Starting phenix.real_space_refine on Thu Mar 14 18:16:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eje_28179/03_2024/8eje_28179.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eje_28179/03_2024/8eje_28179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eje_28179/03_2024/8eje_28179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eje_28179/03_2024/8eje_28179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eje_28179/03_2024/8eje_28179.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eje_28179/03_2024/8eje_28179.pdb" } resolution = 3.69 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= 0.026 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 87 5.16 5 C 5892 2.51 5 N 1497 2.21 5 O 1950 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 TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 310": "OD1" <-> "OD2" Residue "a TYR 362": "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 "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 310": "OD1" <-> "OD2" 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 "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 310": "OD1" <-> "OD2" Residue "c TYR 362": "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" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9426 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1538 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 4, 'TRANS': 190} Chain: "a" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1308 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 4, 'TRANS': 156} Chain: "B" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1538 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 4, 'TRANS': 190} Chain: "b" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1308 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 4, 'TRANS': 156} Chain: "C" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1538 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 4, 'TRANS': 190} Chain: "c" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1308 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 4, 'TRANS': 156} Chain: "D" 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 5.37, per 1000 atoms: 0.57 Number of scatterers: 9426 At special positions: 0 Unit cell: (93.005, 91.96, 100.32, 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 87 16.00 O 1950 8.00 N 1497 7.00 C 5892 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=2.03 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 154 " distance=2.03 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=2.06 Simple disulfide: pdb=" SG CYS a 278 " - pdb=" SG CYS a 291 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 154 " distance=2.03 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=2.06 Simple disulfide: pdb=" SG CYS b 278 " - pdb=" SG CYS b 291 " distance=2.04 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 85 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 154 " distance=2.03 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 211 " distance=2.03 Simple disulfide: pdb=" SG CYS C 206 " - pdb=" SG CYS c 359 " distance=2.06 Simple disulfide: pdb=" SG CYS c 278 " - pdb=" SG CYS c 291 " distance=2.04 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 ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA P 3 " - " MAN P 4 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA P 3 " - " MAN P 5 " " BMA W 3 " - " MAN W 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A 301 " - " ASN A 98 " " NAG A 302 " - " ASN A 223 " " NAG B 301 " - " ASN B 98 " " NAG B 302 " - " ASN B 223 " " NAG C 301 " - " ASN C 98 " " NAG C 302 " - " ASN C 223 " " NAG D 1 " - " ASN A 78 " " NAG E 1 " - " ASN A 88 " " NAG F 1 " - " ASN A 108 " " NAG G 1 " - " ASN A 118 " " NAG H 1 " - " ASN A 166 " " NAG I 1 " - " ASN a 364 " " NAG J 1 " - " ASN a 372 " " NAG K 1 " - " ASN B 78 " " NAG L 1 " - " ASN B 88 " " NAG M 1 " - " ASN B 108 " " NAG N 1 " - " ASN B 118 " " NAG O 1 " - " ASN B 166 " " NAG P 1 " - " ASN b 364 " " NAG Q 1 " - " ASN b 372 " " NAG R 1 " - " ASN C 78 " " NAG S 1 " - " ASN C 88 " " NAG T 1 " - " ASN C 108 " " NAG U 1 " - " ASN C 118 " " NAG V 1 " - " ASN C 166 " " NAG W 1 " - " ASN c 364 " " NAG X 1 " - " ASN c 372 " " NAG a 501 " - " ASN a 394 " " NAG a 502 " - " ASN a 389 " " NAG b 501 " - " ASN b 394 " " NAG b 502 " - " ASN b 389 " " NAG c 501 " - " ASN c 394 " " NAG c 