Starting phenix.real_space_refine on Tue Jun 25 23:20:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rzl_19608/06_2024/8rzl_19608_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rzl_19608/06_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_19608/06_2024/8rzl_19608.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rzl_19608/06_2024/8rzl_19608.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rzl_19608/06_2024/8rzl_19608_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rzl_19608/06_2024/8rzl_19608_updated.pdb" } 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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 5.59, per 1000 atoms: 0.63 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: 6.64 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... running ksdssp... Secondary structure from input PDB file: 10 helices and 20 sheets defined 3.3% alpha, 35.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' 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 48 through 50 No H-bonds generated for 'chain 'E' and resid 48 through 50' Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'A' and resid 48 through 50 No H-bonds generated for 'chain 'A' and resid 48 through 50' 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 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' 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 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' 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= A, first strand: chain 'C' and resid 42 through 45 removed outlier: 3.602A pdb=" N MET C 93 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU C 124 " --> pdb=" O LYS C 138 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LYS C 138 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE C 126 " --> pdb=" O LYS C 136 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LYS C 136 " --> pdb=" O ILE C 126 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 64 through 68 Processing sheet with id= C, first strand: chain 'C' and resid 87 through 89 Processing sheet with id= D, first strand: chain 'C' and resid 154 through 156 removed outlier: 6.691A pdb=" N ASN C 188 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL C 108 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR C 186 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR C 110 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR C 184 " --> pdb=" O TYR C 110 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 42 through 45 removed outlier: 3.602A pdb=" N MET E 93 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU E 124 " --> pdb=" O LYS E 138 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS E 138 " --> pdb=" O LEU E 124 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE E 126 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LYS E 136 " --> pdb=" O ILE E 126 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 64 through 68 Processing sheet with id= G, first strand: chain 'E' and resid 87 through 89 Processing sheet with id= H, first strand: chain 'E' and resid 154 through 156 removed outlier: 6.689A pdb=" N ASN E 188 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL E 108 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR E 186 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR E 110 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR E 184 " --> pdb=" O TYR E 110 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.603A pdb=" N MET A 93 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU A 124 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS A 138 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE A 126 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LYS A 136 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 64 through 68 Processing sheet with id= K, first strand: chain 'A' and resid 87 through 89 Processing sheet with id= L, first strand: chain 'A' and resid 154 through 156 removed outlier: 6.691A pdb=" N ASN A 188 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL A 108 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR A 186 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR A 110 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR A 184 " --> pdb=" O TYR A 110 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 42 through 45 removed outlier: 3.603A pdb=" N MET B 93 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU B 124 " --> pdb=" O LYS B 138 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LYS B 138 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE B 126 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LYS B 136 " --> pdb=" O ILE B 126 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 64 through 68 Processing sheet with id= O, first strand: chain 'B' and resid 87 through 89 Processing sheet with id= P, first strand: chain 'B' and resid 154 through 156 removed outlier: 6.691A pdb=" N ASN B 188 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL B 108 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR B 186 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR B 110 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR B 184 " --> pdb=" O TYR B 110 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 42 through 45 removed outlier: 3.602A pdb=" N MET D 93 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU D 124 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LYS D 138 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE D 126 " --> pdb=" O LYS D 136 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LYS D 136 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 64 through 68 Processing sheet with id= S, first strand: chain 'D' and resid 87 through 89 Processing sheet with id= T, first strand: chain 'D' and resid 154 through 156 removed outlier: 6.690A pdb=" N ASN D 188 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL D 108 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR D 186 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR D 110 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR D 184 " --> pdb=" O TYR D 110 " (cutoff:3.500A) 180 hydrogen bonds defined for protein. 