Starting phenix.real_space_refine on Sun Apr 14 18:37:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkd_13468/04_2024/7pkd_13468_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkd_13468/04_2024/7pkd_13468.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkd_13468/04_2024/7pkd_13468_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkd_13468/04_2024/7pkd_13468_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkd_13468/04_2024/7pkd_13468_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkd_13468/04_2024/7pkd_13468.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkd_13468/04_2024/7pkd_13468.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkd_13468/04_2024/7pkd_13468_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkd_13468/04_2024/7pkd_13468_trim_updated.pdb" } resolution = 3.3 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= 0.002 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: 7 Type Number sf(0) Gaussians Ca 20 9.91 5 P 10 5.49 5 S 40 5.16 5 C 10630 2.51 5 N 2620 2.21 5 O 3140 1.98 5 H 15940 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J GLU 14": "OE1" <-> "OE2" Residue "J TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 42": "OE1" <-> "OE2" Residue "J TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 70": "OD1" <-> "OD2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 140": "OD1" <-> "OD2" Residue "J GLU 147": "OE1" <-> "OE2" Residue "J PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 197": "OE1" <-> "OE2" Residue "J PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 3": "OD1" <-> "OD2" Residue "F TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 60": "OD1" <-> "OD2" Residue "F PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 85": "OE1" <-> "OE2" Residue "F GLU 101": "OE1" <-> "OE2" Residue "F PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 140": "OD1" <-> "OD2" Residue "F GLU 147": "OE1" <-> "OE2" Residue "F PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 193": "OE1" <-> "OE2" Residue "F GLU 197": "OE1" <-> "OE2" Residue "F PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 14": "OE1" <-> "OE2" Residue "G ASP 16": "OD1" <-> "OD2" Residue "G TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 81": "OE1" <-> "OE2" Residue "G GLU 85": "OE1" <-> "OE2" Residue "G GLU 101": "OE1" <-> "OE2" Residue "G PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G GLU 170": "OE1" <-> "OE2" Residue "G PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 16": "OD1" <-> "OD2" Residue "H TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 70": "OD1" <-> "OD2" Residue "H GLU 108": "OE1" <-> "OE2" Residue "H TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 197": "OE1" <-> "OE2" Residue "H PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 3": "OD1" <-> "OD2" Residue "I GLU 42": "OE1" <-> "OE2" Residue "I TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "I PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 85": "OE1" <-> "OE2" Residue "I GLU 101": "OE1" <-> "OE2" Residue "I GLU 130": "OE1" <-> "OE2" Residue "I ASP 140": "OD1" <-> "OD2" Residue "I GLU 170": "OE1" <-> "OE2" Residue "I TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 193": "OE1" <-> "OE2" Residue "I PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 3": "OD1" <-> "OD2" Residue "E TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "E PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 85": "OE1" <-> "OE2" Residue "E PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "E GLU 170": "OE1" <-> "OE2" Residue "E TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 193": "OE1" <-> "OE2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "E PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 16": "OD1" <-> "OD2" Residue "D TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 140": "OD1" <-> "OD2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 60": "OD1" <-> "OD2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 112": "OD1" <-> "OD2" Residue "C TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ASP 140": "OD1" <-> "OD2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 3": "OD1" <-> "OD2" Residue "B ASP 16": "OD1" <-> "OD2" Residue "B TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 3": "OD1" <-> "OD2" Residue "A TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A