Starting phenix.real_space_refine (version: 1.21rc1) on Mon Aug 14 01:50:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7n_29817/08_2023/8g7n_29817_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7n_29817/08_2023/8g7n_29817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7n_29817/08_2023/8g7n_29817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7n_29817/08_2023/8g7n_29817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7n_29817/08_2023/8g7n_29817_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7n_29817/08_2023/8g7n_29817_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.169 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 14 8.98 5 P 42 5.49 5 Mg 14 5.21 5 S 210 5.16 5 C 41468 2.51 5 N 11242 2.21 5 O 13118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 19": "OD1" <-> "OD2" Residue "A ASP 50": "OD1" <-> "OD2" Residue "A ASP 59": "OD1" <-> "OD2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "G ASP 19": "OD1" <-> "OD2" Residue "G ASP 50": "OD1" <-> "OD2" Residue "G ASP 59": "OD1" <-> "OD2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "G TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 212": "OE1" <-> "OE2" Residue "G GLU 250": "OE1" <-> "OE2" Residue "G GLU 387": "OE1" <-> "OE2" Residue "F ASP 19": "OD1" <-> "OD2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F ASP 59": "OD1" <-> "OD2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 212": "OE1" <-> "OE2" Residue "F GLU 250": "OE1" <-> "OE2" Residue "F GLU 387": "OE1" <-> "OE2" Residue "E ASP 19": "OD1" <-> "OD2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E ASP 59": "OD1" <-> "OD2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "E GLU 387": "OE1" <-> "OE2" Residue "D ASP 19": "OD1" <-> "OD2" Residue "D ASP 50": "OD1" <-> "OD2" Residue "D ASP 59": "OD1" <-> "OD2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D GLU 387": "OE1" <-> "OE2" Residue "C ASP 19": "OD1" <-> "OD2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C ASP 59": "OD1" <-> "OD2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C GLU 387": "OE1" <-> "OE2" Residue "B ASP 19": "OD1" <-> "OD2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B ASP 59": "OD1" <-> "OD2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B GLU 387": "OE1" <-> "OE2" Residue "J ASP 19": "OD1" <-> "OD2" Residue "J ASP 50": "OD1" <-> "OD2" Residue "J ASP 59": "OD1" <-> "OD2" Residue "J GLU 103": "OE1" <-> "OE2" Residue "J TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 212": "OE1" <-> "OE2" Residue "J GLU 250": "OE1" <-> "OE2" Residue "J GLU 387": "OE1" <-> "OE2" Residue "I ASP 19": "OD1" <-> "OD2" Residue "I ASP 50": "OD1" <-> "OD2" Residue "I ASP 59": "OD1" <-> "OD2" Residue "I GLU 103": "OE1" <-> "OE2" Residue "I TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 212": "OE1" <-> "OE2" Residue "I GLU 250": "OE1" <-> "OE2" Residue "I GLU 387": "OE1" <-> "OE2" Residue "H ASP 19": "OD1" <-> "OD2" Residue "H ASP 50": "OD1" <-> "OD2" Residue "H ASP 59": "OD1" <-> "OD2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 212": "OE1" <-> "OE2" Residue "H GLU 250": "OE1" <-> "OE2" Residue "H GLU 387": "OE1" <-> "OE2" Residue "N ASP 19": "OD1" <-> "OD2" Residue "N ASP 50": "OD1" <-> "OD2" Residue "N ASP 59": "OD1" <-> "OD2" Residue "N GLU 103": "OE1" <-> "OE2" Residue "N TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 212": "OE1" <-> "OE2" Residue "N GLU 250": "OE1" <-> "OE2" Residue "N GLU 387": "OE1" <-> "OE2" Residue "Y ASP 19": "OD1" <-> "OD2" Residue "Y ASP 50": "OD1" <-> "OD2" Residue "Y ASP 59": "OD1" <-> "OD2" Residue "Y GLU 103": "OE1" <-> "OE2" Residue "Y TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 212": "OE1" <-> "OE2" Residue "Y GLU 250": "OE1" <-> "OE2" Residue "Y GLU 387": "OE1" <-> "OE2" Residue "L ASP 19": "OD1" <-> "OD2" Residue "L ASP 50": "OD1" <-> "OD2" Residue "L ASP 59": "OD1" <-> "OD2" Residue "L GLU 103": "OE1" <-> "OE2" Residue "L TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 212": "OE1" <-> "OE2" Residue "L GLU 250": "OE1" <-> "OE2" Residue "L GLU 387": "OE1" <-> "OE2" Residue "K ASP 19": "OD1" <-> "OD2" Residue "K ASP 50": "OD1" <-> "OD2" Residue "K ASP 59": "OD1" <-> "OD2" Residue "K GLU 103": "OE1" <-> "OE2" Residue "K TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 212": "OE1" <-> "OE2" Residue "K GLU 250": "OE1" <-> "OE2" Residue "K GLU 387": "OE1" <-> "OE2" Residue "O GLU 19": "OE1" <-> "OE2" Residue "O GLU 35": "OE1" <-> "OE2" Residue "O ASP 84": "OD1" <-> "OD2" Residue "O ASP 93": "OD1" <-> "OD2" Residue "U GLU 19": "OE1" <-> "OE2" Residue "U GLU 35": "OE1" <-> "OE2" Residue "U ASP 84": "OD1" <-> "OD2" Residue "U ASP 93": "OD1" <-> "OD2" Residue "T GLU 19": "OE1" <-> "OE2" Residue "T GLU 35": "OE1" <-> "OE2" Residue "T ASP 84": "OD1" <-> "OD2" Residue "T ASP 93": "OD1" <-> "OD2" Residue "S GLU 19": "OE1" <-> "OE2" Residue "S GLU 35": "OE1" <-> "OE2" Residue "S ASP 84": "OD1" <-> "OD2" Residue "S ASP 93": "OD1" <-> "OD2" Residue "R GLU 19": "OE1" <-> "OE2" Residue "R GLU 35": "OE1" <-> "OE2" Residue "R ASP 84": "OD1" <-> "OD2" Residue "R ASP 93": "OD1" <-> "OD2" Residue "Q GLU 19": "OE1" <-> "OE2" Residue "Q GLU 35": "OE1" <-> "OE2" Residue "Q ASP 84": "OD1" <-> "OD2" Residue "Q ASP 93": "OD1" <-> "OD2" Residue "P GLU 19": "OE1" <-> "OE2" Residue "P GLU 35": "OE1" <-> "OE2" Residue "P ASP 84": "OD1" <-> "OD2" Residue "P ASP 93": "OD1" <-> "OD2" Residue "X GLU 19": "OE1" <-> "OE2" Residue "X GLU 35": "OE1" <-> "OE2" Residue "X ASP 84": "OD1" <-> "OD2" Residue "X ASP 93": "OD1" <-> "OD2" Residue "W GLU 19": "OE1" <-> "OE2" Residue "W GLU 35": "OE1" <-> "OE2" Residue "W ASP 84": "OD1" <-> "OD2" Residue "W ASP 93": "OD1" <-> "OD2" Residue "V GLU 19": "OE1" <-> "OE2" Residue "V GLU 35": "OE1" <-> "OE2" Residue "V ASP 84": "OD1" <-> "OD2" Residue "V ASP 93": "OD1" <-> "OD2" Residue "2 GLU 19": "OE1" <-> "OE2" Residue "2 GLU 35": "OE1" <-> "OE2" Residue "2 ASP 84": "OD1" <-> "OD2" Residue "2 ASP 93": "OD1" <-> "OD2" Residue "1 GLU 19": "OE1" <-> "OE2" Residue "1 GLU 35": "OE1" <-> "OE2" Residue "1 ASP 84": "OD1" <-> "OD2" Residue "1 ASP 93": "OD1" <-> "OD2" Residue "Z GLU 19": "OE1" <-> "OE2" Residue "Z GLU 35": "OE1" <-> "OE2" Residue "Z ASP 84": "OD1" <-> "OD2" Residue "Z ASP 93": "OD1" <-> "OD2" Residue "M GLU 19": "OE1" <-> "OE2" Residue "M GLU 35": "OE1" <-> "OE2" Residue "M ASP 84": "OD1" <-> "OD2" Residue "M ASP 93": "OD1" <-> "OD2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 66108 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "G" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "F" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "E" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "D" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "C" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "B" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "J" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "I" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "H" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "N" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "Y" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "L" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "K" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "O" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "U" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "T" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "S" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "R" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "Q" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "P" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "X" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "W" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "V" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "2" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "1" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "Z" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "M" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 23.76, per 1000 atoms: 0.36 Number of scatterers: 66108 At special positions: 0 Unit cell: (160.371, 157.59, 264.195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 14 19.00 S 210 16.00 P 42 15.00 Mg 14 11.99 O 13118 8.00 N 11242 7.00 C 41468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.63 Conformation dependent library (CDL) restraints added in 7.3 seconds 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15876 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 294 helices and 112 sheets defined 45.8% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.54 Creating SS restraints... Processing helix chain 'A' and resid 8 through 28 removed outlier: 3.911A pdb=" N VAL A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N THR A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 57 removed outlier: 3.548A pdb=" N SER A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 83 Processing helix chain 'A' and resid 87 through 104 removed outlier: 3.575A pdb=" N LYS A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 132 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 154 through 167 Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 228 through 241 Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 254 through 267 Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.552A pdb=" N THR A 294 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 338 through 353 removed outlier: 3.732A pdb=" N ASP A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 372 Processing helix chain 'A' and resid 385 through 407 removed outlier: 3.664A pdb=" N ARG A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 427 removed outlier: 3.550A pdb=" N CYS A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Proline residue: A 423 - end of helix removed outlier: 3.785A pdb=" N ASP A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER A 427 " --> pdb=" O PRO A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 456 removed outlier: 4.501A pdb=" N LYS A 447 " --> pdb=" O LYS A 443 