Starting phenix.real_space_refine on Wed Feb 21 23:35:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkf_13470/02_2024/7pkf_13470.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkf_13470/02_2024/7pkf_13470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkf_13470/02_2024/7pkf_13470.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkf_13470/02_2024/7pkf_13470.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkf_13470/02_2024/7pkf_13470.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkf_13470/02_2024/7pkf_13470.pdb" } resolution = 2.8 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: 6 Type Number sf(0) Gaussians Ca 20 9.91 5 S 40 5.16 5 C 10580 2.51 5 N 2610 2.21 5 O 3100 1.98 5 H 15960 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J PHE 11": "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 140": "OD1" <-> "OD2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "J PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 14": "OE1" <-> "OE2" Residue "F TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 140": "OD1" <-> "OD2" Residue "F GLU 170": "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 PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 19": "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 101": "OE1" <-> "OE2" Residue "G GLU 170": "OE1" <-> "OE2" Residue "H ASP 3": "OD1" <-> "OD2" Residue "H PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 14": "OE1" <-> "OE2" Residue "H TYR 19": "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 GLU 101": "OE1" <-> "OE2" Residue "H TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 140": "OD1" <-> "OD2" Residue "H ASP 169": "OD1" <-> "OD2" Residue "H GLU 170": "OE1" <-> "OE2" 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 PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 3": "OD1" <-> "OD2" Residue "I PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 60": "OD1" <-> "OD2" Residue "I PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 101": "OE1" <-> "OE2" Residue "I ASP 140": "OD1" <-> "OD2" Residue "I ASP 163": "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 PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 14": "OE1" <-> "OE2" Residue "E TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 130": "OE1" <-> "OE2" Residue "E ASP 140": "OD1" <-> "OD2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "E ASP 155": "OD1" <-> "OD2" Residue "E GLU 170": "OE1" <-> "OE2" Residue "E PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 193": "OE1" <-> "OE2" Residue "E PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 140": "OD1" <-> "OD2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D ASP 169": "OD1" <-> "OD2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 193": "OE1" <-> "OE2" Residue "C ASP 3": "OD1" <-> "OD2" Residue "C PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C ASP 140": "OD1" <-> "OD2" Residue "C GLU 170": "OE1" <-> "OE2" 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 PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 3": "OD1" <-> "OD2" Residue "B PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 70": "OD1" <-> "OD2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B ASP 155": "OD1" <-> "OD2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A ASP 70": "OD1" <-> "OD2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A ASP 140": "OD1" <-> "OD2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A ASP 163": "OD1" <-> "OD2" Residue "A ASP 169": "OD1" <-> "OD2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32310 Number of models: 1 Model: "" Number of chains: 30 Chain: "J" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "F" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "G" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "H" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "I" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "E" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "D" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "C" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "B" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "A" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 14.02, per 1000 atoms: 0.43 Number of scatterers: 32310 At special positions: 0 Unit cell: (140.448, 131.252, 111.188, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 20 19.99 S 40 16.00 O 3100 8.00 N 2610 7.00 C 10580 6.00 H 15960 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=2.04 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: 26.44 Conformation dependent library (CDL) restraints added in 3.3 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... Secondary structure from input PDB file: 40 helices and 31 sheets defined 12.4% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'J' and resid 42 through 46 removed outlier: 4.051A pdb=" N SER J 45 " --> pdb=" O GLU J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 151 Processing helix chain 'J' and resid 167 through 177 Processing helix chain 'J' and resid 186 through 190 removed outlier: 4.045A pdb=" N LEU J 190 " --> pdb=" O TRP J 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 46 removed outlier: 3.821A pdb=" N SER F 45 " --> pdb=" O GLU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 151 Processing helix chain 'F' and resid 167 through 177 Processing helix chain 'F' and resid 186 through 190 removed outlier: 3.847A pdb=" N LEU F 190 " --> pdb=" O TRP F 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 46 removed