ASP 140": "OD1" <-> "OD2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 32400 Number of models: 1 Model: "" Number of chains: 30 Chain: "J" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "F" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "G" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "H" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "I" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "E" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "D" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "C" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "B" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "A" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "J" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Time building chain proxies: 13.95, per 1000 atoms: 0.43 Number of scatterers: 32400 At special positions: 0 Unit cell: (119.548, 112.024, 144.628, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 20 19.99 S 40 16.00 P 10 15.00 O 3140 8.00 N 2620 7.00 C 10630 6.00 H 15940 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS J 36 " - pdb=" SG CYS J 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 36 " - pdb=" SG CYS F 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 36 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 36 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 36 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 36 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 36 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 27.20 Conformation dependent library (CDL) restraints added in 3.6 seconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3780 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 30 sheets defined 8.0% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.98 Creating SS restraints... Processing helix chain 'J' and resid 43 through 45 No H-bonds generated for 'chain 'J' and resid 43 through 45' Processing helix chain 'J' and resid 148 through 150 No H-bonds generated for 'chain 'J' and resid 148 through 150' Processing helix chain 'J' and resid 168 through 176 Processing helix chain 'F' and resid 43 through 45 No H-bonds generated for 'chain 'F' and resid 43 through 45' Processing helix chain 'F' and resid 148 through 150 No H-bonds generated for 'chain 'F' and resid 148 through 150' Processing helix chain 'F' and resid 168 through 176 Processing helix chain 'F' and resid 187 through 189 No H-bonds generated for 'chain 'F' and resid 187 through 189' Processing helix chain 'G' and resid 43 through 45 No H-bonds generated for 'chain 'G' and resid 43 through 45' Processing helix chain 'G' and resid 148 through 150 No H-bonds generated for 'chain 'G' and resid 148 through 150' Processing helix chain 'G' and resid 168 through 175 Processing helix chain 'H' and resid 43 through 45 No H-bonds generated for 'chain 'H' and resid 43 through 45' Processing helix chain 'H' and resid 148 through 150 No H-bonds generated for 'chain 'H' and resid 148 through 150' Processing helix chain 'H' and resid 168 through 175 Processing helix chain 'I' and resid 43 through 45 No H-bonds generated for 'chain 'I' and resid 43 through 45' Processing helix chain 'I' and resid 148 through 150 No H-bonds generated for 'chain 'I' and resid 148 through 150' Processing helix chain 'I' and resid 168 through 175 Processing helix chain 'I' and resid 187 through 189 No H-bonds generated for 'chain 'I' and resid 187 through 189' Processing helix chain 'E' and resid 43 through 45 No H-bonds generated for 'chain 'E' and resid 43 through 45' Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 168 through 176 Processing helix chain 'E' and resid 187 through 189 No H-bonds generated for 'chain 'E' and resid 187 through 189' Processing helix chain 'D' and resid 43 through 45 No H-bonds generated for 'chain 'D' and resid 43 through 45' Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 168 through 175 Processing helix chain 'D' and resid 187 through 189 No H-bonds generated for 'chain 'D' and resid 187 through 189' Processing helix chain 'C' and resid 43 through 45 No H-bonds generated for 'chain 'C' and resid 43 through 45' Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 168 through 175 Processing helix chain 'C' and resid 187 through 189 No H-bonds generated for 'chain 'C' and resid 187 through 189' Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 168 through 175 Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 168 through 176 Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing sheet with id= A, first strand: chain 'J' and resid 199 through 202 Processing sheet with id= B, first strand: chain 'J' and resid 192 through 195 removed outlier: 3.951A pdb=" N ILE J 133 " --> pdb=" O LEU J 22 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE J 65 " --> pdb=" O ILE J 51 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N SER J 53 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE J 63 " --> pdb=" O SER J 53 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'J' and resid 34 through 36 Processing sheet with id= D, first strand: chain 'F' and resid 199 through 202 Processing sheet with id= E, first strand: chain 'F' and resid 192 through 195 removed outlier: 3.976A pdb=" N ILE F 133 " --> pdb=" O LEU F 22 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE F 65 " --> pdb=" O ILE F 51 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER F 53 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE F 63 " --> pdb=" O SER F 53 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 34 through 36 Processing sheet with id= G, first strand: chain 'G' and resid 199 through 202 Processing sheet with id= H, first strand: chain 'G' and resid 192 through 195 removed outlier: 4.136A pdb=" N ILE G 133 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE G 65 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N SER G 53 " --> pdb=" O ILE G 63 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE G 63 " --> pdb=" O SER G 53 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 34 through 36 Processing sheet with id= J, first strand: chain 'H' and resid 199 through 202 Processing sheet with id= K, first strand: chain 'H' and resid 192 through 195 removed outlier: 3.986A pdb=" N ILE H 133 " --> pdb=" O LEU H 22 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE H 65 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER H 53 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE H 63 " --> pdb=" O SER H 53 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 34 through 36 Processing sheet with id= M, first strand: chain 'I' and resid 199 through 202 Processing sheet with id= N, first strand: chain 'I' and resid 192 through 195 removed outlier: 4.006A pdb=" N ILE I 133 " --> pdb=" O LEU I 22 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE I 65 " --> pdb=" O ILE I 51 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N SER I 53 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE I 63 " --> pdb=" O SER I 53 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 34 through 36 Processing sheet with id= P, first strand: chain 'E' and resid 199 through 202 Processing sheet with id= Q, first strand: chain 'E' and resid 192 through 195 removed outlier: 4.193A pdb=" N ILE E 133 " --> pdb=" O LEU E 22 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE E 65 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER E 53 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE E 63 " --> pdb=" O SER E 53 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 34 through 36 Processing sheet with id= S, first strand: chain 'D' and resid 199 through 202 Processing sheet with id= T, first strand: chain 'D' and resid 192 through 195 removed outlier: 4.126A pdb=" N ILE D 133 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE D 65 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N SER D 53 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE D 63 " --> pdb=" O SER D 53 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 34 through 36 Processing sheet with id= V, first strand: chain 'C' and resid 199 through 202 Processing sheet with id= W, first strand: chain 'C' and resid 192 through 195 removed outlier: 3.919A pdb=" N ILE C 133 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE C 65 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N SER C 53 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE C 63 " --> pdb=" O SER C 53 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 34 through 36 Processing sheet with id= Y, first strand: chain 'B' and resid 199 through 202 Processing sheet with id= Z, first strand: chain 'B' and resid 192 through 195 