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE A 448 " --> pdb=" O ARG A 444 " (cutoff:3.500A) Proline residue: A 449 - end of helix Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 487 through 490 No H-bonds generated for 'chain 'A' and resid 487 through 490' Processing helix chain 'A' and resid 496 through 515 removed outlier: 3.811A pdb=" N LEU A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 28 removed outlier: 3.911A pdb=" N VAL G 27 " --> pdb=" O ASP G 23 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N THR G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 57 removed outlier: 3.549A pdb=" N SER G 57 " --> pdb=" O THR G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 83 Processing helix chain 'G' and resid 87 through 104 removed outlier: 3.575A pdb=" N LYS G 104 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 132 Processing helix chain 'G' and resid 139 through 149 Processing helix chain 'G' and resid 154 through 167 Processing helix chain 'G' and resid 200 through 202 No H-bonds generated for 'chain 'G' and resid 200 through 202' Processing helix chain 'G' and resid 228 through 241 Proline residue: G 233 - end of helix Processing helix chain 'G' and resid 254 through 267 Processing helix chain 'G' and resid 280 through 294 removed outlier: 3.552A pdb=" N THR G 294 " --> pdb=" O ALA G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 310 No H-bonds generated for 'chain 'G' and resid 308 through 310' Processing helix chain 'G' and resid 313 through 315 No H-bonds generated for 'chain 'G' and resid 313 through 315' Processing helix chain 'G' and resid 338 through 353 removed outlier: 3.732A pdb=" N ASP G 353 " --> pdb=" O ILE G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 372 Processing helix chain 'G' and resid 385 through 407 removed outlier: 3.664A pdb=" N ARG G 394 " --> pdb=" O GLU G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 427 removed outlier: 3.550A pdb=" N CYS G 421 " --> pdb=" O ALA G 417 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE G 422 " --> pdb=" O LEU G 418 " (cutoff:3.500A) Proline residue: G 423 - end of helix removed outlier: 3.786A pdb=" N ASP G 426 " --> pdb=" O ILE G 422 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER G 427 " --> pdb=" O PRO G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 456 removed outlier: 4.501A pdb=" N LYS G 447 " --> pdb=" O LYS G 443 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE G 448 " --> pdb=" O ARG G 444 " (cutoff:3.500A) Proline residue: G 449 - end of helix Processing helix chain 'G' and resid 461 through 469 Processing helix chain 'G' and resid 487 through 490 No H-bonds generated for 'chain 'G' and resid 487 through 490' Processing helix chain 'G' and resid 496 through 515 removed outlier: 3.811A pdb=" N LEU G 512 " --> pdb=" O GLY G 508 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR G 515 " --> pdb=" O SER G 511 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 28 removed outlier: 3.911A pdb=" N VAL F 27 " --> pdb=" O ASP F 23 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N THR F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 57 removed outlier: 3.548A pdb=" N SER F 57 " --> pdb=" O THR F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 83 Processing helix chain 'F' and resid 87 through 104 removed outlier: 3.575A pdb=" N LYS F 104 " --> pdb=" O GLU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 132 Processing helix chain 'F' and resid 139 through 149 Processing helix chain 'F' and resid 154 through 167 Processing helix chain 'F' and resid 200 through 202 No H-bonds generated for 'chain 'F' and resid 200 through 202' Processing helix chain 'F' and resid 228 through 241 Proline residue: F 233 - end of helix Processing helix chain 'F' and resid 254 through 267 Processing helix chain 'F' and resid 280 through 294 removed outlier: 3.552A pdb=" N THR F 294 " --> pdb=" O ALA F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 310 No H-bonds generated for 'chain 'F' and resid 308 through 310' Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 338 through 353 removed outlier: 3.732A pdb=" N ASP F 353 " --> pdb=" O ILE F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 372 Processing helix chain 'F' and resid 385 through 407 removed outlier: 3.665A pdb=" N ARG F 394 " --> pdb=" O GLU F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 427 removed outlier: 3.550A pdb=" N CYS F 421 " --> pdb=" O ALA F 417 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE F 422 " --> pdb=" O LEU F 418 " (cutoff:3.500A) Proline residue: F 423 - end of helix removed outlier: 3.786A pdb=" N ASP F 426 " --> pdb=" O ILE F 422 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER F 427 " --> pdb=" O PRO F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 456 removed outlier: 4.501A pdb=" N LYS F 447 " --> pdb=" O LYS F 443 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE F 448 " --> pdb=" O ARG F 444 " (cutoff:3.500A) Proline residue: F 449 - end of helix Processing helix chain 'F' and resid 461 through 469 Processing helix chain 'F' and resid 487 through 490 No H-bonds generated for 'chain 'F' and resid 487 through 490' Processing helix chain 'F' and resid 496 through 515 removed outlier: 3.811A pdb=" N LEU F 512 " --> pdb=" O GLY F 508 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR F 515 " --> pdb=" O SER F 511 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 28 removed outlier: 3.910A pdb=" N VAL E 27 " --> pdb=" O ASP E 23 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N THR E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 57 removed outlier: 3.548A pdb=" N SER E 57 " --> pdb=" O THR E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 83 Processing helix chain 'E' and resid 87 through 104 removed outlier: 3.574A pdb=" N LYS E 104 " --> pdb=" O GLU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 132 Processing helix chain 'E' and resid 139 through 149 Processing helix chain 'E' and resid 154 through 167 Processing helix chain 'E' and resid 200 through 202 No H-bonds generated for 'chain 'E' and resid 200 through 202' Processing helix chain 'E' and resid 228 through 241 Proline residue: E 233 - end of helix Processing helix chain 'E' and resid 254 through 267 Processing helix chain 'E' and resid 280 through 294 removed outlier: 3.551A pdb=" N THR E 294 " --> pdb=" O ALA E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 310 No H-bonds generated for 'chain 'E' and resid 308 through 310' Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 338 through 353 removed outlier: 3.732A pdb=" N ASP E 353 " --> pdb=" O ILE E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 372 Processing helix chain 'E' and resid 385 through 407 removed outlier: 3.664A pdb=" N ARG E 394 " --> pdb=" O GLU E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 427 removed outlier: 3.550A pdb=" N CYS E 421 " --> pdb=" O ALA E 417 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE E 422 " --> pdb=" O LEU E 418 " (cutoff:3.500A) Proline residue: E 423 - end of helix removed outlier: 3.785A pdb=" N ASP E 426 " --> pdb=" O ILE E 422 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER E 427 " --> pdb=" O PRO E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 456 removed outlier: 4.501A pdb=" N LYS E 447 " --> pdb=" O LYS E 443 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE E 448 " --> pdb=" O ARG E 444 " (cutoff:3.500A) Proline residue: E 449 - end of helix Processing helix chain 'E' and resid 461 through 469 Processing helix chain 'E' and resid 487 through 490 No H-bonds generated for 'chain 'E' and resid 487 through 490' Processing helix chain 'E' and resid 496 through 515 removed outlier: 3.811A pdb=" N LEU E 512 " --> pdb=" O GLY E 508 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR E 515 " --> pdb=" O SER E 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 28 removed outlier: 3.911A pdb=" N VAL D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N THR D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 57 removed outlier: 3.548A pdb=" N SER D 57 " --> pdb=" O THR D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 83 Processing helix chain 'D' and resid 87 through 104 removed outlier: 3.574A pdb=" N LYS D 104 " --> pdb=" O GLU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 132 Processing helix chain 'D' and resid 139 through 149 Processing helix chain 'D' and resid 154 through 167 Processing helix chain 'D' and resid 200 through 202 No H-bonds generated for 'chain 'D' and resid 200 through 202' Processing helix chain 'D' and resid 228 through 241 Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 254 through 267 Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.552A pdb=" N THR D 294 " --> pdb=" O ALA D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 310 No H-bonds generated for 'chain 'D' and resid 308 through 310' Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 338 through 353 removed outlier: 3.732A pdb=" N ASP D 353 " --> pdb=" O ILE D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 372 Processing helix chain 'D' and resid 385 through 407 removed outlier: 3.663A pdb=" N ARG D 394 " --> pdb=" O GLU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 427 removed outlier: 3.549A pdb=" N CYS D 421 " --> pdb=" O ALA D 417 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Proline residue: D 423 - end of helix removed outlier: 3.786A pdb=" N ASP D 426 " --> pdb=" O ILE D 422 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER D 427 " --> pdb=" O PRO D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 456 removed outlier: 4.501A pdb=" N LYS D 447 " --> pdb=" O LYS D 443 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE D 448 " --> pdb=" O ARG D 444 " (cutoff:3.500A) Proline residue: D 449 - end of helix Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 487 through 490 No H-bonds generated for 'chain 'D' and resid 487 through 490' Processing helix chain 'D' and resid 496 through 515 removed outlier: 3.811A pdb=" N