Starting phenix.real_space_refine on Thu May 16 08:46:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7n_29817/05_2024/8g7n_29817_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7n_29817/05_2024/8g7n_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_29817/05_2024/8g7n_29817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7n_29817/05_2024/8g7n_29817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7n_29817/05_2024/8g7n_29817_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7n_29817/05_2024/8g7n_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: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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: 26.26, per 1000 atoms: 0.40 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: 19.91 Conformation dependent library (CDL) restraints added in 9.2 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: 11.04 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: 27.45 Time building geometry restraints manager: 21.96 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 - 16.73: 38469 16.73 - 33.45: 2132 33.45 - 50.18: 659 50.18 - 66.91: 194 66.91 - 83.63: 112 Dihedral angle restraints: 41566 sinusoidal: 16814 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 41563 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: 0.000 Normalize map: mean=0, sd=1: 3.970 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: 0.050 Extract box with map and model: 20.080 Check model and map are aligned: 0.400 Set scattering table: 0.460 Process input model: 142.620 Find NCS groups from input model: 4.210 Set up NCS constraints: 0.870 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: 0.010 Load rotamer database and sin/cos tables:10.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 183.100 ------------------------------------------------------------------------------- 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 : 13.363 83.635 25690 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 % Allowed : 0.20 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP Y 42 HIS 0.001 0.000 HIS I 314 PHE 0.006 0.001 PHE Z 89 TYR 0.011 0.001 TYR B 197 ARG 0.002 0.000 ARG I 115 *********************** 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 : 5.741 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: A 212 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6688 (mm-30) REVERT: A 312 GLN cc_start: 0.7586 (mm-40) cc_final: 0.7282 (mm-40) REVERT: G 164 MET cc_start: 0.8562 (mtt) cc_final: 0.8361 (mtt) REVERT: G 212 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6552 (mm-30) REVERT: G 217 TYR cc_start: 0.8463 (m-80) cc_final: 0.8151 (m-80) REVERT: G 312 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7307 (mm-40) REVERT: F 312 GLN cc_start: 0.7624 (mm-40) cc_final: 0.7372 (mm-40) REVERT: E 212 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6613 (mm-30) REVERT: E 340 GLN cc_start: 0.7822 (mm110) cc_final: 0.7601 (mm110) REVERT: D 212 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6610 (mm-30) REVERT: D 270 GLN cc_start: 0.8052 (mt0) cc_final: 0.7838 (mt0) REVERT: D 312 GLN cc_start: 0.7591 (mm-40) cc_final: 0.7342 (mm-40) REVERT: D 340 GLN cc_start: 0.7612 (mm110) cc_final: 0.7237 (mm110) REVERT: D 469 MET cc_start: 0.8622 (mtm) cc_final: 0.8421 (mtp) REVERT: C 212 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6711 (mm-30) REVERT: C 312 GLN cc_start: 0.7539 (mm-40) cc_final: 0.7255 (mm-40) REVERT: B 212 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6550 (mm-30) REVERT: B 323 ILE cc_start: 0.8607 (mt) cc_final: 0.8323 (mt) REVERT: B 469 MET cc_start: 0.8600 (mtm) cc_final: 0.8235 (mtp) REVERT: J 212 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6689 (mm-30) REVERT: J 312 GLN cc_start: 0.7584 (mm-40) cc_final: 0.7280 (mm-40) REVERT: I 212 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6576 (mm-30) REVERT: I 217 TYR cc_start: 0.8463 (m-80) cc_final: 0.8161 (m-80) REVERT: I 312 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7317 (mm-40) REVERT: H 312 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7389 (mm-40) REVERT: N 212 GLU cc_start: 0.6972 (mt-10) cc_final: 0.6609 (mm-30) REVERT: N 340 GLN cc_start: 0.7818 (mm110) cc_final: 0.7485 (mm110) REVERT: Y 212 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6607 (mm-30) REVERT: Y 312 GLN cc_start: 0.7602 (mm-40) cc_final: 0.7363 (mm-40) REVERT: Y 340 GLN cc_start: 0.7615 (mm110) cc_final: 0.7255 (mm110) REVERT: Y 469 MET cc_start: 0.8608 (mtm) cc_final: 0.8394 (mtp) REVERT: L 212 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6618 (mm-30) REVERT: L 312 GLN cc_start: 0.7559 (mm-40) cc_final: 0.7253 (mm-40) REVERT: K 212 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6511 (mm-30) REVERT: K 469 MET cc_start: 0.8578 (mtm) cc_final: 0.8232 (mtp) REVERT: T 19 GLU cc_start: 0.7688 (tt0) cc_final: 0.7434 (tt0) REVERT: S 87 ASP cc_start: 0.7625 (m-30) cc_final: 0.7346 (m-30) REVERT: V 19 GLU cc_start: 0.7671 (tt0) cc_final: 0.7422 (tt0) REVERT: 2 87 ASP cc_start: 0.7624 (m-30) cc_final: 0.7347 (m-30) outliers start: 14 outliers final: 2 residues processed: 1190 average time/residue: 1.5095 time to fit residues: 2306.1268 Evaluate side-chains 898 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 896 time to evaluate : 6.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain Y residue 345 ILE 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 239 ASN Y 346 GLN L 239 ASN L 346 GLN K 214 GLN K 239 ASN S 43 GLN 2 43 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1072 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= 0.141 Angle : 0.463 6.894 90034 Z= 0.253 Chirality : 0.042 0.138 10850 Planarity : 0.004 0.058 11522 Dihedral : 6.497 61.670 9664 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.80 % Allowed : 8.19 % Favored : 90.01 % 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: 1.62 (0.09), residues: 8722 helix: 2.42 (0.08), residues: 3892 sheet: 0.94 (0.15), residues: 1106 loop : -0.34 (0.09), residues: 3724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 42 HIS 0.001 0.000 HIS F 314 PHE 0.008 0.001 PHE N 213 TYR 0.012 0.001 TYR Y 197 ARG 0.002 0.000 ARG E 420 *********************** 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 1064 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 936 time to evaluate : 5.822 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6748 (mm-30) REVERT: A 312 GLN cc_start: 0.7617 (mm-40) cc_final: 0.7382 (mm110) REVERT: G 164 MET cc_start: 0.8613 (mtt) cc_final: 0.8401 (mtt) REVERT: G 212 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6517 (mm-30) REVERT: G 217 TYR cc_start: 0.8426 (m-80) cc_final: 0.8156 (m-80) REVERT: G 312 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7302 (mm-40) REVERT: G 343 LYS cc_start: 0.8185 (mttm) cc_final: 0.7949 (mttp) REVERT: G 393 ASP cc_start: 0.8210 (m-30) cc_final: 0.8000 (m-30) REVERT: F 201 TYR cc_start: 0.7423 (m-80) cc_final: 0.7163 (m-80) REVERT: F 264 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.6102 (tpt90) REVERT: F 312 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7399 (mm-40) REVERT: F 362 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6748 (tt0) REVERT: E 