Starting phenix.real_space_refine on Mon Apr 8 18:33:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t5c_41048/04_2024/8t5c_41048.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t5c_41048/04_2024/8t5c_41048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t5c_41048/04_2024/8t5c_41048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t5c_41048/04_2024/8t5c_41048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t5c_41048/04_2024/8t5c_41048.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t5c_41048/04_2024/8t5c_41048.pdb" } resolution = 4.7 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= 0.005 sd= 0.066 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 104 5.16 5 C 8835 2.51 5 N 2277 2.21 5 O 2973 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 130": "OD1" <-> "OD2" Residue "a ASP 317": "OD1" <-> "OD2" Residue "c ASP 357": "OD1" <-> "OD2" Residue "D ASP 54": "OD1" <-> "OD2" Residue "D ASP 98": "OD1" <-> "OD2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "E ASP 100": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14189 Number of models: 1 Model: "" Number of chains: 35 Chain: "B" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1581 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 197} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "b" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1282 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} Chain: "A" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1548 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 193} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "a" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1282 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} Chain: "C" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1599 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 4, 'TRANS': 197} Chain: "c" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1282 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} Chain: "D" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 906 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 928 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "L" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 851 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "E" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 928 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "I" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 851 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "F" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "N" 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: "O" 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: "P" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'MAN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "S" 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: "T" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.58, per 1000 atoms: 0.53 Number of scatterers: 14189 At special positions: 0 Unit cell: (109.752, 125.892, 139.88, 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 104 16.00 O 2973 8.00 N 2277 7.00 C 8835 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.04 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS a 326 " distance=2.03 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 326 " - pdb=" SG CYS C 207 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.03 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.02 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS c 326 " distance=2.03 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.04 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.03 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.02 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN F 4 " - " MAN F 5 " " MAN O 4 " - " MAN O 5 " ALPHA1-3 " BMA F 3 " - " MAN F 4 " " MAN F 6 " - " MAN F 7 " " BMA M 3 " - " MAN M 6 " " MAN M 4 " - " MAN M 5 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " " MAN P 1 " - " MAN P 2 " " BMA R 3 " - " MAN R 6 " " MAN R 4 " - " MAN R 5 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 6 " " BMA W 3 " - " MAN W 6 " " MAN W 4 " - " MAN W 5 " ALPHA1-6 " BMA F 3 " - " MAN F 6 " " MAN F 6 " - " MAN F 8 " " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 5 " " MAN P 1 " - " MAN P 3 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 5 " " BMA T 3 " - " MAN T 4 " " MAN T 4 " - " MAN T 5 " " BMA W 3 " - " MAN W 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG J 1 " - " BMA J 2 " " NAG K 1 " - " BMA K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " BMA V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG A 301 " - " ASN A 99 " " NAG A 302 " - " ASN A 167 " " NAG A 303 " - " ASN A 224 " " NAG A 304 " - " ASN A 90 " " NAG A 305 " - " ASN A 109 " " NAG B 301 " - " ASN B 99 " " NAG B 302 " - " ASN B 224 " " NAG B 303 " - " ASN B 90 " " NAG B 304 " - " ASN B 109 " " NAG B 305 " - " ASN B 167 " " NAG C 301 " - " ASN C 99 " " NAG C 302 " - " ASN C 224 " " NAG C 303 " - " ASN C 90 " " NAG C 304 " - " ASN C 109 " " NAG C 305 " - " ASN C 167 " " NAG F 1 " - " ASN B 79 " " NAG G 1 " - " ASN B 119 " " NAG I 201 " - " ASN I 72 " " NAG L 201 " - " ASN L 72 " " NAG M 1 " - " ASN b 365 " " NAG N 1 " - " ASN b 373 " " NAG O 1 " - " ASN A 79 " " NAG Q 1 " - " ASN A 119 " " NAG R 1 " - " ASN a 365 " " NAG S 1 " - " ASN a 373 " " NAG T 1 " - " ASN C 79 " " NAG U 1 " - " ASN C 119 " " NAG W 1 " - " ASN c 365 " " NAG X 1 " - " ASN c 373 " " NAG a 501 " - " ASN a 390 " " NAG a 502 " - " ASN a 395 " " NAG b 501 " - " ASN b 390 " " NAG b 502 " - " ASN b 395 " " NAG c 501 " - " ASN c 390 " " NAG c 502 " - " ASN c 395 " Time building additional restraints: 6.71 Conformation dependent library (CDL) restraints added in 2.4 seconds 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3058 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 23 sheets defined 22.2% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'B' and resid 120 through 127 Processing helix chain 'B' and resid 131 through 143 removed outlier: 4.077A pdb=" N SER B 135 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 195 removed outlier: 3.531A pdb=" N ARG B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 249 removed outlier: 3.820A pdb=" N LEU B 244 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing helix chain 'b' and resid 294 through 303 removed outlier: 3.926A pdb=" N LYS b 300 " --> pdb=" O THR b 296 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N CYS b 301 " --> pdb=" O ALA b 297 " (cutoff:3.500A) Processing helix chain 'b' and resid 307 through 324 removed outlier: 3.713A pdb=" N ASP b 311 " --> pdb=" O GLU b 307 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN b 319 " --> pdb=" O LEU b 315 " (cutoff:3.500A) Processing helix chain 'b' and resid 334 through 340 removed outlier: 4.257A pdb=" N ASN b 338 " --> pdb=" O ILE b 334 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS b 339 " --> pdb=" O GLN b 335 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA b 340 " --> pdb=" O LEU b 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 334 through 340' Processing helix chain 'b' and resid 340 through 345 removed outlier: 3.979A pdb=" N ILE b 345 " --> pdb=" O VAL b 341 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 360 removed outlier: 3.610A pdb=" N MET b 351 " --> pdb=" O ASP b 347 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE b 358 " --> pdb=" O HIS b 354 " (cutoff:3.500A) Processing helix chain 'b' and resid 399 through 418 removed outlier: 3.584A pdb=" N ILE b 411 " --> pdb=" O ALA b 407 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN b 416 " --> pdb=" O THR b 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 removed outlier: 3.738A pdb=" N HIS A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 143 removed outlier: 3.748A pdb=" N HIS A 141 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 195 removed outlier: 3.787A pdb=" N LEU A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.550A pdb=" N LEU A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'a' and resid 281 through 285 Processing helix chain 'a' and resid 294 through 305 removed outlier: 3.698A pdb=" N VAL a 298 " --> pdb=" O GLY a 294 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N CYS a 301 " --> pdb=" O ALA a 297 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASN a 302 " --> pdb=" O VAL a 298 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU a 303 " --> pdb=" O ALA a 299 " (cutoff:3.500A) Processing helix chain 'a' and resid 307 through 325 removed outlier: 3.984A pdb=" N ARG a 325 " --> pdb=" O GLN a 321 " (cutoff:3.500A) Processing helix chain 'a' and resid 335 through 339 removed outlier: 3.889A pdb=" N LYS a 339 " --> pdb=" O LEU a 336 " (cutoff:3.500A) Processing helix chain 'a' and resid 340 through 345 Processing helix chain 'a' and resid 346 through 354 removed outlier: 3.526A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 399 through 418 removed outlier: 3.569A pdb=" N ILE a 403 " --> pdb=" O PHE a 399 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE a 411 " --> pdb=" O ALA a 407 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN a 416 " --> pdb=" O THR a 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 124 Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 134 through 143 Processing helix chain 'C' and resid 171 through 175 removed outlier: 3.579A pdb=" N GLY C 174 " --> pdb=" O SER C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 195 removed outlier: 3.625A pdb=" N MET C 192 " --> pdb=" O LEU C 188 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG C 193 " --> pdb=" O GLN C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.710A pdb=" N LEU C 244 " --> pdb=" O GLY C 240 " (cutoff:3.500A) Processing helix chain 'c' and resid 281 through 285 removed outlier: 3.533A pdb=" N MET c 284 " --> pdb=" O THR c 281 " (cutoff:3.500A) Processing helix chain 'c' and resid 299 through 303 Processing helix chain 'c' and resid 307 through 323 Processing helix chain 'c' and resid 333 through 339 removed outlier: 3.870A pdb=" N ILE c 337 " --> pdb=" O SER c 333 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS c 339 " --> pdb=" O GLN c 335 " (cutoff:3.500A) Processing helix chain 'c' and resid 340 through 345 removed outlier: 3.597A pdb=" N LEU c 344 " --> pdb=" O ALA c 340 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE c 345 " --> pdb=" O VAL c 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 340 through 345' Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.516A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS c 354 " --> pdb=" O ILE c 350 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N MET c 359 " --> pdb=" O LEU c 355 " (cutoff:3.500A) Processing helix chain 'c' and resid 399 through 418 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.514A pdb=" N THR E 87 " --> pdb=" O ALA E 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 285 through 286 removed outlier: 4.423A pdb=" N GLU B 72 " --> pdb=" O ILE b 286 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP b 370 " --> pdb=" O LYS b 384 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 84 through 87 Processing sheet with id=AA3, first strand: chain 'B' and resid 106 through 108 Processing sheet with id=AA4, first strand: chain 'b' and resid 279 through 280 removed outlier: 3.920A pdb=" N LEU b 280 " --> pdb=" O LYS b 291 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS b 291 " --> pdb=" O LEU b 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 61 through 62 removed outlier: 3.791A pdb=" N TYR A 62 " --> pdb=" O TYR A 66 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR A 66 " --> pdb=" O TYR A 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA7, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AA8, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AA9, first strand: chain 'C' and resid 84 through 86 removed outlier: 3.633A pdb=" N VAL C 97 " --> pdb=" O THR C 101 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 106 through 108 removed outlier: 3.612A pdb=" N LEU C 220 " --> pdb=" O TYR C 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 279 through 280 removed outlier: 3.625A pdb=" N LYS c 291 " --> pdb=" O LEU c 280 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 6 through 7 removed outlier: 3.526A pdb=" N LEU D 18 " --> pdb=" O MET D 83 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN D 82 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.837A pdb=" N THR D 109 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL D 111 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA D 92 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.255A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER H 7 " --> pdb=" O THR H 21 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 46 through 52 removed outlier: 6.209A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER H 94 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 46 through 52 removed outlier: 6.209A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 4 through 5 removed outlier: 4.047A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.587A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 3 through 7 removed outlier: 4.275A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.820A pdb=" N VAL E 12 " --> pdb=" O PRO E 108 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N THR E 110 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR E 107 " --> pdb=" O TYR E 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.850A pdb=" N GLU E 46 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG E 38 " --> pdb=" O GLU E 46 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 19 through 24 removed outlier: 3.617A pdb=" N ALA I 19 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE I 75 " --> pdb=" O ALA I 19 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 53 through 54 removed outlier: 5.321A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 906 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: 3.58 Time building geometry restraints manager: 7.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4322 1.34 - 1.46: 3863 1.46 - 1.58: 6143 1.58 - 1.71: 0 1.71 - 1.83: 156 Bond restraints: 14484 Sorted by residual: bond pdb=" C6 BMA T 3 " pdb=" O6 BMA T 3 " ideal model delta sigma weight residual 1.411 1.469 -0.058 2.00e-02 2.50e+03 8.39e+00 bond pdb=" C2 MAN O 4 " pdb=" O2 MAN O 4 " ideal model delta sigma weight residual 1.407 1.462 -0.055 2.00e-02 2.50e+03 7.55e+00 bond pdb=" C1 BMA K 2 " pdb=" C2 BMA K 2 " ideal model delta sigma weight residual 1.519 1.573 -0.054 2.00e-02 2.50e+03 7.41e+00 bond pdb=" N HIS b 374 " pdb=" CA HIS b 374 " ideal model delta sigma weight residual 1.462 1.496 -0.035 1.46e-02 4.69e+03 5.62e+00 bond pdb=" C3 BMA N 3 " pdb=" O3 BMA N 3 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.53e+00 ... (remaining 14479 not shown) Histogram of bond angle deviations from ideal: 99.99 - 106.80: 387 106.80 - 113.61: 8384 113.61 - 120.41: 5038 120.41 - 127.22: 5651 127.22 - 134.02: 166 Bond angle restraints: 19626 Sorted by residual: angle pdb=" CA CYS a 292 " pdb=" CB CYS a 292 " pdb=" SG CYS a 292 " ideal model delta sigma weight residual 114.40 129.62 -15.22 2.30e+00 1.89e-01 4.38e+01 angle pdb=" CA THR b 375 " pdb=" C THR b 375 " pdb=" O THR b 375 " ideal model delta sigma weight residual 120.96 115.34 5.62 1.09e+00 8.42e-01 2.66e+01 angle pdb=" C THR b 375 " pdb=" CA THR b 375 " pdb=" CB THR b 375 " ideal model delta sigma weight residual 109.84 116.61 -6.77 1.50e+00 4.44e-01 2.04e+01 angle pdb=" N ILE E 54 " pdb=" CA ILE E 54 " pdb=" C ILE E 54 " ideal model delta sigma weight residual 113.20 109.41 3.79 9.60e-01 1.09e+00 1.55e+01 angle pdb=" C HIS b 374 " pdb=" CA HIS b 374 " pdb=" CB HIS b 374 " ideal model delta sigma weight residual 111.41 105.55 5.86 1.70e+00 3.46e-01 1.19e+01 ... (remaining 19621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.12: 8916 24.12 - 48.24: 584 48.24 - 72.36: 86 72.36 - 96.49: 108 96.49 - 120.61: 75 Dihedral angle restraints: 9769 sinusoidal: 4987 harmonic: 4782 Sorted by residual: dihedral pdb=" CB CYS b 326 " pdb=" SG CYS b 326 " pdb=" SG CYS C 207 " pdb=" CB CYS C 207 " ideal model delta sinusoidal sigma weight residual 93.00 166.94 -73.94 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS B 180 " pdb=" SG CYS B 180 " pdb=" SG CYS B 212 " pdb=" CB CYS B 212 " ideal model delta sinusoidal sigma weight residual -86.00 -27.61 -58.39 1 1.00e+01 1.00e-02 4.57e+01 dihedral pdb=" CB CYS a 364 " pdb=" SG CYS a 364 " pdb=" SG CYS a 385 " pdb=" CB CYS a 385 " ideal model delta sinusoidal sigma weight residual -86.00 -140.89 54.89 1 1.00e+01 1.00e-02 4.08e+01 ... (remaining 9766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2130 0.073 - 0.147: 248 0.147 - 0.220: 14 0.220 - 0.294: 20 0.294 - 0.367: 3 Chirality restraints: 2415 Sorted by residual: chirality pdb=" C1 NAG B 303 " pdb=" ND2 ASN B 90 " pdb=" C2 NAG B 303 " pdb=" O5 NAG B 303 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.59 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 2412 not shown) Planarity restraints: 2394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG b 379 " -0.653 9.50e-02 1.11e+02 2.93e-01 5.23e+01 pdb=" NE ARG b 379 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG b 379 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG b 379 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG b 379 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP L 94 " 0.041 5.00e-02 4.00e+02 6.27e-02 6.30e+00 pdb=" N PRO L 95 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE a 361 " 0.038 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO a 362 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO a 362 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO a 362 " 0.032 5.00e-02 4.00e+02 ... (remaining 2391 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 222 2.61 - 3.19: 13550 3.19 - 3.76: 20846 3.76 - 4.33: 28942 4.33 - 4.90: 46350 Nonbonded interactions: 109910 Sorted by model distance: nonbonded pdb=" O ALA I 25 " pdb=" OG1 THR I 69 " model vdw 2.044 2.440 nonbonded pdb=" O SER L 20 " pdb=" O6 NAG L 201 " model vdw 2.070 2.440 nonbonded pdb=" O LEU A 245 " pdb=" OG1 THR A 249 " model vdw 2.080 2.440 nonbonded pdb=" O GLN L 6 " pdb=" OG1 THR L 102 " model vdw 2.124 2.440 nonbonded pdb=" OD2 ASP A 229 " pdb=" NH2 ARG L 61 " model vdw 2.130 2.520 ... (remaining 109905 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 59 through 252 or (resid 253 and (name N or name CA or nam \ e C or name O or name CB )) or resid 254 through 255 or resid 301 through 305)) selection = (chain 'C' and (resid 59 through 252 or (resid 253 and (name N or name CA or nam \ e C or name O or name CB )) or resid 254 through 255 or resid 301 through 