502 " - " ASN c 389 " Time building additional restraints: 4.44 Conformation dependent library (CDL) restraints added in 1.4 seconds 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 12 sheets defined 40.4% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'A' and resid 118 through 126 Processing helix chain 'A' and resid 129 through 142 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 171 through 178 Processing helix chain 'A' and resid 182 through 194 removed outlier: 3.733A pdb=" N ARG A 192 " --> pdb=" O GLN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 237 through 246 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 325 removed outlier: 3.805A pdb=" N ASP a 310 " --> pdb=" O GLU a 306 " (cutoff:3.500A) Processing helix chain 'a' and resid 333 through 344 removed outlier: 3.551A pdb=" N ASN a 341 " --> pdb=" O ASN a 337 " (cutoff:3.500A) Processing helix chain 'a' and resid 345 through 357 Processing helix chain 'a' and resid 358 through 360 No H-bonds generated for 'chain 'a' and resid 358 through 360' Processing helix chain 'a' and resid 398 through 415 Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 118 through 126 Processing helix chain 'B' and resid 129 through 142 Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 171 through 178 Processing helix chain 'B' and resid 182 through 194 removed outlier: 3.733A pdb=" N ARG B 192 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 237 through 246 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 325 removed outlier: 3.805A pdb=" N ASP b 310 " --> pdb=" O GLU b 306 " (cutoff:3.500A) Processing helix chain 'b' and resid 333 through 344 removed outlier: 3.551A pdb=" N ASN b 341 " --> pdb=" O ASN b 337 " (cutoff:3.500A) Processing helix chain 'b' and resid 345 through 357 Processing helix chain 'b' and resid 358 through 360 No H-bonds generated for 'chain 'b' and resid 358 through 360' Processing helix chain 'b' and resid 398 through 415 Processing helix chain 'C' and resid 73 through 78 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 129 through 142 Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 171 through 178 Processing helix chain 'C' and resid 182 through 194 removed outlier: 3.732A pdb=" N ARG C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'C' and resid 237 through 246 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 325 removed outlier: 3.805A pdb=" N ASP c 310 " --> pdb=" O GLU c 306 " (cutoff:3.500A) Processing helix chain 'c' and resid 333 through 344 removed outlier: 3.550A pdb=" N ASN c 341 " --> pdb=" O ASN c 337 " (cutoff:3.500A) Processing helix chain 'c' and resid 345 through 357 Processing helix chain 'c' and resid 358 through 360 No H-bonds generated for 'chain 'c' and resid 358 through 360' Processing helix chain 'c' and resid 398 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 71 Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 86 Processing sheet with id=AA3, first strand: chain 'a' and resid 277 through 279 Processing sheet with id=AA4, first strand: chain 'a' and resid 387 through 388 Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 71 Processing sheet with id=AA6, first strand: chain 'B' and resid 83 through 86 Processing sheet with id=AA7, first strand: chain 'b' and resid 277 through 279 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 65 through 71 Processing sheet with id=AB1, first strand: chain 'C' and resid 83 through 86 Processing sheet with id=AB2, first strand: chain 'c' and resid 277 through 279 Processing sheet with id=AB3, first strand: chain 'c' and resid 387 through 388 372 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: 2.60 Time building geometry restraints manager: 4.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 2322 1.33 - 1.47: 3215 1.47 - 1.62: 3946 1.62 - 1.77: 12 1.77 - 1.91: 123 Bond restraints: 9618 Sorted by residual: bond pdb=" CB ILE b 419 " pdb=" CG1 ILE b 419 " ideal model delta sigma weight residual 1.530 1.653 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" CB ILE a 419 " pdb=" CG1 ILE a 419 " ideal model delta sigma weight residual 1.530 1.653 -0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" CB ILE c 419 " pdb=" CG1 ILE c 419 " ideal model delta sigma weight residual 1.530 1.653 -0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" NE1 TRP b 385 " pdb=" CE2 TRP b 385 " ideal model