212 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6685 (mm-30) REVERT: E 340 GLN cc_start: 0.7824 (mm110) cc_final: 0.7467 (mm110) REVERT: D 212 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6474 (mm-30) REVERT: D 312 GLN cc_start: 0.7615 (mm-40) cc_final: 0.7310 (mm-40) REVERT: D 330 MET cc_start: 0.7059 (mtm) cc_final: 0.6843 (mmm) REVERT: D 340 GLN cc_start: 0.7584 (mm110) cc_final: 0.7206 (mm110) REVERT: C 212 GLU cc_start: 0.6967 (mt-10) cc_final: 0.6660 (mm-30) REVERT: C 275 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7694 (mtmt) REVERT: C 312 GLN cc_start: 0.7568 (mm-40) cc_final: 0.7246 (mm-40) REVERT: C 342 GLU cc_start: 0.7254 (mm-30) cc_final: 0.7044 (mm-30) REVERT: B 312 GLN cc_start: 0.7969 (mm110) cc_final: 0.7688 (mm110) REVERT: B 469 MET cc_start: 0.8581 (mtm) cc_final: 0.8238 (mtp) REVERT: J 212 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6746 (mm-30) REVERT: J 312 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7379 (mm110) REVERT: I 212 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6548 (mm-30) REVERT: I 217 TYR cc_start: 0.8419 (m-80) cc_final: 0.8164 (m-80) REVERT: I 312 GLN cc_start: 0.7586 (mm-40) cc_final: 0.7295 (mm-40) REVERT: I 343 LYS cc_start: 0.8162 (mttm) cc_final: 0.7926 (mttp) REVERT: H 312 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7412 (mm-40) REVERT: H 362 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6788 (tt0) REVERT: H 392 LYS cc_start: 0.8691 (mtmt) cc_final: 0.8458 (mttm) REVERT: N 212 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6679 (mm-30) REVERT: N 340 GLN cc_start: 0.7778 (mm110) cc_final: 0.7508 (mm110) REVERT: Y 212 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6505 (mm-30) REVERT: Y 312 GLN cc_start: 0.7591 (mm-40) cc_final: 0.7283 (mm-40) REVERT: Y 330 MET cc_start: 0.7057 (mtm) cc_final: 0.6843 (mmm) REVERT: Y 340 GLN cc_start: 0.7592 (mm110) cc_final: 0.7192 (mm110) REVERT: L 212 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6663 (mm-30) REVERT: L 275 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7735 (mtmt) REVERT: L 312 GLN cc_start: 0.7577 (mm-40) cc_final: 0.7256 (mm-40) REVERT: L 342 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6946 (mm-30) REVERT: K 312 GLN cc_start: 0.8023 (mm110) cc_final: 0.7743 (mm110) REVERT: K 469 MET cc_start: 0.8563 (mtm) cc_final: 0.8241 (mtp) REVERT: T 8 LYS cc_start: 0.8069 (mtmm) cc_final: 0.7854 (mtpt) REVERT: T 32 MET cc_start: 0.7396 (mtp) cc_final: 0.7139 (mtp) REVERT: W 80 LYS cc_start: 0.8666 (tppt) cc_final: 0.8141 (tptt) REVERT: W 87 ASP cc_start: 0.7524 (m-30) cc_final: 0.7228 (m-30) REVERT: V 8 LYS cc_start: 0.8092 (mtmm) cc_final: 0.7870 (mtpt) outliers start: 128 outliers final: 41 residues processed: 1022 average time/residue: 1.3920 time to fit residues: 1861.6184 Evaluate side-chains 920 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 874 time to evaluate : 5.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 266 LYS Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 266 LYS Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 350 GLU Chi-restraints excluded: chain F residue 362 GLU Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 264 ARG Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 LYS Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 264 ARG Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 350 GLU Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 266 LYS Chi-restraints excluded: chain I residue 350 GLU Chi-restraints excluded: chain H residue 266 LYS Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain H residue 362 GLU Chi-restraints excluded: chain H residue 366 GLU Chi-restraints excluded: chain N residue 350 GLU Chi-restraints excluded: chain Y residue 223 LYS Chi-restraints excluded: chain Y residue 264 ARG Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 266 LYS Chi-restraints excluded: chain L residue 275 LYS Chi-restraints excluded: chain L residue 322 VAL Chi-restraints excluded: chain L residue 350 GLU Chi-restraints excluded: chain K residue 350 GLU Chi-restraints excluded: chain K residue 383 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 438 optimal weight: 7.9990 chunk 244 optimal weight: 0.9990 chunk 656 optimal weight: 0.8980 chunk 536 optimal weight: 0.7980 chunk 217 optimal weight: 5.9990 chunk 789 optimal weight: 10.0000 chunk 853 optimal weight: 0.0870 chunk 703 optimal weight: 5.9990 chunk 783 optimal weight: 9.9990 chunk 269 optimal weight: 0.9980 chunk 633 optimal weight: 0.8980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN G 214 GLN F 239 ASN E 214 GLN E 239 ASN E 346 GLN ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 ASN C 239 ASN B 239 ASN J 239 ASN H 239 ASN N 214 GLN N 239 ASN N 346 GLN Y 239 ASN L 239 ASN K 214 GLN K 239 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 66710 Z= 0.130 Angle : 0.443 7.130 90034 Z= 0.241 Chirality : 0.042 0.149 10850 Planarity : 0.003 0.037 11522 Dihedral : 6.367 61.442 9660 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.44 % Allowed : 9.96 % Favored : 88.60 % 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: 1.57 (0.09), residues: 8722 helix: 2.28 (0.08), residues: 3920 sheet: 1.02 (0.15), residues: 1190 loop : -0.33 (0.09), residues: 3612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 42 HIS 0.001 0.000 HIS G 314 PHE 0.007 0.001 PHE F 213 TYR 0.010 0.001 TYR A 197 ARG 0.002 0.000 ARG K 34 *********************** 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 1027 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 925 time to evaluate : 5.721 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 revert: symmetry clash REVERT: A 212 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6703 (mm-30) REVERT: A 312 GLN cc_start: 0.7626 (mm-40) cc_final: 0.7304 (mm-40) REVERT: A 326 LYS cc_start: 0.7705 (mppt) cc_final: 0.7494 (tppt) REVERT: A 362 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6428 (tt0) REVERT: G 212 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6512 (mm-30) REVERT: G 312 GLN cc_start: 0.7659 (mm-40) cc_final: 0.7360 (mm-40) REVERT: G 321 GLU cc_start: 0.7406 (tp30) cc_final: 0.7050 (tm-30) REVERT: G 343 LYS cc_start: 0.8162 (mttm) cc_final: 0.7940 (mttp) REVERT: G 393 ASP cc_start: 0.8200 (m-30) cc_final: 0.7985 (m-30) REVERT: F 214 GLN cc_start: 0.7611 (mm-40) cc_final: 0.7410 (mp-120) REVERT: F 312 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7518 (mm110) REVERT: F 321 GLU cc_start: 0.7313 (tp30) cc_final: 0.7082 (tp30) REVERT: F 340 GLN cc_start: 0.7633 (mm110) cc_final: 0.7413 (mp10) REVERT: F 362 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6766 (tt0) REVERT: E 212 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6655 (mm-30) REVERT: E 340 GLN cc_start: 0.7789 (mm110) cc_final: 0.7496 (mm110) REVERT: D 212 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6542 (mm-30) REVERT: D 275 LYS cc_start: 0.8318 (mmmm) cc_final: 0.8030 (mtpm) REVERT: D 312 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7340 (mm-40) REVERT: D 323 ILE cc_start: 0.8698 (mt) cc_final: 0.8435 (mt) REVERT: D 330 MET cc_start: 0.7045 (mtm) cc_final: 0.6834 (mmm) REVERT: D 340 GLN cc_start: 0.7554 (mm110) cc_final: 0.7214 (mm110) REVERT: C 212 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6658 (mm-30) REVERT: C 312 GLN cc_start: 0.7583 (mm-40) cc_final: 0.7249 (mm-40) REVERT: B 212 GLU cc_start: 0.6869 (mt-10) cc_final: 0.6518 (mm-30) REVERT: B 312 GLN cc_start: 0.8013 (mm110) cc_final: 0.7756 (mm110) REVERT: B 321 GLU cc_start: 0.7424 (tp30) cc_final: 0.7218 (tp30) REVERT: B 469 MET cc_start: 0.8571 (mtm) cc_final: 0.8234 (mtp) REVERT: J 212 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6704 (mm-30) REVERT: J 312 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7304 (mm-40) REVERT: J 326 LYS cc_start: 0.7709 (mppt) cc_final: 0.7495 (tppt) REVERT: J 362 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6427 (tt0) REVERT: I 212 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6540 (mm-30) REVERT: I 217 TYR cc_start: 0.8371 (m-80) cc_final: 0.8126 (m-80) REVERT: I 312 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7375 (mm-40) REVERT: I 321 GLU cc_start: 0.7407 (tp30) cc_final: 0.7055 (tm-30) REVERT: H 220 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8453 (mt) REVERT: H 312 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7414 (mm-40) REVERT: H 321 GLU cc_start: 0.7321 (tp30) cc_final: 0.7085 (tp30) REVERT: H 340 GLN cc_start: 0.7629 (mm110) cc_final: 0.7395 (mp10) REVERT: H 362 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6749 (tt0) REVERT: N 212 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6652 (mm-30) REVERT: N 340 GLN cc_start: 0.7743 (mm110) cc_final: 0.7456 (mm110) REVERT: Y 275 LYS cc_start: 0.8306 (mmmm) cc_final: 0.8014 (mtpm) REVERT: Y 312 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7328 (mm-40) REVERT: Y 330 MET cc_start: 0.7053 (mtm) cc_final: 0.6843 (mmm) REVERT: Y 340 GLN cc_start: 0.7603 (mm110) cc_final: 0.7267 (mm110) REVERT: L 212 GLU cc_start: 0.7016 (mt-10) cc_final: 0.6649 (mm-30) REVERT: L 312 GLN cc_start: 0.7610 (mm-40) cc_final: 0.7272 (mm-40) REVERT: K 212 GLU cc_start: 0.6859 (mt-10) cc_final: 0.6509 (mm-30) REVERT: K 312 GLN cc_start: 0.8042 (mm110) cc_final: 0.7740 (mm110) REVERT: K 469 MET cc_start: 0.8562 (mtm) cc_final: 0.8238 (mtp) REVERT: O 80 LYS cc_start: 0.8466 (tmtm) cc_final: 0.7849 (tptt) REVERT: T 8 LYS cc_start: 0.8169 (mtmm) cc_final: 0.7952 (mtpt) REVERT: S 80 LYS cc_start: 0.8527 (tttm) cc_final: 0.7921 (tmtm) REVERT: X 80 LYS cc_start: 0.8469 (tmtm) cc_final: 0.7853 (tptt) REVERT: V 8 LYS cc_start: 0.8179 (mtmm) cc_final: 0.7965 (mtpt) outliers start: 102 outliers final: 31 residues processed: 988 average time/residue: 1.3972 time to fit residues: 1805.6643 Evaluate side-chains 921 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 885 time to evaluate : 5.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 266 LYS Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain F residue 350 GLU Chi-restraints excluded: chain F residue 362 GLU Chi-restraints excluded: chain E residue 214 GLN Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 LYS Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 266 LYS Chi-restraints excluded: chain J residue 350 GLU Chi-restraints excluded: chain J residue 362 GLU Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 266 LYS Chi-restraints excluded: chain I residue 350 GLU Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain H residue 362 GLU Chi-restraints excluded: chain N residue 214 GLN Chi-restraints excluded: chain N residue 350 GLU Chi-restraints excluded: chain Y residue 223 LYS Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 266 LYS Chi-restraints excluded: chain L residue 322 VAL Chi-restraints excluded: chain L residue 350 GLU Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 266 LYS Chi-restraints excluded: chain K residue 350 GLU 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: 9.9990 chunk 409 optimal weight: 2.9990 chunk 87 optimal weight: 0.0970 chunk 376 optimal weight: 4.9990 chunk 530 optimal weight: 0.4980 chunk 792 optimal weight: 7.9990 chunk 839 optimal weight: 7.9990 chunk 414 optimal weight: 1.9990 chunk 751 optimal weight: 30.0000 chunk 226 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 239 ASN H 239 ASN N 239 ASN ** Y 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 239 ASN L 239 ASN K 239 ASN K 346 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 66710 Z= 0.226 Angle : 0.514 8.030 90034 Z= 0.278 Chirality : 0.044 0.150 10850 Planarity : 0.004 0.041 11522 Dihedral : 7.671 69.346 9660 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.09 % Allowed : 10.89 % Favored : 87.02 % 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: 1.32 (0.09), residues: 8722 helix: 1.98 (0.08), residues: 3906 sheet: 1.10 (0.15), residues: 1106 loop : -0.38 (0.09), residues: 3710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 42 HIS 0.002 0.001 HIS H 241 PHE 0.008 0.001 PHE T 89 TYR 0.009 0.001 TYR Z 88 ARG 0.005 0.000 ARG B 420 *********************** 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 1050 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 902 time to evaluate : 5.805 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 REVERT: A 212 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6885 (mm-30) REVERT: A 312 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7336 (mm-40) REVERT: A 362 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6521 (tt0) REVERT: A 392 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8416 (mtmm) REVERT: G 212 GLU cc_start: 0.6889 (mt-10) cc_final: 0.6534 (mt-10) REVERT: G 312 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7381 (mm-40) REVERT: G 321 GLU cc_start: 0.7379 (tp30) cc_final: 0.7006 (tm-30) REVERT: G 326 LYS cc_start: 0.8179 (tmtm) cc_final: 0.7966 (tmtt) REVERT: G 362 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6458 (tt0) REVERT: G 393 ASP cc_start: 0.8227 (m-30) cc_final: 0.7998 (m-30) REVERT: F 195 ARG cc_start: 0.7587 (mmt-90) cc_final: 0.7333 (mmt180) REVERT: F 220 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8450 (mt) REVERT: F 312 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7365 (mm-40) REVERT: F 340 GLN cc_start: 0.7630 (mm110) cc_final: 0.7402 (mp10) REVERT: F 362 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6767 (tt0) REVERT: E 212 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6751 (mm-30) REVERT: E 340 GLN cc_start: 0.7793 (mm110) cc_final: 0.7500 (mm110) REVERT: D 212 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6560 (mm-30) REVERT: D 312 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7440 (mm-40) REVERT: D 340 GLN cc_start: 0.7556 (mm110) cc_final: 0.7217 (mm110) REVERT: D 362 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6269 (tt0) REVERT: C 212 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6812 (mt-10) REVERT: C 312 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7313 (mm-40) REVERT: C 362 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6473 (tt0) REVERT: B 212 GLU cc_start: 0.6972 (mt-10) cc_final: 0.6636 (mm-30) REVERT: B 264 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.6850 (tpt90) REVERT: B 321 GLU cc_start: 0.7419 (tp30) cc_final: 0.7169 (tp30) REVERT: B 362 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6352 (tt0) REVERT: J 212 