305)) } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'Q' selection = chain 'U' selection = chain 'X' } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'V' } ncs_group { reference = chain 'M' selection = chain 'R' selection = chain 'T' selection = chain 'W' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'S' } 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: 1.680 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: 6.360 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 38.800 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14484 Z= 0.301 Angle : 0.839 15.219 19626 Z= 0.374 Chirality : 0.053 0.367 2415 Planarity : 0.007 0.293 2359 Dihedral : 20.844 120.607 6633 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.51 % Favored : 85.94 % Rotamer: Outliers : 1.11 % Allowed : 1.11 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.21), residues: 1629 helix: 0.83 (0.34), residues: 281 sheet: -1.15 (0.34), residues: 286 loop : -2.43 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 103 HIS 0.004 0.001 HIS B 92 PHE 0.015 0.001 PHE C 117 TYR 0.033 0.001 TYR b 363 ARG 0.004 0.000 ARG b 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 568 time to evaluate : 1.583 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: 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: B 82 MET cc_start: 0.7890 (ptp) cc_final: 0.7661 (ptp) REVERT: B 101 THR cc_start: 0.8735 (p) cc_final: 0.8364 (t) REVERT: B 104 GLU cc_start: 0.8762 (tt0) cc_final: 0.7788 (tt0) REVERT: B 119 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7142 (m-40) REVERT: B 130 ASP cc_start: 0.9080 (p0) cc_final: 0.8747 (p0) REVERT: B 133 LEU cc_start: 0.8898 (mt) cc_final: 0.8305 (mp) REVERT: B 187 VAL cc_start: 0.8716 (t) cc_final: 0.8503 (p) REVERT: B 232 GLN cc_start: 0.7532 (tt0) cc_final: 0.6835 (mm-40) REVERT: b 270 GLU cc_start: 0.7855 (mp0) cc_final: 0.7240 (tp30) REVERT: b 284 MET cc_start: 0.8116 (mmm) cc_final: 0.7868 (mmm) REVERT: b 302 ASN cc_start: 0.9073 (OUTLIER) cc_final: 0.8522 (m110) REVERT: b 325 ARG cc_start: 0.7924 (ptt180) cc_final: 0.7690 (ptp90) REVERT: b 344 LEU cc_start: 0.8314 (mp) cc_final: 0.7468 (mp) REVERT: b 372 LEU cc_start: 0.8260 (mt) cc_final: 0.7877 (tp) REVERT: b 380 THR cc_start: 0.9545 (p) cc_final: 0.9045 (t) REVERT: A 73 LEU cc_start: 0.8644 (mt) cc_final: 0.8165 (mp) REVERT: A 82 MET cc_start: 0.8452 (pmm) cc_final: 0.8112 (pmm) REVERT: A 140 PHE cc_start: 0.9454 (m-80) cc_final: 0.9066 (m-80) REVERT: A 179 HIS cc_start: 0.7862 (t70) cc_final: 0.7636 (t70) REVERT: a 325 ARG cc_start: 0.8266 (ptp-170) cc_final: 0.7275 (ptp-170) REVERT: a 344 LEU cc_start: 0.9338 (mt) cc_final: 0.9011 (mt) REVERT: a 363 TYR cc_start: 0.8643 (p90) cc_final: 0.8298 (p90) REVERT: a 369 TYR cc_start: 0.8672 (m-80) cc_final: 0.7280 (m-80) REVERT: a 372 LEU cc_start: 0.8886 (mt) cc_final: 0.8659 (tp) REVERT: a 387 LEU cc_start: 0.8574 (mt) cc_final: 0.7928 (tp) REVERT: C 75 MET cc_start: 0.8858 (mtm) cc_final: 0.8599 (mtm) REVERT: C 80 MET cc_start: 0.7185 (mtt) cc_final: 0.6745 (mtt) REVERT: C 92 HIS cc_start: 0.8218 (m-70) cc_final: 0.7776 (m-70) REVERT: c 268 ASP cc_start: 0.7462 (p0) cc_final: 0.6885 (p0) REVERT: c 282 ARG cc_start: 0.7594 (ttt180) cc_final: 0.6465 (ptp-170) REVERT: c 321 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8427 (mm110) REVERT: c 338 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8273 (t0) REVERT: c 356 ARG cc_start: 0.7352 (mtt180) cc_final: 0.6725 (mmm-85) REVERT: c 361 ILE cc_start: 0.8690 (tp) cc_final: 0.8060 (tp) REVERT: c 369 TYR cc_start: 0.7736 (m-80) cc_final: 0.6100 (m-10) REVERT: c 387 LEU cc_start: 0.9031 (mt) cc_final: 0.8612 (mp) REVERT: c 404 GLU cc_start: 0.9408 (mm-30) cc_final: 0.9079 (mm-30) REVERT: c 410 MET cc_start: 0.9022 (mmt) cc_final: 0.8534 (tpt) REVERT: c 416 GLN cc_start: 0.8502 (tt0) cc_final: 0.8180 (tt0) REVERT: D 37 GLU cc_start: 0.6292 (mt-10) cc_final: 0.5755 (mm-30) REVERT: D 46 GLU cc_start: 0.8520 (pt0) cc_final: 0.7579 (pm20) REVERT: D 107 GLN cc_start: 0.8366 (pt0) cc_final: 0.8123 (pt0) REVERT: H 67 LEU cc_start: 0.8212 (mt) cc_final: 0.7968 (mm) REVERT: H 91 TYR cc_start: 0.7697 (m-80) cc_final: 0.7377 (m-80) REVERT: H 102 TYR cc_start: 0.8907 (m-80) cc_final: 0.7245 (m-80) REVERT: H 103 TRP cc_start: 0.9161 (m100) cc_final: 0.8779 (m-10) REVERT: H 105 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8563 (pm20) REVERT: L 6 GLN cc_start: 0.6431 (mt0) cc_final: 0.5798 (mp-120) REVERT: L 23 CYS cc_start: 0.6676 (t) cc_final: 0.4958 (t) REVERT: L 47 VAL cc_start: 0.9026 (m) cc_final: 0.8805 (m) REVERT: L 48 ILE cc_start: 0.9498 (mm) cc_final: 0.9179 (tt) REVERT: L 57 ASP cc_start: 0.8468 (t0) cc_final: 0.8267 (t0) REVERT: L 58 ILE cc_start: 0.9288 (mm) cc_final: 0.8791 (mt) REVERT: L 98 PHE cc_start: 0.8542 (m-80) cc_final: 0.8323 (m-10) REVERT: E 3 GLN cc_start: 0.8539 (tt0) cc_final: 0.8092 (tm-30) REVERT: E 77 GLN cc_start: 0.8740 (tt0) cc_final: 0.8324 (tm-30) REVERT: E 86 ASP cc_start: 0.8665 (m-30) cc_final: 0.8222 (m-30) REVERT: I 38 GLN cc_start: 0.7902 (tt0) cc_final: 0.7537 (tt0) REVERT: I 75 ILE cc_start: 0.9250 (mt) cc_final: 0.8509 (tt) REVERT: I 78 MET cc_start: 0.8871 (tpp) cc_final: 0.8481 (tpt) REVERT: I 93 ASN cc_start: 0.9082 (m-40) cc_final: 0.8571 (p0) outliers start: 16 outliers final: 3 residues processed: 578 average time/residue: 0.2706 time to fit residues: 225.4362 Evaluate side-chains 334 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 328 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 80 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 HIS B 189 GLN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 321 GLN b 342 ASN b 354 HIS ** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN a 409 ASN C 141 HIS C 223 GLN c 305 HIS c 406 GLN D 84 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 14484 Z= 0.440 Angle : 0.970 11.695 19626 Z= 0.470 Chirality : 0.056 0.425 2415 Planarity : 0.005 0.057 2359 Dihedral : 16.678 112.692 3617 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.49 % Allowed : 16.08 % Favored : 83.43 % Rotamer: Outliers : 0.69 % Allowed : 8.31 % Favored : 91.00 % 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: -2.84 (0.20), residues: 1629 helix: -0.52 (0.29), residues: 296 sheet: -1.11 (0.32), residues: 291 loop : -2.70 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP E 103 HIS 0.016 0.002 HIS B 170 PHE 0.024 0.003 PHE c 318 TYR 0.025 0.003 TYR E 98 ARG 0.008 0.001 ARG D 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 390 time to evaluate : 1.654 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 MET cc_start: 0.8642 (mtm) cc_final: 0.8344 (mtm) REVERT: B 101 THR cc_start: 0.8779 (p) cc_final: 0.8503 (t) REVERT: B 104 GLU cc_start: 0.8460 (tt0) cc_final: 0.8197 (tt0) REVERT: B 142 LEU cc_start: 0.9278 (mp) cc_final: 0.8902 (tp) REVERT: B 157 PHE cc_start: 0.9096 (m-80) cc_final: 0.8713 (m-80) REVERT: B 218 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8127 (mp10) REVERT: B 248 ARG cc_start: 0.7743 (tpp80) cc_final: 0.7518 (tpp80) REVERT: b 270 GLU cc_start: 0.7903 (mp0) cc_final: 0.7180 (tp30) REVERT: b 311 ASP cc_start: 0.8884 (m-30) cc_final: 0.8437 (m-30) REVERT: b 325 ARG cc_start: 0.7743 (ptt180) cc_final: 0.7355 (ptp90) REVERT: b 345 ILE cc_start: 0.9522 (tp) cc_final: 0.9311 (tp) REVERT: b 346 ASN cc_start: 0.9013 (t0) cc_final: 0.8559 (t0) REVERT: b 357 ASP cc_start: 0.9099 (t70) cc_final: 0.8600 (t0) REVERT: b 380 THR cc_start: 0.9559 (p) cc_final: 0.9340 (t) REVERT: b 414 MET cc_start: 0.9286 (tmm) cc_final: 0.8642 (tmm) REVERT: A 75 MET cc_start: 0.8848 (mtp) cc_final: 0.7999 (ttm) REVERT: A 82 MET cc_start: 0.8485 (pmm) cc_final: 0.8160 (pmm) REVERT: A 134 MET cc_start: 0.8516 (mmm) cc_final: 0.8133 (mmm) REVERT: A 140 PHE cc_start: 0.9305 (m-80) cc_final: 0.8782 (m-80) REVERT: A 223 GLN cc_start: 0.8575 (mm110) cc_final: 0.8144 (mm110) REVERT: a 281 THR cc_start: 0.7972 (p) cc_final: 0.6956 (p) REVERT: a 284 MET cc_start: 0.9230 (mtm) cc_final: 0.8923 (mtt) REVERT: a 287 GLU cc_start: 0.8610 (mt-10) cc_final: 0.7758 (tm-30) REVERT: a 325 ARG cc_start: 0.8256 (ptp-170) cc_final: 0.7788 (ptp-170) REVERT: a 334 ILE cc_start: 0.9495 (mm) cc_final: 0.9277 (pt) REVERT: a 363 TYR cc_start: 0.8716 (p90) cc_final: 0.8299 (p90) REVERT: a 369 TYR cc_start: 0.9042 (m-80) cc_final: 0.8669 (m-80) REVERT: a 387 LEU cc_start: 0.8706 (mt) cc_final: 0.8459 (mt) REVERT: a 397 THR cc_start: 0.8807 (p) cc_final: 0.8515 (p) REVERT: C 75 MET cc_start: 0.9062 (mtm) cc_final: 0.8680 (mtm) REVERT: C 82 MET cc_start: 0.8218 (mmm) cc_final: 0.7696 (mmm) REVERT: C 92 HIS cc_start: 0.8411 (m-70) cc_final: 0.8088 (m90) REVERT: C 241 TYR cc_start: 0.8746 (t80) cc_final: 0.8409 (t80) REVERT: c 268 ASP cc_start: 0.7443 (p0) cc_final: 0.7019 (p0) REVERT: c 282 ARG cc_start: 0.7974 (ttt180) cc_final: 0.6795 (ptp-170) REVERT: c 311 ASP cc_start: 0.9389 (m-30) cc_final: 0.9054 (m-30) REVERT: c 337 ILE cc_start: 0.8952 (mt) cc_final: 0.8016 (mt) REVERT: c 349 LEU cc_start: 0.9222 (tp) cc_final: 0.8946 (tp) REVERT: c 359 MET cc_start: 0.8846 (mtp) cc_final: 0.8426 (mmm) REVERT: c 369 TYR cc_start: 0.8379 (m-80) cc_final: 0.6293 (m-80) REVERT: c 387 LEU cc_start: 0.9063 (mt) cc_final: 0.8653 (mp) REVERT: D 34 MET cc_start: 0.8140 (mtm) cc_final: 0.7735 (mtp) REVERT: D 37 GLU cc_start: 0.6148 (mt-10) cc_final: 0.5716 (mt-10) REVERT: D 46 GLU cc_start: 0.8414 (pt0) cc_final: 0.7481 (pm20) REVERT: D 95 TYR cc_start: 0.7686 (m-10) cc_final: 0.7036 (m-80) REVERT: D 99 LEU cc_start: 0.9387 (mp) cc_final: 0.9157 (mp) REVERT: D 105 ARG cc_start: 0.8160 (ptp-110) cc_final: 0.7732 (ptp-110) REVERT: H 13 LYS cc_start: 0.9682 (tppt) cc_final: 0.9460 (tppt) REVERT: L 6 GLN cc_start: 0.7262 (mt0) cc_final: 0.6211 (mp-120) REVERT: L 23 CYS cc_start: 0.7676 (t) cc_final: 0.5679 (t) REVERT: L 37 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7438 (tm-30) REVERT: L 78 MET cc_start: 0.8473 (tmm) cc_final: 0.8044 (tmm) REVERT: E 3 GLN cc_start: 0.8771 (tt0) cc_final: 0.8137 (tm-30) REVERT: E 67 LEU cc_start: 0.8430 (mm) cc_final: 0.7935 (mm) REVERT: E 77 GLN cc_start: 0.8821 (tt0) cc_final: 0.8602 (tm-30) REVERT: E 86 ASP cc_start: 0.8965 (m-30) cc_final: 0.8428 (m-30) REVERT: I 37 GLN cc_start: 0.7832 (pp30) cc_final: 0.7538 (tm-30) REVERT: I 66 ARG cc_start: 0.8811 (tmt170) cc_final: 0.8545 (tmt170) REVERT: I 78 MET cc_start: 0.8813 (tpp) cc_final: 0.8392 (tpp) REVERT: I 93 ASN cc_start: 0.9314 (m-40) cc_final: 0.8754 (p0) outliers start: 10 outliers final: 3 residues processed: 399 average time/residue: 0.2772 time to fit residues: 163.2147 Evaluate side-chains 297 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 292 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 118 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 142 optimal weight: 0.1980 chunk 154 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 141 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 342 ASN b 405 GLN A 131 HIS ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 353 ASN a 409 ASN C 124 HIS C 148 ASN c 331 GLN D 39 GLN L 90 GLN ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 14484 Z= 0.296 Angle : 0.804 12.707 19626 Z= 0.396 Chirality : 0.051 0.356 2415 Planarity : 0.005 0.091 2359 Dihedral : 14.206 111.324 3617 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.49 % Allowed : 14.86 % Favored : 84.65 % Rotamer: Outliers : 0.35 % Allowed : 3.88 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.20), residues: 1629 helix: -0.19 (0.30), residues: 296 sheet: -1.34 (0.32), residues: 267 loop : -2.64 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 210 HIS 0.012 0.002 HIS B 170 PHE 0.017 0.002 PHE D 68 TYR 0.022 0.002 TYR c 393 ARG 0.010 0.001 ARG E 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 372 time to evaluate : 1.744 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 MET cc_start: 0.8734 (mtm) cc_final: 0.8388 (mtm) REVERT: B 101 THR cc_start: 0.8817 (p) cc_final: 0.8459 (t) REVERT: B 104 GLU cc_start: 0.8358 (tt0) cc_final: 0.8085 (tt0) REVERT: B 142 LEU cc_start: 0.9239 (mp) cc_final: 0.8871 (tp) REVERT: B 149 GLN cc_start: 0.8514 (tm-30) cc_final: 0.7901 (tm-30) REVERT: B 150 TYR cc_start: 0.7423 (m-80) cc_final: 0.7100 (m-80) REVERT: B 157 PHE cc_start: 0.9063 (m-80) cc_final: 0.8632 (m-80) REVERT: B 183 VAL cc_start: 0.8515 (t) cc_final: 0.8099 (m) REVERT: b 270 GLU cc_start: 0.7871 (mp0) cc_final: 0.7126 (tp30) REVERT: b 303 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8446 (tm-30) REVERT: b 311 ASP cc_start: 0.8828 (m-30) cc_final: 0.8419 (m-30) REVERT: b 317 ASP cc_start: 0.9411 (t0) cc_final: 0.9201 (t70) REVERT: b 345 ILE cc_start: 0.9553 (tp) cc_final: 0.9347 (tp) REVERT: b 346 ASN cc_start: 0.8927 (t0) cc_final: 0.8353 (t0) REVERT: b 357 ASP cc_start: 0.9173 (t70) cc_final: 0.8696 (t0) REVERT: A 62 TYR cc_start: 0.8361 (m-10) cc_final: 0.7987 (m-10) REVERT: A 75 MET cc_start: 0.9065 (mtp) cc_final: 0.8545 (ttm) REVERT: A 82 MET cc_start: 0.8435 (pmm) cc_final: 0.8094 (pmm) REVERT: A 134 MET cc_start: 0.8806 (mmm) cc_final: 0.8391 (mmm) REVERT: A 140 PHE cc_start: 0.9282 (m-80) cc_final: 0.8789 (m-80) REVERT: A 193 ARG cc_start: 0.5127 (ptm160) cc_final: 0.4497 (ttp80) REVERT: A 223 GLN cc_start: 0.8537 (mm110) cc_final: 0.8308 (mm110) REVERT: a 266 LEU cc_start: 0.8815 (mp) cc_final: 0.8556 (tp) REVERT: a 281 THR cc_start: 0.7996 (p) cc_final: 0.6856 (p) REVERT: a 283 TRP cc_start: 0.8809 (p-90) cc_final: 0.8581 (p-90) REVERT: a 284 MET cc_start: 0.9300 (mtm) cc_final: 0.8926 (mtt) REVERT: a 287 GLU cc_start: 0.8720 (mt-10) cc_final: 0.7793 (tm-30) REVERT: a 324 GLN cc_start: 0.9188 (tm-30) cc_final: 0.8841 (tm-30) REVERT: a 325 ARG cc_start: 0.8195 (ptp-170) cc_final: 0.7308 (ptp-170) REVERT: a 363 TYR cc_start: 0.8642 (p90) cc_final: 0.8177 (p90) REVERT: a 369 TYR cc_start: 0.9145 (m-80) cc_final: 0.8804 (m-80) REVERT: a 372 LEU cc_start: 0.9240 (mm) cc_final: 0.8728 (tp) REVERT: a 387 LEU cc_start: 0.8642 (mt) cc_final: 0.8422 (mt) REVERT: C 75 MET cc_start: 0.9014 (mtm) cc_final: 0.8705 (mtm) REVERT: C 242 LEU cc_start: 0.8678 (mm) cc_final: 0.8460 (tp) REVERT: c 268 ASP cc_start: 0.7664 (p0) cc_final: 0.7269 (p0) REVERT: c 282 ARG cc_start: 0.7966 (ttt180) cc_final: 0.6749 (ptp-170) REVERT: c 304 LYS cc_start: 0.7797 (mptt) cc_final: 0.7391 (mttt) REVERT: c 311 ASP cc_start: 0.9435 (m-30) cc_final: 0.9033 (m-30) REVERT: c 337 ILE cc_start: 0.9111 (mt) cc_final: 0.8618 (mt) REVERT: c 349 LEU cc_start: 0.9212 (tp) cc_final: 0.8903 (tt) REVERT: c 369 TYR cc_start: 0.8520 (m-80) cc_final: 0.6427 (m-80) REVERT: c 387 LEU cc_start: 0.9139 (mt) cc_final: 0.8757 (mp) REVERT: c 403 ILE cc_start: 0.8863 (mt) cc_final: 0.8641 (mt) REVERT: c 404 GLU cc_start: 0.9371 (mm-30) cc_final: 0.9039 (mm-30) REVERT: c 409 ASN cc_start: 0.9599 (t0) cc_final: 0.9284 (m110) REVERT: D 34 MET cc_start: 0.7998 (mtm) cc_final: 0.7245 (mtp) REVERT: D 37 GLU cc_start: 0.6161 (mt-10) cc_final: 0.5853 (mt-10) REVERT: D 46 GLU cc_start: 0.8352 (pt0) cc_final: 0.7540 (pm20) REVERT: D 62 ASP cc_start: 0.9139 (m-30) cc_final: 0.8411 (p0) REVERT: D 99 LEU cc_start: 0.9382 (mp) cc_final: 0.9073 (mp) REVERT: D 104 LEU cc_start: 0.7859 (pp) cc_final: 0.7552 (pp) REVERT: D 105 ARG cc_start: 0.8185 (ptp-110) cc_final: 0.7464 (ptp90) REVERT: H 67 LEU cc_start: 0.8110 (mm) cc_final: 0.7891 (mm) REVERT: H 96 PHE cc_start: 0.8364 (m-80) cc_final: 0.7775 (m-80) REVERT: H 101 ASP cc_start: 0.7599 (p0) cc_final: 0.7374 (p0) REVERT: L 6 GLN cc_start: 0.7322 (mt0) cc_final: 0.6498 (mp-120) REVERT: L 74 THR cc_start: 0.8313 (m) cc_final: 0.7986 (t) REVERT: L 78 MET cc_start: 0.8767 (tmm) cc_final: 0.8227 (tmm) REVERT: E 3 GLN cc_start: 0.8655 (tt0) cc_final: 0.7937 (tm-30) REVERT: E 47 TRP cc_start: 0.9177 (t60) cc_final: 0.7788 (t60) REVERT: E 67 LEU cc_start: 0.8333 (mm) cc_final: 0.7842 (mm) REVERT: E 86 ASP cc_start: 0.9065 (m-30) cc_final: 0.8537 (m-30) REVERT: E 91 TYR cc_start: 0.8838 (m-10) cc_final: 0.8618 (m-80) REVERT: E 100 ASP cc_start: 0.7891 (t70) cc_final: 0.7678 (t0) REVERT: I 23 CYS cc_start: 0.5167 (t) cc_final: 0.4815 (t) REVERT: I 48 ILE cc_start: 0.8794 (tp) cc_final: 0.8580 (tp) REVERT: I 77 ARG cc_start: 0.8868 (ptp90) cc_final: 0.8412 (ptp-170) REVERT: I 78 MET cc_start: 0.8805 (tpp) cc_final: 0.8272 (tpp) REVERT: I 93 ASN cc_start: 0.9259 (m-40) cc_final: 0.8536 (p0) outliers start: 5 outliers final: 1 residues processed: 376 average time/residue: 0.2696 time to fit residues: 147.8425 Evaluate side-chains 292 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 291 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 15 optimal weight: 0.0370 chunk 68 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 151 optimal weight: 0.0770 chunk 135 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 overall best weight: 2.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 405 GLN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 409 ASN C 149 GLN C 189 GLN D 39 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 14484 Z= 0.294 Angle : 0.807 11.178 19626 Z= 0.397 Chirality : 0.051 0.361 2415 Planarity : 0.005 0.120 2359 Dihedral : 12.992 111.614 3617 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.49 % Allowed : 15.29 % Favored : 84.22 % Rotamer: Outliers : 0.14 % Allowed : 3.74 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.77 (0.20), residues: 1629 helix: -0.31 (0.29), residues: 307 sheet: -1.18 (0.32), residues: 264 loop : -2.67 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 210 HIS 0.013 0.002 HIS B 230 PHE 0.016 0.002 PHE c 318 TYR 0.028 0.002 TYR H 102 ARG 0.013 0.001 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 349 time to evaluate : 1.697 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 MET cc_start: 0.8741 (mtm) cc_final: 0.8393 (mtm) REVERT: B 82 MET cc_start: 0.8107 (ptp) cc_final: 0.7860 (ptp) REVERT: B 101 THR cc_start: 0.8789 (p) cc_final: 0.8485 (t) REVERT: B 104 GLU cc_start: 0.8398 (tt0) cc_final: 0.7772 (tt0) REVERT: B 142 LEU cc_start: 0.9204 (mp) cc_final: 0.8957 (tp) REVERT: B 149 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8087 (tm-30) REVERT: B 157 PHE cc_start: 0.9035 (m-80) cc_final: 0.8572 (m-80) REVERT: b 270 GLU cc_start: 0.7830 (mp0) cc_final: 0.7050 (tp30) REVERT: b 303 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8459 (tm-30) REVERT: b 311 ASP cc_start: 0.8857 (m-30) cc_final: 0.8500 (m-30) REVERT: b 317 ASP cc_start: 0.9400 (t0) cc_final: 0.9193 (t0) REVERT: b 324 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8448 (tm-30) REVERT: b 346 ASN cc_start: 0.8940 (t0) cc_final: 0.8331 (t0) REVERT: b 357 ASP cc_start: 0.9191 (t70) cc_final: 0.8678 (t0) REVERT: A 75 MET cc_start: 0.9125 (mtp) cc_final: 0.8511 (ttm) REVERT: A 82 MET cc_start: 0.8432 (pmm) cc_final: 0.8231 (pmm) REVERT: A 140 PHE cc_start: 0.9293 (m-80) cc_final: 