removed outlier: 3.916A pdb=" N ILE B 133 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B 65 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N SER B 53 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ILE B 63 " --> pdb=" O SER B 53 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 34 through 36 Processing sheet with id= AB, first strand: chain 'A' and resid 199 through 202 Processing sheet with id= AC, first strand: chain 'A' and resid 192 through 195 removed outlier: 4.076A pdb=" N ILE A 133 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE A 65 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER A 53 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE A 63 " --> pdb=" O SER A 53 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 34 through 36 584 hydrogen bonds defined for protein. 1461 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: 15.19 Time building geometry restraints manager: 28.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 15940 1.02 - 1.21: 0 1.21 - 1.41: 7107 1.41 - 1.61: 9712 1.61 - 1.80: 61 Bond restraints: 32820 Sorted by residual: bond pdb=" O4 PC B 303 " pdb=" P1 PC B 303 " ideal model delta sigma weight residual 1.510 1.608 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" O4 PC G 303 " pdb=" P1 PC G 303 " ideal model delta sigma weight residual 1.510 1.607 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" O1 PC C 303 " pdb=" P1 PC C 303 " ideal model delta sigma weight residual 1.510 1.606 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" O4 PC E 303 " pdb=" P1 PC E 303 " ideal model delta sigma weight residual 1.510 1.606 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" O4 PC J 303 " pdb=" P1 PC J 303 " ideal model delta sigma weight residual 1.510 1.606 -0.096 2.00e-02 2.50e+03 2.31e+01 ... (remaining 32815 not shown) Histogram of bond angle deviations from ideal: 80.01 - 90.82: 63 90.82 - 101.64: 21 101.64 - 112.45: 37329 112.45 - 123.27: 18521 123.27 - 134.08: 3286 Bond angle restraints: 59220 Sorted by residual: angle pdb=" CG2 THR B 46 " pdb=" CB THR B 46 " pdb=" HB THR B 46 " ideal model delta sigma weight residual 108.00 80.01 27.99 3.00e+00 1.11e-01 8.71e+01 angle pdb=" CG2 THR D 126 " pdb=" CB THR D 126 " pdb=" HB THR D 126 " ideal model delta sigma weight residual 108.00 80.26 27.74 3.00e+00 1.11e-01 8.55e+01 angle pdb=" CG2 THR A 46 " pdb=" CB THR A 46 " pdb=" HB THR A 46 " ideal model delta sigma weight residual 108.00 80.44 27.56 3.00e+00 1.11e-01 8.44e+01 angle pdb=" CG2 THR A 173 " pdb=" CB THR A 173 " pdb=" HB THR A 173 " ideal model delta sigma weight residual 108.00 80.53 27.47 3.00e+00 1.11e-01 8.38e+01 angle pdb=" CG2 THR F 173 " pdb=" CB THR F 173 " pdb=" HB THR F 173 " ideal model delta sigma weight residual 108.00 80.60 27.40 3.00e+00 1.11e-01 8.34e+01 ... (remaining 59215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 14112 17.97 - 35.95: 901 35.95 - 53.92: 337 53.92 - 71.89: 214 71.89 - 89.86: 16 Dihedral angle restraints: 15580 sinusoidal: 8230 harmonic: 7350 Sorted by residual: dihedral pdb=" CA SER F 80 " pdb=" C SER F 80 " pdb=" N GLU F 81 " pdb=" CA GLU F 81 " ideal model delta harmonic sigma weight residual -180.00 -151.90 -28.10 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA GLU A 62 " pdb=" C GLU A 62 " pdb=" N ILE A 63 " pdb=" CA ILE A 63 " ideal model delta harmonic sigma weight residual 180.00 152.53 27.47 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA GLU F 62 " pdb=" C GLU F 62 " pdb=" N ILE F 63 " pdb=" CA ILE F 63 " ideal model delta harmonic sigma weight residual 180.00 152.70 27.30 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 15577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.395: 2449 0.395 - 0.790: 0 0.790 - 1.185: 0 1.185 - 1.580: 16 1.580 - 1.976: 5 Chirality restraints: 2470 Sorted by residual: chirality pdb=" CG LEU I 83 " pdb=" CB LEU I 83 " pdb=" CD1 LEU I 83 " pdb=" CD2 LEU I 83 " both_signs ideal model delta sigma weight residual False -2.59 -0.61 -1.98 2.00e-01 2.50e+01 9.76e+01 chirality pdb=" CG LEU D 83 " pdb=" CB LEU D 83 " pdb=" CD1 LEU D 83 " pdb=" CD2 LEU D 83 " both_signs ideal model delta sigma weight residual False -2.59 -0.80 -1.79 2.00e-01 2.50e+01 7.99e+01 chirality pdb=" CG LEU F 83 " pdb=" CB LEU F 83 " pdb=" CD1 LEU F 83 " pdb=" CD2 LEU F 83 " both_signs ideal model delta sigma