465 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: 2.07 Time building geometry restraints manager: 6.92 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: 767 2.76 - 3.47: 11926 3.47 - 4.19: 22411 4.19 - 4.90: 36053 Nonbonded interactions: 71160 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 2.520 nonbonded pdb=" N ASP C 24 " pdb=" OD1 ASN A 57 " model vdw 2.247 2.520 ... (remaining 71155 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 1.280 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: 3.680 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 28.530 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.800 ------------------------------------------------------------------------------- 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= 0.704 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 : 0.892 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: 1.1474 time to fit residues: 106.8771 Evaluate side-chains 52 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 40 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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: 0.9990 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 0.0020 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 21.9990 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9095 Z= 0.223 Angle : 0.731 8.170 12530 Z= 0.322 Chirality : 0.048 0.226 1870 Planarity : 0.005 0.032 1330 Dihedral : 12.056 112.074 4134 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.31 % Allowed : 9.87 % Favored : 87.82 % 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: 1.39 (0.29), residues: 905 helix: None (None), residues: 0 sheet: 0.69 (0.25), residues: 410 loop : 1.35 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE D 92 TYR 0.017 0.002 TYR A 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 56 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 38 time to evaluate : 0.864 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 52 average time/residue: 1.1754 time to fit residues: 66.0981 Evaluate side-chains 48 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 38 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 E residue 187 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 187 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: 6.9990 chunk 25 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 0.0060 chunk 65 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 overall best weight: 3.2004 ------------------------------------------------------------------------------- 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 A 129 GLN ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9095 Z= 0.379 Angle : 0.696 6.178 12530 Z= 0.308 Chirality : 0.045 0.187 1870 Planarity : 0.004 0.033 1330 Dihedral : 9.823 112.932 4125 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.18 % Allowed : 11.41 % Favored : 86.41 % 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: 1.33 (0.29), residues: 905 helix: None (None), residues: 0 sheet: 0.55 (0.26), residues: 380 loop : 1.37 (0.31), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE C 92 TYR 0.012 0.002 TYR B 88 *********************** 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 60 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 43 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8224 (ptpt) cc_final: 0.7993 (ptmm) outliers start: 17 outliers final: 10 residues processed: 59 average time/residue: 1.1126 time to fit residues: 70.9911 Evaluate side-chains 52 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 E residue 187 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 187 VAL Chi-restraints excluded: chain D residue 87 ASN 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: 6.9990 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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 37 ASN E 120 GLN ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 9095 Z= 0.404 Angle : 0.681 8.503 12530 Z= 0.299 Chirality : 0.045 0.213 1870 Planarity : 0.004 0.034 1330 Dihedral : 9.664 112.092 4125 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.21 % Allowed : 10.64 % Favored : 86.15 % 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: 1.45 (0.29), residues: 905 helix: None (None), residues: 0 sheet: 0.76 (0.27), residues: 350 loop : 1.31 (0.29), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE B 92 TYR 0.011 0.001 TYR B 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 67 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 42 time to evaluate : 0.793 Fit side-chains REVERT: E 53 LYS cc_start: 0.9553 (OUTLIER) cc_final: 0.9175 (mtpp) REVERT: A 99 LYS cc_start: 0.8226 (ptpt) cc_final: 0.7962 (ptmm) outliers start: 25 outliers final: 16 residues processed: 63 average time/residue: 0.9405 time to fit residues: 64.4503 Evaluate side-chains 58 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 41 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 187 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 187 VAL Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 148 THR 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: 0.7980 chunk 35 optimal weight: 4.9990 chunk 74 optimal weight: 0.3980 chunk 60 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 GLN ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9095 Z= 0.234 Angle : 0.617 5.555 12530 Z= 0.270 Chirality : 0.044 0.206 1870 Planarity : 0.004 0.030 1330 Dihedral : 9.261 107.432 4125 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.69 % Allowed : 10.90 % Favored : 86.41 % 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: 1.71 (0.29), residues: 905 helix: None (None), residues: 0 sheet: 0.98 (0.27), residues: 340 loop : 1.45 (0.29), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE B 92 TYR 0.011 0.001 TYR B 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 64 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 43 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8251 (ptpt) cc_final: 0.7982 (ptmm) outliers start: 21 outliers final: 13 residues processed: 63 average time/residue: 0.9269 time to fit residues: 63.8490 Evaluate side-chains 54 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 41 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 C residue 187 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 79 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 79 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: 10.0000 chunk 21 optimal weight: 10.0000 chunk 87 optimal weight: 0.4980 chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 GLN A 180 ASN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9095 Z= 0.218 Angle : 0.607 5.787 12530 Z= 0.264 Chirality : 0.044 0.219 1870 Planarity : 0.004 0.029 1330 Dihedral : 9.097 106.910 4125 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.31 % Allowed : 11.03 % 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: 1.71 (0.29), residues: 905 helix: None (None), residues: 0 sheet: 0.97 (0.27), residues: 340 loop : 1.46 (0.29), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE B 92 TYR 0.010 