0.8844 (m-80) REVERT: A 223 GLN cc_start: 0.8617 (mm110) cc_final: 0.8353 (mm110) REVERT: a 281 THR cc_start: 0.8016 (p) cc_final: 0.7495 (p) REVERT: a 284 MET cc_start: 0.9371 (mtm) cc_final: 0.9080 (mtm) REVERT: a 286 ILE cc_start: 0.8930 (tt) cc_final: 0.8708 (tt) REVERT: a 287 GLU cc_start: 0.8621 (mt-10) cc_final: 0.7843 (tm-30) REVERT: a 324 GLN cc_start: 0.9169 (tm-30) cc_final: 0.8893 (tm-30) REVERT: a 325 ARG cc_start: 0.8347 (ptp-170) cc_final: 0.7853 (ptp-170) REVERT: a 332 MET cc_start: 0.7118 (mtt) cc_final: 0.6895 (mtt) REVERT: a 369 TYR cc_start: 0.9048 (m-80) cc_final: 0.8830 (m-80) REVERT: a 387 LEU cc_start: 0.8601 (mt) cc_final: 0.8361 (mt) REVERT: C 75 MET cc_start: 0.9011 (mtm) cc_final: 0.8762 (mtm) REVERT: C 82 MET cc_start: 0.8339 (mmm) cc_final: 0.8062 (mmm) REVERT: C 122 ASP cc_start: 0.8208 (p0) cc_final: 0.7994 (p0) REVERT: C 124 HIS cc_start: 0.8177 (m170) cc_final: 0.7842 (m-70) REVERT: C 192 MET cc_start: 0.8453 (mmt) cc_final: 0.8201 (mmt) REVERT: c 268 ASP cc_start: 0.7757 (p0) cc_final: 0.7342 (p0) REVERT: c 282 ARG cc_start: 0.8078 (ttt180) cc_final: 0.6855 (ptp-170) REVERT: c 304 LYS cc_start: 0.7938 (mptt) cc_final: 0.7576 (mttt) REVERT: c 311 ASP cc_start: 0.9428 (m-30) cc_final: 0.9132 (m-30) REVERT: c 314 ARG cc_start: 0.9070 (mtt90) cc_final: 0.8361 (ttm110) REVERT: c 337 ILE cc_start: 0.8995 (mt) cc_final: 0.8467 (mt) REVERT: c 349 LEU cc_start: 0.9245 (tp) cc_final: 0.9020 (tp) REVERT: c 359 MET cc_start: 0.9057 (mmm) cc_final: 0.8466 (mmm) REVERT: c 369 TYR cc_start: 0.8438 (m-80) cc_final: 0.6351 (m-80) REVERT: c 387 LEU cc_start: 0.9134 (mt) cc_final: 0.8801 (mt) REVERT: c 403 ILE cc_start: 0.8822 (mt) cc_final: 0.8618 (mt) REVERT: c 404 GLU cc_start: 0.9386 (mm-30) cc_final: 0.9068 (mm-30) REVERT: c 409 ASN cc_start: 0.9585 (t0) cc_final: 0.9248 (m110) REVERT: c 410 MET cc_start: 0.8818 (tpt) cc_final: 0.8301 (tpt) REVERT: D 34 MET cc_start: 0.8018 (mtm) cc_final: 0.7599 (mtp) REVERT: D 37 GLU cc_start: 0.6202 (mt-10) cc_final: 0.5950 (mt-10) REVERT: D 46 GLU cc_start: 0.8569 (pt0) cc_final: 0.7625 (pm20) REVERT: D 95 TYR cc_start: 0.7607 (m-10) cc_final: 0.7279 (m-80) REVERT: D 99 LEU cc_start: 0.9381 (mp) cc_final: 0.9081 (mp) REVERT: D 104 LEU cc_start: 0.8129 (pp) cc_final: 0.7923 (pp) REVERT: D 105 ARG cc_start: 0.8283 (ptp-110) cc_final: 0.7668 (ptp-110) REVERT: H 30 ARG cc_start: 0.8262 (ptt-90) cc_final: 0.7880 (ttp-170) REVERT: H 48 ILE cc_start: 0.9200 (mt) cc_final: 0.8971 (mt) REVERT: H 64 LYS cc_start: 0.9185 (mmtm) cc_final: 0.8983 (tmtt) REVERT: H 67 LEU cc_start: 0.7984 (mm) cc_final: 0.7688 (mm) REVERT: H 86 ASP cc_start: 0.8876 (m-30) cc_final: 0.8423 (m-30) REVERT: H 96 PHE cc_start: 0.8250 (m-80) cc_final: 0.7994 (m-80) REVERT: H 101 ASP cc_start: 0.7754 (p0) cc_final: 0.7458 (p0) REVERT: L 6 GLN cc_start: 0.7560 (mt0) cc_final: 0.6992 (mp-120) REVERT: L 74 THR cc_start: 0.8235 (m) cc_final: 0.7943 (t) REVERT: L 78 MET cc_start: 0.8890 (tmm) cc_final: 0.8438 (tmm) REVERT: E 3 GLN cc_start: 0.8636 (tt0) cc_final: 0.7967 (tm-30) REVERT: E 47 TRP cc_start: 0.9123 (t60) cc_final: 0.7576 (t60) REVERT: E 67 LEU cc_start: 0.8377 (mm) cc_final: 0.7880 (mm) REVERT: I 23 CYS cc_start: 0.5144 (t) cc_final: 0.4812 (t) REVERT: I 37 GLN cc_start: 0.7992 (pp30) cc_final: 0.7669 (tm-30) REVERT: I 77 ARG cc_start: 0.8872 (ptp90) cc_final: 0.8492 (ptp-170) REVERT: I 78 MET cc_start: 0.8879 (tpp) cc_final: 0.8269 (tpp) outliers start: 2 outliers final: 1 residues processed: 350 average time/residue: 0.2638 time to fit residues: 134.8414 Evaluate side-chains 284 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 283 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN a 409 ASN D 39 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 14484 Z= 0.292 Angle : 0.790 16.481 19626 Z= 0.388 Chirality : 0.050 0.425 2415 Planarity : 0.005 0.078 2359 Dihedral : 12.165 111.640 3617 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.55 % Allowed : 15.35 % Favored : 84.10 % Rotamer: Outliers : 0.14 % Allowed : 4.78 % Favored : 95.08 % 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: -2.71 (0.20), residues: 1629 helix: -0.13 (0.29), residues: 312 sheet: -1.10 (0.31), residues: 263 loop : -2.70 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 210 HIS 0.018 0.002 HIS B 170 PHE 0.015 0.002 PHE D 68 TYR 0.015 0.002 TYR E 59 ARG 0.008 0.001 ARG E 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 361 time to evaluate : 1.616 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8097 (ptp) cc_final: 0.7866 (ptp) REVERT: B 101 THR cc_start: 0.8786 (p) cc_final: 0.8492 (t) REVERT: B 104 GLU cc_start: 0.8413 (tt0) cc_final: 0.7775 (tt0) REVERT: B 142 LEU cc_start: 0.9258 (mp) cc_final: 0.9034 (tp) REVERT: B 149 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8102 (tm-30) REVERT: B 157 PHE cc_start: 0.8960 (m-80) cc_final: 0.8567 (m-80) REVERT: b 270 GLU cc_start: 0.7915 (mp0) cc_final: 0.7050 (tp30) REVERT: b 311 ASP cc_start: 0.8916 (m-30) cc_final: 0.8586 (m-30) REVERT: b 317 ASP cc_start: 0.9368 (t0) cc_final: 0.9093 (t0) REVERT: b 325 ARG cc_start: 0.7637 (ptp90) cc_final: 0.7427 (ptp90) REVERT: b 346 ASN cc_start: 0.9006 (t0) cc_final: 0.8524 (t0) REVERT: b 357 ASP cc_start: 0.9236 (t70) cc_final: 0.8719 (t0) REVERT: A 75 MET cc_start: 0.9119 (mtp) cc_final: 0.8420 (ttm) REVERT: A 140 PHE cc_start: 0.9260 (m-80) cc_final: 0.8850 (m-80) REVERT: A 191 PHE cc_start: 0.8692 (t80) cc_final: 0.8382 (t80) REVERT: A 219 TYR cc_start: 0.8057 (m-80) cc_final: 0.7725 (m-80) REVERT: a 266 LEU cc_start: 0.8704 (mp) cc_final: 0.8449 (tp) REVERT: a 284 MET cc_start: 0.9281 (mtm) cc_final: 0.9073 (mtt) REVERT: a 317 ASP cc_start: 0.9456 (t0) cc_final: 0.9206 (t0) REVERT: a 324 GLN cc_start: 0.9206 (tm-30) cc_final: 0.8890 (tm-30) REVERT: a 325 ARG cc_start: 0.8544 (ptp-170) cc_final: 0.7948 (ptp-170) REVERT: a 369 TYR cc_start: 0.9075 (m-80) cc_final: 0.8829 (m-80) REVERT: a 372 LEU cc_start: 0.9317 (mm) cc_final: 0.8777 (tp) REVERT: a 387 LEU cc_start: 0.8654 (mt) cc_final: 0.8426 (mt) REVERT: C 122 ASP cc_start: 0.8339 (p0) cc_final: 0.8064 (p0) REVERT: C 124 HIS cc_start: 0.8193 (m170) cc_final: 0.7877 (m-70) REVERT: C 151 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7636 (tm-30) REVERT: C 164 VAL cc_start: 0.7690 (t) cc_final: 0.7413 (t) REVERT: C 192 MET cc_start: 0.8452 (mmt) cc_final: 0.8206 (mmt) REVERT: c 268 ASP cc_start: 0.7798 (p0) cc_final: 0.7342 (p0) REVERT: c 282 ARG cc_start: 0.8092 (ttt180) cc_final: 0.6818 (ptp-170) REVERT: c 304 LYS cc_start: 0.7921 (mptt) cc_final: 0.7594 (mttt) REVERT: c 311 ASP cc_start: 0.9398 (m-30) cc_final: 0.8960 (m-30) REVERT: c 337 ILE cc_start: 0.9118 (mt) cc_final: 0.8584 (mt) REVERT: c 349 LEU cc_start: 0.9255 (tp) cc_final: 0.9039 (tp) REVERT: c 359 MET cc_start: 0.9135 (mmm) cc_final: 0.8639 (mmm) REVERT: c 369 TYR cc_start: 0.8474 (m-80) cc_final: 0.6383 (m-80) REVERT: c 387 LEU cc_start: 0.9129 (mt) cc_final: 0.8803 (mt) REVERT: c 404 GLU cc_start: 0.9400 (mm-30) cc_final: 0.9073 (mm-30) REVERT: c 409 ASN cc_start: 0.9584 (t0) cc_final: 0.9240 (m-40) REVERT: c 410 MET cc_start: 0.8853 (tpt) cc_final: 0.8312 (tpt) REVERT: D 30 SER cc_start: 0.8475 (p) cc_final: 0.8119 (m) REVERT: D 34 MET cc_start: 0.7968 (mtm) cc_final: 0.7586 (mtp) REVERT: D 37 GLU cc_start: 0.6170 (mt-10) cc_final: 0.5901 (mt-10) REVERT: D 46 GLU cc_start: 0.8591 (pt0) cc_final: 0.7593 (pm20) REVERT: D 95 TYR cc_start: 0.7592 (m-10) cc_final: 0.7259 (m-80) REVERT: D 99 LEU cc_start: 0.9393 (mp) cc_final: 0.8946 (mm) REVERT: D 105 ARG cc_start: 0.8199 (ptp-110) cc_final: 0.7686 (ptp-110) REVERT: H 30 ARG cc_start: 0.8296 (ptt-90) cc_final: 0.7884 (ttp-170) REVERT: H 48 ILE cc_start: 0.9197 (mt) cc_final: 0.8974 (mt) REVERT: H 64 LYS cc_start: 0.9185 (mmtm) cc_final: 0.8966 (tmtt) REVERT: H 67 LEU cc_start: 0.7876 (mm) cc_final: 0.7558 (mm) REVERT: H 86 ASP cc_start: 0.8867 (m-30) cc_final: 0.8395 (m-30) REVERT: H 96 PHE cc_start: 0.8378 (m-80) cc_final: 0.7948 (m-80) REVERT: H 101 ASP cc_start: 0.7783 (p0) cc_final: 0.6404 (p0) REVERT: H 102 TYR cc_start: 0.7870 (m-10) cc_final: 0.7285 (m-80) REVERT: L 6 GLN cc_start: 0.7532 (mt0) cc_final: 0.7032 (mp-120) REVERT: L 31 ASP cc_start: 0.8621 (p0) cc_final: 0.8352 (p0) REVERT: L 74 THR cc_start: 0.8321 (m) cc_final: 0.7995 (t) REVERT: L 78 MET cc_start: 0.8925 (tmm) cc_final: 0.8608 (tmm) REVERT: E 3 GLN cc_start: 0.8559 (tt0) cc_final: 0.7915 (tm-30) REVERT: E 47 TRP cc_start: 0.9103 (t60) cc_final: 0.6964 (t60) REVERT: E 67 LEU cc_start: 0.8449 (mm) cc_final: 0.7955 (mm) REVERT: E 100 ASP cc_start: 0.7731 (t70) cc_final: 0.7420 (t0) REVERT: I 23 CYS cc_start: 0.5736 (t) cc_final: 0.5450 (t) REVERT: I 77 ARG cc_start: 0.8881 (ptp90) cc_final: 0.8514 (ptp-170) REVERT: I 78 MET cc_start: 0.8823 (tpp) cc_final: 0.8186 (tpp) REVERT: I 83 PHE cc_start: 0.7552 (m-80) cc_final: 0.7265 (m-80) outliers start: 2 outliers final: 0 residues processed: 363 average time/residue: 0.2707 time to fit residues: 143.9503 Evaluate side-chains 285 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 126 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 305 HIS ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN a 409 ASN c 331 GLN D 39 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14484 Z= 0.264 Angle : 0.799 13.509 19626 Z= 0.391 Chirality : 0.050 0.370 2415 Planarity : 0.005 0.078 2359 Dihedral : 11.566 111.206 3617 