LEU D 512 " --> pdb=" O GLY D 508 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR D 515 " --> pdb=" O SER D 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 28 removed outlier: 3.911A pdb=" N VAL C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N THR C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 57 removed outlier: 3.548A pdb=" N SER C 57 " --> pdb=" O THR C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 83 Processing helix chain 'C' and resid 87 through 104 removed outlier: 3.575A pdb=" N LYS C 104 " --> pdb=" O GLU C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 132 Processing helix chain 'C' and resid 139 through 149 Processing helix chain 'C' and resid 154 through 167 Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 228 through 241 Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 254 through 267 Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.552A pdb=" N THR C 294 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 310 No H-bonds generated for 'chain 'C' and resid 308 through 310' Processing helix chain 'C' and resid 313 through 315 No H-bonds generated for 'chain 'C' and resid 313 through 315' Processing helix chain 'C' and resid 338 through 353 removed outlier: 3.733A pdb=" N ASP C 353 " --> pdb=" O ILE C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 372 Processing helix chain 'C' and resid 385 through 407 removed outlier: 3.664A pdb=" N ARG C 394 " --> pdb=" O GLU C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 427 removed outlier: 3.550A pdb=" N CYS C 421 " --> pdb=" O ALA C 417 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) Proline residue: C 423 - end of helix removed outlier: 3.785A pdb=" N ASP C 426 " --> pdb=" O ILE C 422 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER C 427 " --> pdb=" O PRO C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 456 removed outlier: 4.501A pdb=" N LYS C 447 " --> pdb=" O LYS C 443 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE C 448 " --> pdb=" O ARG C 444 " (cutoff:3.500A) Proline residue: C 449 - end of helix Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 487 through 490 No H-bonds generated for 'chain 'C' and resid 487 through 490' Processing helix chain 'C' and resid 496 through 515 removed outlier: 3.811A pdb=" N LEU C 512 " --> pdb=" O GLY C 508 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR C 515 " --> pdb=" O SER C 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 28 removed outlier: 3.911A pdb=" N VAL B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N THR B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 57 removed outlier: 3.548A pdb=" N SER B 57 " --> pdb=" O THR B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 83 Processing helix chain 'B' and resid 87 through 104 removed outlier: 3.575A pdb=" N LYS B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 132 Processing helix chain 'B' and resid 139 through 149 Processing helix chain 'B' and resid 154 through 167 Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 228 through 241 Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 254 through 267 Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.552A pdb=" N THR B 294 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 338 through 353 removed outlier: 3.732A pdb=" N ASP B 353 " --> pdb=" O ILE B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 372 Processing helix chain 'B' and resid 385 through 407 removed outlier: 3.664A pdb=" N ARG B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 427 removed outlier: 3.550A pdb=" N CYS B 421 " --> pdb=" O ALA B 417 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Proline residue: B 423 - end of helix removed outlier: 3.785A pdb=" N ASP B 426 " --> pdb=" O ILE B 422 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER B 427 " --> pdb=" O PRO B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 456 removed outlier: 4.500A pdb=" N LYS B 447 " --> pdb=" O LYS B 443 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE B 448 " --> pdb=" O ARG B 444 " (cutoff:3.500A) Proline residue: B 449 - end of helix Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 487 through 490 No H-bonds generated for 'chain 'B' and resid 487 through 490' Processing helix chain 'B' and resid 496 through 515 removed outlier: 3.811A pdb=" N LEU B 512 " --> pdb=" O GLY B 508 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR B 515 " --> pdb=" O SER B 511 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 28 removed outlier: 3.911A pdb=" N VAL J 27 " --> pdb=" O ASP J 23 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N THR J 28 " --> pdb=" O ALA J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 57 removed outlier: 3.548A pdb=" N SER J 57 " --> pdb=" O THR J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 83 Processing helix chain 'J' and resid 87 through 104 removed outlier: 3.575A pdb=" N LYS J 104 " --> pdb=" O GLU J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 132 Processing helix chain 'J' and resid 139 through 149 Processing helix chain 'J' and resid 154 through 167 Processing helix chain 'J' and resid 200 through 202 No H-bonds generated for 'chain 'J' and resid 200 through 202' Processing helix chain 'J' and resid 228 through 241 Proline residue: J 233 - end of helix Processing helix chain 'J' and resid 254 through 267 Processing helix chain 'J' and resid 280 through 294 removed outlier: 3.552A pdb=" N THR J 294 " --> pdb=" O ALA J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 310 No H-bonds generated for 'chain 'J' and resid 308 through 310' Processing helix chain 'J' and resid 313 through 315 No H-bonds generated for 'chain 'J' and resid 313 through 315' Processing helix chain 'J' and resid 338 through 353 removed outlier: 3.732A pdb=" N ASP J 353 " --> pdb=" O ILE J 349 " (cutoff:3.500A) Processing helix chain 'J' and resid 358 through 372 Processing helix chain 'J' and resid 385 through 407 removed outlier: 3.664A pdb=" N ARG J 394 " --> pdb=" O GLU J 390 " (cutoff:3.500A) Processing helix chain 'J' and resid 416 through 427 removed outlier: 3.550A pdb=" N CYS J 421 " --> pdb=" O ALA J 417 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE J 422 " --> pdb=" O LEU J 418 " (cutoff:3.500A) Proline residue: J 423 - end of helix removed outlier: 3.785A pdb=" N ASP J 426 " --> pdb=" O ILE J 422 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER J 427 " --> pdb=" O PRO J 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 433 through 456 removed outlier: 4.501A pdb=" N LYS J 447 " --> pdb=" O LYS J 443 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE J 448 " --> pdb=" O ARG J 444 " (cutoff:3.500A) Proline residue: J 449 - end of helix Processing helix chain 'J' and resid 461 through 469 Processing helix chain 'J' and resid 487 through 490 No H-bonds generated for 'chain 'J' and resid 487 through 490' Processing helix chain 'J' and resid 496 through 515 removed outlier: 3.811A pdb=" N LEU J 512 " --> pdb=" O GLY J 508 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR J 515 " --> pdb=" O SER J 511 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 28 removed outlier: 3.911A pdb=" N VAL I 27 " --> pdb=" O ASP I 23 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N THR I 28 " --> pdb=" O ALA I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 57 removed outlier: 3.547A pdb=" N SER I 57 " --> pdb=" O THR I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 83 Processing helix chain 'I' and resid 87 through 104 removed outlier: 3.575A pdb=" N LYS I 104 " --> pdb=" O GLU I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 132 Processing helix chain 'I' and resid 139 through 149 Processing helix chain 'I' and resid 154 through 167 Processing helix chain 'I' and resid 200 through 202 No H-bonds generated for 'chain 'I' and resid 200 through 202' Processing helix chain 'I' and resid 228 through 241 Proline residue: I 233 - end of helix Processing helix chain 'I' and resid 254 through 267 Processing helix chain 'I' and resid 280 through 294 removed outlier: 3.551A pdb=" N THR I 294 " --> pdb=" O ALA I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 310 No H-bonds generated for 'chain 'I' and resid 308 through 310' Processing helix chain 'I' and resid 313 through 315 No H-bonds generated for 'chain 'I' and resid 313 through 315' Processing helix chain 'I' and resid 338 through 353 removed outlier: 3.732A pdb=" N ASP I 353 " --> pdb=" O ILE I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 372 Processing helix chain 'I' and resid 385 through 407 removed outlier: 3.664A pdb=" N ARG I 394 " --> pdb=" O GLU I 390 " (cutoff:3.500A) Processing helix chain 'I' and resid 416 through 427 removed outlier: 3.550A pdb=" N CYS I 421 " --> pdb=" O ALA I 417 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE I 422 " --> pdb=" O LEU I 418 " (cutoff:3.500A) Proline residue: I 423 - end of helix removed outlier: 3.785A pdb=" N ASP I 426 " --> pdb=" O ILE I 422 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER I 427 " --> pdb=" O PRO I 423 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 456 removed outlier: 4.500A pdb=" N LYS I 447 " --> pdb=" O LYS I 443 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE I 448 " --> pdb=" O ARG I 444 " (cutoff:3.500A) Proline residue: I 449 - end of helix Processing helix chain 'I' and resid 461 through 469 Processing helix chain 'I' and resid 487 through 490 No H-bonds generated for 'chain 'I' and resid 487 through 490' Processing helix chain 'I' and resid 496 through 515 removed outlier: 3.811A pdb=" N LEU I 512 " --> pdb=" O GLY I 508 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR I 515 " --> pdb=" O SER I 511 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 28 removed outlier: 3.911A pdb=" N VAL H 27 " --> pdb=" O ASP H 23 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N THR H 28 " --> pdb=" O ALA H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 57 removed outlier: 3.547A pdb=" N SER H 57 " --> pdb=" O THR