outlier: 3.800A pdb=" N SER G 45 " --> pdb=" O GLU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 151 Processing helix chain 'G' and resid 167 through 177 Processing helix chain 'G' and resid 186 through 190 removed outlier: 3.986A pdb=" N LEU G 190 " --> pdb=" O TRP G 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 46 removed outlier: 3.583A pdb=" N SER H 45 " --> pdb=" O GLU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 151 Processing helix chain 'H' and resid 167 through 177 Processing helix chain 'H' and resid 186 through 190 removed outlier: 3.809A pdb=" N LEU H 190 " --> pdb=" O TRP H 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 46 removed outlier: 3.682A pdb=" N SER I 45 " --> pdb=" O GLU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 151 Processing helix chain 'I' and resid 167 through 176 Processing helix chain 'I' and resid 186 through 190 removed outlier: 3.803A pdb=" N LEU I 190 " --> pdb=" O TRP I 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 46 Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 167 through 177 Processing helix chain 'E' and resid 186 through 190 removed outlier: 3.776A pdb=" N LEU E 190 " --> pdb=" O TRP E 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 46 removed outlier: 3.995A pdb=" N SER D 45 " --> pdb=" O GLU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 151 Processing helix chain 'D' and resid 167 through 176 Processing helix chain 'D' and resid 186 through 190 removed outlier: 3.946A pdb=" N LEU D 190 " --> pdb=" O TRP D 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 46 removed outlier: 3.854A pdb=" N SER C 45 " --> pdb=" O GLU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 186 through 190 removed outlier: 3.624A pdb=" N LEU C 190 " --> pdb=" O TRP C 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.757A pdb=" N SER B 45 " --> pdb=" O GLU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'B' and resid 167 through 177 Processing helix chain 'B' and resid 186 through 190 removed outlier: 3.825A pdb=" N LEU B 190 " --> pdb=" O TRP B 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.770A pdb=" N SER A 45 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 167 through 177 Processing helix chain 'A' and resid 186 through 190 removed outlier: 3.936A pdb=" N LEU A 190 " --> pdb=" O TRP A 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 114 through 115 Processing sheet with id=AA2, first strand: chain 'J' and resid 114 through 115 removed outlier: 3.508A pdb=" N ILE J 106 " --> pdb=" O GLU J 101 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR J 34 " --> pdb=" O MET J 161 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET J 161 " --> pdb=" O THR J 34 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N CYS J 36 " --> pdb=" O VAL J 159 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL J 159 " --> pdb=" O CYS J 36 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASN J 158 " --> pdb=" O LYS J 7 " (cutoff:3.500A) removed outlier: 9.955A pdb=" N LYS J 7 " --> pdb=" O ASN J 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 80 through 85 removed outlier: 6.518A pdb=" N TRP J 67 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N SER J 50 " --> pdb=" O TRP J 67 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE J 133 " --> pdb=" O LEU J 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'F' and resid 114 through 115 removed outlier: 6.541A pdb=" N THR F 34 " --> pdb=" O MET F 161 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N MET F 161 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N CYS F 36 " --> pdb=" O VAL F 159 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL F 159 " --> pdb=" O CYS F 36 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASN F 158 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N LYS F 7 " --> pdb=" O ASN F 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 80 through 85 removed outlier: 3.507A pdb=" N TYR F 73 " --> pdb=" O PHE F 84 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASN F 61 " --> pdb=" O THR F 56 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR F 56 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP F 67 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N SER F 50 " --> pdb=" O TRP F 67 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE F 133 " --> pdb=" O LEU F 22 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 139 through 141 removed outlier: 7.462A pdb=" N GLN F 139 " --> pdb=" O PHE F 146 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE F 146 " --> pdb=" O GLN F 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 114 through 115 Processing sheet with id=AA9, first strand: chain 'G' and resid 114 through 115 removed outlier: 3.766A pdb=" N ILE G 106 " --> pdb=" O GLU G 101 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR G 34 " --> pdb=" O MET G 161 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N MET G 161 " --> pdb=" O THR G 34 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N CYS G 36 " --> pdb=" O VAL G 159 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL G 159 " --> pdb=" O CYS G 36 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASN G 158 " --> pdb=" O LYS G 7 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N LYS G 7 " --> pdb=" O ASN G 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 80 through 85 removed outlier: 3.680A pdb=" N TYR G 73 " --> pdb=" O PHE G 84 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASN G 61 " --> pdb=" O THR G 56 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N THR G 56 " --> pdb=" O ASN G 61 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP G 67 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N SER G 50 " --> pdb=" O TRP G 67 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE G 133 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 114 through 115 Processing sheet with id=AB3, first strand: chain 'H' and resid 114 through 115 removed outlier: 3.631A pdb=" N ILE H 106 " --> pdb=" O GLU H 101 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR H 34 " --> pdb=" O MET H 161 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET H 161 " --> pdb=" O THR H 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N CYS H 36 " --> pdb=" O VAL H 159 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL H 159 " --> pdb=" O CYS H 36 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASN H 158 " --> pdb=" O LYS H 7 " (cutoff:3.500A) removed outlier: 10.222A pdb=" N LYS H 7 " --> pdb=" O ASN H 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 80 through 85 removed outlier: 3.556A pdb=" N TYR H 73 " --> pdb=" O PHE H 84 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ASN H 61 " --> pdb=" O THR H 56 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR H 56 " --> pdb=" O ASN H 61 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TRP H 67 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N SER H 50 " --> pdb=" O TRP H 67 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE H 133 " --> pdb=" O LEU H 22 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 114 through 115 Processing sheet with id=AB6, first strand: chain 'I' and resid 114 through 115 removed outlier: 3.602A pdb=" N ILE I 106 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N HIS I 38 " --> pdb=" O ASN I 158 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASN I 158 " --> pdb=" O HIS I 38 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N TYR I 40 " --> pdb=" O ILE I 156 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE I 156 " --> pdb=" O TYR I 40 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ASN I 158 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N LYS I 7 " --> pdb=" O ASN I 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 80 through 85 removed outlier: 6.511A pdb=" N TRP I 67 " --> pdb=" O SER I 50 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N SER I 50 " --> pdb=" O TRP I 67 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE I 133 " --> pdb=" O LEU I 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 114 through 115 Processing sheet with id=AB9, first strand: chain 'E' and resid 114 through 115 removed outlier: 3.605A pdb=" N ILE E 106 " --> pdb=" O GLU E 101 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR E 34 " --> pdb=" O MET E 161 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N MET E 161 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS E 36 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL E 159 " --> pdb=" O CYS E 36 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ASN E 158 " --> pdb=" O LYS E 7 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N LYS E 7 " --> pdb=" O ASN E 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 80 through 85 removed outlier: 3.552A pdb=" N TYR E 73 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ASN E 61 " --> pdb=" O THR E 56 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THR E 56 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N TRP E 67 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N SER E 50 " --> pdb=" O TRP E 67 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE E 133 " --> pdb=" O LEU E 22 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AC3, first strand: chain 'D' and resid 114 through 115 removed outlier: 3.646A pdb=" N ILE D 106 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR D 34 " --> pdb=" O MET D 161 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET D 161 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N CYS D 36 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL D 159 " --> pdb=" O CYS D 36 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ASN D 158 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 10.054A pdb=" N LYS D 7 " --> pdb=" O ASN D 158 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 80 through 85 removed outlier: 6.036A pdb=" N ASN D 61 " --> pdb=" O THR D 56 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR D 56 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP D 67 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N SER D 50 " --> pdb=" O TRP D 67 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE D 133 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LYS D 191 " --> pdb=" O LYS D 23 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 114 through 115 Processing sheet with id=AC6, first strand: chain 'C' and resid 114 through 115 removed outlier: 3.594A pdb=" N ILE C 106 " --> pdb=" O GLU C 101 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR C 34 " --> pdb=" O MET C 161 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N MET C 161 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N CYS C 36 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL C 159 " --> pdb=" O CYS C 36 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASN C 158 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 10.034A pdb=" N LYS C 7 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 