delta sigma weight residual 1.370 1.304 0.066 1.10e-02 8.26e+03 3.61e+01 bond pdb=" NE1 TRP c 385 " pdb=" CE2 TRP c 385 " ideal model delta sigma weight residual 1.370 1.304 0.066 1.10e-02 8.26e+03 3.57e+01 ... (remaining 9613 not shown) Histogram of bond angle deviations from ideal: 97.94 - 110.54: 3381 110.54 - 123.15: 8781 123.15 - 135.75: 861 135.75 - 148.35: 0 148.35 - 160.95: 9 Bond angle restraints: 13032 Sorted by residual: angle pdb=" C2 NAG V 2 " pdb=" N2 NAG V 2 " pdb=" C7 NAG V 2 " ideal model delta sigma weight residual 124.56 160.95 -36.39 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG H 2 " pdb=" N2 NAG H 2 " pdb=" C7 NAG H 2 " ideal model delta sigma weight residual 124.56 160.94 -36.38 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG A 301 " pdb=" N2 NAG A 301 " pdb=" C7 NAG A 301 " ideal model delta sigma weight residual 124.56 160.94 -36.38 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG C 301 " pdb=" N2 NAG C 301 " pdb=" C7 NAG C 301 " ideal model delta sigma weight residual 124.56 160.93 -36.37 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG B 301 " pdb=" N2 NAG B 301 " pdb=" C7 NAG B 301 " ideal model delta sigma weight residual 124.56 160.93 -36.37 3.00e+00 1.11e-01 1.47e+02 ... (remaining 13027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.37: 6246 21.37 - 42.73: 226 42.73 - 64.10: 44 64.10 - 85.47: 45 85.47 - 106.83: 30 Dihedral angle restraints: 6591 sinusoidal: 3456 harmonic: 3135 Sorted by residual: dihedral pdb=" CA CYS B 117 " pdb=" CB CYS B 117 " pdb=" SG CYS B 117 " pdb=" SG CYS B 154 " ideal model delta sinusoidal sigma weight residual 79.00 13.37 65.63 1 2.00e+01 2.50e-03 1.41e+01 dihedral pdb=" CA CYS C 117 " pdb=" CB CYS C 117 " pdb=" SG CYS C 117 " pdb=" SG CYS C 154 " ideal model delta sinusoidal sigma weight residual 79.00 13.39 65.61 1 2.00e+01 2.50e-03 1.41e+01 dihedral pdb=" CA CYS A 117 " pdb=" CB CYS A 117 " pdb=" SG CYS A 117 " pdb=" SG CYS A 154 " ideal model delta sinusoidal sigma weight residual 79.00 13.42 65.58 1 2.00e+01 2.50e-03 1.41e+01 ... (remaining 6588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 1072 0.121 - 0.242: 359 0.242 - 0.363: 135 0.363 - 0.483: 51 0.483 - 0.604: 15 Chirality restraints: 1632 Sorted by residual: chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-02 2.50e+03 9.13e+02 chirality pdb=" C1 BMA R 3 " pdb=" O4 NAG R 2 " pdb=" C2 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-02 2.50e+03 9.13e+02 chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-02 2.50e+03 9.08e+02 ... (remaining 1629 not shown) Planarity restraints: 1590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " -0.226 2.00e-02 2.50e+03 1.85e-01 4.28e+02 pdb=" C7 NAG K 2 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " -0.163 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " 0.298 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.226 2.00e-02 2.50e+03 1.85e-01 4.28e+02 pdb=" C7 NAG D 2 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.163 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.298 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " 0.226 2.00e-02 2.50e+03 1.85e-01 4.28e+02 pdb=" C7 NAG R 2 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " 0.163 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " -0.298 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " -0.026 2.00e-02 2.50e+03 ... (remaining 1587 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2756 2.83 - 3.35: 9323 3.35 - 3.87: 15841 3.87 - 4.38: 19496 4.38 - 4.90: 30060 Nonbonded interactions: 77476 Sorted by model distance: nonbonded pdb=" N ALA B 201 " pdb=" N LEU B 202 " model vdw 2.317 2.560 nonbonded pdb=" N ALA A 201 " pdb=" N LEU A 202 " model vdw 2.317 2.560 nonbonded pdb=" N ALA C 201 " pdb=" N LEU C 202 " model vdw 2.317 2.560 nonbonded pdb=" O GLY B 207 " pdb=" C SER B 208 " model vdw 2.403 3.270 nonbonded pdb=" O GLY C 207 " pdb=" C SER C 208 " model vdw 2.403 3.270 ... (remaining 77471 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 'K' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'I' selection = chain 'P' selection = chain 'W' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 3.990 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.470 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.130 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 : 0.023 0.123 9618 