H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 83 Processing helix chain 'H' and resid 87 through 104 removed outlier: 3.575A pdb=" N LYS H 104 " --> pdb=" O GLU H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 132 Processing helix chain 'H' and resid 139 through 149 Processing helix chain 'H' and resid 154 through 167 Processing helix chain 'H' and resid 200 through 202 No H-bonds generated for 'chain 'H' and resid 200 through 202' Processing helix chain 'H' and resid 228 through 241 Proline residue: H 233 - end of helix Processing helix chain 'H' and resid 254 through 267 Processing helix chain 'H' and resid 280 through 294 removed outlier: 3.552A pdb=" N THR H 294 " --> pdb=" O ALA H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 310 No H-bonds generated for 'chain 'H' and resid 308 through 310' Processing helix chain 'H' and resid 313 through 315 No H-bonds generated for 'chain 'H' and resid 313 through 315' Processing helix chain 'H' and resid 338 through 353 removed outlier: 3.732A pdb=" N ASP H 353 " --> pdb=" O ILE H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 358 through 372 Processing helix chain 'H' and resid 385 through 407 removed outlier: 3.664A pdb=" N ARG H 394 " --> pdb=" O GLU H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 427 removed outlier: 3.551A pdb=" N CYS H 421 " --> pdb=" O ALA H 417 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE H 422 " --> pdb=" O LEU H 418 " (cutoff:3.500A) Proline residue: H 423 - end of helix removed outlier: 3.785A pdb=" N ASP H 426 " --> pdb=" O ILE H 422 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER H 427 " --> pdb=" O PRO H 423 " (cutoff:3.500A) Processing helix chain 'H' and resid 433 through 456 removed outlier: 4.501A pdb=" N LYS H 447 " --> pdb=" O LYS H 443 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE H 448 " --> pdb=" O ARG H 444 " (cutoff:3.500A) Proline residue: H 449 - end of helix Processing helix chain 'H' and resid 461 through 469 Processing helix chain 'H' and resid 487 through 490 No H-bonds generated for 'chain 'H' and resid 487 through 490' Processing helix chain 'H' and resid 496 through 515 removed outlier: 3.811A pdb=" N LEU H 512 " --> pdb=" O GLY H 508 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR H 515 " --> pdb=" O SER H 511 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 28 removed outlier: 3.910A pdb=" N VAL N 27 " --> pdb=" O ASP N 23 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N THR N 28 " --> pdb=" O ALA N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 57 removed outlier: 3.548A pdb=" N SER N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 83 Processing helix chain 'N' and resid 87 through 104 removed outlier: 3.575A pdb=" N LYS N 104 " --> pdb=" O GLU N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 132 Processing helix chain 'N' and resid 139 through 149 Processing helix chain 'N' and resid 154 through 167 Processing helix chain 'N' and resid 200 through 202 No H-bonds generated for 'chain 'N' and resid 200 through 202' Processing helix chain 'N' and resid 228 through 241 Proline residue: N 233 - end of helix Processing helix chain 'N' and resid 254 through 267 Processing helix chain 'N' and resid 280 through 294 removed outlier: 3.552A pdb=" N THR N 294 " --> pdb=" O ALA N 291 " (cutoff:3.500A) Processing helix chain 'N' and resid 308 through 310 No H-bonds generated for 'chain 'N' and resid 308 through 310' Processing helix chain 'N' and resid 313 through 315 No H-bonds generated for 'chain 'N' and resid 313 through 315' Processing helix chain 'N' and resid 338 through 353 removed outlier: 3.732A pdb=" N ASP N 353 " --> pdb=" O ILE N 349 " (cutoff:3.500A) Processing helix chain 'N' and resid 358 through 372 Processing helix chain 'N' and resid 385 through 407 removed outlier: 3.663A pdb=" N ARG N 394 " --> pdb=" O GLU N 390 " (cutoff:3.500A) Processing helix chain 'N' and resid 416 through 427 removed outlier: 3.550A pdb=" N CYS N 421 " --> pdb=" O ALA N 417 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE N 422 " --> pdb=" O LEU N 418 " (cutoff:3.500A) Proline residue: N 423 - end of helix removed outlier: 3.786A pdb=" N ASP N 426 " --> pdb=" O ILE N 422 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER N 427 " --> pdb=" O PRO N 423 " (cutoff:3.500A) Processing helix chain 'N' and resid 433 through 456 removed outlier: 4.501A pdb=" N LYS N 447 " --> pdb=" O LYS N 443 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE N 448 " --> pdb=" O ARG N 444 " (cutoff:3.500A) Proline residue: N 449 - end of helix Processing helix chain 'N' and resid 461 through 469 Processing helix chain 'N' and resid 487 through 490 No H-bonds generated for 'chain 'N' and resid 487 through 490' Processing helix chain 'N' and resid 496 through 515 removed outlier: 3.811A pdb=" N LEU N 512 " --> pdb=" O GLY N 508 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR N 515 " --> pdb=" O SER N 511 " (cutoff:3.500A) Processing helix chain 'Y' and resid 8 through 28 removed outlier: 3.910A pdb=" N VAL Y 27 " --> pdb=" O ASP Y 23 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N THR Y 28 " --> pdb=" O ALA Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 57 removed outlier: 3.548A pdb=" N SER Y 57 " --> pdb=" O THR Y 53 " (cutoff:3.500A) Processing helix chain 'Y' and resid 65 through 83 Processing helix chain 'Y' and resid 87 through 104 removed outlier: 3.574A pdb=" N LYS Y 104 " --> pdb=" O GLU Y 100 " (cutoff:3.500A) Processing helix chain 'Y' and resid 111 through 132 Processing helix chain 'Y' and resid 139 through 149 Processing helix chain 'Y' and resid 154 through 167 Processing helix chain 'Y' and resid 200 through 202 No H-bonds generated for 'chain 'Y' and resid 200 through 202' Processing helix chain 'Y' and resid 228 through 241 Proline residue: Y 233 - end of helix Processing helix chain 'Y' and resid 254 through 267 Processing helix chain 'Y' and resid 280 through 294 removed outlier: 3.552A pdb=" N THR Y 294 " --> pdb=" O ALA Y 291 " (cutoff:3.500A) Processing helix chain 'Y' and resid 308 through 310 No H-bonds generated for 'chain 'Y' and resid 308 through 310' Processing helix chain 'Y' and resid 313 through 315 No H-bonds generated for 'chain 'Y' and resid 313 through 315' Processing helix chain 'Y' and resid 338 through 353 removed outlier: 3.732A pdb=" N ASP Y 353 " --> pdb=" O ILE Y 349 " (cutoff:3.500A) Processing helix chain 'Y' and resid 358 through 372 Processing helix chain 'Y' and resid 385 through 407 removed outlier: 3.664A pdb=" N ARG Y 394 " --> pdb=" O GLU Y 390 " (cutoff:3.500A) Processing helix chain 'Y' and resid 416 through 427 removed outlier: 3.550A pdb=" N CYS Y 421 " --> pdb=" O ALA Y 417 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE Y 422 " --> pdb=" O LEU Y 418 " (cutoff:3.500A) Proline residue: Y 423 - end of helix removed outlier: 3.785A pdb=" N ASP Y 426 " --> pdb=" O ILE Y 422 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER Y 427 " --> pdb=" O PRO Y 423 " (cutoff:3.500A) Processing helix chain 'Y' and resid 433 through 456 removed outlier: 4.501A pdb=" N LYS Y 447 " --> pdb=" O LYS Y 443 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE Y 448 " --> pdb=" O ARG Y 444 " (cutoff:3.500A) Proline residue: Y 449 - end of helix Processing helix chain 'Y' and resid 461 through 469 Processing helix chain 'Y' and resid 487 through 490 No H-bonds generated for 'chain 'Y' and resid 487 through 490' Processing helix chain 'Y' and resid 496 through 515 removed outlier: 3.811A pdb=" N LEU Y 512 " --> pdb=" O GLY Y 508 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR Y 515 " --> pdb=" O SER Y 511 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 28 removed outlier: 3.910A pdb=" N VAL L 27 " --> pdb=" O ASP L 23 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N THR L 28 " --> pdb=" O ALA L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 57 removed outlier: 3.548A pdb=" N SER L 57 " --> pdb=" O THR L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 83 Processing helix chain 'L' and resid 87 through 104 removed outlier: 3.575A pdb=" N LYS L 104 " --> pdb=" O GLU L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 132 Processing helix chain 'L' and resid 139 through 149 Processing helix chain 'L' and resid 154 through 167 Processing helix chain 'L' and resid 200 through 202 No H-bonds generated for 'chain 'L' and resid 200 through 202' Processing helix chain 'L' and resid 228 through 241 Proline residue: L 233 - end of helix Processing helix chain 'L' and resid 254 through 267 Processing helix chain 'L' and resid 280 through 294 removed outlier: 3.552A pdb=" N THR L 294 " --> pdb=" O ALA L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 310 No H-bonds generated for 'chain 'L' and resid 308 through 310' Processing helix chain 'L' and resid 313 through 315 No H-bonds generated for 'chain 'L' and resid 313 through 315' Processing helix chain 'L' and resid 338 through 353 removed outlier: 3.733A pdb=" N ASP L 353 " --> pdb=" O ILE L 349 " (cutoff:3.500A) Processing helix chain 'L' and resid 358 through 372 Processing helix chain 'L' and resid 385 through 407 removed outlier: 3.664A pdb=" N ARG L 394 " --> pdb=" O GLU L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 416 through 427 removed outlier: 3.550A pdb=" N CYS L 421 " --> pdb=" O ALA L 417 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE L 422 " --> pdb=" O LEU L 418 " (cutoff:3.500A) Proline residue: L 423 - end of helix removed outlier: 3.786A pdb=" N ASP L 426 " --> pdb=" O ILE L 422 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER L 427 " --> pdb=" O PRO L 423 " (cutoff:3.500A) Processing helix chain 'L' and resid 433 through 456 removed outlier: 4.501A pdb=" N LYS L 447 " --> pdb=" O LYS L 443 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE L 448 " --> pdb=" O ARG L 444 " (cutoff:3.500A) Proline residue: L 449 - end of helix Processing helix chain 'L' and resid 461 through 469 Processing helix chain 'L' and resid 487 through 490 No