chains 192 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 HIS 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 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 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 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 394 ASN Chi-restraints excluded: chain c residue 398 PHE Chi-restraints excluded: chain c residue 420 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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** ** A 184 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 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10158 Z= 0.340 Angle : 0.814 11.556 13755 Z= 0.381 Chirality : 0.051 0.350 1812 Planarity : 0.004 0.040 1596 Dihedral : 10.376 62.934 2886 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.80 % Favored : 89.92 % Rotamer: Outliers : 4.35 % Allowed : 16.25 % Favored : 79.40 % 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: -0.77 (0.25), residues: 1071 helix: 0.36 (0.27), residues: 408 sheet: 1.45 (0.51), residues: 96 loop : -1.58 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 263 HIS 0.030 0.002 HIS A 178 PHE 0.016 0.002 PHE b 398 TYR 0.016 0.002 TYR B 65 ARG 0.011 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 217 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 175 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 HIS cc_start: 0.7099 (p90) cc_final: 0.6894 (p90) REVERT: a 331 MET cc_start: 0.7098 (tmm) cc_final: 0.6715 (tmm) REVERT: C 150 GLU cc_start: 0.8036 (pm20) cc_final: 0.7454 (tm-30) outliers start: 42 outliers final: 31 residues processed: 198 average time/residue: 0.2378 time to fit residues: 64.0565 Evaluate side-chains 196 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 165 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 210 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 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 375 SER Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain a residue 404 GLN Chi-restraints excluded: chain B residue 121 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 211 CYS 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 394 ASN 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: 5.9990 chunk 11 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 63 optimal weight: 20.0000 chunk 61 optimal weight: 0.7980 chunk 46 optimal weight: 30.0000 chunk 62 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 334 GLN b 337 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10158 Z= 0.198 Angle : 0.781 11.411 13755 Z= 0.362 Chirality : 0.048 0.346 1812 Planarity : 0.004 0.040 1596 Dihedral : 9.590 57.513 2886 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.12 % Favored : 91.60 % Rotamer: Outliers : 3.62 % Allowed : 17.91 % Favored : 78.47 % 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: 0.46 (0.27), residues: 417 sheet: 1.48 (0.53), residues: 96 loop : -1.56 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 263 HIS 0.006 0.001 HIS C 169 PHE 0.015 0.001 PHE b 398 TYR 0.023 0.001 TYR B 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 214 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 179 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 HIS cc_start: 0.7165 (p90) cc_final: 0.6888 (p90) REVERT: a 331 MET cc_start: 0.7029 (tmm) cc_final: 0.6633 (tmm) REVERT: C 150 GLU cc_start: 0.7971 (pm20) cc_final: 0.7355 (tm-30) REVERT: b 330 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7812 (mm110) REVERT: c 338 LYS cc_start: 0.8892 (mptt) cc_final: 0.8687 (mtmm) outliers start: 35 outliers final: 22 residues processed: 198 average time/residue: 0.2425 time to fit residues: 65.2037 Evaluate side-chains 193 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 170 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 303 LYS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 332 SER 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 136 LEU 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 323 GLN Chi-restraints excluded: chain b residue 330 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 304 HIS Chi-restraints excluded: chain c residue 344 ILE Chi-restraints excluded: chain c residue 375 SER Chi-restraints excluded: chain c residue 394 ASN Chi-restraints excluded: chain c residue 398 PHE Chi-restraints excluded: chain c residue 400 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 10158 Z= 0.268 Angle : 0.816 12.695 13755 Z= 0.384 Chirality : 0.049 0.345 1812 Planarity : 0.004 0.040 1596 Dihedral : 9.332 55.996 2886 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.62 % Favored : 90.10 % Rotamer: Outliers : 3.42 % Allowed : 18.53 % Favored : 78.05 % 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: -0.70 (0.26), residues: 1071 helix: 0.47 (0.27), residues: 417 sheet: 0.93 (0.52), residues: 114 loop : -1.58 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 263 HIS 0.005 0.001 HIS C 169 PHE 0.018 0.002 PHE C 116 TYR 0.020 0.001 TYR B 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 211 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 178 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: a 331 MET cc_start: 0.7105 (tmm) cc_final: 0.6729 (tmm) REVERT: C 150 GLU