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 58 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 40 time to evaluate : 0.858 Fit side-chains REVERT: A 99 LYS cc_start: 0.8288 (ptpt) cc_final: 0.8021 (ptmm) outliers start: 18 outliers final: 13 residues processed: 58 average time/residue: 1.0485 time to fit residues: 65.9594 Evaluate side-chains 53 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 C residue 187 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 B residue 79 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL 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: 8.9990 chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 0.1980 chunk 48 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9063 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9095 Z= 0.295 Angle : 0.629 6.223 12530 Z= 0.274 Chirality : 0.044 0.197 1870 Planarity : 0.004 0.030 1330 Dihedral : 9.139 107.538 4125 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.44 % Allowed : 10.77 % 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: 1.42 (0.30), residues: 905 helix: None (None), residues: 0 sheet: 0.35 (0.26), residues: 380 loop : 1.67 (0.31), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE B 92 TYR 0.010 0.001 TYR B 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 59 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 40 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8312 (ptpt) cc_final: 0.8024 (ptmm) outliers start: 19 outliers final: 16 residues processed: 59 average time/residue: 1.1529 time to fit residues: 73.8078 Evaluate side-chains 56 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 40 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 C residue 187 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 B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain D residue 24 ASP 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: 6.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9095 Z= 0.173 Angle : 0.588 6.527 12530 Z= 0.256 Chirality : 0.044 0.227 1870 Planarity : 0.004 0.028 1330 Dihedral : 8.788 103.061 4125 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.31 % Allowed : 10.38 % Favored : 87.31 % 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: 1.79 (0.29), residues: 905 helix: None (None), residues: 0 sheet: 0.97 (0.27), residues: 340 loop : 1.56 (0.29), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE B 92 TYR 0.009 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 59 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 41 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: E 138 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8964 (mttp) REVERT: A 99 LYS cc_start: 0.8383 (ptpt) cc_final: 0.8148 (ptmm) outliers start: 18 outliers final: 13 residues processed: 58 average time/residue: 1.1056 time to fit residues: 69.3775 Evaluate side-chains 54 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 40 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 C residue 187 VAL Chi-restraints excluded: chain E residue 138 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 B residue 187 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: 0.9990 chunk 83 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 GLN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9081 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 9095 Z= 0.391 Angle : 0.667 7.067 12530 Z= 0.290 Chirality : 0.044 0.187 1870 Planarity : 0.004 0.029 1330 Dihedral : 9.108 107.566 4124 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.31 % Allowed : 10.51 % 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: 1.41 (0.30), residues: 905 helix: None (None), residues: 0 sheet: 0.33 (0.26), residues: 380 loop : 1.68 (0.31), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE B 92 TYR 0.011 0.001 TYR B 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 59 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 41 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8370 (ptpt) cc_final: 0.8112 (ptmm) outliers start: 18 outliers final: 13 residues processed: 56 average time/residue: 1.1449 time to fit residues: 69.2110 Evaluate side-chains 53 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 C residue 187 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 B residue 184 THR Chi-restraints excluded: chain B residue 187 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: 3.9990 chunk 89 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 56 optimal weight: 0.0020 chunk 76 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 GLN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9095 Z= 0.180 Angle : 0.595 7.072 12530 Z= 0.259 Chirality : 0.044 0.226 1870 Planarity : 0.004 0.029 1330 Dihedral : 8.744 102.620 4124 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.92 % Allowed : 10.51 % 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: 1.77 (0.29), residues: 905 helix: None (None), residues: 0 sheet: 0.92 (0.28), residues: 340 loop : 1.56 (0.29), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE C 92 TYR 0.009 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 54 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 39 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8478 (ptpt) cc_final: 0.8250 (ptmm) outliers start: 15 outliers final: 12 residues processed: 54 average time/residue: 1.0923 time to fit residues: 63.9806 Evaluate side-chains 52 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 40 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 187 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 B residue 184 THR Chi-restraints excluded: chain B residue 187 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: 4.9990 chunk 10 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 GLN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.072505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.045865 restraints weight = 23273.267| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 4.00 r_work: 0.2547 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9095 Z= 0.191 Angle : 0.594 7.001 12530 Z= 0.257 Chirality : 0.043 0.207 1870 Planarity : 0.004 0.028 1330 Dihedral : 8.549 101.648 4123 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.05 % Allowed : 10.51 % 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: 1.66 (0.30), residues: 905 helix: None (None), residues: 0 sheet: 0.74 (0.28), residues: 350 loop : 1.58 (0.30), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE B 92 TYR 0.009 0.001 TYR B 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2333.01 seconds wall clock time: 42 minutes 17.05 seconds (2537.05 seconds total)