H-bonds generated for 'chain 'L' and resid 487 through 490' Processing helix chain 'L' and resid 496 through 515 removed outlier: 3.811A pdb=" N LEU L 512 " --> pdb=" O GLY L 508 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR L 515 " --> pdb=" O SER L 511 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 28 removed outlier: 3.910A pdb=" N VAL K 27 " --> pdb=" O ASP K 23 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N THR K 28 " --> pdb=" O ALA K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 57 removed outlier: 3.548A pdb=" N SER K 57 " --> pdb=" O THR K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 83 Processing helix chain 'K' and resid 87 through 104 removed outlier: 3.575A pdb=" N LYS K 104 " --> pdb=" O GLU K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 132 Processing helix chain 'K' and resid 139 through 149 Processing helix chain 'K' and resid 154 through 167 Processing helix chain 'K' and resid 200 through 202 No H-bonds generated for 'chain 'K' and resid 200 through 202' Processing helix chain 'K' and resid 228 through 241 Proline residue: K 233 - end of helix Processing helix chain 'K' and resid 254 through 267 Processing helix chain 'K' and resid 280 through 294 removed outlier: 3.552A pdb=" N THR K 294 " --> pdb=" O ALA K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 310 No H-bonds generated for 'chain 'K' and resid 308 through 310' Processing helix chain 'K' and resid 313 through 315 No H-bonds generated for 'chain 'K' and resid 313 through 315' Processing helix chain 'K' and resid 338 through 353 removed outlier: 3.732A pdb=" N ASP K 353 " --> pdb=" O ILE K 349 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 372 Processing helix chain 'K' and resid 385 through 407 removed outlier: 3.664A pdb=" N ARG K 394 " --> pdb=" O GLU K 390 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 427 removed outlier: 3.551A pdb=" N CYS K 421 " --> pdb=" O ALA K 417 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE K 422 " --> pdb=" O LEU K 418 " (cutoff:3.500A) Proline residue: K 423 - end of helix removed outlier: 3.786A pdb=" N ASP K 426 " --> pdb=" O ILE K 422 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER K 427 " --> pdb=" O PRO K 423 " (cutoff:3.500A) Processing helix chain 'K' and resid 433 through 456 removed outlier: 4.500A pdb=" N LYS K 447 " --> pdb=" O LYS K 443 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE K 448 " --> pdb=" O ARG K 444 " (cutoff:3.500A) Proline residue: K 449 - end of helix Processing helix chain 'K' and resid 461 through 469 Processing helix chain 'K' and resid 487 through 490 No H-bonds generated for 'chain 'K' and resid 487 through 490' Processing helix chain 'K' and resid 496 through 515 removed outlier: 3.811A pdb=" N LEU K 512 " --> pdb=" O GLY K 508 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR K 515 " --> pdb=" O SER K 511 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 2 through 6 Processing sheet with id= B, first strand: chain 'A' and resid 36 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 172 through 177 Processing sheet with id= D, first strand: chain 'A' and resid 211 through 214 Processing sheet with id= E, first strand: chain 'A' and resid 317 through 319 Processing sheet with id= F, first strand: chain 'A' and resid 410 through 412 Processing sheet with id= G, first strand: chain 'A' and resid 475 through 478 Processing sheet with id= H, first strand: chain 'G' and resid 2 through 6 Processing sheet with id= I, first strand: chain 'G' and resid 36 through 38 Processing sheet with id= J, first strand: chain 'G' and resid 172 through 177 Processing sheet with id= K, first strand: chain 'G' and resid 211 through 214 Processing sheet with id= L, first strand: chain 'G' and resid 317 through 319 Processing sheet with id= M, first strand: chain 'G' and resid 410 through 412 Processing sheet with id= N, first strand: chain 'G' and resid 475 through 478 Processing sheet with id= O, first strand: chain 'F' and resid 2 through 6 Processing sheet with id= P, first strand: chain 'F' and resid 36 through 38 Processing sheet with id= Q, first strand: chain 'F' and resid 172 through 177 Processing sheet with id= R, first strand: chain 'F' and resid 211 through 214 Processing sheet with id= S, first strand: chain 'F' and resid 317 through 319 Processing sheet with id= T, first strand: chain 'F' and resid 410 through 412 Processing sheet with id= U, first strand: chain 'F' and resid 475 through 478 Processing sheet with id= V, first strand: chain 'E' and resid 2 through 6 Processing sheet with id= W, first strand: chain 'E' and resid 36 through 38 Processing sheet with id= X, first strand: chain 'E' and resid 172 through 177 Processing sheet with id= Y, first strand: chain 'E' and resid 211 through 214 Processing sheet with id= Z, first strand: chain 'E' and resid 317 through 319 Processing sheet with id= AA, first strand: chain 'E' and resid 410 through 412 Processing sheet with id= AB, first strand: chain 'E' and resid 475 through 478 Processing sheet with id= AC, first strand: chain 'D' and resid 2 through 6 Processing sheet with id= AD, first strand: chain 'D' and resid 36 through 38 Processing sheet with id= AE, first strand: chain 'D' and resid 172 through 177 Processing sheet with id= AF, first strand: chain 'D' and resid 211 through 214 Processing sheet with id= AG, first strand: chain 'D' and resid 317 through 319 Processing sheet with id= AH, first strand: chain 'D' and resid 410 through 412 Processing sheet with id= AI, first strand: chain 'D' and resid 475 through 478 Processing sheet with id= AJ, first strand: chain 'C' and resid 2 through 6 Processing sheet with id= AK, first strand: chain 'C' and resid 36 through 38 Processing sheet with id= AL, first strand: chain 'C' and resid 172 through 177 Processing sheet with id= AM, first strand: chain 'C' and resid 211 through 214 Processing sheet with id= AN, first strand: chain 'C' and resid 317 through 319 Processing sheet with id= AO, first strand: chain 'C' and resid 410 through 412 Processing sheet with id= AP, first strand: chain 'C' and resid 475 through 478 Processing sheet with id= AQ, first strand: chain 'B' and resid 2 through 6 Processing sheet with id= AR, first strand: chain 'B' and resid 36 through 38 Processing sheet with id= AS, first strand: chain 'B' and resid 172 through 177 Processing sheet with id= AT, first strand: chain 'B' and resid 211 through 214 Processing sheet with id= AU, first strand: chain 'B' and resid 317 through 319 Processing sheet with id= AV, first strand: chain 'B' and resid 410 through 412 Processing sheet with id= AW, first strand: chain 'B' and resid 475 through 478 Processing sheet with id= AX, first strand: chain 'J' and resid 2 through 6 Processing sheet with id= AY, first strand: chain 'J' and resid 36 through 38 Processing sheet with id= AZ, first strand: chain 'J' and resid 172 through 177 Processing sheet with id= BA, first strand: chain 'J' and resid 211 through 214 Processing sheet with id= BB, first strand: chain 'J' and resid 317 through 319 Processing sheet with id= BC, first strand: chain 'J' and resid 410 through 412 Processing sheet with id= BD, first strand: chain 'J' and resid 475 through 478 Processing sheet with id= BE, first strand: chain 'I' and resid 2 through 6 Processing sheet with id= BF, first strand: chain 'I' and resid 36 through 38 Processing sheet with id= BG, first strand: chain 'I' and resid 172 through 177 Processing sheet with id= BH, first strand: chain 'I' and resid 211 through 214 Processing sheet with id= BI, first strand: chain 'I' and resid 317 through 319 Processing sheet with id= BJ, first strand: chain 'I' and resid 410 through 412 Processing sheet with id= BK, first strand: chain 'I' and resid 475 through 478 Processing sheet with id= BL, first strand: chain 'H' and resid 2 through 6 Processing sheet with id= BM, first strand: chain 'H' and resid 36 through 38 Processing sheet with id= BN, first strand: chain 'H' and resid 172 through 177 Processing sheet with id= BO, first strand: chain 'H' and resid 211 through 214 Processing sheet with id= BP, first strand: chain 'H' and resid 317 through 319 Processing sheet with id= BQ, first strand: chain 'H' and resid 410 through 412 Processing sheet with id= BR, first strand: chain 'H' and resid 475 through 478 Processing sheet with id= BS, first strand: chain 'N' and resid 2 through 6 Processing sheet with id= BT, first strand: chain 'N' and resid 36 through 38 Processing sheet with id= BU, first strand: chain 'N' and resid 172 through 177 Processing sheet with id= BV, first strand: chain 'N' and resid 211 through 214 Processing sheet with id= BW, first strand: chain 'N' and resid 317 through 319 Processing sheet with id= BX, first strand: chain 'N' and resid 410 through 412 Processing sheet with id= BY, first strand: chain 'N' and resid 475 through 478 Processing sheet with id= BZ, first strand: chain 'Y' and resid 2 through 6 Processing sheet with id= CA, first strand: chain 'Y' and resid 36 through 38 Processing sheet with id= CB, first strand: chain 'Y' and resid 172 through 177 Processing sheet with id= CC, first strand: chain 'Y' and resid 211 through 214 Processing sheet with id= CD, first strand: chain 'Y' and resid 317 through 319 Processing sheet with id= CE, first strand: chain 'Y' and resid 410 through 412 Processing sheet with id= CF, first strand: chain 'Y' and resid 475 through 478 Processing sheet with id= CG, first strand: chain 'L' and resid 2 through 6 Processing sheet with id= CH, first strand: chain 'L' and resid 36 through 38 Processing sheet with id= CI, first strand: chain 'L' and resid 172 through 177 Processing sheet with id= CJ, first strand: chain 'L' and resid 211 through 214 Processing sheet with id= CK, first strand: chain 'L' and resid 317 through 319 Processing sheet with id= CL, first strand: chain 'L' and resid 410 through 412 Processing sheet with id= CM, first strand: chain 'L' and resid 475 through 478 Processing sheet with