Starting phenix.real_space_refine on Sat Aug 3 19:38:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rzl_19608/08_2024/8rzl_19608.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rzl_19608/08_2024/8rzl_19608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rzl_19608/08_2024/8rzl_19608.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rzl_19608/08_2024/8rzl_19608.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rzl_19608/08_2024/8rzl_19608.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rzl_19608/08_2024/8rzl_19608.cif" } resolution = 2.65 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= 0.000 sd= 0.006 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 45 5.16 5 C 5545 2.51 5 N 1145 2.21 5 O 2160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8895 Number of models: 1 Model: "" Number of chains: 35 Chain: "C" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "G" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "H" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "I" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "J" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "K" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "L" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "M" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "O" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "P" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "Q" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "R" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "T" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "V" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "W" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "Y" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "Z" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "a" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "b" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "c" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "d" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 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: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 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: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 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: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 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: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 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: 5.43, per 1000 atoms: 0.61 Number of scatterers: 8895 At special positions: 0 Unit cell: (82.071, 78.755, 214.711, 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 45 16.00 O 2160 8.00 N 1145 7.00 C 5545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 ?1-3 " NAG F 2 " - " YZT F 3 " " NAG G 2 " - " YZT G 3 " " NAG H 2 " - " YZT H 3 " " NAG I 2 " - " YZT I 3 " " NAG J 2 " - " YZT J 3 " " NAG K 2 " - " YZT K 3 " " NAG L 2 " - " YZT L 3 " " NAG M 2 " - " YZT M 3 " " NAG N 2 " - " YZT N 3 " " NAG O 2 " - " YZT O 3 " " NAG P 2 " - " YZT P 3 " " NAG Q 2 " - " YZT Q 3 " " NAG R 2 " - " YZT R 3 " " NAG S 2 " - " YZT S 3 " " NAG T 2 " - " YZT T 3 " " NAG U 2 " - " YZT U 3 " " NAG V 2 " - " YZT V 3 " " NAG W 2 " - " YZT W 3 " " NAG X 2 " - " YZT X 3 " " NAG Y 2 " - " YZT Y 3 " " NAG Z 2 " - " YZT Z 3 " " NAG a 2 " - " YZT a 3 " " NAG b 2 " - " YZT b 3 " " NAG c 2 " - " YZT c 3 " " NAG d 2 " - " YZT d 3 " ALPHA1-4 " NAG F 2 " - " MAN F 5 " " NAG G 2 " - " MAN G 5 " " NAG H 2 " - " MAN H 5 " " NAG I 2 " - " MAN I 5 " " NAG J 2 " - " MAN J 5 " " NAG K 2 " - " MAN K 5 " " NAG L 2 " - " MAN L 5 " " NAG M 2 " - " MAN M 5 " " NAG N 2 " - " MAN N 5 " " NAG O 2 " - " MAN O 5 " " NAG P 2 " - " MAN P 5 " " NAG Q 2 " - " MAN Q 5 " " NAG R 2 " - " MAN R 5 " " NAG S 2 " - " MAN S 5 " " NAG T 2 " - " MAN T 5 " " NAG U 2 " - " MAN U 5 " " NAG V 2 " - " MAN V 5 " " NAG W 2 " - " MAN W 5 " " NAG X 2 " - " MAN X 5 " " NAG Y 2 " - " MAN Y 5 " " NAG Z 2 " - " MAN Z 5 " " NAG a 2 " - " MAN a 5 " " NAG b 2 " - " MAN b 5 " " NAG c 2 " - " MAN c 5 " " NAG d 2 " - " MAN d 5 " ALPHA1-6 " NAG F 2 " - " MAN F 6 " " NAG G 2 " - " MAN G 6 " " NAG H 2 " - " MAN H 6 " " NAG I 2 " - " MAN I 6 " " NAG J 2 " - " MAN J 6 " " NAG K 2 " - " MAN K 6 " " NAG L 2 " - " MAN L 6 " " NAG M 2 " - " MAN M 6 " " NAG N 2 " - " MAN N 6 " " NAG O 2 " - " MAN O 6 " " NAG P 2 " - " MAN P 6 " " NAG Q 2 " - " MAN Q 6 " " NAG R 2 " - " MAN R 6 " " NAG S 2 " - " MAN S 6 " " NAG T 2 " - " MAN T 6 " " NAG U 2 " - " MAN U 6 " " NAG V 2 " - " MAN V 6 " " NAG W 2 " - " MAN W 6 " " NAG X 2 " - " MAN X 6 " " NAG Y 2 " - " MAN Y 6 " " NAG Z 2 " - " MAN Z 6 " " NAG a 2 " - " MAN a 6 " " NAG b 2 " - " MAN b 6 " " NAG c 2 " - " MAN c 6 " " NAG d 2 " - " MAN d 6 " BETA1-4 " NAG F 1 " - " NAG F 2 " " YZT F 3 " - " BGC F 4 " " NAG G 1 " - " NAG G 2 " " YZT G 3 " - " BGC G 4 " " NAG H 1 " - " NAG H 2 " " YZT H 3 " - " BGC H 4 " " NAG I 1 " - " NAG I 2 " " YZT I 3 " - " BGC I 4 " " NAG J 1 " - " NAG J 2 " " YZT J 3 " - " BGC J 4 " " NAG K 1 " - " NAG K 2 " " YZT K 3 " - " BGC K 4 " " NAG L 1 " - " NAG L 2 " " YZT L 3 " - " BGC L 4 " " NAG M 1 " - " NAG M 2 " " YZT M 3 " - " BGC M 4 " " NAG N 1 " - " NAG N 2 " " YZT N 3 " - " BGC N 4 " " NAG O 1 " - " NAG O 2 " " YZT O 3 " - " BGC O 4 " " NAG P 1 " - " NAG P 2 " " YZT P 3 " - " BGC P 4 " " NAG Q 1 " - " NAG Q 2 " " YZT Q 3 " - " BGC Q 4 " " NAG R 1 " - " NAG R 2 " " YZT R 3 " - " BGC R 4 " " NAG S 1 " - " NAG S 2 " " YZT S 3 " - " BGC S 4 " " NAG T 1 " - " NAG T 2 " " YZT T 3 " - " BGC T 4 " " NAG U 1 " - " NAG U 2 " " YZT U 3 " - " BGC U 4 " " NAG V 1 " - " NAG V 2 " " YZT V 3 " - " BGC V 4 " " NAG W 1 " - " NAG W 2 " " YZT W 3 " - " BGC W 4 " " NAG X 1 " - " NAG X 2 " " YZT X 3 " - " BGC X 4 " " NAG Y 1 " - " NAG Y 2 " " YZT Y 3 " - " BGC Y 4 " " NAG Z 1 " - " NAG Z 2 " " YZT Z 3 " - " BGC Z 4 " " NAG a 1 " - " NAG a 2 " " YZT a 3 " - " BGC a 4 " " NAG b 1 " - " NAG b 2 " " YZT b 3 " - " BGC b 4 " " NAG c 1 " - " NAG c 2 " " YZT c 3 " - " BGC c 4 " " NAG d 1 " - " NAG d 2 " " YZT d 3 " - " BGC d 4 " MAN-THR " MAN A 311 " - " THR A 195 " " MAN B 311 " - " THR B 195 " " MAN C 311 " - " THR C 195 " " MAN D 311 " - " THR D 195 " " MAN E 311 " - " THR E 195 " NAG-ASN " NAG F 1 " - " ASN C 56 " " NAG G 1 " - " ASN C 80 " " NAG H 1 " - " ASN C 83 " " NAG I 1 " - " ASN C 146 " " NAG J 1 " - " ASN C 121 " " NAG K 1 " - " ASN E 56 " " NAG L 1 " - " ASN E 80 " " NAG M 1 " - " ASN E 83 " " NAG N 1 " - " ASN E 146 " " NAG O 1 " - " ASN E 121 " " NAG P 1 " - " ASN A 56 " " NAG Q 1 " - " ASN A 80 " " NAG R 1 " - " ASN A 83 " " NAG S 1 " - " ASN A 146 " " NAG T 1 " - " ASN A 121 " " NAG U 1 " - " ASN B 56 " " NAG V 1 " - " ASN B 80 " " NAG W 1 " - " ASN B 83 " " NAG X 1 " - " ASN B 146 " " NAG Y 1 " - " ASN B 121 " " NAG Z 1 " - " ASN D 56 " " NAG a 1 " - " ASN D 80 " " NAG b 1 " - " ASN D 83 " " NAG c 1 " - " ASN D 146 " " NAG d 1 " - " ASN D 121 " Time building additional restraints: 6.73 Conformation dependent library (CDL) restraints added in 1.3 seconds 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1690 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 11 sheets defined 4.5% alpha, 54.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'C' and resid 47 through 51 Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'E' and resid 47 through 51 Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'D' and resid 47 through 51 Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 145 removed outlier: 6.428A pdb=" N ALA A 122 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL A 141 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N GLN A 120 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY A 159 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LEU A 95 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N TYR A 161 " --> pdb=" O MET A 93 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N MET A 93 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL A 163 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 91 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ASN C 37 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASP B 181 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLY B 190 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU B 105 " --> pdb=" O GLY B 190 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N SER B 192 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE B 103 " --> pdb=" O SER B 192 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 45 Processing sheet with id=AA4, first strand: chain 'C' and