80 through 85 removed outlier: 6.125A pdb=" N ASN C 61 " --> pdb=" O THR C 56 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR C 56 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP C 67 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N SER C 50 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE C 133 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AC9, first strand: chain 'B' and resid 114 through 115 removed outlier: 3.569A pdb=" N ILE B 106 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR B 34 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N MET B 161 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N CYS B 36 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL B 159 " --> pdb=" O CYS B 36 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASN B 158 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N LYS B 7 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 80 through 85 removed outlier: 3.562A pdb=" N TYR B 73 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASN B 61 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR B 54 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE B 63 " --> pdb=" O PHE B 52 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE B 52 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE B 65 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N SER B 50 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE B 133 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AD3, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.627A pdb=" N ILE A 106 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR A 34 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET A 161 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N CYS A 36 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL A 159 " --> pdb=" O CYS A 36 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ASN A 158 " --> pdb=" O LYS A 7 " (cutoff:3.500A) removed outlier: 10.160A pdb=" N LYS A 7 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 80 through 85 removed outlier: 6.497A pdb=" N TRP A 67 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N SER A 50 " --> pdb=" O TRP A 67 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE A 133 " --> pdb=" O LEU A 22 " (cutoff:3.500A) 684 hydrogen bonds defined for protein. 1638 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: 13.02 Time building geometry restraints manager: 27.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 15960 1.03 - 1.22: 2 1.22 - 1.42: 7288 1.42 - 1.62: 9430 1.62 - 1.81: 60 Bond restraints: 32740 Sorted by residual: bond pdb=" CB PHE F 109 " pdb=" CG PHE F 109 " ideal model delta sigma weight residual 1.502 1.437 0.065 2.30e-02 1.89e+03 7.88e+00 bond pdb=" CD1 PHE F 109 " pdb=" CE1 PHE F 109 " ideal model delta sigma weight residual 1.382 1.328 0.054 3.00e-02 1.11e+03 3.27e+00 bond pdb=" CE1 PHE F 109 " pdb=" CZ PHE F 109 " ideal model delta sigma weight residual 1.382 1.330 0.052 3.00e-02 1.11e+03 2.99e+00 bond pdb=" CG PHE F 109 " pdb=" CD2 PHE F 109 " ideal model delta sigma weight residual 1.384 1.352 0.032 2.10e-02 2.27e+03 2.39e+00 bond pdb=" CB PRO E 25 " pdb=" CG PRO E 25 " ideal model delta sigma weight residual 1.492 1.560 -0.068 5.00e-02 4.00e+02 1.84e+00 ... (remaining 32735 not shown) Histogram of bond angle deviations from ideal: 78.23 - 89.92: 82 89.92 - 101.61: 21 101.61 - 113.31: 38327 113.31 - 125.00: 19870 125.00 - 136.69: 810 Bond angle restraints: 59110 Sorted by residual: angle pdb=" CG GLU J 147 " pdb=" CB GLU J 147 " pdb=" HB3 GLU J 147 " ideal model delta sigma weight residual 108.00 78.23 29.77 3.00e+00 1.11e-01 9.85e+01 angle pdb=" CG GLU J 147 " pdb=" CB GLU J 147 " pdb=" HB2 GLU J 147 " ideal model delta sigma weight residual 108.00 78.26 29.74 3.00e+00 1.11e-01 9.82e+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 79.19 28.81 3.00e+00 1.11e-01 9.22e+01 angle pdb=" OG1 THR A 46 " pdb=" CB THR A 46 " pdb=" HB THR A 46 " ideal model delta sigma weight residual 109.00 81.16 27.84 3.00e+00 1.11e-01 8.61e+01 angle pdb=" CA GLU J 147 " pdb=" CB GLU J 147 " pdb=" HB3 GLU J 147 " ideal model delta sigma weight residual 109.00 81.35 27.65 3.00e+00 1.11e-01 8.50e+01 ... (remaining 59105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 14102 17.89 - 35.79: 924 35.79 - 53.68: 290 53.68 - 71.57: 228 71.57 - 89.46: 26 Dihedral angle restraints: 15570 sinusoidal: 8200 harmonic: 7370 Sorted by residual: dihedral pdb=" CA ASP I 140 " pdb=" C ASP I 140 " pdb=" N SER I 141 " pdb=" CA SER I 141 " ideal model delta harmonic sigma weight residual 180.00 152.41 27.59 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA ASP H 140 " pdb=" C ASP H 140 " pdb=" N SER H 141 " pdb=" CA SER H 141 " ideal model delta harmonic sigma weight residual 180.00 152.80 27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA GLU E 62 " pdb=" C GLU E 62 " pdb=" N ILE E 63 " pdb=" CA ILE E 63 " ideal model delta harmonic sigma weight residual 180.00 152.93 27.07 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 15567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.412: 2444 0.412 - 0.825: 0 0.825 - 1.237: 2 1.237 - 1.650: 19 1.650 - 2.062: 5 Chirality restraints: 2470 Sorted by residual: 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 -0.53 -2.06 2.00e-01 2.50e+01 1.06e+02 chirality pdb=" CG LEU A 83 " pdb=" CB LEU A 83 " pdb=" CD1 LEU A 83 " pdb=" CD2 LEU A 83 " both_signs ideal model delta sigma weight residual False -2.59 -0.86 -1.73 2.00e-01 2.50e+01 