id= CN, first strand: chain 'K' and resid 2 through 6 Processing sheet with id= CO, first strand: chain 'K' and resid 36 through 38 Processing sheet with id= CP, first strand: chain 'K' and resid 172 through 177 Processing sheet with id= CQ, first strand: chain 'K' and resid 211 through 214 Processing sheet with id= CR, first strand: chain 'K' and resid 317 through 319 Processing sheet with id= CS, first strand: chain 'K' and resid 410 through 412 Processing sheet with id= CT, first strand: chain 'K' and resid 475 through 478 Processing sheet with id= CU, first strand: chain 'O' and resid 79 through 83 removed outlier: 8.392A pdb=" N ASP O 87 " --> pdb=" O ARG O 20 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG O 20 " --> pdb=" O ASP O 87 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLU O 19 " --> pdb=" O VAL O 46 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL O 46 " --> pdb=" O GLU O 19 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS O 70 " --> pdb=" O TYR O 100 " (cutoff:3.500A) Processing sheet with id= CV, first strand: chain 'U' and resid 79 through 83 removed outlier: 8.392A pdb=" N ASP U 87 " --> pdb=" O ARG U 20 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG U 20 " --> pdb=" O ASP U 87 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU U 19 " --> pdb=" O VAL U 46 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL U 46 " --> pdb=" O GLU U 19 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS U 70 " --> pdb=" O TYR U 100 " (cutoff:3.500A) Processing sheet with id= CW, first strand: chain 'T' and resid 79 through 83 removed outlier: 8.392A pdb=" N ASP T 87 " --> pdb=" O ARG T 20 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG T 20 " --> pdb=" O ASP T 87 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLU T 19 " --> pdb=" O VAL T 46 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL T 46 " --> pdb=" O GLU T 19 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS T 70 " --> pdb=" O TYR T 100 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain 'S' and resid 79 through 83 removed outlier: 8.391A pdb=" N ASP S 87 " --> pdb=" O ARG S 20 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG S 20 " --> pdb=" O ASP S 87 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU S 19 " --> pdb=" O VAL S 46 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL S 46 " --> pdb=" O GLU S 19 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS S 70 " --> pdb=" O TYR S 100 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain 'R' and resid 79 through 83 removed outlier: 8.392A pdb=" N ASP R 87 " --> pdb=" O ARG R 20 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG R 20 " --> pdb=" O ASP R 87 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU R 19 " --> pdb=" O VAL R 46 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL R 46 " --> pdb=" O GLU R 19 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS R 70 " --> pdb=" O TYR R 100 " (cutoff:3.500A) Processing sheet with id= CZ, first strand: chain 'Q' and resid 79 through 83 removed outlier: 8.392A pdb=" N ASP Q 87 " --> pdb=" O ARG Q 20 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ARG Q 20 " --> pdb=" O ASP Q 87 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLU Q 19 " --> pdb=" O VAL Q 46 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL Q 46 " --> pdb=" O GLU Q 19 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS Q 70 " --> pdb=" O TYR Q 100 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'P' and resid 79 through 83 removed outlier: 8.393A pdb=" N ASP P 87 " --> pdb=" O ARG P 20 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG P 20 " --> pdb=" O ASP P 87 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU P 19 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL P 46 " --> pdb=" O GLU P 19 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS P 70 " --> pdb=" O TYR P 100 " (cutoff:3.500A) Processing sheet with id= DB, first strand: chain 'X' and resid 79 through 83 removed outlier: 8.392A pdb=" N ASP X 87 " --> pdb=" O ARG X 20 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG X 20 " --> pdb=" O ASP X 87 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLU X 19 " --> pdb=" O VAL X 46 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL X 46 " --> pdb=" O GLU X 19 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS X 70 " --> pdb=" O TYR X 100 " (cutoff:3.500A) Processing sheet with id= DC, first strand: chain 'W' and resid 79 through 83 removed outlier: 8.392A pdb=" N ASP W 87 " --> pdb=" O ARG W 20 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG W 20 " --> pdb=" O ASP W 87 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU W 19 " --> pdb=" O VAL W 46 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL W 46 " --> pdb=" O GLU W 19 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS W 70 " --> pdb=" O TYR W 100 " (cutoff:3.500A) Processing sheet with id= DD, first strand: chain 'V' and resid 79 through 83 removed outlier: 8.392A pdb=" N ASP V 87 " --> pdb=" O ARG V 20 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG V 20 " --> pdb=" O ASP V 87 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLU V 19 " --> pdb=" O VAL V 46 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL V 46 " --> pdb=" O GLU V 19 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS V 70 " --> pdb=" O TYR V 100 " (cutoff:3.500A) Processing sheet with id= DE, first strand: chain '2' and resid 79 through 83 removed outlier: 8.391A pdb=" N ASP 2 87 " --> pdb=" O ARG 2 20 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG 2 20 " --> pdb=" O ASP 2 87 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLU 2 19 " --> pdb=" O VAL 2 46 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL 2 46 " --> pdb=" O GLU 2 19 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS 2 70 " --> pdb=" O TYR 2 100 " (cutoff:3.500A) Processing sheet with id= DF, first strand: chain '1' and resid 79 through 83 removed outlier: 8.391A pdb=" N ASP 1 87 " --> pdb=" O ARG 1 20 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG 1 20 " --> pdb=" O ASP 1 87 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLU 1 19 " --> pdb=" O VAL 1 46 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL 1 46 " --> pdb=" O GLU 1 19 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS 1 70 " --> pdb=" O TYR 1 100 " (cutoff:3.500A) Processing sheet with id= DG, first strand: chain 'Z' and resid 79 through 83 removed outlier: 8.392A pdb=" N ASP Z 87 " --> pdb=" O ARG Z 20 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ARG Z 20 " --> pdb=" O ASP Z 87 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLU Z 19 " --> pdb=" O VAL Z 46 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL Z 46 " --> pdb=" O GLU Z 19 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS Z 70 " --> pdb=" O TYR Z 100 " (cutoff:3.500A) Processing sheet with id= DH, first strand: chain 'M' and resid 79 through 83 removed outlier: 8.392A pdb=" N ASP M 87 " --> pdb=" O ARG M 20 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ARG M 20 " --> pdb=" O ASP M 87 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLU M 19 " --> pdb=" O VAL M 46 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL M 46 " --> pdb=" O GLU M 19 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS M 70 " --> pdb=" O TYR M 100 " (cutoff:3.500A) 3402 hydrogen bonds defined for protein. 9282 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: 32.13 Time building geometry restraints manager: 22.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 22188 1.34 - 1.46: 8777 1.46 - 1.57: 35297 1.57 - 1.69: 70 1.69 - 1.81: 378 Bond restraints: 66710 Sorted by residual: bond pdb=" CD GLN K 286 " pdb=" OE1 GLN K 286 " ideal model delta sigma weight residual 1.231 1.327 -0.096 1.90e-02 2.77e+03 2.55e+01 bond pdb=" CD GLN E 286 " pdb=" OE1 GLN E 286 " ideal model delta sigma weight residual 1.231 1.327 -0.096 1.90e-02 2.77e+03 2.54e+01 bond pdb=" CD GLN F 286 " pdb=" OE1 GLN F 286 " ideal model delta sigma weight residual 1.231 1.327 -0.096 1.90e-02 2.77e+03 2.54e+01 bond pdb=" CD GLN C 286 " pdb=" OE1 GLN C 286 " ideal model delta sigma weight residual 1.231 1.326 -0.095 1.90e-02 2.77e+03 2.52e+01 bond pdb=" CD GLN G 286 " pdb=" OE1 GLN G 286 " ideal model delta sigma weight residual 1.231 1.326 -0.095 1.90e-02 2.77e+03 2.52e+01 ... (remaining 66705 not shown) Histogram of bond angle deviations from ideal: 99.37 - 107.48: 1724 107.48 - 115.59: 43755 115.59 - 123.69: 43544 123.69 - 131.80: 955 131.80 - 139.91: 56 Bond angle restraints: 90034 Sorted by residual: angle pdb=" O ILE A 228 " pdb=" C ILE A 228 " pdb=" N GLN A 229 " ideal model delta sigma weight residual 121.80 115.43 6.37 1.13e+00 7.83e-01 3.18e+01 angle pdb=" CA ILE A 228 " pdb=" C ILE A 228 " pdb=" N GLN A 229 " ideal model delta sigma weight residual 117.69 123.85 -6.16 1.27e+00 6.20e-01 2.36e+01 angle pdb=" O ILE G 228 " pdb=" C ILE G 228 " pdb=" N GLN G 229 " ideal model delta sigma weight residual 121.80 116.64 5.16 1.13e+00 7.83e-01 2.08e+01 angle pdb=" O ILE I 228 " pdb=" C ILE I 228 " pdb=" N GLN I 229 " ideal model delta sigma weight residual 121.80 116.68 5.12 1.13e+00 7.83e-01 2.05e+01 angle pdb=" C PHE T 13 " pdb=" CA PHE T 13 " pdb=" CB PHE T 13 " ideal model delta sigma weight residual 117.23 111.17 6.06 1.36e+00 5.41e-01 1.98e+01 ... (remaining 90029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.09: 38241 16.09 - 32.18: 2160 32.18 - 48.27: 507 48.27 - 64.37: 126 64.37 - 80.46: 98 Dihedral angle restraints: 41132 sinusoidal: 16380 harmonic: 24752 Sorted by residual: dihedral pdb=" CA GLY Y 7 " pdb=" C GLY Y 7 " pdb=" N ALA Y 8 " pdb=" CA ALA Y 8 " ideal model delta harmonic sigma weight residual -180.00 -162.62 -17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA GLY L 7 " pdb=" C GLY L 7 " pdb=" N ALA L 8 " pdb=" CA ALA L 8 " ideal model delta harmonic sigma weight residual 180.00 -162.63 -17.37 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA GLY I 7 " pdb=" C GLY I 7 " pdb=" N