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.49 % Allowed : 15.96 % Favored : 83.55 % Rotamer: Outliers : 0.14 % Allowed : 2.56 % Favored : 97.30 % 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: -2.56 (0.20), residues: 1629 helix: -0.10 (0.29), residues: 312 sheet: -0.86 (0.32), residues: 276 loop : -2.62 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 210 HIS 0.018 0.002 HIS B 170 PHE 0.022 0.002 PHE C 147 TYR 0.038 0.002 TYR b 393 ARG 0.011 0.001 ARG a 282 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 350 time to evaluate : 1.837 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 THR cc_start: 0.8736 (p) cc_final: 0.8465 (t) REVERT: B 104 GLU cc_start: 0.8403 (tt0) cc_final: 0.7780 (tt0) REVERT: B 142 LEU cc_start: 0.9215 (mp) cc_final: 0.8984 (tp) REVERT: B 149 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8206 (tm-30) REVERT: B 157 PHE cc_start: 0.8921 (m-80) cc_final: 0.8469 (m-80) REVERT: B 185 ASN cc_start: 0.8496 (p0) cc_final: 0.8195 (p0) REVERT: b 270 GLU cc_start: 0.7874 (mp0) cc_final: 0.7011 (tp30) REVERT: b 311 ASP cc_start: 0.8926 (m-30) cc_final: 0.8608 (m-30) REVERT: b 324 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8399 (tm-30) REVERT: b 325 ARG cc_start: 0.7684 (ptp90) cc_final: 0.7393 (ptp90) REVERT: b 346 ASN cc_start: 0.8788 (t0) cc_final: 0.8230 (t0) REVERT: b 357 ASP cc_start: 0.9133 (t70) cc_final: 0.8139 (t70) REVERT: b 414 MET cc_start: 0.9140 (tmm) cc_final: 0.8665 (tmm) REVERT: A 75 MET cc_start: 0.9026 (mtp) cc_final: 0.8512 (ttm) REVERT: A 76 GLU cc_start: 0.8811 (tt0) cc_final: 0.7756 (tp30) REVERT: A 82 MET cc_start: 0.8632 (pmm) cc_final: 0.8277 (pmm) REVERT: A 134 MET cc_start: 0.9003 (mmm) cc_final: 0.8491 (mmm) REVERT: A 140 PHE cc_start: 0.9278 (m-80) cc_final: 0.8879 (m-80) REVERT: A 191 PHE cc_start: 0.8662 (t80) cc_final: 0.8360 (t80) REVERT: A 219 TYR cc_start: 0.8043 (m-80) cc_final: 0.7807 (m-80) REVERT: a 266 LEU cc_start: 0.8642 (mp) cc_final: 0.8394 (tp) REVERT: a 317 ASP cc_start: 0.9425 (t0) cc_final: 0.9155 (t0) REVERT: a 324 GLN cc_start: 0.9232 (tm-30) cc_final: 0.8905 (tm-30) REVERT: a 325 ARG cc_start: 0.8638 (ptp-170) cc_final: 0.8167 (ptp-170) REVERT: a 369 TYR cc_start: 0.9075 (m-80) cc_final: 0.8800 (m-80) REVERT: a 387 LEU cc_start: 0.8618 (mt) cc_final: 0.8388 (mt) REVERT: C 82 MET cc_start: 0.8360 (mmm) cc_final: 0.8128 (mmm) REVERT: C 122 ASP cc_start: 0.8216 (p0) cc_final: 0.7983 (p0) REVERT: C 124 HIS cc_start: 0.8237 (m170) cc_final: 0.7930 (m-70) REVERT: C 192 MET cc_start: 0.8480 (mmt) cc_final: 0.8227 (mmt) REVERT: C 242 LEU cc_start: 0.8773 (mm) cc_final: 0.8504 (tp) REVERT: c 268 ASP cc_start: 0.7681 (p0) cc_final: 0.7211 (p0) REVERT: c 282 ARG cc_start: 0.8235 (ttt180) cc_final: 0.7043 (ptp-170) REVERT: c 311 ASP cc_start: 0.9385 (m-30) cc_final: 0.9053 (m-30) REVERT: c 320 LYS cc_start: 0.9246 (ttpt) cc_final: 0.9013 (ttmt) REVERT: c 337 ILE cc_start: 0.9108 (mt) cc_final: 0.8422 (mt) REVERT: c 359 MET cc_start: 0.9165 (mmm) cc_final: 0.8776 (mmm) REVERT: c 369 TYR cc_start: 0.8473 (m-80) cc_final: 0.6321 (m-80) REVERT: c 387 LEU cc_start: 0.9110 (mt) cc_final: 0.8804 (mt) REVERT: c 404 GLU cc_start: 0.9402 (mm-30) cc_final: 0.9093 (mm-30) REVERT: c 409 ASN cc_start: 0.9585 (t0) cc_final: 0.9185 (m110) REVERT: c 410 MET cc_start: 0.8878 (tpt) cc_final: 0.8331 (tpt) REVERT: D 30 SER cc_start: 0.8466 (p) cc_final: 0.8165 (m) REVERT: D 34 MET cc_start: 0.7973 (mtm) cc_final: 0.7577 (mtp) REVERT: D 37 GLU cc_start: 0.6208 (mt-10) cc_final: 0.5877 (mt-10) REVERT: D 46 GLU cc_start: 0.8647 (pt0) cc_final: 0.7685 (pm20) REVERT: D 85 ASP cc_start: 0.8210 (t70) cc_final: 0.7803 (t70) REVERT: D 99 LEU cc_start: 0.9383 (mp) cc_final: 0.8942 (mm) REVERT: H 13 LYS cc_start: 0.9681 (tppt) cc_final: 0.9470 (tppt) REVERT: H 30 ARG cc_start: 0.8219 (ptt-90) cc_final: 0.7843 (ttp-170) REVERT: H 48 ILE cc_start: 0.9173 (mt) cc_final: 0.8947 (mt) REVERT: H 67 LEU cc_start: 0.7898 (mm) cc_final: 0.7634 (mm) REVERT: H 86 ASP cc_start: 0.8858 (m-30) cc_final: 0.8387 (m-30) REVERT: H 96 PHE cc_start: 0.8652 (m-80) cc_final: 0.8351 (m-80) REVERT: L 6 GLN cc_start: 0.7461 (mt0) cc_final: 0.7094 (mp-120) REVERT: L 31 ASP cc_start: 0.8526 (p0) cc_final: 0.8253 (p0) REVERT: L 74 THR cc_start: 0.8305 (m) cc_final: 0.7976 (t) REVERT: L 78 MET cc_start: 0.8969 (tmm) cc_final: 0.8644 (tmm) REVERT: E 3 GLN cc_start: 0.8450 (tt0) cc_final: 0.7876 (tm-30) REVERT: E 47 TRP cc_start: 0.9105 (t60) cc_final: 0.7062 (t60) REVERT: E 50 TYR cc_start: 0.8832 (p90) cc_final: 0.8600 (p90) REVERT: E 67 LEU cc_start: 0.8489 (mm) cc_final: 0.8000 (mm) REVERT: E 89 VAL cc_start: 0.8508 (t) cc_final: 0.8250 (p) REVERT: I 23 CYS cc_start: 0.5630 (t) cc_final: 0.5344 (t) REVERT: I 37 GLN cc_start: 0.8117 (pp30) cc_final: 0.7747 (tm-30) REVERT: I 53 THR cc_start: 0.8916 (m) cc_final: 0.8262 (p) REVERT: I 75 ILE cc_start: 0.9235 (mt) cc_final: 0.8472 (tt) REVERT: I 77 ARG cc_start: 0.8883 (ptp90) cc_final: 0.8487 (ptp-170) REVERT: I 78 MET cc_start: 0.8786 (tpp) cc_final: 0.8061 (tpp) outliers start: 2 outliers final: 0 residues processed: 352 average time/residue: 0.2942 time to fit residues: 151.9316 Evaluate side-chains 282 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 84 optimal weight: 0.0570 chunk 151 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 92 optimal weight: 0.0000 chunk 69 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 405 GLN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 409 ASN H 77 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14484 Z= 0.201 Angle : 0.779 12.346 19626 Z= 0.380 Chirality : 0.050 0.362 2415 Planarity : 0.004 0.061 2359 Dihedral : 10.881 111.367 3617 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.49 % Allowed : 14.18 % Favored : 85.33 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.46 (0.20), residues: 1629 helix: 0.06 (0.29), residues: 308 sheet: -0.67 (0.33), residues: 259 loop : -2.59 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 210 HIS 0.011 0.001 HIS B 170 PHE 0.014 0.001 PHE C 117 TYR 0.043 0.002 TYR B 94 ARG 0.009 0.001 ARG a 282 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 1.652 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 MET cc_start: 0.8687 (mtm) cc_final: 0.8371 (mtm) REVERT: B 82 MET cc_start: 0.7770 (ptp) cc_final: 0.6934 (pmm) REVERT: B 101 THR cc_start: 0.8681 (p) cc_final: 0.8395 (t) REVERT: B 104 GLU cc_start: 0.8366 (tt0) cc_final: 0.7763 (tt0) REVERT: B 142 LEU cc_start: 0.9211 (mp) cc_final: 0.8936 (tp) REVERT: B 149 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8247 (tm-30) REVERT: B 150 TYR cc_start: 0.7440 (m-80) cc_final: 0.6935 (m-80) REVERT: B 157 PHE cc_start: 0.8927 (m-80) cc_final: 0.8493 (m-80) REVERT: B 185 ASN cc_start: 0.8359 (p0) cc_final: 0.8108 (p0) REVERT: b 270 GLU cc_start: 0.7866 (mp0) cc_final: 0.7025 (tp30) REVERT: b 311 ASP cc_start: 0.8999 (m-30) cc_final: 0.8761 (m-30) REVERT: b 317 ASP cc_start: 0.9310 (t0) cc_final: 0.8904 (t0) REVERT: b 318 PHE cc_start: 0.9377 (t80) cc_final: 0.9149 (t80) REVERT: b 325 ARG cc_start: 0.7738 (ptp90) cc_final: 0.7486 (ptp90) REVERT: b 346 ASN cc_start: 0.8770 (t0) cc_final: 0.8184 (t0) REVERT: b 353 ASN cc_start: 0.9034 (m-40) cc_final: 0.8567 (m-40) REVERT: b 357 ASP cc_start: 0.9040 (t70) cc_final: 0.8318 (t0) REVERT: b 369 TYR cc_start: 0.8584 (m-80) cc_final: 0.8261 (m-10) REVERT: b 410 MET cc_start: 0.9459 (mmm) cc_final: 0.9025 (mmm) REVERT: A 75 MET cc_start: 0.8926 (mtp) cc_final: 0.8390 (ttm) REVERT: A 82 MET cc_start: 0.8487 (pmm) cc_final: 0.8226 (pmm) REVERT: A 104 GLU cc_start: 0.7567 (tp30) cc_final: 0.6866 (tp30) REVERT: A 134 MET cc_start: 0.9036 (mmm) cc_final: 0.8565 (mmm) REVERT: A 140 PHE cc_start: 0.9269 (m-80) cc_final: 0.8870 (m-80) REVERT: A 191 PHE cc_start: 0.8723 (t80) cc_final: 0.7953 (t80) REVERT: A 219 TYR cc_start: 0.8003 (m-80) cc_final: 0.7785 (m-80) REVERT: a 266 LEU cc_start: 0.8643 (mp) cc_final: 0.8368 (tp) REVERT: a 289 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7919 (mm-30) REVERT: a 324 GLN cc_start: 0.9255 (tm-30) cc_final: 0.8822 (tm-30) REVERT: a 325 ARG cc_start: 0.8636 (ptp-170) cc_final: 0.7813 (ptp-170) REVERT: a 369 TYR cc_start: 0.9054 (m-80) cc_final: 0.8714 (m-80) REVERT: a 372 LEU cc_start: 0.9296 (mm) cc_final: 0.8839 (tp) REVERT: C 72 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8754 (mm-30) REVERT: C 124 HIS cc_start: 0.8300 (m170) cc_final: 0.7945 (m-70) REVERT: C 164 VAL cc_start: 0.7428 (t) cc_final: 0.7211 (t) REVERT: C 192 MET cc_start: 0.8310 (mmt) cc_final: 0.8004 (mmt) REVERT: c 311 ASP cc_start: 0.9388 (m-30) cc_final: 0.9012 (m-30) REVERT: c 320 LYS cc_start: 0.9237 (ttpt) cc_final: 0.8950 (ttmt) REVERT: c 337 ILE cc_start: 0.9066 (mt) cc_final: 0.8304 (mt) REVERT: c 359 MET cc_start: 0.9227 (mmm) cc_final: 0.8861 (mmm) REVERT: c 369 TYR cc_start: 0.8549 (m-80) cc_final: 0.6356 (m-80) REVERT: c 387 LEU cc_start: 0.9118 (mt) cc_final: 0.8809 (mt) REVERT: c 404 GLU cc_start: 0.9387 (mm-30) cc_final: 0.9099 (mm-30) REVERT: c 409 ASN cc_start: 0.9546 (t0) cc_final: 0.9174 (m110) REVERT: c 410 MET cc_start: 0.8848 (tpt) cc_final: 0.8313 (tpt) REVERT: D 30 SER cc_start: 0.8517 (p) cc_final: 0.8138 (m) REVERT: D 34 MET cc_start: 0.7799 (mtm) cc_final: 0.7516 (mtp) REVERT: D 46 GLU cc_start: 0.8737 (pt0) cc_final: 0.8286 (pm20) REVERT: D 75 TRP cc_start: 0.8809 (t-100) cc_final: 0.8573 (t-100) REVERT: D 85 ASP cc_start: 0.8205 (t70) cc_final: 0.7766 (t70) REVERT: D 99 LEU cc_start: 0.9300 (mp) cc_final: 0.8837 (mm) REVERT: H 13 LYS cc_start: 0.9697 (tppt) cc_final: 0.9454 (tppt) REVERT: H 20 LEU cc_start: 0.9299 (mm) cc_final: 0.9085 (mt) REVERT: H 30 ARG cc_start: 0.8197 (ptt-90) cc_final: 0.7803 (ttp-170) REVERT: H 48 ILE cc_start: 0.9076 (mt) cc_final: 0.8875 (mt) REVERT: H 86 ASP cc_start: 0.8687 (m-30) cc_final: 0.8253 (m-30) REVERT: H 96 PHE cc_start: 0.8553 (m-80) cc_final: 0.8170 (m-80) REVERT: L 6 GLN cc_start: 0.7490 (mt0) cc_final: 0.7103 (mp-120) REVERT: L 31 ASP cc_start: 0.8660 (p0) cc_final: 0.8396 (p0) REVERT: L 74 THR cc_start: 0.8220 (m) cc_final: 0.7889 (t) REVERT: L 78 MET cc_start: 0.8867 (tmm) cc_final: 0.8515 (tmm) REVERT: E 3 GLN cc_start: 0.8410 (tt0) cc_final: 0.7851 (tm-30) REVERT: E 47 TRP cc_start: 0.9009 (t60) cc_final: 0.8047 (t60) REVERT: E 50 TYR cc_start: 0.8653 (p90) cc_final: 0.8390 (p90) REVERT: E 67 LEU cc_start: 0.8492 (mm) cc_final: 0.8031 (mm) REVERT: I 37 GLN cc_start: 0.8032 (pp30) cc_final: 0.7818 (tm-30) REVERT: I 74 THR cc_start: 0.8318 (t) cc_final: 0.7757 (t) REVERT: I 75 ILE cc_start: 0.9201 (mt) cc_final: 0.8510 (tt) REVERT: I 77 ARG cc_start: 0.8836 (ptp90) cc_final: 0.8455 (ptp-170) REVERT: I 78 MET cc_start: 0.8756 (tpp) cc_final: 0.8148 (tpp) REVERT: I 83 PHE cc_start: 0.7638 (m-80) cc_final: 0.7022 (m-80) REVERT: I 104 LEU cc_start: 0.9199 (tt) cc_final: 0.8910 (tt) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.2788 time to fit residues: 149.9393 Evaluate side-chains 293 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 74 optimal weight: 0.0970 chunk 14 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 137 optimal weight: 0.0070 chunk 144 optimal weight: 4.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 409 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14484 Z= 0.233 Angle : 0.785 12.966 19626 Z= 0.381 Chirality : 0.050 0.361 2415 Planarity : 0.005 0.070 2359 Dihedral : 10.600 110.786 3617 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.49 % Allowed : 15.22 % Favored : 84.28 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.44 (0.21), residues: 1629 helix: 0.08 (0.30), residues: 309 sheet: -0.55 (0.34), residues: 255 loop : -2.61 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP C 210 HIS 0.012 0.001 HIS B 170 PHE 0.018 0.001 PHE D 68 TYR 0.056 0.002 TYR D 95 ARG 0.011 0.001 ARG D 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 1.758 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: 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: B 101 THR cc_start: 0.8702 (p) cc_final: 0.8414 (t) REVERT: B 104 GLU cc_start: 0.8263 (tt0) cc_final: 0.7678 (tt0) REVERT: B 142 LEU cc_start: 0.9200 (mp) cc_final: 0.8955 (tp) REVERT: B 149 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8292 (tm-30) REVERT: B 150 TYR cc_start: 0.7061 (m-80) cc_final: 0.6561 (m-80) REVERT: B 153 MET cc_start: 0.8090 (tpp) cc_final: 0.7742 (tpp) REVERT: B 185 ASN cc_start: 0.8311 (p0) cc_final: 0.8052 (p0) REVERT: b 270 GLU cc_start: 0.7767 (mp0) cc_final: 0.6991 (tp30) REVERT: b 311 ASP cc_start: 0.9011 (m-30) cc_final: 0.8772 (m-30) REVERT: b 325 ARG cc_start: 0.7817 (ptp90) cc_final: 0.7582 (ptp90) REVERT: b 346 ASN cc_start: 0.8808 (t0) cc_final: 0.8180 (t0) REVERT: b 357 ASP cc_start: 0.9029 (t70) cc_final: 0.8494 (t0) REVERT: b 369 TYR cc_start: 0.8828 (m-80) cc_final: 0.8589 (m-10) REVERT: b 410 MET cc_start: 0.9461 (mmm) cc_final: 0.9020 (mmm) REVERT: A 62 TYR cc_start: 0.8174 (m-10) cc_final: 0.7951 (m-10) REVERT: A 72 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8428 (mm-30) REVERT: A 75 MET cc_start: 0.9019 (mtp) cc_final: 0.8409 (ttm) REVERT: A 76 GLU cc_start: 0.8847 (tt0) cc_final: 0.7677 (tp30) REVERT: A 82 MET cc_start: 0.8581 (pmm) cc_final: 0.8277 (pmm) REVERT: A 134 MET cc_start: 0.9066 (mmm) cc_final: 0.8746 (mmm) REVERT: A 140 PHE cc_start: 0.9288 (m-80) cc_final: 0.8879 (m-80) REVERT: A 219 TYR cc_start: 0.7988 (m-80) cc_final: 0.7715 (m-80) REVERT: a 265 THR cc_start: 0.7825 (m) cc_final: 0.7497 (p) REVERT: a 266 LEU cc_start: 0.8671 (mp) cc_final: 0.8360 (tp) REVERT: a 324 GLN cc_start: 0.9251 (tm-30) cc_final: 0.8885 (tm-30) REVERT: a 325 ARG cc_start: 0.8605 (ptp-170) cc_final: 0.7931 (ptp-170) REVERT: a 369 TYR cc_start: 0.9027 (m-80) cc_final: 0.8785 (m-80) REVERT: a 372 LEU cc_start: 0.9300 (mm) cc_final: 0.8842 (tp) REVERT: C 68 LEU cc_start: 0.8315 (tp) cc_final: 0.7683 (tp) REVERT: C 72 GLU cc_start: 0.9278 (mm-30) cc_final: 0.8801 (mm-30) REVERT: C 124 HIS cc_start: 0.8283 (m170) cc_final: 0.7964 (m-70) REVERT: C 142 LEU cc_start: 0.8845 (mp) cc_final: 0.8464 (tp) REVERT: C 149 GLN cc_start: 0.9194 (tp-100) cc_final: 0.8963 (tp-100) REVERT: c 311 ASP cc_start: 0.9365 (m-30) cc_final: 0.8891 (m-30) REVERT: c 320 LYS cc_start: 0.9288 (ttpt) cc_final: 0.9031 (ttmt) REVERT: c 359 MET cc_start: 0.9146 (mmm) cc_final: 0.8848 (mmm) REVERT: c 369 TYR cc_start: 0.8556 (m-80) cc_final: 0.6311 (m-80) REVERT: c 387 LEU cc_start: 0.9109 (mt) cc_final: 0.8801 (mt) REVERT: c 404 GLU cc_start: 0.9398 (mm-30) cc_final: 0.9105 (mm-30) REVERT: c 409 ASN cc_start: 0.9548 (t0) cc_final: 0.9173 (m110) REVERT: c 410 MET cc_start: 0.8820 (tpt) cc_final: 0.8393 (tpt) REVERT: D 30 SER cc_start: 0.8355 (p) cc_final: 0.7832 (m) REVERT: D 46 GLU cc_start: 0.8630 (pt0) cc_final: 0.8068 (pm20) REVERT: D 85 ASP cc_start: 0.8227 (t70) cc_final: 0.7788 (t70) REVERT: D 99 LEU cc_start: 0.9251 (mp) cc_final: 0.8815 (mm) REVERT: H 30 ARG cc_start: 0.8208 (ptt-90) cc_final: 0.7767 (ttp-170) REVERT: H 86 ASP cc_start: 0.8748 (m-30) cc_final: 0.8262 (m-30) REVERT: H 96 PHE cc_start: 0.8670 (m-80) cc_final: 0.8381 (m-80) REVERT: L 6 GLN cc_start: 0.7373 (mt0) cc_final: 0.7107 (mp-120) REVERT: L 31 ASP cc_start: 0.8668 (p0) cc_final: 0.8421 (p0) REVERT: L 42 GLN cc_start: 0.8659 (mp10) cc_final: 0.8445 (mp10) REVERT: L 74 THR cc_start: 0.8278 (m) cc_final: 0.7929 (t) REVERT: L 78 MET cc_start: 0.8910 (tmm) cc_final: 0.8552 (tmm) REVERT: E 3 GLN cc_start: 0.8380 (tt0) cc_final: 0.7836 (tm-30) REVERT: E 47 TRP cc_start: 0.9030 (t60) cc_final: 0.8083 (t60) REVERT: E 67 LEU cc_start: 0.8473 (mm) cc_final: 0.7992 (mm) REVERT: E 89 VAL cc_start: 0.8559 (t) cc_final: 0.8332 (p) REVERT: I 74 THR cc_start: 0.8349 (t) cc_final: 0.7741 (t) REVERT: I 75 ILE cc_start: 0.9181 (mt) cc_final: 0.8405 (tp) REVERT: I 77 ARG cc_start: 0.8824 (ptp90) cc_final: 0.8414 (ptp-170) REVERT: I 78 MET cc_start: 0.8771 (tpp) cc_final: 0.8161 (tpp) REVERT: I 83 PHE cc_start: 0.7660 (m-80) cc_final: 0.6994 (m-80) REVERT: I 104 LEU cc_start: 0.9198 (tt) cc_final: 0.8905 (tt) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.2611 time to fit residues: 138.6003 Evaluate side-chains 283 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 144 optimal weight: 0.4980 chunk 84 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 409 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14484 Z= 0.210 Angle : 0.787 13.042 19626 Z= 0.385 Chirality : 0.050 0.373 2415 Planarity : 0.004 0.054 2359 Dihedral : 10.221 110.226 3617 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.43 % Allowed : 14.61 % Favored : 84.96 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.47 (0.21), residues: 1629 helix: 0.01 (0.30), residues: 311 sheet: -0.81 (0.34), residues: 270 loop : -2.56 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP C 210 HIS 0.012 0.001 HIS B 170 PHE 0.025 0.002 PHE A 140 TYR 0.051 0.002 TYR D 95 ARG 0.008 0.001 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 1.473 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 THR cc_start: 0.8684 (p) cc_final: 0.8347 (t) REVERT: B 142 LEU cc_start: 0.9190 (mp) cc_final: 0.8924 (tp) REVERT: B 149 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8383 (tm-30) REVERT: B 185 ASN cc_start: 0.8079 (p0) cc_final: 0.7860 (p0) REVERT: b 262 PHE cc_start: 0.6879 (m-80) cc_final: 0.6612 (m-80) REVERT: b 270 GLU cc_start: 0.7772 (mp0) cc_final: 0.6975 (tp30) REVERT: b 311 ASP cc_start: 0.8978 (m-30) cc_final: 0.8720 (m-30) REVERT: b 317 ASP cc_start: 0.9314 (t0) cc_final: 0.8862 (t0) REVERT: b 318 PHE cc_start: 0.9512 (t80) cc_final: 0.9284 (t80) REVERT: b 325 ARG cc_start: 0.7716 (ptp90) cc_final: 0.7415 (ptp90) REVERT: b 334 ILE cc_start: 0.9226 (tt) cc_final: 0.8938 (pt) REVERT: b 346 ASN cc_start: 0.8803 (t0) cc_final: 0.8154 (t0) REVERT: b 357 ASP cc_start: 0.8965 (t70) cc_final: 0.8458 (t0) REVERT: b 410 MET cc_start: 0.9445 (mmm) cc_final: 0.9033 (mmm) REVERT: A 72 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8441 (mm-30) REVERT: A 75 MET cc_start: 0.8989 (mtp) cc_final: 0.8634 (ttm) REVERT: A 76 GLU cc_start: 0.8857 (tt0) cc_final: 0.7675 (tp30) REVERT: A 82 MET cc_start: 0.8571 (pmm) cc_final: 0.8269 (pmm) REVERT: A 134 MET cc_start: 0.8973 (mmm) cc_final: 0.8619 (mmm) REVERT: A 191 PHE cc_start: 0.8515 (t80) cc_final: 0.8281 (t80) REVERT: A 219 TYR cc_start: 0.8000 (m-80) cc_final: 0.7728 (m-80) REVERT: a 265 THR cc_start: 0.7766 (m) cc_final: 0.7424 (p) REVERT: a 266 LEU cc_start: 0.8652 (mp) cc_final: 0.8333 (tp) REVERT: a 284 MET cc_start: 0.8639 (pmm) cc_final: 0.8392 (pmm) REVERT: a 324 GLN cc_start: 0.9215 (tm-30) cc_final: 0.8784 (tm-30) REVERT: a 325 ARG cc_start: 0.8693 (ptp-170) cc_final: 0.8041 (ptp-170) REVERT: a 369 TYR cc_start: 0.9053 (m-80) cc_final: 0.8804 (m-80) REVERT: a 372 LEU cc_start: 0.9292 (mm) cc_final: 0.8865 (tp) REVERT: C 72 