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6884 (mm-30) REVERT: J 312 GLN cc_start: 0.7651 (mm-40) cc_final: 0.7355 (mm-40) REVERT: J 362 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6519 (tt0) REVERT: J 392 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8416 (mtmm) REVERT: I 212 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6560 (mt-10) REVERT: I 217 TYR cc_start: 0.8390 (m-80) cc_final: 0.8162 (m-80) REVERT: I 312 GLN cc_start: 0.7709 (mm-40) cc_final: 0.7398 (mm-40) REVERT: I 321 GLU cc_start: 0.7382 (tp30) cc_final: 0.7009 (tm-30) REVERT: I 362 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6444 (tt0) REVERT: H 220 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8424 (mt) REVERT: H 264 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.6293 (tpt90) REVERT: H 312 GLN cc_start: 0.7730 (mm-40) cc_final: 0.7498 (mm110) REVERT: H 362 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6836 (tt0) REVERT: N 212 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6737 (mm-30) REVERT: N 262 LEU cc_start: 0.8403 (tt) cc_final: 0.8191 (tm) REVERT: N 340 GLN cc_start: 0.7796 (mm110) cc_final: 0.7505 (mm110) REVERT: N 362 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6279 (tt0) REVERT: Y 312 GLN cc_start: 0.7789 (mm-40) cc_final: 0.7441 (mm-40) REVERT: Y 340 GLN cc_start: 0.7582 (mm110) cc_final: 0.7240 (mm110) REVERT: Y 362 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6266 (tt0) REVERT: L 212 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6799 (mt-10) REVERT: L 312 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7329 (mm-40) REVERT: L 343 LYS cc_start: 0.8048 (mttp) cc_final: 0.7770 (mtpp) REVERT: L 362 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6449 (tt0) REVERT: K 212 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6608 (mm-30) REVERT: K 264 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.6748 (tpt90) REVERT: K 312 GLN cc_start: 0.8083 (mm110) cc_final: 0.7713 (mm110) REVERT: K 321 GLU cc_start: 0.7472 (tp30) cc_final: 0.7213 (tp30) REVERT: K 342 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7336 (mm-30) REVERT: K 362 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6456 (tt0) REVERT: U 32 MET cc_start: 0.7286 (mtm) cc_final: 0.7079 (mtm) REVERT: T 80 LYS cc_start: 0.8724 (tptm) cc_final: 0.8369 (tptt) REVERT: T 87 ASP cc_start: 0.7457 (m-30) cc_final: 0.6794 (m-30) REVERT: Q 80 LYS cc_start: 0.8659 (tptt) cc_final: 0.7795 (tptt) REVERT: P 45 THR cc_start: 0.8723 (m) cc_final: 0.8346 (m) REVERT: W 45 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8312 (m) REVERT: W 70 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8068 (mmtt) REVERT: W 80 LYS cc_start: 0.8731 (tttm) cc_final: 0.8003 (tptt) REVERT: W 87 ASP cc_start: 0.7469 (m-30) cc_final: 0.7218 (m-30) REVERT: V 80 LYS cc_start: 0.8721 (tptm) cc_final: 0.8155 (tptt) REVERT: V 87 ASP cc_start: 0.7401 (m-30) cc_final: 0.6826 (m-30) REVERT: M 45 THR cc_start: 0.8729 (m) cc_final: 0.8372 (m) outliers start: 148 outliers final: 52 residues processed: 989 average time/residue: 1.4409 time to fit residues: 1847.0892 Evaluate side-chains 948 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 874 time to evaluate : 5.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 266 LYS Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain G residue 362 GLU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 266 LYS Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 350 GLU Chi-restraints excluded: chain F residue 362 GLU Chi-restraints excluded: chain F residue 514 THR Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 264 ARG Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 LYS Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 362 GLU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 266 LYS Chi-restraints excluded: chain J residue 350 GLU Chi-restraints excluded: chain J residue 362 GLU Chi-restraints excluded: chain J residue 392 LYS Chi-restraints excluded: chain J residue 469 MET Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 264 ARG Chi-restraints excluded: chain I residue 266 LYS Chi-restraints excluded: chain I residue 350 GLU Chi-restraints excluded: chain I residue 362 GLU Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 264 ARG Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain H residue 362 GLU Chi-restraints excluded: chain H residue 514 THR Chi-restraints excluded: chain N residue 350 GLU Chi-restraints excluded: chain N residue 362 GLU Chi-restraints excluded: chain Y residue 223 LYS Chi-restraints excluded: chain Y residue 264 ARG Chi-restraints excluded: chain Y residue 362 GLU Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 266 LYS Chi-restraints excluded: chain L residue 322 VAL Chi-restraints excluded: chain L residue 350 GLU Chi-restraints excluded: chain L residue 362 GLU Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 264 ARG Chi-restraints excluded: chain K residue 266 LYS Chi-restraints excluded: chain K residue 350 GLU Chi-restraints excluded: chain K residue 362 GLU Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 522 GLU Chi-restraints excluded: chain U residue 19 GLU Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain W residue 70 LYS Chi-restraints excluded: chain 1 residue 33 LEU 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: 0.9990 chunk 624 optimal weight: 3.9990 chunk 346 optimal weight: 3.9990 chunk 715 optimal weight: 4.9990 chunk 579 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 428 optimal weight: 2.9990 chunk 753 optimal weight: 0.0370 chunk 211 optimal weight: 4.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- 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 239 ASN D 239 ASN C 239 ASN B 239 ASN J 239 ASN H 239 ASN N 239 ASN Y 239 ASN L 239 ASN K 239 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 66710 Z= 0.270 Angle : 0.545 8.417 90034 Z= 0.295 Chirality : 0.045 0.158 10850 Planarity : 0.004 0.043 11522 Dihedral : 8.058 72.355 9660 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.23 % Allowed : 11.23 % Favored : 86.55 % 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: 1.07 (0.09), residues: 8722 helix: 1.75 (0.08), residues: 3906 sheet: 0.98 (0.15), residues: 1106 loop : -0.47 (0.09), residues: 3710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 42 HIS 0.002 0.001 HIS C 241 PHE 0.010 0.001 PHE T 89 TYR 0.010 0.001 TYR Q 88 ARG 0.007 0.001 ARG N 420 *********************** 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 1049 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 891 time to evaluate : 5.783 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 REVERT: A 212 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6892 (mm-30) REVERT: A 312 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7373 (mm-40) REVERT: A 362 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6625 (tt0) REVERT: A 392 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8419 (mtmm) REVERT: G 212 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6534 (mm-30) REVERT: G 312 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7391 (mm-40) REVERT: G 321 GLU cc_start: 0.7337 (tp30) cc_final: 0.7036 (tm-30) REVERT: G 362 