Z= 1.470 Angle : 2.139 36.392 13032 Z= 1.262 Chirality : 0.155 0.604 1632 Planarity : 0.012 0.185 1557 Dihedral : 15.070 106.833 4512 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: -0.11 (0.24), residues: 1056 helix: -0.09 (0.24), residues: 339 sheet: 1.95 (0.48), residues: 99 loop : -0.34 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.005 TRP B 226 HIS 0.009 0.003 HIS C 140 PHE 0.025 0.006 PHE C 146 TYR 0.043 0.009 TYR B 218 ARG 0.006 0.001 ARG C 125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 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 316 ASP cc_start: 0.8681 (t70) cc_final: 0.8398 (t0) REVERT: a 350 MET cc_start: 0.9295 (mmm) cc_final: 0.9083 (tpp) REVERT: a 401 ASP cc_start: 0.8451 (m-30) cc_final: 0.8054 (m-30) REVERT: B 129 ASP cc_start: 0.8208 (t0) cc_final: 0.7996 (t0) REVERT: B 182 ILE cc_start: 0.8049 (mt) cc_final: 0.7778 (mp) REVERT: b 316 ASP cc_start: 0.8636 (t70) cc_final: 0.8306 (t0) REVERT: b 350 MET cc_start: 0.9260 (mmm) cc_final: 0.9051 (tpp) REVERT: b 401 ASP cc_start: 0.8477 (m-30) cc_final: 0.7988 (m-30) REVERT: C 129 ASP cc_start: 0.8023 (t0) cc_final: 0.7811 (t0) REVERT: C 193 MET cc_start: 0.7914 (tpp) cc_final: 0.7609 (tpp) REVERT: C 210 ASP cc_start: 0.6558 (p0) cc_final: 0.6077 (t0) REVERT: c 316 ASP cc_start: 0.8627 (t70) cc_final: 0.8389 (t0) REVERT: c 401 ASP cc_start: 0.8410 (m-30) cc_final: 0.8075 (m-30) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.2642 time to fit residues: 123.0480 Evaluate side-chains 195 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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: 0.7980 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 HIS ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 HIS c 330 GLN c 353 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 9618 Z= 0.305 Angle : 1.029 10.655 13032 Z= 0.526 Chirality : 0.056 0.293 1632 Planarity : 0.004 0.029 1557 Dihedral : 13.559 84.962 2514 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.10 % Allowed : 12.09 % Favored : 83.81 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.13 (0.25), residues: 1056 helix: 0.63 (0.27), residues: 336 sheet: 0.68 (0.43), residues: 144 loop : -0.70 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 195 HIS 0.021 0.002 HIS C 123 PHE 0.026 0.003 PHE A 116 TYR 0.022 0.002 TYR B 149 ARG 0.004 0.001 ARG C 125 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 240 time to evaluate : 1.059 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 171 TYR cc_start: 0.6992 (OUTLIER) cc_final: 0.5264 (p90) REVERT: a 291 CYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6806 (m) REVERT: B 129 ASP cc_start: 0.7952 (t0) cc_final: 0.7711 (m-30) REVERT: b 401 ASP cc_start: 0.8247 (m-30) cc_final: 0.7846 (m-30) REVERT: C 62 LYS cc_start: 0.8315 (mtmm) cc_final: 0.7051 (mtmm) REVERT: C 149 TYR cc_start: 0.6585 (m-80) cc_final: 0.5956 (m-10) REVERT: C 193 MET cc_start: 0.8138 (tpp) cc_final: 0.7682 (tpp) REVERT: c 323 ARG cc_start: 0.8556 (tpm170) cc_final: 0.8324 (tpm170) REVERT: c 401 ASP cc_start: 0.8298 (m-30) cc_final: 0.7873 (m-30) REVERT: c 409 MET cc_start: 0.6982 (mtp) cc_final: 0.6686 (mtp) outliers start: 39 outliers final: 24 residues processed: 263 average time/residue: 0.2467 time to fit residues: 86.1475 Evaluate side-chains 206 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 180 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 333 ILE Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 283 MET Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 357 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 0.0170 chunk 29 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 64 optimal weight: 0.3980 chunk 26 optimal weight: 0.2980 chunk 95 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 94 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN a 415 GLN ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN c 334 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 9618 Z= 0.261 Angle : 0.889 9.496 13032 Z= 0.450 Chirality : 0.052 0.286 1632 Planarity : 0.003 0.023 1557 Dihedral : 11.695 77.109 2514 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 5.57 % Allowed : 13.56 % Favored : 80.86 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.26), residues: 1056 helix: 0.67 (0.28), residues: 333 sheet: 0.20 (0.45), residues: 144 loop : -0.71 