7.52e+01 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 -0.87 -1.72 2.00e-01 2.50e+01 7.37e+01 ... (remaining 2467 not shown) Planarity restraints: 4840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS G 38 " -0.011 2.00e-02 2.50e+03 4.06e-02 4.12e+01 pdb=" CG HIS G 38 " 0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS G 38 " 0.059 2.00e-02 2.50e+03 pdb=" CD2 HIS G 38 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 HIS G 38 " 0.027 2.00e-02 2.50e+03 pdb=" NE2 HIS G 38 " 0.025 2.00e-02 2.50e+03 pdb=" HD1 HIS G 38 " -0.072 2.00e-02 2.50e+03 pdb=" HD2 HIS G 38 " -0.054 2.00e-02 2.50e+03 pdb=" HE1 HIS G 38 " -0.022 2.00e-02 2.50e+03 pdb=" HE2 HIS G 38 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 38 " 0.010 2.00e-02 2.50e+03 3.88e-02 3.76e+01 pdb=" CG HIS F 38 " -0.035 2.00e-02 2.50e+03 pdb=" ND1 HIS F 38 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 HIS F 38 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 HIS F 38 " -0.026 2.00e-02 2.50e+03 pdb=" NE2 HIS F 38 " -0.023 2.00e-02 2.50e+03 pdb=" HD1 HIS F 38 " 0.068 2.00e-02 2.50e+03 pdb=" HD2 HIS F 38 " 0.053 2.00e-02 2.50e+03 pdb=" HE1 HIS F 38 " 0.021 2.00e-02 2.50e+03 pdb=" HE2 HIS F 38 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 38 " -0.011 2.00e-02 2.50e+03 3.76e-02 3.53e+01 pdb=" CG HIS D 38 " 0.039 2.00e-02 2.50e+03 pdb=" ND1 HIS D 38 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 HIS D 38 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 HIS D 38 " 0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS D 38 " 0.022 2.00e-02 2.50e+03 pdb=" HD1 HIS D 38 " -0.067 2.00e-02 2.50e+03 pdb=" HD2 HIS D 38 " -0.049 2.00e-02 2.50e+03 pdb=" HE1 HIS D 38 " -0.018 2.00e-02 2.50e+03 pdb=" HE2 HIS D 38 " -0.020 2.00e-02 2.50e+03 ... (remaining 4837 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 1261 2.13 - 2.75: 58974 2.75 - 3.37: 92737 3.37 - 3.98: 128567 3.98 - 4.60: 197830 Nonbonded interactions: 479369 Sorted by model distance: nonbonded pdb=" OD1 ASP F 3 " pdb=" HG SER F 5 " model vdw 1.513 1.850 nonbonded pdb=" OD1 ASP E 3 " pdb=" HG SER E 5 " model vdw 1.533 1.850 nonbonded pdb=" OD1 ASP A 3 " pdb=" HG SER A 5 " model vdw 1.536 1.850 nonbonded pdb=" H SER D 167 " pdb=" OE1 GLU D 170 " model vdw 1.548 1.850 nonbonded pdb=" HG SER F 74 " pdb=" OE2 GLU F 81 " model vdw 1.562 1.850 ... (remaining 479364 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.160 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: 11.450 Check model and map are aligned: 0.490 Set scattering table: 0.260 Process input model: 101.860 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.200 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:13.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 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 : 0.004 0.068 16780 Z= 0.249 Angle : 0.901 14.670 22810 Z= 0.495 Chirality : 0.160 2.062 2470 Planarity : 0.006 0.124 2900 Dihedral : 13.325 89.463 5980 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.26 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -0.68 (0.18), residues: 2040 helix: -0.96 (0.40), residues: 100 sheet: -0.13 (0.17), residues: 830 loop : -0.57 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.006 TRP E 205 HIS 0.042 0.006 HIS E 38 PHE 0.048 0.003 PHE F 84 TYR 0.026 0.005 TYR E 54 ARG 0.045 0.009 ARG A 118 *********************** 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 223 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 2.534 Fit side-chains revert: symmetry clash REVERT: H 193 GLU cc_start: 0.7342 (tt0) cc_final: 0.7122 (tt0) REVERT: I 88 GLU cc_start: 0.7100 (pp20) cc_final: 0.6846 (pm20) REVERT: D 4 MET cc_start: 0.8484 (mmm) cc_final: 0.8220 (mmm) REVERT: C 81 GLU cc_start: 0.7828 (tt0) cc_final: 0.7565 (tt0) REVERT: C 91 VAL cc_start: 0.8276 (t) cc_final: 0.8010 (m) outliers start: 0 outliers final: 1 residues processed: 223 average time/residue: 3.1847 time to fit residues: 778.9925 Evaluate side-chains 148 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 172 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.0050 chunk 151 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 95 HIS E 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16780 Z= 0.180 Angle : 0.761 16.214 22810 Z= 0.395 Chirality : 0.161 1.756 2470 Planarity : 0.004 0.073 2900 Dihedral : 6.200 38.757 2202 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.67 % Allowed : 5.89 % Favored : 93.44 % 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: -0.19 (0.18), residues: 2040 helix: 1.38 (0.40), residues: 110 sheet: 0.22 (0.16), residues: 890 loop : -0.54 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 110 HIS 0.007 0.002 HIS I 38 PHE 0.019 0.002 PHE F 66 TYR 0.020 0.001 TYR J 54 ARG 0.005 0.001 ARG G 6 *********************** 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 176 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 164 time to evaluate : 2.527 Fit side-chains revert: symmetry clash REVERT: J 193 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6776 (tp30) REVERT: F 163 ASP cc_start: 0.8230 (p0) cc_final: 0.8026 (p0) REVERT: H 155 ASP cc_start: 0.7978 (m-30) cc_final: 0.7711 (m-30) REVERT: H 193 GLU cc_start: 0.7376 (tt0) cc_final: 0.7150 (tt0) REVERT: I 6 ARG cc_start: 0.7754 (mmm160) cc_final: 0.7533 (mmm-85) REVERT: I 13 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8074 (mtmm) REVERT: I 88 GLU cc_start: 0.7059 (pp20) cc_final: 0.6758 (pm20) REVERT: I 155 ASP cc_start: 0.8307 (m-30) cc_final: 