ALA I 8 " pdb=" CA ALA I 8 " ideal model delta harmonic sigma weight residual -180.00 -162.63 -17.37 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 41129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 9146 0.056 - 0.112: 1345 0.112 - 0.167: 317 0.167 - 0.223: 0 0.223 - 0.279: 42 Chirality restraints: 10850 Sorted by residual: chirality pdb=" C2' ATP L 601 " pdb=" C1' ATP L 601 " pdb=" C3' ATP L 601 " pdb=" O2' ATP L 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C2' ATP H 601 " pdb=" C1' ATP H 601 " pdb=" C3' ATP H 601 " pdb=" O2' ATP H 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C2' ATP N 601 " pdb=" C1' ATP N 601 " pdb=" C3' ATP N 601 " pdb=" O2' ATP N 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 10847 not shown) Planarity restraints: 11522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 199 " -0.064 5.00e-02 4.00e+02 9.52e-02 1.45e+01 pdb=" N PRO D 200 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO D 200 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO D 200 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 199 " 0.064 5.00e-02 4.00e+02 9.52e-02 1.45e+01 pdb=" N PRO H 200 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO H 200 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO H 200 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 199 " -0.064 5.00e-02 4.00e+02 9.52e-02 1.45e+01 pdb=" N PRO F 200 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO F 200 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO F 200 " -0.052 5.00e-02 4.00e+02 ... (remaining 11519 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.72: 1748 2.72 - 3.32: 75199 3.32 - 3.93: 124814 3.93 - 4.53: 169307 4.53 - 5.14: 263213 Nonbonded interactions: 634281 Sorted by model distance: nonbonded pdb=" O2G ATP N 601 " pdb="MG MG N 602 " model vdw 2.109 2.170 nonbonded pdb=" O2G ATP B 601 " pdb="MG MG B 602 " model vdw 2.110 2.170 nonbonded pdb=" O2G ATP Y 601 " pdb="MG MG Y 602 " model vdw 2.110 2.170 nonbonded pdb=" O2G ATP D 601 " pdb="MG MG D 602 " model vdw 2.110 2.170 nonbonded pdb=" O2G ATP I 601 " pdb="MG MG I 602 " model vdw 2.110 2.170 ... (remaining 634276 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 '1' selection = chain '2' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' } 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' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.730 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: 0.040 Extract box with map and model: 22.010 Check model and map are aligned: 0.710 Set scattering table: 0.430 Process input model: 139.300 Find NCS groups from input model: 3.860 Set up NCS constraints: 0.810 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: 0.020 Load rotamer database and sin/cos tables:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 182.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 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 : 0.003 0.097 66710 Z= 0.227 Angle : 0.573 6.369 90034 Z= 0.344 Chirality : 0.045 0.279 10850 Planarity : 0.005 0.095 11522 Dihedral : 12.310 80.456 25256 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer Outliers : 0.20 % 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: 1.66 (0.09), residues: 8722 helix: 2.55 (0.08), residues: 3850 sheet: 0.80 (0.15), residues: 1106 loop : -0.33 (0.09), residues: 3766 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1190 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1176 time to evaluate : 5.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 1190 average time/residue: 1.5177 time to fit residues: 2328.7863 Evaluate side-chains 879 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 877 time to evaluate : 5.700 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 7.8692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 732 optimal weight: 0.4980 chunk 657 optimal weight: 0.6980 chunk 365 optimal weight: 3.9990 chunk 224 optimal weight: 0.9990 chunk 443 optimal weight: 10.0000 chunk 351 optimal weight: 5.9990 chunk 680 optimal weight: 0.9990 chunk 263 optimal weight: 2.9990 chunk 413 optimal weight: 0.7980 chunk 506 optimal weight: 3.9990 chunk 788 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN G 239 ASN F 239 ASN F 346 GLN E 214 GLN E 239 ASN D 214 GLN D 239 ASN D 346 GLN C 239 ASN C 346 GLN B 239 ASN J 239 ASN I 239 ASN H 239 ASN H 346 GLN N 214 GLN N 239 ASN Y 214 GLN Y 239 ASN Y 346 GLN L 239 ASN L 346 GLN K 239 ASN S 43 GLN 2 43 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 66710 Z= 0.143 Angle : 0.462 6.842 90034 Z= 0.252 Chirality : 0.042 0.174 10850 Planarity : 0.004 0.058 11522 Dihedral : 5.500 81.262 9226 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer Outliers : 1.90 % 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: 1.61 (0.09), residues: 8722 helix: 2.41 (0.08), residues: 3892 sheet: 0.93 (0.15), residues: 1106 loop : -0.34 (0.09), residues: 3724 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1054 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 919 time to evaluate : 5.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 135 outliers final: 42 residues processed: 1008 average time/residue: 1.3923 time to fit residues: 1852.6283 Evaluate side-chains 886 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 844 time to evaluate : 5.720 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 31 residues processed: 14 average time/residue: 1.5301 time to fit residues: 35.7211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 438 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 656 optimal weight: 20.0000 chunk 536 optimal weight: 0.9980 chunk 217 optimal weight: 4.9990 chunk 789 optimal weight: 9.9990 chunk 853 optimal weight: 0.0970 chunk 703 optimal weight: 8.9990 chunk 783 optimal weight: 8.9990 chunk 269 optimal weight: 0.9990 chunk 633 optimal weight: 0.9980 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN F 239 ASN E 214 GLN E 239 ASN E 346 GLN D 239 ASN C 239 ASN B 239 ASN B 312 GLN J 239 ASN I 214 GLN H 239 ASN N 214 GLN N 239 ASN N 346 GLN ** Y 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 239 ASN L 239 ASN K 214 GLN K 239 ASN K 312 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 66710 Z= 0.204 Angle : 0.499 7.543 90034 Z= 0.271 Chirality : 0.043 0.158 10850 Planarity : 0.004 0.040 11522 Dihedral : 5.679 87.331 9226 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.09), residues: 8722 helix: 2.06 (0.08), residues: 3934 sheet: 1.01 (0.15), residues: 1106 loop : -0.39 (0.09), residues: 3682 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1018 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 892 time to evaluate : 5.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 126 outliers final: 43 residues processed: 969 average time/residue: 1.4501 time to fit residues: 1832.9563 Evaluate side-chains 903 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 860 time to evaluate : 5.792 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 32 residues processed: 14 average time/residue: 1.0633 time to fit residues: 28.9855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 780 optimal weight: 20.0000 chunk 593 optimal weight: 10.0000 chunk 409 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 376 optimal weight: 4.9990 chunk 530 optimal weight: 0.3980 chunk 792 optimal weight: 4.9990 chunk 839 optimal weight: 7.9990 chunk 414 optimal weight: 3.9990 chunk 751 optimal weight: 20.0000 chunk 226 optimal weight: 10.0000 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN G 239 ASN F 239 ASN E 239 ASN ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 ASN C 239 ASN B 239 ASN J 239 ASN I 214 GLN I 239 ASN H 239 ASN N 239 ASN Y 239 ASN L 239 ASN K 214 GLN K 239 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 66710 Z= 0.256 Angle : 0.538 8.225 90034 Z= 0.291 Chirality : 0.045 0.156 10850 Planarity : 0.004 0.044 11522 Dihedral : 5.835 89.057 9226 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer Outliers : 1.86 % 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: 1.15 (0.09), residues: 8722 helix: 1.83 (0.08), residues: 3906 sheet: 0.94 (0.15), residues: 1106 loop : -0.42 (0.09), residues: 3710 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 890 time to evaluate : 5.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 132 outliers final: 53 residues processed: 969 average time/residue: 1.4577 time to fit residues: 1847.7121 Evaluate side-chains 920 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 867 time to evaluate : 5.802 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 42 residues processed: 13 average time/residue: 1.1999 time to fit residues: 29.4726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 698 optimal weight: 9.9990 chunk 476 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 624 optimal weight: 1.9990 chunk 346 optimal weight: 5.9990 chunk 715 optimal weight: 4.9990 chunk 579 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 428 optimal weight: 1.9990 chunk 753 optimal weight: 0.0010 chunk 211 optimal weight: 3.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN G 239 ASN F 239 ASN E 214 GLN E 239 ASN ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 ASN C 239 ASN B 239 ASN B 312 GLN J 239 ASN I 214 GLN I 239 ASN H 239 ASN N 214 GLN N 239 ASN ** Y 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 239 ASN L 239 ASN K 239 ASN K 312 GLN K 346 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 66710 Z= 0.251 Angle : 0.531 8.168 90034 Z= 0.287 Chirality : 0.044 0.156 10850 Planarity : 0.004 0.044 11522 Dihedral : 5.829 89.391 9226 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 1.70 % 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: 1.05 (0.09), residues: 8722 helix: 1.75 (0.08), residues: 3906 sheet: 0.90 (0.15), residues: 1106 loop : -0.50 (0.09), residues: 3710 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 987 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 866 time to evaluate : 5.