resid 144 through 145 removed outlier: 6.428A pdb=" N ALA C 122 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL C 141 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLN C 120 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY C 159 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU C 95 " --> pdb=" O GLY C 159 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N TYR C 161 " --> pdb=" O MET C 93 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N MET C 93 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL C 163 " --> pdb=" O ASN C 91 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN C 91 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ASN E 37 " --> pdb=" O ASP D 181 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASP D 181 " --> pdb=" O ASN E 37 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLY D 190 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU D 105 " --> pdb=" O GLY D 190 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N SER D 192 " --> pdb=" O ILE D 103 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ILE D 103 " --> pdb=" O SER D 192 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.589A pdb=" N PHE C 75 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N THR D 34 " --> pdb=" O PHE C 75 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA C 77 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLY D 36 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL C 79 " --> pdb=" O GLY D 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 154 through 156 removed outlier: 5.638A pdb=" N ILE C 103 " --> pdb=" O SER C 192 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N SER C 192 " --> pdb=" O ILE C 103 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU C 105 " --> pdb=" O GLY C 190 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLY C 190 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ASP C 181 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ASN D 37 " --> pdb=" O ASP C 181 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN B 91 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL B 163 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N MET B 93 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N TYR B 161 " --> pdb=" O MET B 93 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LEU B 95 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY B 159 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLN B 120 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL B 141 " --> pdb=" O GLN B 120 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA B 122 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 42 through 45 removed outlier: 3.514A pdb=" N ASN E 91 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N VAL E 163 " --> pdb=" O ASN E 91 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N MET E 93 " --> pdb=" O TYR E 161 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N TYR E 161 " --> pdb=" O MET E 93 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU E 95 " --> pdb=" O GLY E 159 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY E 159 " --> pdb=" O LEU E 95 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN E 120 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL E 141 " --> pdb=" O GLN E 120 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA E 122 " --> pdb=" O LEU E 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 59 through 60 Processing sheet with id=AA9, first strand: chain 'E' and resid 154 through 156 removed outlier: 5.637A pdb=" N ILE E 103 " --> pdb=" O SER E 192 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N SER E 192 " --> pdb=" O ILE E 103 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU E 105 " --> pdb=" O GLY E 190 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLY E 190 " --> pdb=" O LEU E 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.529A pdb=" N PHE A 75 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N THR B 34 " --> pdb=" O PHE A 75 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA A 77 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N GLY B 36 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL A 79 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ASN B 37 