weight residual False -2.59 -0.84 -1.75 2.00e-01 2.50e+01 7.69e+01 ... (remaining 2467 not shown) Planarity restraints: 4840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 188 " 0.073 9.50e-02 1.11e+02 4.50e-02 3.28e+01 pdb=" NE ARG E 188 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG E 188 " 0.058 2.00e-02 2.50e+03 pdb=" NH1 ARG E 188 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 188 " -0.069 2.00e-02 2.50e+03 pdb="HH11 ARG E 188 " 0.011 2.00e-02 2.50e+03 pdb="HH12 ARG E 188 " -0.035 2.00e-02 2.50e+03 pdb="HH21 ARG E 188 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG E 188 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 58 " 0.065 9.50e-02 1.11e+02 4.25e-02 3.04e+01 pdb=" NE ARG C 58 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG C 58 " 0.046 2.00e-02 2.50e+03 pdb=" NH1 ARG C 58 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 58 " -0.073 2.00e-02 2.50e+03 pdb="HH11 ARG C 58 " 0.010 2.00e-02 2.50e+03 pdb="HH12 ARG C 58 " -0.029 2.00e-02 2.50e+03 pdb="HH21 ARG C 58 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG C 58 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 188 " -0.007 9.50e-02 1.11e+02 3.55e-02 2.83e+01 pdb=" NE ARG D 188 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG D 188 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG D 188 " -0.052 2.00e-02 2.50e+03 pdb=" NH2 ARG D 188 " 0.052 2.00e-02 2.50e+03 pdb="HH11 ARG D 188 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG D 188 " 0.057 2.00e-02 2.50e+03 pdb="HH21 ARG D 188 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG D 188 " -0.051 2.00e-02 2.50e+03 ... (remaining 4837 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 755 2.08 - 2.71: 53257 2.71 - 3.34: 93806 3.34 - 3.97: 127399 3.97 - 4.60: 199990 Nonbonded interactions: 475207 Sorted by model distance: nonbonded pdb=" OE2 GLU D 193 " pdb="HE21 GLN D 195 " model vdw 1.446 1.850 nonbonded pdb=" HG SER B 132 " pdb="HE22 GLN B 139 " model vdw 1.491 2.100 nonbonded pdb=" OE1 GLU G 197 " pdb=" HZ3 LYS H 123 " model vdw 1.534 1.850 nonbonded pdb=" HG SER H 102 " pdb=" O TYR H 125 " model vdw 1.541 1.850 nonbonded pdb=" OD1 ASP F 163 " pdb="HD22 ASN F 183 " model vdw 1.563 1.850 ... (remaining 475202 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' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 2.640 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: 0.510 Extract box with map and model: 11.470 Check model and map are aligned: 0.520 Set scattering table: 0.320 Process input model: 110.790 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 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 : 0.009 0.098 16880 Z= 0.552 Angle : 0.900 15.349 22960 Z= 0.469 Chirality : 0.147 1.976 2470 Planarity : 0.005 0.051 2900 Dihedral : 13.299 89.862 6010 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.18), residues: 2040 helix: -0.09 (0.39), residues: 110 sheet: -0.16 (0.17), residues: 810 loop : -0.84 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP B 187 HIS 0.030 0.004 HIS J 38 PHE 0.027 0.003 PHE G 66 TYR 0.026 0.005 TYR F 54 ARG 0.066 0.009 ARG E 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 2.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 180 PHE cc_start: 0.8529 (p90) cc_final: 0.8167 (p90) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.8898 time to fit residues: 232.3721 Evaluate side-chains 140 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 181 optimal weight: 0.1980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 38 HIS G 38 HIS G 195 GLN H 38 HIS H 95 HIS H 186 ASN D 38 HIS D 145 ASN C 38 HIS B 38 HIS B 59 GLN B 95 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16880 Z= 0.245 Angle : 0.723 16.065 22960 Z= 0.377 Chirality : 0.147 1.763 2470 Planarity : 0.004 0.052 2900 Dihedral : 6.278 45.964 2230 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.94 % Allowed : 3.28 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.18), residues: 2040 helix: 1.90 (0.44), residues: 110 sheet: 0.18 (0.16), residues: 890 loop : -0.49 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 110 HIS 0.006 0.002 HIS C 38 PHE 0.014 0.001 PHE H 39 TYR 0.019 0.001 TYR A 54 ARG 0.007 0.000 ARG I 58 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 165 time to evaluate : 2.817 Fit side-chains revert: symmetry clash REVERT: I 18 SER