cc_start: 0.7938 (pm20) cc_final: 0.7296 (tm-30) outliers start: 33 outliers final: 27 residues processed: 197 average time/residue: 0.2448 time to fit residues: 65.8394 Evaluate side-chains 195 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 168 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 210 ASP Chi-restraints excluded: chain A residue 211 CYS 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 a residue 398 PHE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 136 LEU 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 C residue 211 CYS 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 394 ASN Chi-restraints excluded: chain c residue 398 PHE Chi-restraints excluded: chain c residue 400 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS ** A 184 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 10158 Z= 0.241 Angle : 0.833 19.973 13755 Z= 0.389 Chirality : 0.049 0.342 1812 Planarity : 0.004 0.041 1596 Dihedral : 8.976 56.903 2886 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.03 % Favored : 91.69 % Rotamer: Outliers : 3.62 % Allowed : 18.22 % 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: -0.74 (0.26), residues: 1071 helix: 0.49 (0.26), residues: 417 sheet: 0.77 (0.53), residues: 114 loop : -1.61 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 263 HIS 0.009 0.001 HIS A 178 PHE 0.015 0.001 PHE b 398 TYR 0.023 0.001 TYR C 65 ARG 0.007 0.001 ARG B 192 *********************** 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 215 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 180 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: a 331 MET cc_start: 0.7119 (tmm) cc_final: 0.6872 (tmm) REVERT: C 150 GLU cc_start: 0.7894 (pm20) cc_final: 0.7336 (tm-30) REVERT: C 152 MET cc_start: 0.7984 (tmm) cc_final: 0.7649 (ttp) outliers start: 35 outliers final: 27 residues processed: 198 average time/residue: 0.2408 time to fit residues: 65.0094 Evaluate side-chains 193 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 166 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 CYS 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 136 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain b residue 295 THR 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 375 SER 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 394 ASN 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 99 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 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 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 10158 Z= 0.334 Angle : 0.876 17.607 13755 Z= 0.410 Chirality : 0.050 0.341 1812 Planarity : 0.004 0.042 1596 Dihedral : 8.997 58.360 2886 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.15 % Favored : 90.48 % Rotamer: Outliers : 3.11 % Allowed : 19.05 % Favored : 77.85 % 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: -0.92 (0.26), residues: 1071 helix: 0.37 (0.26), residues: 417 sheet: 0.58 (0.52), residues: 114 loop : -1.71 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 263 HIS 0.008 0.001 HIS A 178 PHE 0.015 0.002 PHE b 398 TYR 0.019 0.001 TYR C 65 ARG 0.008 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 197 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 167 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: a 331 MET cc_start: 0.7149 (tmm) cc_final: 0.6859 (tmm) REVERT: a 400 ASP cc_start: 0.7770 (p0) cc_final: 0.7467 (p0) REVERT: B 150 GLU cc_start: 0.8074 (pm20) cc_final: 0.7658 (tm-30) REVERT: C 150 GLU cc_start: 0.7915 (pm20) cc_final: 0.7357 (tm-30) REVERT: C 152 MET cc_start: 0.7964 (tmm) cc_final: 0.7500 (ttp) outliers start: 30 outliers final: 28 residues processed: 183 average time/residue: 0.2351 time to fit residues: 59.3073 Evaluate side-chains 195 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 332 SER 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 a residue 398 PHE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 96 VAL 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 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 394 ASN 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: 0.2980 chunk 25 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 334 GLN ** b 408 ASN ** 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 = 0.3737 r_free = 0.3737 target = 0.089621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.063663 restraints weight = 28145.076| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 4.40 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 10158 Z= 0.218 Angle : 0.830 16.166 13755 Z= 0.387 Chirality : 0.049 0.337 1812 Planarity : 0.004 0.042 1596 Dihedral : 8.587 57.492 2886 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.84 % Favored : 91.78 % Rotamer: Outliers : 2.80 % Allowed : 19.67 % Favored : 77.54 % 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: 0.58 (0.27), residues: 417 sheet: 0.74 (0.53), residues: 114 loop : -1.72 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP c 263 HIS 0.014 0.001 HIS A 178 PHE 0.017 0.001 PHE b 398 TYR 0.017 0.001 TYR c 418 ARG 0.008 0.001 ARG a 421 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2148.23 seconds wall clock time: 40 minutes 19.25 seconds (2419.25 seconds total)