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ASP A 181 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLY A 190 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU A 105 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N SER A 192 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE A 103 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 42 through 45 removed outlier: 3.512A pdb=" N ASN D 91 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL D 163 " --> pdb=" O ASN D 91 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N MET D 93 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N TYR D 161 " --> pdb=" O MET D 93 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LEU D 95 " --> pdb=" O GLY D 159 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY D 159 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN D 120 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL D 141 " --> pdb=" O GLN D 120 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA D 122 " --> pdb=" O LEU D 139 " (cutoff:3.500A) 284 hydrogen bonds defined for protein. 732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 6.82 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: 1416 1.34 - 1.46: 3025 1.46 - 1.58: 4589 1.58 - 1.70: 0 1.70 - 1.81: 65 Bond restraints: 9095 Sorted by residual: bond pdb=" CA SER A 58 " pdb=" CB SER A 58 " ideal model delta sigma weight residual 1.529 1.449 0.080 1.74e-02 3.30e+03 2.10e+01 bond pdb=" CA SER D 58 " pdb=" CB SER D 58 " ideal model delta sigma weight residual 1.529 1.450 0.079 1.74e-02 3.30e+03 2.08e+01 bond pdb=" CA SER B 58 " pdb=" CB SER B 58 " ideal model delta sigma weight residual 1.529 1.451 0.079 1.74e-02 3.30e+03 2.04e+01 bond pdb=" CA SER E 58 " pdb=" CB SER E 58 " ideal model delta sigma weight residual 1.529 1.451 0.078 1.74e-02 3.30e+03 2.02e+01 bond pdb=" CA SER C 58 " pdb=" CB SER C 58 " ideal model delta sigma weight residual 1.529 1.451 0.078 1.74e-02 3.30e+03 2.01e+01 ... (remaining 9090 not shown) Histogram of bond angle deviations from ideal: 99.61 - 105.24: 385 105.24 - 110.88: 3345 110.88 - 116.51: 3686 116.51 - 122.14: 3377 122.14 - 127.77: 1737 Bond angle restraints: 12530 Sorted by residual: angle pdb=" C ASN A 57 " pdb=" N SER A 58 " pdb=" CA SER A 58 " ideal model delta sigma weight residual 120.72 109.13 11.59 1.67e+00 3.59e-01 4.82e+01 angle pdb=" C ASN D 57 " pdb=" N SER D 58 " pdb=" CA SER D 58 " ideal model delta sigma weight residual 120.72 109.14 11.58 1.67e+00 3.59e-01 4.81e+01 angle pdb=" C ASN E 57 " pdb=" N SER E 58 " pdb=" CA SER E 58 " ideal model delta sigma weight residual 120.72 109.14 11.58 1.67e+00 3.59e-01 4.81e+01 angle pdb=" C ASN C 57 " pdb=" N SER C 58 " pdb=" CA SER C 58 " ideal model delta sigma weight residual 120.72 109.19 11.53 1.67e+00 3.59e-01 4.77e+01 angle pdb=" C ASN B 57 " pdb=" N SER B 58 " pdb=" CA SER B 58 " ideal model delta sigma weight residual 120.72 109.19 11.53 1.67e+00 3.59e-01 4.77e+01 ... (remaining 12525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.52: 7034 23.52 - 47.05: 221 47.05 - 70.57: 45 70.57 - 94.09: 25 94.09 - 117.61: 45 Dihedral angle restraints: 7370 sinusoidal: 4685 harmonic: 2685 Sorted by residual: dihedral pdb=" CA VAL A 60 " pdb=" C VAL A 60 " pdb=" N PRO A 61 " pdb=" CA PRO A 61 " ideal model delta harmonic sigma weight residual 180.00 -152.84 -27.16 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA VAL D 60 " pdb=" C VAL D 60 " pdb=" N PRO D 61 " pdb=" CA PRO D 61 " ideal model delta harmonic sigma weight residual -180.00 -153.36 -26.64 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA VAL E 60 " pdb=" C VAL E 60 " pdb=" N PRO E 61 " pdb=" CA PRO E 61 " ideal model delta harmonic sigma weight residual -180.00 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 7367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1302 0.095 - 0.191: 473 0.191 - 0.286: 65 0.286 - 0.381: 16 0.381 - 0.477: 14 Chirality restraints: 1870 Sorted by residual: chirality pdb=" C1 MAN R 6 " pdb=" O6 NAG R 2 " pdb=" C2 MAN R 6 " pdb=" O5 MAN R 6 " both_signs ideal model delta sigma weight residual False 2.40 2.00 0.40 2.00e-02 2.50e+03 3.96e+02 chirality pdb=" C1 MAN b 6 " pdb=" O6 NAG b 2 " pdb=" C2 MAN b 6 " pdb=" O5 MAN b 6 " both_signs ideal model delta sigma weight residual False 