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 195 HIS 0.011 0.001 HIS B 123 PHE 0.015 0.002 PHE c 292 TYR 0.019 0.001 TYR C 149 ARG 0.006 0.001 ARG b 383 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 214 time to evaluate : 1.022 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: A 171 TYR cc_start: 0.7264 (OUTLIER) cc_final: 0.5500 (p90) REVERT: A 193 MET cc_start: 0.8310 (tpp) cc_final: 0.7856 (tpp) REVERT: a 262 THR cc_start: 0.9475 (OUTLIER) cc_final: 0.9231 (m) REVERT: a 291 CYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6764 (m) REVERT: B 74 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7913 (mtm) REVERT: b 262 THR cc_start: 0.9503 (OUTLIER) cc_final: 0.9274 (m) REVERT: b 306 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7941 (mm-30) REVERT: b 401 ASP cc_start: 0.8327 (m-30) cc_final: 0.7967 (m-30) REVERT: C 152 MET cc_start: 0.8269 (tmm) cc_final: 0.8009 (tmm) REVERT: C 230 CYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7390 (m) REVERT: c 356 ASP cc_start: 0.8216 (t0) cc_final: 0.8003 (t0) REVERT: c 401 ASP cc_start: 0.8243 (m-30) cc_final: 0.7943 (m-30) outliers start: 53 outliers final: 32 residues processed: 247 average time/residue: 0.2586 time to fit residues: 83.9420 Evaluate side-chains 213 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 175 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 283 MET Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 283 MET Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 0.1980 chunk 95 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 0.0020 chunk 27 optimal weight: 0.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 ASN c 404 GLN ** c 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9618 Z= 0.255 Angle : 0.841 9.209 13032 Z= 0.424 Chirality : 0.052 0.302 1632 Planarity : 0.003 0.041 1557 Dihedral : 10.785 70.379 2514 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 5.05 % Allowed : 15.14 % Favored : 79.81 % Cbeta Deviations : 0.10 % 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: -0.29 (0.26), residues: 1056 helix: 0.78 (0.28), residues: 336 sheet: 0.01 (0.44), residues: 144 loop : -0.81 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 195 HIS 0.007 0.001 HIS B 123 PHE 0.016 0.002 PHE c 292 TYR 0.021 0.001 TYR B 149 ARG 0.005 0.001 ARG b 383 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 191 time to evaluate : 1.310 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: A 95 MET cc_start: 0.7258 (ttt) cc_final: 0.6988 (ttt) REVERT: A 99 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7677 (mp0) REVERT: A 115 LYS cc_start: 0.8333 (mmtm) cc_final: 0.8066 (mmtm) REVERT: A 152 MET cc_start: 0.8285 (tmm) cc_final: 0.7959 (tmm) REVERT: A 171 TYR cc_start: 0.7180 (OUTLIER) cc_final: 0.5602 (p90) REVERT: A 199 TYR cc_start: 0.6603 (OUTLIER) cc_final: 0.5076 (m-80) REVERT: B 193 MET cc_start: 0.8296 (tpp) cc_final: 0.7292 (tpp) REVERT: b 401 ASP cc_start: 0.8360 (m-30) cc_final: 0.7980 (m-30) REVERT: b 409 MET cc_start: 0.7330 (mtp) cc_final: 0.7089 (mtp) REVERT: C 191 MET cc_start: 0.8308 (mmm) cc_final: 0.8010 (mmm) REVERT: c 356 ASP cc_start: 0.8244 (t0) cc_final: 0.7912 (t0) REVERT: c 401 ASP cc_start: 0.8389 (m-30) cc_final: 0.8100 (m-30) outliers start: 48 outliers final: 37 residues processed: 220 average time/residue: 0.2467 time to fit residues: 72.3068 Evaluate side-chains 204 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 165 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 283 MET Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 334 GLN Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 404 GLN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 405 GLN c 404 GLN ** c 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 9618 Z= 0.263 Angle : 0.826 12.917 13032 Z= 0.412 Chirality : 0.052 0.325 1632 Planarity : 0.003 0.028 1557 Dihedral : 10.330 65.512 2514 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.05 % Favored : 91.86 % Rotamer: Outliers : 5.47 % Allowed : 16.30 % Favored : 78.23 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.26), residues: 1056 helix: 0.95 (0.28), residues: 336 sheet: -0.12 (0.44), residues: 138 loop : -0.90 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 195 HIS 0.013 0.001 HIS B 123 PHE 0.015 0.002 PHE c 292 TYR 0.018 0.001 TYR B 149 ARG 0.007 0.001 ARG c 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 