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8831 (mm-30) REVERT: C 104 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7372 (mm-30) REVERT: C 124 HIS cc_start: 0.8258 (m170) cc_final: 0.7966 (m-70) REVERT: C 142 LEU cc_start: 0.8836 (mp) cc_final: 0.8530 (tp) REVERT: C 149 GLN cc_start: 0.9190 (tp-100) cc_final: 0.8951 (tp-100) REVERT: C 164 VAL cc_start: 0.7358 (t) cc_final: 0.7143 (t) REVERT: C 192 MET cc_start: 0.8292 (mmt) cc_final: 0.7618 (mmt) REVERT: c 311 ASP cc_start: 0.9228 (m-30) cc_final: 0.8874 (m-30) REVERT: c 320 LYS cc_start: 0.9286 (ttpt) cc_final: 0.9028 (ttmt) REVERT: c 359 MET cc_start: 0.9154 (mmm) cc_final: 0.8864 (mmm) REVERT: c 369 TYR cc_start: 0.8462 (m-80) cc_final: 0.6351 (m-80) REVERT: c 387 LEU cc_start: 0.9075 (mt) cc_final: 0.8752 (mt) REVERT: c 404 GLU cc_start: 0.9391 (mm-30) cc_final: 0.9130 (mm-30) REVERT: c 409 ASN cc_start: 0.9554 (t0) cc_final: 0.9183 (m110) REVERT: c 410 MET cc_start: 0.8823 (tpt) cc_final: 0.8224 (tpt) REVERT: c 414 MET cc_start: 0.8884 (ptp) cc_final: 0.8668 (ptp) REVERT: D 30 SER cc_start: 0.8382 (p) cc_final: 0.7842 (m) REVERT: D 46 GLU cc_start: 0.8660 (pt0) cc_final: 0.8030 (pm20) REVERT: D 85 ASP cc_start: 0.8218 (t70) cc_final: 0.7787 (t70) REVERT: D 99 LEU cc_start: 0.9148 (mp) cc_final: 0.8797 (mp) REVERT: H 20 LEU cc_start: 0.9279 (mm) cc_final: 0.9063 (mt) REVERT: H 30 ARG cc_start: 0.8185 (ptt-90) cc_final: 0.7790 (ttp-170) REVERT: H 86 ASP cc_start: 0.8745 (m-30) cc_final: 0.8240 (m-30) REVERT: H 96 PHE cc_start: 0.8687 (m-80) cc_final: 0.8197 (m-80) REVERT: L 31 ASP cc_start: 0.8656 (p0) cc_final: 0.8139 (p0) REVERT: L 74 THR cc_start: 0.8255 (m) cc_final: 0.7902 (t) REVERT: L 78 MET cc_start: 0.8830 (tmm) cc_final: 0.8556 (tmm) REVERT: E 3 GLN cc_start: 0.8367 (tt0) cc_final: 0.7816 (tm-30) REVERT: E 18 LEU cc_start: 0.9258 (tt) cc_final: 0.8853 (mt) REVERT: E 19 SER cc_start: 0.9152 (m) cc_final: 0.8557 (p) REVERT: E 30 ARG cc_start: 0.8334 (tpm170) cc_final: 0.7972 (tpm170) REVERT: E 47 TRP cc_start: 0.8984 (t60) cc_final: 0.8082 (t60) REVERT: E 50 TYR cc_start: 0.8609 (p90) cc_final: 0.8394 (p90) REVERT: E 67 LEU cc_start: 0.8516 (mm) cc_final: 0.8058 (mm) REVERT: E 89 VAL cc_start: 0.8501 (t) cc_final: 0.8097 (p) REVERT: I 53 THR cc_start: 0.8849 (m) cc_final: 0.8351 (p) REVERT: I 74 THR cc_start: 0.8355 (t) cc_final: 0.7766 (t) REVERT: I 75 ILE cc_start: 0.9154 (mt) cc_final: 0.8398 (tp) REVERT: I 78 MET cc_start: 0.8776 (tpp) cc_final: 0.8123 (tpp) REVERT: I 83 PHE cc_start: 0.7657 (m-80) cc_final: 0.7004 (m-80) REVERT: I 104 LEU cc_start: 0.9153 (tt) cc_final: 0.8847 (tt) outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.2760 time to fit residues: 146.6599 Evaluate side-chains 281 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 6.9990 chunk 91 optimal weight: 0.0570 chunk 70 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 HIS ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 305 HIS ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 409 ASN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14484 Z= 0.223 Angle : 0.788 11.607 19626 Z= 0.386 Chirality : 0.049 0.371 2415 Planarity : 0.005 0.075 2359 Dihedral : 10.056 110.235 3617 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.49 % Allowed : 14.86 % Favored : 84.65 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.21), residues: 1629 helix: 0.04 (0.30), residues: 310 sheet: -0.86 (0.32), residues: 287 loop : -2.52 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP C 210 HIS 0.013 0.002 HIS B 170 PHE 0.016 0.001 PHE D 68 TYR 0.035 0.002 TYR b 393 ARG 0.009 0.001 ARG a 282 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 1.678 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 THR cc_start: 0.9461 (p) cc_final: 0.9140 (t) REVERT: B 82 MET cc_start: 0.7778 (ptt) cc_final: 0.6738 (pmm) REVERT: B 101 THR cc_start: 0.8687 (p) cc_final: 0.8369 (t) REVERT: B 104 GLU cc_start: 0.8465 (tt0) cc_final: 0.7632 (tt0) REVERT: B 142 LEU cc_start: 0.9221 (mp) cc_final: 0.8998 (tp) REVERT: B 149 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8176 (tm-30) REVERT: B 153 MET cc_start: 0.7617 (tpp) cc_final: 0.7137 (tpp) REVERT: b 262 PHE cc_start: 0.6929 (m-80) cc_final: 0.6655 (m-80) REVERT: b 270 GLU cc_start: 0.7732 (mp0) cc_final: 0.6978 (tp30) REVERT: b 311 ASP cc_start: 0.8839 (m-30) cc_final: 0.8596 (m-30) REVERT: b 317 ASP cc_start: 0.9380 (t0) cc_final: 0.8904 (t0) REVERT: b 324 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8305 (tm-30) REVERT: b 325 ARG cc_start: 0.7787 (ptp90) cc_final: 0.7474 (ptp90) REVERT: b 334 ILE cc_start: 0.9221 (tt) cc_final: 0.8962 (pt) REVERT: b 346 ASN cc_start: 0.8740 (t0) cc_final: 0.8129 (t0) REVERT: b 357 ASP cc_start: 0.8965 (t70) cc_final: 0.8401 (t0) REVERT: b 410 MET cc_start: 0.9458 (mmm) cc_final: 0.9060 (mmm) REVERT: A 72 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8482 (mm-30) REVERT: A 75 MET cc_start: 0.9006 (mtp) cc_final: 0.8620 (ttm) REVERT: A 76 GLU cc_start: 0.8883 (tt0) cc_final: 0.7749 (tp30) REVERT: A 82 MET cc_start: 0.8654 (pmm) cc_final: 0.8296 (pmm) REVERT: A 191 PHE cc_start: 0.9021 (t80) cc_final: 0.8690 (t80) REVERT: A 219 TYR cc_start: 0.7959 (m-80) cc_final: 0.7684 (m-80) REVERT: a 266 LEU cc_start: 0.8653 (mp) cc_final: 0.8374 (tp) REVERT: a 284 MET cc_start: 0.8686 (pmm) cc_final: 0.8415 (pmm) REVERT: a 324 GLN cc_start: 0.9266 (tm-30) cc_final: 0.8935 (tm-30) REVERT: a 325 ARG cc_start: 0.8718 (ptp-170) cc_final: 0.8220 (ptp-170) REVERT: a 369 TYR cc_start: 0.9070 (m-80) cc_final: 0.8798 (m-80) REVERT: a 372 LEU cc_start: 0.9362 (mm) cc_final: 0.8870 (tp) REVERT: a 387 LEU cc_start: 0.8434 (mt) cc_final: 0.7604 (mt) REVERT: C 72 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8818 (mm-30) REVERT: C 124 HIS cc_start: 0.8281 (m170) cc_final: 0.7977 (m-70) REVERT: C 149 GLN cc_start: 0.9211 (tp-100) cc_final: 0.8947 (tp-100) REVERT: C 164 VAL cc_start: 0.7350 (t) cc_final: 0.7129 (t) REVERT: C 192 MET cc_start: 0.8344 (mmt) cc_final: 0.7608 (mmt) REVERT: c 311 ASP cc_start: 0.9230 (m-30) cc_final: 0.8897 (m-30) REVERT: c 320 LYS cc_start: 0.9296 (ttpt) cc_final: 0.9025 (ttmt) REVERT: c 321 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8410 (mm110) REVERT: c 359 MET cc_start: 0.9127 (mmm) cc_final: 0.8865 (mmm) REVERT: c 369 TYR cc_start: 0.8504 (m-80) cc_final: 0.6421 (m-80) REVERT: c 387 LEU cc_start: 0.9068 (mt) cc_final: 0.8742 (mt) REVERT: c 404 GLU cc_start: 0.9428 (mm-30) cc_final: 0.9162 (mm-30) REVERT: c 409 ASN cc_start: 0.9548 (t0) cc_final: 0.9180 (m110) REVERT: c 410 MET cc_start: 0.8837 (tpt) cc_final: 0.8302 (tpt) REVERT: D 46 GLU cc_start: 0.8683 (pt0) cc_final: 0.7935 (pm20) REVERT: D 85 ASP cc_start: 0.8228 (t70) cc_final: 0.7775 (t70) REVERT: D 99 LEU cc_start: 0.9210 (mp) cc_final: 0.8841 (mp) REVERT: H 20 LEU cc_start: 0.9298 (mm) cc_final: 0.9091 (mt) REVERT: H 30 ARG cc_start: 0.8250 (ptt-90) cc_final: 0.7815 (ttp-170) REVERT: H 67 LEU cc_start: 0.7546 (mm) cc_final: 0.7341 (mm) REVERT: H 86 ASP cc_start: 0.8830 (m-30) cc_final: 0.8307 (m-30) REVERT: H 96 PHE cc_start: 0.8519 (m-80) cc_final: 0.8152 (m-80) REVERT: L 31 ASP cc_start: 0.8537 (p0) cc_final: 0.8248 (p0) REVERT: L 74 THR cc_start: 0.8230 (m) cc_final: 0.7896 (t) REVERT: L 78 MET cc_start: 0.8831 (tmm) cc_final: 0.8509 (tmm) REVERT: E 3 GLN cc_start: 0.8367 (tt0) cc_final: 0.7792 (tm-30) REVERT: E 30 ARG cc_start: 0.8371 (tpm170) cc_final: 0.8024 (tpm170) REVERT: E 47 TRP cc_start: 0.8932 (t60) cc_final: 0.8059 (t60) REVERT: E 50 TYR cc_start: 0.8615 (p90) cc_final: 0.8369 (p90) REVERT: E 67 LEU cc_start: 0.8577 (mm) cc_final: 0.8100 (mm) REVERT: E 103 TRP cc_start: 0.7698 (t-100) cc_final: 0.7415 (m-90) REVERT: I 53 THR cc_start: 0.8822 (m) cc_final: 0.8266 (p) REVERT: I 74 THR cc_start: 0.8346 (t) cc_final: 0.8025 (t) REVERT: I 78 MET cc_start: 0.8779 (tpp) cc_final: 0.8179 (tpp) REVERT: I 83 PHE cc_start: 0.7700 (m-80) cc_final: 0.7050 (m-80) REVERT: I 93 ASN cc_start: 0.9110 (m110) cc_final: 0.8898 (m110) REVERT: I 104 LEU cc_start: 0.9115 (tt) cc_final: 0.8766 (tt) outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.2723 time to fit residues: 140.0428 Evaluate side-chains 272 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 52 optimal weight: 0.0980 chunk 128 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 409 ASN C 141 HIS E 53 ASN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.089045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.069650 restraints weight = 52434.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.071198 restraints weight = 37043.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.072433 restraints weight = 27011.053| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14484 Z= 0.202 Angle : 0.779 10.812 19626 Z= 0.381 Chirality : 0.049 0.380 2415 Planarity : 0.005 0.075 2359 Dihedral : 9.753 109.315 3617 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.49 % Allowed : 14.92 % Favored : 84.59 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: -2.38 (0.21), residues: 1629 helix: 0.10 (0.30), residues: 309 sheet: -0.86 (0.33), residues: 274 loop : -2.47 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP C 210 HIS 0.012 0.002 HIS B 170 PHE 0.016 0.001 PHE A 140 TYR 0.031 0.002 TYR b 393 ARG 0.008 0.001 ARG a 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3408.67 seconds wall clock time: 67 minutes 51.40 seconds (4071.40 seconds total)