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 121 outliers final: 58 residues processed: 943 average time/residue: 1.4642 time to fit residues: 1803.3303 Evaluate side-chains 890 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 832 time to evaluate : 5.688 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 48 residues processed: 12 average time/residue: 1.1284 time to fit residues: 26.6435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 282 optimal weight: 9.9990 chunk 755 optimal weight: 3.9990 chunk 165 optimal weight: 0.6980 chunk 492 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 chunk 839 optimal weight: 7.9990 chunk 697 optimal weight: 9.9990 chunk 388 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 277 optimal weight: 5.9990 chunk 440 optimal weight: 5.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN G 239 ASN G 312 GLN F 239 ASN E 214 GLN E 239 ASN ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 ASN C 239 ASN B 239 ASN J 239 ASN I 214 GLN I 239 ASN H 239 ASN ** N 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 239 ASN ** Y 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 239 ASN L 239 ASN K 239 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 66710 Z= 0.336 Angle : 0.590 8.574 90034 Z= 0.318 Chirality : 0.046 0.163 10850 Planarity : 0.005 0.045 11522 Dihedral : 6.006 89.485 9226 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.09), residues: 8722 helix: 1.55 (0.08), residues: 3906 sheet: 0.81 (0.15), residues: 1106 loop : -0.60 (0.09), residues: 3710 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1002 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 873 time to evaluate : 5.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 129 outliers final: 61 residues processed: 951 average time/residue: 1.4729 time to fit residues: 1833.4594 Evaluate side-chains 909 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 848 time to evaluate : 5.767 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 44 residues processed: 17 average time/residue: 0.9860 time to fit residues: 32.1369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 809 optimal weight: 6.9990 chunk 94 optimal weight: 0.1980 chunk 478 optimal weight: 0.9990 chunk 613 optimal weight: 4.9990 chunk 475 optimal weight: 0.5980 chunk 706 optimal weight: 2.9990 chunk 468 optimal weight: 0.9990 chunk 836 optimal weight: 0.5980 chunk 523 optimal weight: 2.9990 chunk 510 optimal weight: 0.0970 chunk 386 optimal weight: 10.0000 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN G 239 ASN F 214 GLN F 239 ASN E 214 GLN E 239 ASN ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 ASN C 239 ASN B 239 ASN B 312 GLN B 346 GLN J 239 ASN I 239 ASN I 312 GLN H 214 GLN H 239 ASN ** N 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 239 ASN Y 239 ASN L 239 ASN K 214 GLN K 239 ASN K 312 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 66710 Z= 0.124 Angle : 0.452 8.006 90034 Z= 0.242 Chirality : 0.041 0.158 10850 Planarity : 0.004 0.041 11522 Dihedral : 5.482 88.242 9226 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer Outliers : 1.32 % 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: 1.20 (0.09), residues: 8722 helix: 1.95 (0.08), residues: 3934 sheet: 0.84 (0.15), residues: 1190 loop : -0.51 (0.09), residues: 3598 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 910 time to evaluate : 5.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 51 residues processed: 971 average time/residue: 1.4151 time to fit residues: 1812.4959 Evaluate side-chains 914 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 863 time to evaluate : 5.906 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 44 residues processed: 8 average time/residue: 0.8684 time to fit residues: 18.9066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 517 optimal weight: 0.9980 chunk 334 optimal weight: 9.9990 chunk 499 optimal weight: 8.9990 chunk 252 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 chunk 531 optimal weight: 3.9990 chunk 569 optimal weight: 0.9980 chunk 413 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 657 optimal weight: 9.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN G 239 ASN F 214 GLN F 239 ASN E 239 ASN D 239 ASN C 239 ASN B 239 ASN J 239 ASN I 239 ASN H 214 GLN H 239 ASN ** N 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 239 ASN Y 239 ASN L 239 ASN K 239 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 66710 Z= 0.291 Angle : 0.562 8.622 90034 Z= 0.302 Chirality : 0.045 0.196 10850 Planarity : 0.004 0.045 11522 Dihedral : 5.845 88.021 9226 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 1.25 % 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: 0.94 (0.09), residues: 8722 helix: 1.68 (0.08), residues: 3906 sheet: 0.87 (0.16), residues: 1106 loop : -0.58 (0.09), residues: 3710 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 987 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 898 time to evaluate : 6.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 63 residues processed: 959 average time/residue: 1.4244 time to fit residues: 1799.5235 Evaluate side-chains 929 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 866 time to evaluate : 5.737 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 50 residues processed: 14 average time/residue: 1.2174 time to fit residues: 31.1697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 761 optimal weight: 7.9990 chunk 801 optimal weight: 8.9990 chunk 731 optimal weight: 9.9990 chunk 779 optimal weight: 8.9990 chunk 469 optimal weight: 0.9990 chunk 339 optimal weight: 7.9990 chunk 612 optimal weight: 0.4980 chunk 239 optimal weight: 2.9990 chunk 704 optimal weight: 3.9990 chunk 737 optimal weight: 8.9990 chunk 776 optimal weight: 5.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN A 239 ASN G 239 ASN G 312 GLN F 214 GLN F 239 ASN E 239 ASN D 239 ASN C 239 ASN B 312 GLN J 214 GLN J 239 ASN I 239 ASN H 214 GLN H 239 ASN ** N 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 239 ASN Y 239 ASN L 214 GLN L 239 ASN K 239 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 66710 Z= 0.317 Angle : 0.586 10.015 90034 Z= 0.315 Chirality : 0.046 0.178 10850 Planarity : 0.005 0.045 11522 Dihedral : 5.990 87.905 9226 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 1.04 % 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: 0.74 (0.09), residues: 8722 helix: 1.50 (0.08), residues: 3906 sheet: 0.78 (0.16), residues: 1106 loop : -0.67 (0.09), residues: 3710 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 895 time to evaluate : 5.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 57 residues processed: 948 average time/residue: 1.4579 time to fit residues: 1816.2888 Evaluate side-chains 935 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 878 time to evaluate : 5.744 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 46 residues processed: 11 average time/residue: 1.0889 time to fit residues: 24.7287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 511 optimal weight: 0.9980 chunk 824 optimal weight: 20.0000 chunk 503 optimal weight: 7.9990 chunk 391 optimal weight: 5.9990 chunk 573 optimal weight: 1.9990 chunk 864 optimal weight: 9.9990 chunk 795 optimal weight: 3.9990 chunk 688 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 531 optimal weight: 0.9980 chunk 422 optimal weight: 0.4980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN A 239 ASN G 239 ASN F 239 ASN E 214 GLN E 239 ASN E 340 GLN D 214 GLN D 239 ASN ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN J 214 GLN J 239 ASN I 239 ASN H 214 GLN H 239 ASN N 239 ASN Y 214 GLN Y 239 ASN ** L 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 239 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 66710 Z= 0.164 Angle : 0.495 9.715 90034 Z= 0.263 Chirality : 0.043 0.166 10850 Planarity : 0.004 0.043 11522 Dihedral : 5.680 88.112 9226 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.09), residues: 8722 helix: 1.77 (0.08), residues: 3934 sheet: 0.79 (0.16), residues: 1050 loop : -0.62 (0.09), residues: 3738 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 879 time to evaluate : 5.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 51 residues processed: 928 average time/residue: 1.3916 time to fit residues: 1714.7225 Evaluate side-chains 913 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 862 time to evaluate : 5.799 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 46 residues processed: 5 average time/residue: 1.3971 time to fit residues: 17.3310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 546 optimal weight: 0.0770 chunk 733 optimal weight: 30.0000 chunk 210 optimal weight: 0.6980 chunk 634 optimal weight: 0.9980 chunk 101 optimal weight: 0.0020 chunk 191 optimal weight: 4.9990 chunk 689 optimal weight: 0.9990 chunk 288 optimal weight: 6.9990 chunk 708 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 overall best weight: 0.5546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 241 HIS G 239 ASN G 312 GLN F 40 GLN F 239 ASN E 214 GLN E 239 ASN E 340 GLN D 40 GLN D 239 ASN C 40 GLN C 214 GLN C 239 ASN B 40 GLN B 312 GLN J 239 ASN J 241 HIS I 239 ASN H 40 GLN H 214 GLN H 239 ASN N 239 ASN N 340 GLN Y 40 GLN Y 214 GLN Y 239 ASN L 40 GLN L 214 GLN L 239 ASN K 40 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.180279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.134748 restraints weight = 68551.897| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.45 r_work: 0.3149 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 66710 Z= 0.127 Angle : 0.460 9.586 90034 Z= 0.242 Chirality : 0.042 0.167 10850 Planarity : 0.004 0.040 11522 Dihedral : 5.293 88.151 9226 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 0.83 % 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: 1.14 (0.09), residues: 8722 helix: 2.00 (0.08), residues: 3920 sheet: 0.67 (0.17), residues: 910 loop : -0.51 (0.09), residues: 3892 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25123.95 seconds wall clock time: 435 minutes 49.00 seconds (26149.00 seconds total)