0.7976 (m-30) REVERT: I 197 GLU cc_start: 0.6903 (tt0) cc_final: 0.6538 (tt0) REVERT: E 138 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6919 (tm-30) REVERT: D 4 MET cc_start: 0.8439 (mmm) cc_final: 0.8189 (mmm) outliers start: 12 outliers final: 3 residues processed: 172 average time/residue: 3.0115 time to fit residues: 571.2740 Evaluate side-chains 144 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 138 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 193 GLU Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 82 ILE 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: 0.7980 chunk 151 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16780 Z= 0.270 Angle : 0.755 15.743 22810 Z= 0.391 Chirality : 0.161 1.737 2470 Planarity : 0.004 0.067 2900 Dihedral : 5.792 38.593 2200 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.39 % Allowed : 7.06 % 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: -0.12 (0.18), residues: 2040 helix: 2.37 (0.46), residues: 110 sheet: 0.21 (0.16), residues: 890 loop : -0.55 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 110 HIS 0.010 0.003 HIS F 38 PHE 0.013 0.002 PHE E 52 TYR 0.023 0.002 TYR J 54 ARG 0.007 0.001 ARG B 188 *********************** 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 172 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 2.597 Fit side-chains REVERT: F 88 GLU cc_start: 0.7639 (pp20) cc_final: 0.7240 (mm-30) REVERT: F 163 ASP cc_start: 0.8241 (p0) cc_final: 0.8015 (p0) REVERT: F 197 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7439 (mt-10) REVERT: G 193 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6545 (tm-30) REVERT: H 193 GLU cc_start: 0.7386 (tt0) cc_final: 0.7146 (tt0) REVERT: I 13 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8113 (mtmm) REVERT: I 88 GLU cc_start: 0.7114 (pp20) cc_final: 0.6757 (pm20) REVERT: I 155 ASP cc_start: 0.8337 (m-30) cc_final: 0.8137 (m-30) REVERT: I 172 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7832 (m-40) REVERT: E 138 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6743 (tm-30) REVERT: D 4 MET cc_start: 0.8526 (mmm) cc_final: 0.8324 (mmm) REVERT: B 88 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6673 (tm-30) outliers start: 25 outliers final: 13 residues processed: 167 average time/residue: 3.2723 time to fit residues: 601.6648 Evaluate side-chains 158 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 139 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 169 ASP Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 172 ASN Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain A residue 46 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 94 optimal weight: 0.0770 chunk 20 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 122 optimal weight: 0.0970 chunk 182 optimal weight: 0.9980 chunk 193 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 95 HIS I 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16780 Z= 0.166 Angle : 0.718 15.772 22810 Z= 0.368 Chirality : 0.161 1.722 2470 Planarity : 0.004 0.076 2900 Dihedral : 5.341 33.539 2200 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.06 % Allowed : 7.83 % Favored : 91.11 % 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: 2.77 (0.47), residues: 110 sheet: 0.24 (0.16), residues: 890 loop : -0.47 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 110 HIS 0.007 0.002 HIS F 38 PHE 0.011 0.001 PHE B 39 TYR 0.019 0.001 TYR J 54 ARG 0.009 0.000 ARG J 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 166 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 2.608 Fit side-chains revert: symmetry clash REVERT: J 193 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6788 (tp30) REVERT: F 163 ASP cc_start: 0.8153 (p0) cc_final: 0.7945 (p0) REVERT: G 193 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6417 (tm-30) REVERT: H 193 GLU cc_start: 0.7303 (tt0) cc_final: 0.7079 (tt0) REVERT: I 13 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8082 (mtmm) REVERT: I 88 GLU cc_start: 0.7118 (pp20) cc_final: 0.6744 (pm20) REVERT: I 155 ASP cc_start: 0.8271 (m-30) cc_final: 0.8042 (m-30) REVERT: I 197 GLU cc_start: 0.7123 (tt0) cc_final: 0.6785 (tt0) REVERT: E 138 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6667 (tm-30) REVERT: D 4 MET cc_start: 0.8541 (mmm) cc_final: 0.8334 (mmm) outliers start: 19 outliers final: 11 residues processed: 163 average time/residue: 3.1214 time to fit residues: 561.1379 Evaluate side-chains 151 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 193 GLU Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain A residue 46 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 173 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16780 Z= 0.299 Angle : 0.751 15.756 22810 Z= 0.388 Chirality : 0.161 1.747 2470 Planarity : 0.004 0.081 2900 Dihedral : 5.533 38.824 2200 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.39 % Allowed : 8.56 % Favored : 90.06 % 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: -0.18 (0.18), residues: 2040 helix: 2.50 (0.48), residues: 110 sheet: 0.20 (0.16), residues: 890 loop : -0.64 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 162 HIS 0.010 0.002 HIS F 38 PHE 0.014 0.002 PHE G 52 TYR 0.025 0.002 TYR J 54 ARG 0.011 0.001 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 169 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 2.604 Fit side-chains revert: symmetry clash REVERT: F 88 GLU cc_start: 0.7687 (pp20) cc_final: 0.7234 (mm-30) REVERT: F 163 ASP cc_start: 0.8224 (p0) cc_final: 0.8013 (p0) REVERT: F 197 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7481 (mt-10) REVERT: G 147 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6914 (mt-10) REVERT: H 193 GLU cc_start: 0.7397 (tt0) cc_final: 0.7132 (tt0) REVERT: I 13 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8125 (mtmm) REVERT: I 88 GLU cc_start: 0.7158 (pp20) cc_final: 0.6738 (pm20) REVERT: E 138 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7028 (tm-30) REVERT: C 57 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8362 (mttt) REVERT: B 88 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6659 (tm-30) outliers start: 25 outliers final: 14 residues processed: 165 average time/residue: 3.0575 time to fit residues: 556.2322 Evaluate side-chains 159 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 169 ASP Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain A residue 46 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 89 optimal weight: 0.0270 chunk 16 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16780 Z= 0.234 Angle : 0.729 15.669 22810 Z= 0.374 Chirality : 0.161 1.737 2470 Planarity : 0.004 0.083 2900 Dihedral : 5.364 38.973 2200 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.33 % Allowed : 9.22 % Favored : 89.44 % 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: -0.17 (0.18), residues: 2040 helix: 2.59 (0.47), residues: 110 sheet: 0.23 (0.16), residues: 890 loop : -0.67 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 162 HIS 0.009 0.002 HIS F 38 PHE 0.012 0.001 PHE E 52 TYR 0.022 0.001 TYR J 54 ARG 0.011 0.001 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 165 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 2.670 Fit side-chains revert: symmetry clash REVERT: F 163 ASP cc_start: 0.8172 (p0) cc_final: 0.7965 (p0) REVERT: F 197 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7487 (mt-10) REVERT: G 147 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6915 (mt-10) REVERT: H 193 GLU cc_start: 0.7364 (tt0) cc_final: 0.7105 (tt0) REVERT: I 13 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8109 (mtmm) REVERT: I 88 GLU cc_start: 0.7258 (pp20) cc_final: 0.6827 (pm20) REVERT: E 138 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6837 (tm-30) REVERT: C 57 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8362 (mttt) REVERT: B 88 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6634 (tm-30) outliers start: 24 outliers final: 14 residues processed: 160 average time/residue: 3.1028 time to fit residues: 550.2695 Evaluate side-chains 155 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 136 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain A residue 46 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 141 optimal weight: 0.5980 chunk 109 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 192 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 88 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16780 Z= 0.182 Angle : 0.711 15.731 22810 Z= 0.363 Chirality : 0.161 1.780 2470 Planarity : 0.004 0.088 2900 Dihedral : 5.058 34.297 2200 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.17 % Allowed : 9.56 % Favored : 89.28 % 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: -0.03 (0.18), residues: 2040 helix: 2.86 (0.48), residues: 110 sheet: 0.30 (0.16), residues: 890 loop : -0.57 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 162 HIS 0.008 0.002 HIS F 38 PHE 0.010 0.001 PHE H 39 TYR 0.021 0.001 TYR H 54 ARG 0.014 0.001 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 169 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 148 time to evaluate : 2.665 Fit side-chains REVERT: J 193 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6765 (tp30) REVERT: F 88 GLU cc_start: 0.7694 (pp20) cc_final: 0.7259 (mm-30) REVERT: F 163 ASP cc_start: 0.8123 (p0) cc_final: 0.7914 (p0) REVERT: F 197 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: G 147 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6926 (mt-10) REVERT: H 193 GLU cc_start: 0.7350 (tt0) cc_final: 0.7076 (tt0) REVERT: I 88 GLU cc_start: 0.7349 (pp20) cc_final: 0.6882 (pm20) REVERT: E 138 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6663 (tm-30) outliers start: 21 outliers final: 11 residues processed: 167 average time/residue: 2.9651 time to fit residues: 547.7993 Evaluate side-chains 151 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 2.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 193 GLU Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain A residue 46 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 151 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16780 Z= 0.209 Angle : 0.716 15.672 22810 Z= 0.366 Chirality : 0.161 1.798 2470 Planarity : 0.004 0.087 2900 Dihedral : 5.078 35.309 2200 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.00 % Allowed : 9.78 % Favored : 89.22 % 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: -0.04 (0.18), residues: 2040 helix: 2.75 (0.48), residues: 110 sheet: 0.31 (0.16), residues: 890 loop : -0.58 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 162 HIS 0.008 0.002 HIS F 38 PHE 0.011 0.001 PHE G 52 TYR 0.021 0.001 TYR H 54 ARG 0.013 0.001 ARG B 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 155 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 2.545 Fit side-chains REVERT: F 163 ASP cc_start: 0.8151 (p0) cc_final: 0.7950 (p0) REVERT: G 147 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6915 (mt-10) REVERT: H 193 GLU cc_start: 