188 time to evaluate : 1.176 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: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8213 (mmtm) cc_final: 0.7916 (mmtm) REVERT: A 171 TYR cc_start: 0.7424 (OUTLIER) cc_final: 0.5922 (p90) REVERT: A 199 TYR cc_start: 0.6669 (OUTLIER) cc_final: 0.5134 (m-80) REVERT: a 262 THR cc_start: 0.9498 (OUTLIER) cc_final: 0.9269 (m) REVERT: a 356 ASP cc_start: 0.8198 (t0) cc_final: 0.7991 (t0) REVERT: b 352 ASN cc_start: 0.8857 (m-40) cc_final: 0.8514 (m-40) REVERT: b 401 ASP cc_start: 0.8372 (m-30) cc_final: 0.8016 (m-30) REVERT: C 191 MET cc_start: 0.8248 (mmm) cc_final: 0.7927 (mmm) REVERT: c 356 ASP cc_start: 0.8246 (t0) cc_final: 0.7889 (t0) REVERT: c 401 ASP cc_start: 0.8422 (m-30) cc_final: 0.8135 (m-30) outliers start: 52 outliers final: 35 residues processed: 223 average time/residue: 0.2489 time to fit residues: 73.8404 Evaluate side-chains 204 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 166 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 336 ILE Chi-restraints excluded: chain a residue 360 ILE Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 354 LEU Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** 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: 0.7879 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9618 Z= 0.248 Angle : 0.802 10.657 13032 Z= 0.399 Chirality : 0.051 0.333 1632 Planarity : 0.003 0.035 1557 Dihedral : 9.967 62.375 2514 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 5.68 % Allowed : 16.19 % Favored : 78.13 % Cbeta Deviations : 0.10 % 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: -0.25 (0.26), residues: 1056 helix: 1.19 (0.28), residues: 336 sheet: -0.18 (0.45), residues: 138 loop : -0.98 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 195 HIS 0.010 0.001 HIS B 91 PHE 0.014 0.002 PHE c 292 TYR 0.023 0.001 TYR B 149 ARG 0.007 0.001 ARG b 383 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 180 time to evaluate : 1.135 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.6006 (p90) REVERT: A 199 TYR cc_start: 0.6680 (OUTLIER) cc_final: 0.5201 (m-80) REVERT: a 356 ASP cc_start: 0.8197 (t0) cc_final: 0.7958 (t0) REVERT: B 193 MET cc_start: 0.8391 (tpp) cc_final: 0.8178 (tpp) REVERT: b 352 ASN cc_start: 0.8861 (m-40) cc_final: 0.8581 (m-40) REVERT: b 401 ASP cc_start: 0.8448 (m-30) cc_final: 0.8064 (m-30) REVERT: C 152 MET cc_start: 0.8236 (tmm) cc_final: 0.7796 (tmm) REVERT: C 191 MET cc_start: 0.8276 (mmm) cc_final: 0.7947 (mmm) REVERT: c 261 PHE cc_start: 0.8535 (m-80) cc_final: 0.8240 (m-10) REVERT: c 401 ASP cc_start: 0.8478 (m-30) cc_final: 0.8218 (m-30) outliers start: 54 outliers final: 40 residues processed: 221 average time/residue: 0.2498 time to fit residues: 73.8607 Evaluate side-chains 214 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 172 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 336 ILE Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 336 ILE Chi-restraints excluded: chain c residue 359 CYS Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 3.9990 chunk 11 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 46 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 404 GLN a 408 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.5751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9618 Z= 0.263 Angle : 0.812 13.458 13032 Z= 0.399 Chirality : 0.053 0.364 1632 Planarity : 0.003 0.031 1557 Dihedral : 9.875 60.404 2514 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 5.36 % Allowed : 17.77 % Favored : 76.87 % 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: -0.47 (0.26), residues: 1056 helix: 0.93 (0.27), residues: 357 sheet: -0.23 (0.44), residues: 144 loop : -1.18 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 195 HIS 0.008 0.001 HIS B 123 PHE 0.036 0.002 PHE A 116 TYR 0.019 0.001 TYR B 149 ARG 0.006 0.001 ARG a 383 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 175 time to evaluate : 1.146 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 171 TYR cc_start: 0.7438 (OUTLIER) cc_final: 0.5994 (p90) REVERT: a 356 ASP cc_start: 0.8195 (t0) cc_final: 0.7958 (t0) REVERT: b 261 PHE cc_start: 0.8548 (m-80) cc_final: 0.8230 (m-80) REVERT: b 352 ASN cc_start: 0.8856 (m-40) cc_final: 0.8525 (m-40) REVERT: b 401 ASP cc_start: 0.8457 (m-30) cc_final: 0.8090 (m-30) REVERT: C 148 GLN cc_start: 0.8171 (mm110) cc_final: 0.7944 (tm-30) REVERT: C 193 MET cc_start: 0.8197 (tpp) cc_final: 0.7478 (ttm) REVERT: c 261 PHE cc_start: 0.8599 (m-80) cc_final: 0.8347 (m-10) outliers start: 51 outliers final: 41 residues processed: 214 average time/residue: 0.2538 time to fit residues: 72.3371 Evaluate side-chains 200 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 158 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 336 ILE Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain a residue 360 ILE Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 299 LYS Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 336 ILE Chi-restraints excluded: chain c residue 341 ASN Chi-restraints excluded: chain c residue 359 CYS Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.0770 chunk 60 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 50 optimal weight: 0.1980 chunk 9 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 92 optimal weight: 0.1980 chunk 96 optimal weight: 0.8980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS ** a 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 353 HIS a 408 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 9618 Z= 0.240 Angle : 0.844 12.403 13032 Z= 0.415 Chirality : 0.053 0.346 1632 Planarity : 0.003 0.031 1557 Dihedral : 9.745 59.754 2514 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 3.89 % Allowed : 18.93 % Favored : 77.18 % 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: -0.56 (0.26), residues: 1056 helix: 0.79 (0.27), residues: 363 sheet: -0.21 (0.45), residues: 144 loop : -1.22 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 195 HIS 0.007 0.001 HIS B 123 PHE 0.039 0.002 PHE C 116 TYR 0.019 0.001 TYR B 149 ARG 0.008 0.001 ARG b 383 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 179 time to evaluate : 1.159 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: A 95 MET cc_start: 0.7234 (ttt) cc_final: 0.6933 (ttt) REVERT: A 171 TYR cc_start: 0.7509 (OUTLIER) cc_final: 0.5781 (p90) REVERT: A 193 MET cc_start: 0.8293 (tpp) cc_final: 0.7606 (ttm) REVERT: A 199 TYR cc_start: 0.6675 (OUTLIER) cc_final: 0.5188 (m-80) REVERT: a 356 ASP cc_start: 0.8081 (t0) cc_final: 0.7809 (t0) REVERT: B 193 MET cc_start: 0.8430 (tpp) cc_final: 0.7398 (tpp) REVERT: b 261 PHE cc_start: 0.8533 (m-80) cc_final: 0.8237 (m-80) REVERT: b 306 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8153 (mm-30) REVERT: b 352 ASN cc_start: 0.8768 (m-40) cc_final: 0.8445 (m-40) REVERT: b 401 ASP cc_start: 0.8415 (m-30) cc_final: 0.8023 (m-30) REVERT: C 148 GLN cc_start: 0.8107 (mm110) cc_final: 0.7889 (tm-30) outliers start: 37 outliers final: 25 residues processed: 206 average time/residue: 0.2524 time to fit residues: 68.9034 Evaluate side-chains 192 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 165 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 292 PHE Chi-restraints excluded: chain c residue 299 LYS Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 61 optimal weight: 0.0470 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS ** a 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 404 GLN ** c 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.6191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 9618 Z= 0.262 Angle : 0.872 15.000 13032 Z= 0.426 Chirality : 0.054 0.352 1632 Planarity : 0.003 0.032 1557 Dihedral : 9.858 59.026 2514 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 3.89 % Allowed : 18.51 % Favored : 77.60 % 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: -0.61 (0.26), residues: 1056 helix: 0.81 (0.28), residues: 363 sheet: -0.51 (0.43), residues: 153 loop : -1.23 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 195 HIS 0.006 0.001 HIS B 123 PHE 0.022 0.002 PHE B 116 TYR 0.020 0.001 TYR B 149 ARG 0.007 0.001 ARG b 383 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 186 time to evaluate : 1.075 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: A 171 TYR cc_start: 0.7529 (OUTLIER) cc_final: 0.5808 (p90) REVERT: A 199 TYR cc_start: 0.6683 (OUTLIER) cc_final: 0.5212 (m-80) REVERT: A 246 GLN cc_start: 0.7336 (tm-30) cc_final: 0.6934 (tm-30) REVERT: a 352 ASN cc_start: 0.8922 (m-40) cc_final: 0.8704 (m-40) REVERT: a 356 ASP cc_start: 0.8095 (t0) cc_final: 0.7841 (t0) REVERT: B 152 MET cc_start: 0.8216 (tmm) cc_final: 0.7993 (tmm) REVERT: B 191 MET cc_start: 0.8151 (mmt) cc_final: 0.7898 (mmt) REVERT: b 261 PHE cc_start: 0.8559 (m-80) cc_final: 0.8302 (m-80) REVERT: b 352 ASN cc_start: 0.8746 (m-40) cc_final: 0.8499 (m-40) REVERT: b 401 ASP cc_start: 0.8425 (m-30) cc_final: 0.8060 (m-30) REVERT: C 193 MET cc_start: 0.8051 (tpp) cc_final: 0.7414 (ttm) REVERT: c 404 GLN cc_start: 0.7931 (tp40) cc_final: 0.7359 (tp40) outliers start: 37 outliers final: 30 residues processed: 215 average time/residue: 0.2539 time to fit residues: 72.1288 Evaluate side-chains 201 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 169 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 336 ILE Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 341 ASN Chi-restraints excluded: chain c residue 359 CYS Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 96 optimal weight: 0.0980 chunk 83 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS ** a 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 HIS b 352 ASN ** c 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.6323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 9618 Z= 0.274 Angle : 0.885 14.249 13032 Z= 0.433 Chirality : 0.054 0.355 1632 Planarity : 0.003 0.033 1557 Dihedral : 9.858 59.736 2514 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.19 % Favored : 90.72 % Rotamer: Outliers : 3.47 % Allowed : 20.19 % Favored : 76.34 % 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: -0.55 (0.26), residues: 1056 helix: 0.86 (0.28), residues: 357 sheet: -0.18 (0.50), residues: 123 loop : -1.22 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 195 HIS 0.007 0.001 HIS B 123 PHE 0.037 0.002 PHE B 116 TYR 0.020 0.001 TYR B 149 ARG 0.009 0.001 ARG b 383 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 176 time to evaluate : 1.166 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: A 95 MET cc_start: 0.7316 (ttt) cc_final: 0.7041 (ttt) REVERT: A 171 TYR cc_start: 0.7482 (OUTLIER) cc_final: 0.5736 (p90) REVERT: A 193 MET cc_start: 0.8236 (tpp) cc_final: 0.7844 (ttm) REVERT: A 199 TYR cc_start: 0.6709 (OUTLIER) cc_final: 0.5227 (m-80) REVERT: A 246 GLN cc_start: 0.7411 (tm-30) cc_final: 0.6941 (tm-30) REVERT: a 358 MET cc_start: 0.8619 (mtm) cc_final: 0.8263 (ptp) REVERT: a 404 GLN cc_start: 0.7909 (tp-100) cc_final: 0.7486 (tp40) REVERT: B 152 MET cc_start: 0.8262 (tmm) cc_final: 0.8059 (tmm) REVERT: B 191 MET cc_start: 0.8138 (mmt) cc_final: 0.7878 (mmt) REVERT: B 193 MET cc_start: 0.8305 (tpp) cc_final: 0.7376 (tpp) REVERT: b 261 PHE cc_start: 0.8550 (m-80) cc_final: 0.8311 (m-80) REVERT: b 401 ASP cc_start: 0.8400 (m-30) cc_final: 0.7999 (m-30) REVERT: C 193 MET cc_start: 0.8068 (tpp) cc_final: 0.7413 (ttm) REVERT: c 404 GLN cc_start: 0.7981 (tp40) cc_final: 0.7642 (tp40) outliers start: 33 outliers final: 26 residues processed: 202 average time/residue: 0.2622 time to fit residues: 70.0762 Evaluate side-chains 201 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 173 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 334 GLN Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 341 ASN Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 0.0060 chunk 83 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS ** a 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 352 ASN ** c 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.124160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.098679 restraints weight = 18968.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.101620 restraints weight = 13340.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.103644 restraints weight = 10644.071| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.6464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9618 Z= 0.257 Angle : 0.855 11.756 13032 Z= 0.421 Chirality : 0.053 0.356 1632 Planarity : 0.003 0.041 1557 Dihedral : 9.750 58.676 2514 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.09 % Favored : 90.72 % Rotamer: Outliers : 3.58 % Allowed : 20.19 % Favored : 76.24 % 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: -0.52 (0.27), residues: 1056 helix: 0.90 (0.28), residues: 357 sheet: -0.15 (0.50), residues: 123 loop : -1.22 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 195 HIS 0.006 0.001 HIS B 123 PHE 0.032 0.002 PHE C 116 TYR 0.021 0.001 TYR B 149 ARG 0.008 0.001 ARG B 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2190.27 seconds wall clock time: 40 minutes 34.92 seconds (2434.92 seconds total)