2.40 2.01 0.39 2.00e-02 2.50e+03 3.87e+02 chirality pdb=" C1 MAN H 6 " pdb=" O6 NAG H 2 " pdb=" C2 MAN H 6 " pdb=" O5 MAN H 6 " both_signs ideal model delta sigma weight residual False 2.40 2.01 0.39 2.00e-02 2.50e+03 3.84e+02 ... (remaining 1867 not shown) Planarity restraints: 1355 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " -0.107 2.00e-02 2.50e+03 8.79e-02 9.65e+01 pdb=" C7 NAG R 1 " 0.034 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " -0.082 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " 0.138 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 1 " -0.099 2.00e-02 2.50e+03 8.13e-02 8.26e+01 pdb=" C7 NAG b 1 " 0.028 2.00e-02 2.50e+03 pdb=" C8 NAG b 1 " -0.075 2.00e-02 2.50e+03 pdb=" N2 NAG b 1 " 0.128 2.00e-02 2.50e+03 pdb=" O7 NAG b 1 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 1 " -0.099 2.00e-02 2.50e+03 8.10e-02 8.20e+01 pdb=" C7 NAG W 1 " 0.028 2.00e-02 2.50e+03 pdb=" C8 NAG W 1 " -0.075 2.00e-02 2.50e+03 pdb=" N2 NAG W 1 " 0.128 2.00e-02 2.50e+03 pdb=" O7 NAG W 1 " 0.018 2.00e-02 2.50e+03 ... (remaining 1352 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.05: 3 2.05 - 2.76: 740 2.76 - 3.47: 11860 3.47 - 4.19: 22169 4.19 - 4.90: 36020 Nonbonded interactions: 70792 Sorted by model distance: nonbonded pdb=" N ASP C 24 " pdb=" CG ASN A 57 " model vdw 1.332 3.350 nonbonded pdb=" CG ASN B 57 " pdb=" N ASP D 24 " model vdw 1.334 3.350 nonbonded pdb=" CG ASN C 57 " pdb=" N ASP E 24 " model vdw 1.335 3.350 nonbonded pdb=" OD1 ASN B 57 " pdb=" N ASP D 24 " model vdw 2.246 3.120 nonbonded pdb=" N ASP C 24 " pdb=" OD1 ASN A 57 " model vdw 2.247 3.120 ... (remaining 70787 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 29.060 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 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:11.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 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 : 0.012 0.080 9095 Z= 0.709 Angle : 1.571 11.592 12530 Z= 0.841 Chirality : 0.102 0.477 1870 Planarity : 0.009 0.088 1330 Dihedral : 15.365 117.611 5680 Min Nonbonded Distance : 1.332 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.21 % Allowed : 4.49 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.27), residues: 905 helix: None (None), residues: 0 sheet: 1.22 (0.25), residues: 380 loop : 0.28 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.003 PHE A 191 TYR 0.052 0.009 TYR A 89 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 62 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 87 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8449 (m-40) outliers start: 25 outliers final: 11 residues processed: 87 average time/residue: 1.1542 time to fit residues: 107.4912 Evaluate side-chains 52 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 40 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 195 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 GLN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 GLN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN D 78 GLN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9095 Z= 0.266 Angle : 0.767 8.015 12530 Z= 0.345 Chirality : 0.047 0.203 1870 Planarity : 0.005 0.032 1330 Dihedral : 12.200 113.191 4134 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.67 % Allowed : 10.26 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.28), residues: 905 helix: None (None), residues: 0 sheet: 0.61 (0.25), residues: 405 loop : 1.24 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE B 189 TYR 0.016 0.002 TYR D 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 41 time to evaluate : 0.955 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 51 average time/residue: 1.1870 time to fit residues: 65.3256 Evaluate side-chains 47 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain D residue 163 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 22 optimal weight: 0.0770 chunk 81 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 GLN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9095 Z= 0.203 Angle : 0.645 5.399 12530 Z= 0.292 Chirality : 0.044 0.204 1870 Planarity : 0.005 0.035 1330 Dihedral : 9.497 108.313 4125 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.28 % Allowed : 12.05 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.28), residues: 