cc_start: 0.9216 (m) cc_final: 0.8636 (p) REVERT: D 180 PHE cc_start: 0.8480 (p90) cc_final: 0.8048 (p90) REVERT: C 38 HIS cc_start: 0.9028 (OUTLIER) cc_final: 0.8802 (m-70) outliers start: 17 outliers final: 15 residues processed: 177 average time/residue: 0.7466 time to fit residues: 190.0881 Evaluate side-chains 155 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 169 ASP Chi-restraints excluded: chain J residue 193 GLU Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 155 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 151 optimal weight: 0.0070 chunk 123 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 overall best weight: 1.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 HIS E 145 ASN D 145 ASN C 38 HIS C 95 HIS A 38 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16880 Z= 0.258 Angle : 0.686 15.771 22960 Z= 0.356 Chirality : 0.147 1.836 2470 Planarity : 0.003 0.051 2900 Dihedral : 5.759 36.377 2230 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.00 % Allowed : 4.56 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.18), residues: 2040 helix: 2.20 (0.44), residues: 110 sheet: 0.17 (0.16), residues: 890 loop : -0.46 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 110 HIS 0.012 0.003 HIS G 95 PHE 0.012 0.001 PHE F 52 TYR 0.018 0.001 TYR F 54 ARG 0.003 0.000 ARG F 6 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 153 time to evaluate : 2.673 Fit side-chains revert: symmetry clash REVERT: J 188 ARG cc_start: 0.8319 (mtp85) cc_final: 0.8084 (mtt-85) REVERT: G 188 ARG cc_start: 0.8341 (mmt90) cc_final: 0.7957 (mmt-90) REVERT: I 18 SER cc_start: 0.9213 (m) cc_final: 0.8753 (p) REVERT: D 180 PHE cc_start: 0.8474 (p90) cc_final: 0.8016 (p90) outliers start: 18 outliers final: 15 residues processed: 166 average time/residue: 0.8058 time to fit residues: 187.8904 Evaluate side-chains 153 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 169 ASP Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 155 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 0.0870 chunk 136 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 122 optimal weight: 0.2980 chunk 182 optimal weight: 0.5980 chunk 193 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16880 Z= 0.163 Angle : 0.655 15.732 22960 Z= 0.337 Chirality : 0.146 1.798 2470 Planarity : 0.003 0.037 2900 Dihedral : 5.259 35.655 2230 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.94 % Allowed : 5.17 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.18), residues: 2040 helix: 2.56 (0.45), residues: 110 sheet: 0.44 (0.17), residues: 840 loop : -0.37 (0.19), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 110 HIS 0.008 0.002 HIS C 38 PHE 0.015 0.001 PHE G 39 TYR 0.012 0.001 TYR F 54 ARG 0.003 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 2.712 Fit side-chains REVERT: I 18 SER cc_start: 0.9198 (m) cc_final: 0.8737 (p) REVERT: D 38 HIS cc_start: 0.8986 (OUTLIER) cc_final: 0.8686 (m90) REVERT: D 180 PHE cc_start: 0.8466 (p90) cc_final: 0.8030 (p90) outliers start: 17 outliers final: 15 residues processed: 167 average time/residue: 0.8119 time to fit residues: 193.2608 Evaluate side-chains 158 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 193 GLU Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain I residue 38 HIS Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain A residue 76 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 173 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 38 HIS ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16880 Z= 0.265 Angle : 0.667 15.727 22960 Z= 0.344 Chirality : 0.147 1.806 2470 Planarity : 0.003 0.049 2900 Dihedral : 5.315 40.358 2230 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.06 % Allowed : 5.67 % Favored : 93.