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6420 (tt0) REVERT: F 195 ARG cc_start: 0.7636 (mmt-90) cc_final: 0.7399 (mmt180) REVERT: F 220 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8480 (mt) REVERT: F 264 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.6286 (tpt90) REVERT: F 312 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7532 (mm110) REVERT: F 321 GLU cc_start: 0.7273 (tp30) cc_final: 0.7014 (tp30) REVERT: F 362 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6678 (tt0) REVERT: E 212 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6785 (mm-30) REVERT: E 264 ARG cc_start: 0.8159 (tpt90) cc_final: 0.7871 (tpt90) REVERT: E 286 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7549 (mt0) REVERT: E 340 GLN cc_start: 0.7766 (mm110) cc_final: 0.7486 (mm110) REVERT: D 212 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6698 (mm-30) REVERT: D 312 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7454 (mm-40) REVERT: D 362 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6240 (tt0) REVERT: C 212 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6813 (mt-10) REVERT: C 312 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7282 (mm-40) REVERT: C 321 GLU cc_start: 0.7443 (tp30) cc_final: 0.7158 (tp30) REVERT: C 343 LYS cc_start: 0.8084 (mtpp) cc_final: 0.7508 (mttp) REVERT: C 362 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6460 (tt0) REVERT: B 212 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6611 (mm-30) REVERT: B 321 GLU cc_start: 0.7385 (tp30) cc_final: 0.7163 (tp30) REVERT: J 212 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6893 (mm-30) REVERT: J 312 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7377 (mm-40) REVERT: J 362 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6625 (tt0) REVERT: J 392 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8436 (mtmm) REVERT: I 212 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6522 (mm-30) REVERT: I 217 TYR cc_start: 0.8395 (m-80) cc_final: 0.8156 (m-80) REVERT: I 312 GLN cc_start: 0.7706 (mm-40) cc_final: 0.7381 (mm-40) REVERT: I 321 GLU cc_start: 0.7337 (tp30) cc_final: 0.7039 (tm-30) REVERT: I 362 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6443 (tt0) REVERT: H 195 ARG cc_start: 0.7632 (mmt-90) cc_final: 0.7390 (mmt180) REVERT: H 220 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8460 (mt) REVERT: H 264 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.6221 (tpt90) REVERT: H 312 GLN cc_start: 0.7730 (mm-40) cc_final: 0.7479 (mm110) REVERT: H 362 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6788 (tt0) REVERT: N 212 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6792 (mm-30) REVERT: N 264 ARG cc_start: 0.8174 (tpt90) cc_final: 0.7916 (tpt90) REVERT: N 286 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7531 (mt0) REVERT: N 362 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6225 (tt0) REVERT: Y 312 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7454 (mm-40) REVERT: Y 362 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6248 (tt0) REVERT: L 312 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7303 (mm-40) REVERT: L 342 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7228 (mm-30) REVERT: L 362 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6527 (tt0) REVERT: K 212 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6600 (mm-30) REVERT: U 45 THR cc_start: 0.8732 (m) cc_final: 0.7825 (m) REVERT: U 70 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7319 (mmpt) REVERT: T 8 LYS cc_start: 0.8172 (mtmm) cc_final: 0.7891 (mtpt) REVERT: T 80 LYS cc_start: 0.8802 (tptm) cc_final: 0.8087 (tptt) REVERT: T 87 ASP cc_start: 0.7485 (m-30) cc_final: 0.7183 (m-30) REVERT: V 8 LYS cc_start: 0.8147 (mtmm) cc_final: 0.7871 (mtpt) REVERT: V 80 LYS cc_start: 0.8812 (tptm) cc_final: 0.8202 (tptt) REVERT: V 87 ASP cc_start: 0.7342 (m-30) cc_final: 0.6842 (m-30) outliers start: 158 outliers final: 73 residues processed: 994 average time/residue: 1.4321 time to fit residues: 1847.6483 Evaluate side-chains 958 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 865 time to evaluate : 5.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 264 ARG Chi-restraints excluded: chain G residue 311 VAL Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain G residue 362 GLU Chi-restraints excluded: chain G residue 514 THR Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 266 LYS Chi-restraints excluded: chain F residue 350 GLU Chi-restraints excluded: chain F residue 362 GLU Chi-restraints excluded: chain F residue 514 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 LYS Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 362 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain J residue 266 LYS Chi-restraints excluded: chain J residue 350 GLU Chi-restraints excluded: chain J residue 362 GLU Chi-restraints excluded: chain J residue 392 LYS Chi-restraints excluded: chain J residue 469 MET Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 266 LYS Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain I residue 350 GLU Chi-restraints excluded: chain I residue 362 GLU Chi-restraints excluded: chain I residue 514 THR Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 264 ARG Chi-restraints excluded: chain H residue 308 LEU Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain H residue 362 GLU Chi-restraints excluded: chain H residue 514 THR Chi-restraints excluded: chain N residue 246 VAL Chi-restraints excluded: chain N residue 266 LYS Chi-restraints excluded: chain N residue 286 GLN Chi-restraints excluded: chain N residue 350 GLU Chi-restraints excluded: chain N residue 362 GLU Chi-restraints excluded: chain Y residue 223 LYS Chi-restraints excluded: chain Y residue 246 VAL Chi-restraints excluded: chain Y residue 311 VAL Chi-restraints excluded: chain Y residue 362 GLU Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 266 LYS Chi-restraints excluded: chain L residue 322 VAL Chi-restraints excluded: chain L residue 350 GLU Chi-restraints excluded: chain L residue 362 GLU Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 246 VAL Chi-restraints excluded: chain K residue 266 LYS Chi-restraints excluded: chain K residue 311 VAL Chi-restraints excluded: chain K residue 350 GLU Chi-restraints excluded: chain K residue 514 THR Chi-restraints excluded: chain K residue 522 GLU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain U residue 99 LYS Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain 2 residue 73 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 282 optimal weight: 10.0000 chunk 755 optimal weight: 5.9990 chunk 165 optimal weight: 0.6980 chunk 492 optimal weight: 0.0060 chunk 207 optimal weight: 1.9990 chunk 839 optimal weight: 5.9990 chunk 697 optimal weight: 8.9990 chunk 388 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 277 optimal weight: 5.9990 chunk 440 optimal weight: 9.9990 overall best weight: 2.3402 ------------------------------------------------------------------------------- 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 D 214 GLN D 239 ASN C 239 ASN B 214 GLN B 239 ASN J 239 ASN H 239 ASN N 214 GLN 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: 0.8303 