905 helix: None (None), residues: 0 sheet: 0.80 (0.26), residues: 340 loop : 1.20 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE A 189 TYR 0.013 0.001 TYR B 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8209 (ptpt) cc_final: 0.7932 (ptmm) outliers start: 10 outliers final: 6 residues processed: 56 average time/residue: 1.3081 time to fit residues: 78.4520 Evaluate side-chains 47 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain D residue 163 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 GLN E 37 ASN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9061 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9095 Z= 0.324 Angle : 0.666 5.889 12530 Z= 0.300 Chirality : 0.044 0.193 1870 Planarity : 0.004 0.032 1330 Dihedral : 9.452 112.830 4125 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.05 % Allowed : 11.28 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.28), residues: 905 helix: None (None), residues: 0 sheet: 0.55 (0.26), residues: 340 loop : 1.41 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE B 92 TYR 0.012 0.001 TYR C 89 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 41 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8214 (ptpt) cc_final: 0.7954 (ptmm) outliers start: 16 outliers final: 10 residues processed: 56 average time/residue: 1.1794 time to fit residues: 71.3945 Evaluate side-chains 51 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain D residue 163 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 GLN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9095 Z= 0.358 Angle : 0.671 6.095 12530 Z= 0.301 Chirality : 0.044 0.192 1870 Planarity : 0.004 0.033 1330 Dihedral : 9.327 111.252 4125 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.92 % Allowed : 11.28 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.28), residues: 905 helix: None (None), residues: 0 sheet: 0.30 (0.26), residues: 340 loop : 1.45 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE B 92 TYR 0.013 0.001 TYR C 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 41 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: E 53 LYS cc_start: 0.9595 (OUTLIER) cc_final: 0.9214 (mtpp) REVERT: A 99 LYS cc_start: 0.8243 (ptpt) cc_final: 0.7989 (ptmm) outliers start: 15 outliers final: 9 residues processed: 52 average time/residue: 1.2077 time to fit residues: 67.9181 Evaluate side-chains 51 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain D residue 163 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 87 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 GLN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9095 Z= 0.285 Angle : 0.645 5.695 12530 Z= 0.288 Chirality : 0.043 0.197 1870 Planarity : 0.004 0.031 1330 Dihedral : 9.168 109.378 4125 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.44 % Allowed : 10.38 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.28), residues: 905 helix: None (None), residues: 0 sheet: -0.17 (0.25), residues: 370 loop : 1.59 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE D 75 TYR 0.013 0.001 TYR B 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 41 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8283 (ptpt) cc_final: 0.8033 (ptmm) outliers start: 19 outliers final: 14 residues processed: 58 average time/residue: 1.0815 time to fit residues: 68.0982 Evaluate side-chains 55 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 41 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 163 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 GLN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9114 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.067 9095 Z= 0.639 Angle : 0.797 7.263 12530 Z= 0.353 Chirality : 0.046 0.165 1870 Planarity : 0.004 0.033 1330 Dihedral : 9.647 114.006 4125 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.56 % Allowed : 10.77 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.28), residues: 905 helix: None (None), residues: 0 sheet: 0.17 (0.26), residues: 320 loop : 1.12 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE C 92 TYR 0.014 0.002 TYR C 89 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 42 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: E 53 LYS cc_start: 0.9571 (OUTLIER) cc_final: 