0.7360 (tt0) cc_final: 0.7088 (tt0) REVERT: I 88 GLU cc_start: 0.7369 (pp20) cc_final: 0.6894 (pm20) REVERT: I 149 SER cc_start: 0.8180 (p) cc_final: 0.7792 (m) REVERT: E 138 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6753 (tm-30) outliers start: 18 outliers final: 14 residues processed: 153 average time/residue: 3.1505 time to fit residues: 543.0665 Evaluate side-chains 150 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain E residue 38 HIS Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 126 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 141 optimal weight: 0.0980 chunk 55 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 169 optimal weight: 0.0870 chunk 117 optimal weight: 0.6980 chunk 189 optimal weight: 0.3980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16780 Z= 0.164 Angle : 0.703 15.672 22810 Z= 0.358 Chirality : 0.161 1.734 2470 Planarity : 0.004 0.102 2900 Dihedral : 4.884 31.418 2200 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.11 % Allowed : 9.94 % Favored : 88.94 % 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: 0.07 (0.18), residues: 2040 helix: 2.96 (0.48), residues: 110 sheet: 0.35 (0.16), residues: 890 loop : -0.49 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 162 HIS 0.007 0.002 HIS F 38 PHE 0.010 0.001 PHE H 39 TYR 0.020 0.001 TYR H 54 ARG 0.015 0.001 ARG B 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 171 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 151 time to evaluate : 2.551 Fit side-chains revert: symmetry clash REVERT: J 193 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6760 (tp30) REVERT: F 88 GLU cc_start: 0.7748 (pp20) cc_final: 0.7211 (mm-30) REVERT: F 163 ASP cc_start: 0.8056 (p0) cc_final: 0.7847 (p0) REVERT: G 58 ARG cc_start: 0.6647 (mtm110) cc_final: 0.6432 (mtm-85) REVERT: G 147 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6940 (mt-10) REVERT: G 172 ASN cc_start: 0.7972 (m110) cc_final: 0.7667 (m110) REVERT: H 193 GLU cc_start: 0.7315 (tt0) cc_final: 0.7043 (tt0) REVERT: I 149 SER cc_start: 0.8109 (p) cc_final: 0.7728 (m) REVERT: E 138 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6675 (tm-30) outliers start: 20 outliers final: 15 residues processed: 168 average time/residue: 2.8499 time to fit residues: 531.6603 Evaluate side-chains 156 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 2.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 193 GLU Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain E residue 38 HIS Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 1.9990 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: 0.5980 chunk 122 optimal weight: 0.0040 chunk 97 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 169 optimal weight: 0.9980 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16780 Z= 0.208 Angle : 0.714 15.705 22810 Z= 0.365 Chirality : 0.161 1.751 2470 Planarity : 0.004 0.092 2900 Dihedral : 4.940 33.405 2200 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.94 % Allowed : 10.44 % Favored : 88.61 % 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: 2.78 (0.47), residues: 110 sheet: 0.34 (0.17), residues: 890 loop : -0.52 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 162 HIS 0.008 0.002 HIS F 38 PHE 0.011 0.001 PHE G 52 TYR 0.021 0.001 TYR H 54 ARG 0.013 0.001 ARG J 58 ********************** 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: 17 poor density : 145 time to evaluate : 2.597 Fit side-chains revert: symmetry clash REVERT: F 88 GLU cc_start: 0.7753 (pp20) cc_final: 0.7204 (mm-30) REVERT: F 163 ASP cc_start: 0.8120 (p0) cc_final: 0.7916 (p0) REVERT: G 58 ARG cc_start: 0.6632 (mtm110) cc_final: 0.6409 (mtm-85) REVERT: G 147 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6950 (mt-10) REVERT: H 193 GLU cc_start: 0.7357 (tt0) cc_final: 0.7080 (tt0) REVERT: I 88 GLU cc_start: 0.7415 (pp20) cc_final: 0.6966 (pm20) REVERT: I 149 SER cc_start: 0.8199 (p) cc_final: 0.7829 (m) REVERT: I 206 PRO cc_start: 0.7928 (Cg_endo) cc_final: 0.7608 (Cg_exo) REVERT: E 138 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6733 (tm-30) REVERT: B 13 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7924 (mtmm) outliers start: 17 outliers final: 15 residues processed: 160 average time/residue: 2.8171 time to fit residues: 503.0345 Evaluate side-chains 157 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 2.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain E residue 38 HIS Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 0.3980 chunk 146 optimal weight: 0.0170 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.100582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.081014 restraints weight = 64306.660| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 1.88 r_work: 0.2746 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16780 Z= 0.166 Angle : 0.703 15.692 22810 Z= 0.358 Chirality : 0.161 1.728 2470 Planarity : 0.004 0.095 2900 Dihedral : 4.805 30.496 2200 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.00 % Allowed : 10.61 % Favored : 88.39 % 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: 0.14 (0.18), residues: 2040 helix: 2.93 (0.47), residues: 110 sheet: 0.39 (0.17), residues: 890 loop : -0.44 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 162 HIS 0.007 0.002 HIS F 38 PHE 0.010 0.001 PHE H 39 TYR 0.021 0.001 TYR H 54 ARG 0.019 0.001 ARG B 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10660.66 seconds wall clock time: 187 minutes 51.14 seconds (11271.14 seconds total)