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.18), residues: 2040 helix: 2.43 (0.45), residues: 110 sheet: 0.38 (0.17), residues: 840 loop : -0.51 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 162 HIS 0.008 0.002 HIS C 38 PHE 0.012 0.001 PHE G 39 TYR 0.016 0.001 TYR G 54 ARG 0.010 0.000 ARG J 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 2.683 Fit side-chains REVERT: F 38 HIS cc_start: 0.8988 (OUTLIER) cc_final: 0.8075 (m90) REVERT: I 18 SER cc_start: 0.9248 (m) cc_final: 0.8808 (p) REVERT: E 94 VAL cc_start: 0.9087 (OUTLIER) cc_final: 0.8846 (p) REVERT: D 38 HIS cc_start: 0.9025 (OUTLIER) cc_final: 0.8683 (m90) outliers start: 19 outliers final: 15 residues processed: 161 average time/residue: 0.7785 time to fit residues: 178.4746 Evaluate side-chains 156 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain I residue 38 HIS Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 155 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 38 optimal weight: 0.0970 chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16880 Z= 0.272 Angle : 0.664 15.678 22960 Z= 0.342 Chirality : 0.146 1.753 2470 Planarity : 0.003 0.042 2900 Dihedral : 5.372 39.436 2230 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.17 % Allowed : 6.44 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.18), residues: 2040 helix: 2.41 (0.45), residues: 110 sheet: 0.33 (0.17), residues: 840 loop : -0.57 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 162 HIS 0.009 0.002 HIS C 38 PHE 0.019 0.001 PHE D 180 TYR 0.015 0.001 TYR F 54 ARG 0.007 0.000 ARG J 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 146 time to evaluate : 2.567 Fit side-chains REVERT: F 38 HIS cc_start: 0.8977 (OUTLIER) cc_final: 0.8052 (m90) REVERT: I 18 SER cc_start: 0.9254 (m) cc_final: 0.8812 (p) REVERT: E 94 VAL cc_start: 0.9059 (OUTLIER) cc_final: 0.8817 (p) REVERT: D 38 HIS cc_start: 0.9048 (OUTLIER) cc_final: 0.8672 (m90) outliers start: 21 outliers final: 18 residues processed: 162 average time/residue: 0.7503 time to fit residues: 174.9717 Evaluate side-chains 159 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 138 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 169 ASP Chi-restraints excluded: chain J residue 193 GLU Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain I residue 38 HIS Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 155 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16880 Z= 0.207 Angle : 0.649 15.679 22960 Z= 0.333 Chirality : 0.146 1.747 2470 Planarity : 0.003 0.053 2900 Dihedral : 5.212 38.662 2230 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.28 % Allowed : 6.94 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.18), residues: 2040 helix: 2.55 (0.45), residues: 110 sheet: 0.34 (0.17), residues: 840 loop : -0.55 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 162 HIS 0.007 0.002 HIS C 38 PHE 0.010 0.001 PHE G 39 TYR 0.013 0.001 TYR F 54 ARG 0.007 0.000 ARG J 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 145 time to evaluate : 2.891 Fit side-chains REVERT: F 38 HIS cc_start: 0.8956 (OUTLIER) cc_final: 0.7991 (m90) REVERT: I 18 SER cc_start: 0.9224 (m) cc_final: 0.8797 (p) REVERT: E 94 VAL cc_start: 0.9045 (OUTLIER) cc_final: 0.8809 (p) REVERT: D 38 HIS cc_start: 0.9027 (OUTLIER) cc_final: 0.8647 (m90) outliers start: 23 outliers final: 18 residues processed: 162 average time/residue: 0.7467 time to fit residues: 174.3323 Evaluate side-chains 160 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 139 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 169 ASP Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain I residue 38 HIS Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 155 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 151 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16880 Z= 0.268 Angle : 0.660 15.640 22960 Z= 0.340 Chirality : 0.146 1.747 2470 Planarity : 0.004 0.061 2900 Dihedral : 5.354 47.992 2230 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.22 % Allowed : 7.22 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.18), residues: 2040 helix: 2.40 (0.45), residues: 110 sheet: 0.09 (0.18), residues: 740 loop : -0.58 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 162 HIS 0.008 0.002 HIS G 38 PHE 0.011 0.001 PHE G 39 TYR 0.015 0.001 TYR G 54 ARG 0.008 0.000 ARG J 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 2.762 Fit side-chains REVERT: F 38 HIS cc_start: 0.8970 (OUTLIER) cc_final: 0.8066 (m90) REVERT: I 18 SER cc_start: 0.9263 (m) cc_final: 0.8831 (p) REVERT: E 94 VAL cc_start: 0.9058 (OUTLIER) cc_final: 0.8816 (p) REVERT: D 38 HIS cc_start: 0.9050 (OUTLIER) cc_final: 0.8671 (m90) outliers start: 22 outliers final: 19 residues processed: 159 average time/residue: 0.7704 time to fit residues: 176.8233 Evaluate side-chains 159 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 169 ASP Chi-restraints excluded: chain J residue 193 