0.9163 (mtpp) REVERT: A 99 LYS cc_start: 0.8217 (ptpt) cc_final: 0.7967 (ptmm) outliers start: 20 outliers final: 14 residues processed: 58 average time/residue: 1.1715 time to fit residues: 73.3918 Evaluate side-chains 57 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 42 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 184 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 78 optimal weight: 0.4980 chunk 83 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9095 Z= 0.172 Angle : 0.633 6.355 12530 Z= 0.282 Chirality : 0.043 0.216 1870 Planarity : 0.004 0.030 1330 Dihedral : 9.005 104.941 4125 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.67 % Allowed : 10.77 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.28), residues: 905 helix: None (None), residues: 0 sheet: 0.03 (0.26), residues: 340 loop : 1.36 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE D 75 TYR 0.012 0.001 TYR B 89 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 53 LYS cc_start: 0.9574 (OUTLIER) cc_final: 0.9193 (mtpp) REVERT: A 99 LYS cc_start: 0.8331 (ptpt) cc_final: 0.8092 (ptmm) outliers start: 13 outliers final: 12 residues processed: 52 average time/residue: 1.1273 time to fit residues: 63.4975 Evaluate side-chains 52 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 39 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 184 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 76 optimal weight: 0.0670 chunk 53 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9095 Z= 0.283 Angle : 0.649 7.041 12530 Z= 0.288 Chirality : 0.043 0.193 1870 Planarity : 0.004 0.029 1330 Dihedral : 9.014 107.242 4125 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.92 % Allowed : 10.64 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.29), residues: 905 helix: None (None), residues: 0 sheet: -0.36 (0.25), residues: 370 loop : 1.54 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE D 75 TYR 0.012 0.001 TYR C 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 40 time to evaluate : 0.804 Fit side-chains REVERT: E 53 LYS cc_start: 0.9579 (OUTLIER) cc_final: 0.9172 (mtpp) REVERT: A 99 LYS cc_start: 0.8325 (ptpt) cc_final: 0.8077 (ptmm) outliers start: 15 outliers final: 12 residues processed: 52 average time/residue: 1.1295 time to fit residues: 63.7142 Evaluate side-chains 53 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 184 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 0.1980 chunk 82 optimal weight: 3.9990 chunk 71 optimal weight: 0.0870 chunk 7 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9095 Z= 0.161 Angle : 0.608 7.105 12530 Z= 0.271 Chirality : 0.043 0.214 1870 Planarity : 0.004 0.029 1330 Dihedral : 8.688 102.883 4125 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.67 % Allowed : 10.64 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.29), residues: 905 helix: None (None), residues: 0 sheet: -0.00 (0.27), residues: 340 loop : 1.40 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE C 92 TYR 0.011 0.001 TYR B 89 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 0.886 Fit side-chains REVERT: A 99 LYS cc_start: 0.8516 (ptpt) cc_final: 0.8284 (ptmm) outliers start: 13 outliers final: 12 residues processed: 52 average time/residue: 1.1729 time to fit residues: 66.0113 Evaluate side-chains 52 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 40 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 184 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.074269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.048511 restraints weight = 23524.652| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 3.85 r_work: 0.2568 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9095 Z= 0.199 Angle : 0.610 6.201 12530 Z= 0.272 Chirality : 0.043 0.197 1870 Planarity : 0.004 0.028 1330 Dihedral : 8.646 103.487 4125 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.79 % Allowed : 10.51 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.29), residues: 905 helix: None (None), residues: 0 sheet: 0.04 (0.26), residues: 340 loop : 1.40 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE C 92 TYR 0.012 0.001 TYR C 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2416.32 seconds wall clock time: 43 minutes 54.62 seconds (2634.62 seconds total)