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 66710 Z= 0.263 Angle : 0.543 8.358 90034 Z= 0.292 Chirality : 0.044 0.159 10850 Planarity : 0.004 0.044 11522 Dihedral : 7.906 71.132 9660 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.07 % Allowed : 12.44 % Favored : 85.49 % 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: 1.69 (0.08), residues: 3906 sheet: 0.92 (0.15), residues: 1106 loop : -0.56 (0.09), residues: 3710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 42 HIS 0.002 0.001 HIS F 241 PHE 0.010 0.001 PHE 1 89 TYR 0.012 0.001 TYR Q 88 ARG 0.006 0.001 ARG L 420 *********************** 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 1010 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 863 time to evaluate : 5.796 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: A 212 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6906 (mm-30) REVERT: A 312 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7324 (mm-40) REVERT: A 362 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6528 (tt0) REVERT: A 392 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8423 (mtmm) REVERT: G 212 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6585 (mm-30) REVERT: G 312 GLN cc_start: 0.7765 (mm-40) cc_final: 0.7423 (mm-40) REVERT: G 330 MET cc_start: 0.7302 (mtm) cc_final: 0.7095 (mtm) REVERT: G 362 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6435 (tt0) REVERT: F 195 ARG cc_start: 0.7637 (mmt-90) cc_final: 0.7390 (mmt180) REVERT: F 214 GLN cc_start: 0.7552 (mp-120) cc_final: 0.7063 (mp10) REVERT: F 220 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8470 (mt) REVERT: F 223 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7308 (mtpp) REVERT: F 264 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.6305 (tpt90) REVERT: F 312 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7533 (mm110) REVERT: F 321 GLU cc_start: 0.7148 (tp30) cc_final: 0.6471 (tp30) REVERT: F 362 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6679 (tt0) REVERT: E 212 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6775 (mm-30) REVERT: E 264 ARG cc_start: 0.8091 (tpt90) cc_final: 0.7772 (tpt90) REVERT: E 286 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7529 (mt0) REVERT: D 131 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8073 (mtmt) REVERT: D 212 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6651 (mm-30) REVERT: D 312 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7433 (mm-40) REVERT: D 330 MET cc_start: 0.7062 (ttp) cc_final: 0.6815 (tpp) REVERT: D 362 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6292 (tt0) REVERT: C 312 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7308 (mm-40) REVERT: C 343 LYS cc_start: 0.8077 (mtpp) cc_final: 0.7514 (mttp) REVERT: C 362 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6532 (tt0) REVERT: B 212 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6611 (mm-30) REVERT: B 321 GLU cc_start: 0.7393 (tp30) cc_final: 0.7165 (tp30) REVERT: B 362 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6784 (tt0) REVERT: J 212 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6902 (mm-30) REVERT: J 312 GLN cc_start: 0.7711 (mm-40) cc_final: 0.7328 (mm-40) REVERT: J 362 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6528 (tt0) REVERT: J 392 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8423 (mtmm) REVERT: I 212 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6557 (mm-30) REVERT: I 217 TYR cc_start: 0.8388 (m-80) cc_final: 0.8168 (m-80) REVERT: I 312 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7454 (mm-40) REVERT: I 362 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6426 (tt0) REVERT: H 195 ARG cc_start: 0.7630 (mmt-90) cc_final: 0.7384 (mmt180) REVERT: H 220 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8457 (mt) REVERT: H 264 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.6190 (tpt90) REVERT: H 312 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7538 (mm110) REVERT: H 362 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6811 (tt0) REVERT: N 212 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6780 (mm-30) REVERT: N 262 LEU cc_start: 0.8413 (tt) cc_final: 0.8204 (tm) REVERT: N 264 ARG cc_start: 0.8140 (tpt90) cc_final: 0.7834 (tpt90) REVERT: N 286 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7527 (mt0) REVERT: N 340 GLN cc_start: 0.7772 (mm110) cc_final: 0.7418 (mm110) REVERT: N 362 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6204 (tt0) REVERT: Y 131 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8075 (mtmt) REVERT: Y 312 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7432 (mm-40) REVERT: Y 323 ILE cc_start: 0.8735 (mp) cc_final: 0.8064 (mp) REVERT: Y 362 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6286 (tt0) REVERT: L 212 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6800 (mt-10) REVERT: L 312 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7307 (mm-40) REVERT: L 342 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7249 (mm-30) REVERT: L 343 LYS cc_start: 0.8075 (mttp) cc_final: 0.7796 (mtpp) REVERT: L 362 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6538 (tt0) REVERT: K 212 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6653 (mm-30) REVERT: K 312 GLN cc_start: 0.8036 (mm110) cc_final: 0.7696 (mm110) REVERT: K 362 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6787 (tt0) REVERT: T 80 LYS cc_start: 0.8802 (tptm) cc_final: 0.8068 (tptt) REVERT: T 87 ASP cc_start: 0.7467 (m-30) cc_final: 0.7166 (m-30) REVERT: W 80 LYS cc_start: 0.8749 (tttm) cc_final: 0.8465 (tptt) REVERT: V 80 LYS cc_start: 0.8828 (tptm) cc_final: 0.8199 (tptt) REVERT: V 87 ASP cc_start: 0.7301 (m-30) cc_final: 0.6847 (m-30) outliers start: 147 outliers final: 74 residues processed: 962 average time/residue: 1.4288 time to fit residues: 1794.3925 Evaluate side-chains 953 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 855 time to evaluate : 5.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 264 ARG Chi-restraints excluded: chain G residue 311 VAL Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain G residue 362 GLU Chi-restraints excluded: chain G residue 514 THR Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 223 LYS Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 266 LYS Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 350 GLU Chi-restraints excluded: chain F residue 362 GLU Chi-restraints excluded: chain F residue 514 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 LYS Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 362 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain J residue 266 LYS Chi-restraints excluded: chain J residue 350 GLU Chi-restraints excluded: chain J residue 362 GLU Chi-restraints excluded: chain J residue 392 LYS Chi-restraints excluded: chain J residue 469 MET Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 264 ARG Chi-restraints excluded: chain I residue 266 LYS Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain I residue 350 GLU Chi-restraints excluded: chain I residue 362 GLU Chi-restraints excluded: chain I residue 514 THR Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 264 ARG Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain H residue 362 GLU Chi-restraints excluded: chain H residue 514 THR Chi-restraints excluded: chain N residue 246 VAL Chi-restraints excluded: chain N residue 266 LYS Chi-restraints excluded: chain N residue 286 GLN Chi-restraints excluded: chain N residue 350 GLU Chi-restraints excluded: chain N residue 362 GLU Chi-restraints excluded: chain Y residue 131 LYS Chi-restraints excluded: chain Y residue 223 LYS Chi-restraints excluded: chain Y residue 246 VAL Chi-restraints excluded: chain Y residue 311 VAL Chi-restraints excluded: chain Y residue 362 GLU Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 350 GLU Chi-restraints excluded: chain L residue 362 GLU Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 246 VAL Chi-restraints excluded: chain K residue 266 LYS Chi-restraints excluded: chain K residue 311 VAL Chi-restraints excluded: chain K residue 350 GLU Chi-restraints excluded: chain K residue 362 GLU Chi-restraints excluded: chain K residue 514 THR Chi-restraints excluded: chain K residue 522 GLU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain U residue 19 GLU Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain U residue 99 LYS Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain 2 residue 73 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 809 optimal weight: 7.9990 chunk 94 optimal weight: 0.2980 chunk 478 optimal weight: 0.8980 chunk 613 optimal weight: 0.9980 chunk 475 optimal weight: 0.8980 chunk 706 optimal weight: 0.8980 chunk 468 optimal weight: 0.3980 chunk 836 optimal weight: 0.2980 chunk 523 optimal weight: 3.9990 chunk 510 optimal weight: 1.9990 chunk 386 optimal weight: 10.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 D 239 ASN C 239 ASN B 214 GLN B 239 ASN J 239 ASN H 239 ASN N 214 GLN N 239 ASN Y 214 GLN Y 239 ASN L 239 ASN K 239 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 66710 Z= 0.122 Angle : 0.452 8.540 90034 Z= 0.241 Chirality : 0.041 0.160 10850 Planarity : 0.004 0.040 11522 Dihedral : 6.270 60.731 9660 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.80 % Allowed : 13.02 % Favored : 85.18 % 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: 1.28 (0.09), residues: 8722 helix: 2.01 (0.08), residues: 3934 sheet: 0.93 (0.15), residues: 1190 loop : -0.48 (0.09), residues: 3598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP N 42 HIS 0.001 0.001 HIS H 241 PHE 0.008 0.001 PHE Y 213 TYR 0.010 0.001 TYR Q 88 ARG 0.002 0.000 ARG J 195 *********************** 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 1020 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 892 time to evaluate : 5.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6835 (mm-30) REVERT: A 312 GLN cc_start: 0.7665 (mm-40) cc_final: 0.7282 (mm-40) REVERT: A 362 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6468 (tt0) REVERT: A 392 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8463 (mtmm) REVERT: G 212 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6560 (mt-10) REVERT: G 312 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7420 (mm-40) REVERT: G 321 GLU cc_start: 0.7272 (tp30) cc_final: 0.7066 (tp30) REVERT: F 212 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6725 (mm-30) REVERT: F 220 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8451 (mt) REVERT: F 312 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7560 (mm110) REVERT: F 362 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6665 (tt0) REVERT: E 212 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6761 (mm-30) REVERT: E 264 ARG cc_start: 0.8082 (tpt90) cc_final: 0.7780 (tpt90) REVERT: D 212 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6625 (mm-30) REVERT: D 284 LYS cc_start: 0.7734 (mttt) cc_final: 0.7457 (tttp) REVERT: D 312 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7469 (mm-40) REVERT: D 362 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6165 (tt0) REVERT: C 212 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6897 (mt-10) REVERT: C 312 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7312 (mm-40) REVERT: C 343 LYS cc_start: 0.8040 (mtpp) cc_final: 0.7497 (mttp) REVERT: B 212 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6516 (mm-30) REVERT: B 283 ARG cc_start: 0.7504 (ttp-170) cc_final: 0.7238 (ttp-170) REVERT: B 312 GLN cc_start: 0.8038 (mm110) cc_final: 0.7667 (mm110) REVERT: B 321 GLU cc_start: 0.7365 (tp30) cc_final: 0.7104 (tp30) REVERT: J 212 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6837 (mm-30) REVERT: J 312 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7328 (mm-40) REVERT: J 362 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6464 (tt0) REVERT: J 392 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8463 (mtmm) REVERT: I 212 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6567 (mm-30) REVERT: I 217 TYR cc_start: 0.8314 (m-80) cc_final: 0.8096 (m-80) REVERT: I 312 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7433 (mm-40) REVERT: I 362 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6288 (tt0) REVERT: H 212 GLU cc_start: 0.7068 (mt-10) cc_final: 0.6732 (mm-30) REVERT: H 214 GLN cc_start: 0.7491 (mp10) cc_final: 0.7139 (mp-120) REVERT: H 220 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8463 (mt) REVERT: H 312 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7548 (mm110) REVERT: H 362 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6733 (tt0) REVERT: N 212 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6780 (mm-30) REVERT: N 262 LEU cc_start: 0.8468 (tt) cc_final: 0.8265 (tm) REVERT: N 264 ARG cc_start: 0.8167 (tpt90) cc_final: 0.7921 (tpt90) REVERT: Y 284 LYS cc_start: 0.7724 (mttt) cc_final: 0.7460 (tttp) REVERT: Y 312 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7452 (mm-40) REVERT: Y 362 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6157 (tt0) REVERT: L 212 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6828 (mt-10) REVERT: L 312 GLN cc_start: 0.7647 (mm-40) cc_final: 0.7309 (mm-40) REVERT: L 323 ILE cc_start: 0.8758 (mt) cc_final: 0.8542 (mp) REVERT: L 342 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7224 (mm-30) REVERT: L 343 LYS cc_start: 0.8010 (mttp) cc_final: 0.7713 (mtpp) REVERT: K 283 ARG cc_start: 0.7501 (ttp-170) cc_final: 0.7239 (ttp-170) REVERT: K 312 GLN cc_start: 0.8022 (mm110) cc_final: 0.7692 (mm110) REVERT: U 45 THR cc_start: 0.8709 (m) cc_final: 0.8330 (m) REVERT: U 70 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7910 (mmtt) REVERT: T 8 LYS cc_start: 0.8202 (mtmm) cc_final: 0.7911 (mtpt) REVERT: T 80 LYS cc_start: 0.8699 (tptm) cc_final: 0.7992 (tptt) REVERT: T 87 ASP cc_start: 0.7378 (m-30) cc_final: 0.7107 (m-30) REVERT: T 93 ASP cc_start: 0.8280 (t0) cc_final: 0.7837 (t0) REVERT: R 73 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8314 (mt) REVERT: P 32 MET cc_start: 0.7369 (mtm) cc_final: 0.7143 (ptp) REVERT: W 45 THR cc_start: 0.8707 (m) cc_final: 0.8304 (m) REVERT: W 70 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7930 (mmtt) REVERT: W 80 LYS cc_start: 0.8712 (tttm) cc_final: 0.8508 (tppt) REVERT: V 8 LYS cc_start: 0.8206 (mtmm) cc_final: 0.7915 (mtpt) REVERT: V 80 LYS cc_start: 0.8799 (tptm) cc_final: 0.8184 (tptt) REVERT: V 87 ASP cc_start: 0.7222 (m-30) cc_final: 0.6798 (m-30) REVERT: V 93 ASP cc_start: 0.8284 (t0) cc_final: 0.7841 (t0) REVERT: 1 32 MET cc_start: 0.7371 (mtm) cc_final: 0.7064 (ptp) REVERT: 1 73 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8324 (mt) outliers start: 128 outliers final: 53 residues processed: 975 average time/residue: 1.3823 time to fit residues: 1765.1748 Evaluate side-chains 929 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 861 time to evaluate : 5.