GLU Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain I residue 38 HIS Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 155 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 2.9990 chunk 168 optimal weight: 0.0370 chunk 179 optimal weight: 0.1980 chunk 108 optimal weight: 0.2980 chunk 78 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 169 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 189 optimal weight: 0.5980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16880 Z= 0.148 Angle : 0.640 15.676 22960 Z= 0.327 Chirality : 0.145 1.743 2470 Planarity : 0.003 0.060 2900 Dihedral : 5.029 48.746 2230 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.00 % Allowed : 7.83 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.18), residues: 2040 helix: 2.73 (0.45), residues: 110 sheet: 0.22 (0.18), residues: 740 loop : -0.46 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 162 HIS 0.007 0.002 HIS G 38 PHE 0.011 0.001 PHE C 39 TYR 0.010 0.001 TYR G 54 ARG 0.008 0.000 ARG J 58 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 2.749 Fit side-chains revert: symmetry clash REVERT: F 38 HIS cc_start: 0.8897 (OUTLIER) cc_final: 0.7932 (m90) REVERT: I 18 SER cc_start: 0.9178 (m) cc_final: 0.8752 (p) REVERT: E 94 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8783 (p) REVERT: D 38 HIS cc_start: 0.9004 (OUTLIER) cc_final: 0.8674 (m90) outliers start: 18 outliers final: 14 residues processed: 169 average time/residue: 0.7144 time to fit residues: 175.9565 Evaluate side-chains 162 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain I residue 38 HIS Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain A residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 97 optimal weight: 0.0870 chunk 126 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16880 Z= 0.289 Angle : 0.660 15.673 22960 Z= 0.340 Chirality : 0.147 1.773 2470 Planarity : 0.004 0.065 2900 Dihedral : 5.330 55.817 2230 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.17 % Allowed : 7.78 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.18), residues: 2040 helix: 2.42 (0.45), residues: 110 sheet: 0.14 (0.19), residues: 740 loop : -0.55 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 162 HIS 0.008 0.002 HIS G 38 PHE 0.011 0.001 PHE E 52 TYR 0.014 0.001 TYR G 54 ARG 0.010 0.000 ARG I 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 2.756 Fit side-chains revert: symmetry clash REVERT: F 38 HIS cc_start: 0.8970 (OUTLIER) cc_final: 0.8058 (m90) REVERT: I 18 SER cc_start: 0.9250 (m) cc_final: 0.8822 (p) REVERT: E 94 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8820 (p) REVERT: D 38 HIS cc_start: 0.9054 (OUTLIER) cc_final: 0.8660 (m90) outliers start: 21 outliers final: 17 residues processed: 159 average time/residue: 0.7596 time to fit residues: 173.1423 Evaluate side-chains 160 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 time to evaluate : 2.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain I residue 38 HIS Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 155 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 0.5980 chunk 146 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 9 optimal weight: 0.0370 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 139 GLN ** 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 = 0.2757 r_free = 0.2757 target = 0.076943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.063682 restraints weight = 76146.696| |-----------------------------------------------------------------------------| r_work (start): 0.2541 rms_B_bonded: 1.85 r_work: 0.2446 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2319 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16880 Z= 0.202 Angle : 0.646 15.645 22960 Z= 0.331 Chirality : 0.146 1.765 2470 Planarity : 0.003 0.060 2900 Dihedral : 5.239 58.218 2230 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.17 % Allowed : 7.89 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.18), residues: 2040 helix: 2.56 (0.45), residues: 110 sheet: 0.18 (0.18), residues: 740 loop : -0.52 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 162 HIS 0.007 0.002 HIS G 38 PHE 0.010 0.001 PHE E 52 TYR 0.013 0.001 TYR F 54 ARG 0.009 0.000 ARG I 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6975.16 seconds wall clock time: 125 minutes 14.71 seconds (7514.71 seconds total)