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 264 ARG Chi-restraints excluded: chain G residue 311 VAL Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 350 GLU Chi-restraints excluded: chain F residue 362 GLU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 LYS Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain J residue 266 LYS Chi-restraints excluded: chain J residue 350 GLU Chi-restraints excluded: chain J residue 362 GLU Chi-restraints excluded: chain J residue 392 LYS Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 264 ARG Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain I residue 350 GLU Chi-restraints excluded: chain I residue 362 GLU Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain H residue 362 GLU Chi-restraints excluded: chain N residue 246 VAL Chi-restraints excluded: chain N residue 350 GLU Chi-restraints excluded: chain Y residue 246 VAL Chi-restraints excluded: chain Y residue 362 GLU Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 322 VAL Chi-restraints excluded: chain L residue 350 GLU Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain K residue 246 VAL Chi-restraints excluded: chain K residue 266 LYS Chi-restraints excluded: chain K residue 311 VAL Chi-restraints excluded: chain K residue 350 GLU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain W residue 19 GLU Chi-restraints excluded: chain W residue 70 LYS Chi-restraints excluded: chain 2 residue 73 LEU Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 1 residue 73 LEU Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 33 LEU 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: 8.9990 chunk 499 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 162 optimal weight: 2.9990 chunk 531 optimal weight: 3.9990 chunk 569 optimal weight: 0.7980 chunk 413 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 657 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 D 239 ASN C 239 ASN B 239 ASN J 239 ASN I 239 ASN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 239 ASN N 239 ASN Y 214 GLN Y 239 ASN L 214 GLN L 239 ASN K 239 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 66710 Z= 0.230 Angle : 0.520 8.728 90034 Z= 0.278 Chirality : 0.044 0.174 10850 Planarity : 0.004 0.043 11522 Dihedral : 7.534 70.112 9660 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.49 % Allowed : 13.99 % Favored : 84.52 % 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: 1.08 (0.09), residues: 8722 helix: 1.78 (0.08), residues: 3962 sheet: 0.95 (0.15), residues: 1106 loop : -0.53 (0.09), residues: 3654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 42 HIS 0.002 0.001 HIS B 241 PHE 0.012 0.001 PHE B 213 TYR 0.011 0.001 TYR J 197 ARG 0.007 0.000 ARG H 264 *********************** 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 984 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 878 time to evaluate : 6.678 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: A 212 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6885 (mm-30) REVERT: A 312 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7323 (mm-40) REVERT: A 362 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6526 (tt0) REVERT: A 392 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8416 (mtmm) REVERT: A 469 MET cc_start: 0.8552 (mtp) cc_final: 0.8228 (mtp) REVERT: G 212 GLU cc_start: 0.6907 (mt-10) cc_final: 0.6522 (mm-30) REVERT: G 312 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7454 (mm-40) REVERT: G 362 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6429 (tt0) REVERT: F 212 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6700 (mm-30) REVERT: F 220 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8438 (mt) REVERT: F 223 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7296 (mtpp) REVERT: F 264 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.6271 (tpt90) REVERT: F 312 GLN cc_start: 0.7789 (mm-40) cc_final: 0.7545 (mm110) REVERT: F 362 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6723 (tt0) REVERT: E 212 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6784 (mm-30) REVERT: D 212 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6731 (mm-30) REVERT: D 312 GLN cc_start: 0.7838 (mm-40) cc_final: 0.7416 (mm-40) REVERT: C 212 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6900 (mm-30) REVERT: C 312 GLN cc_start: 0.7690 (mm-40) cc_final: 0.7355 (mm-40) REVERT: C 343 LYS cc_start: 0.8032 (mtpp) cc_final: 0.7455 (mttp) REVERT: B 212 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6550 (mm-30) REVERT: B 283 ARG cc_start: 0.7519 (ttp-170) cc_final: 0.7234 (ttp-170) REVERT: B 321 GLU cc_start: 0.7413 (tp30) cc_final: 0.7129 (tp30) REVERT: B 362 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6668 (tt0) REVERT: J 212 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6884 (mm-30) REVERT: J 312 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7326 (mm-40) REVERT: J 362 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6527 (tt0) REVERT: J 392 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8416 (mtmm) REVERT: J 469 MET cc_start: 0.8554 (mtp) cc_final: 0.8224 (mtp) REVERT: I 212 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6533 (mm-30) REVERT: I 217 TYR cc_start: 0.8329 (m-80) cc_final: 0.8110 (m-80) REVERT: I 312 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7435 (mm-40) REVERT: I 362 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6492 (tt0) REVERT: H 212 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6774 (mm-30) REVERT: H 220 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8482 (mt) REVERT: H 312 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7549 (mm110) REVERT: H 362 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6749 (tt0) REVERT: N 212 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6787 (mm-30) REVERT: N 264 ARG cc_start: 0.8158 (tpt90) cc_final: 0.7880 (tpt90) REVERT: Y 312 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7415 (mm-40) REVERT: L 212 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6806 (mt-10) REVERT: L 312 GLN cc_start: 0.7690 (mm-40) cc_final: 0.7353 (mm-40) REVERT: L 323 ILE cc_start: 0.8667 (mt) cc_final: 0.8429 (mp) REVERT: L 342 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7211 (mm-30) REVERT: L 343 LYS cc_start: 0.8041 (mttp) cc_final: 0.7756 (mtpp) REVERT: K 283 ARG cc_start: 0.7503 (ttp-170) cc_final: 0.7218 (ttp-170) REVERT: K 312 GLN cc_start: 0.8041 (mm110) cc_final: 0.7700 (mm110) REVERT: K 362 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6675 (tt0) REVERT: O 80 LYS cc_start: 0.8729 (tptp) cc_final: 0.8370 (tptt) REVERT: T 93 ASP cc_start: 0.8285 (t0) cc_final: 0.7829 (t0) REVERT: X 80 LYS cc_start: 0.8705 (tptp) cc_final: 0.8351 (tptt) REVERT: W 80 LYS cc_start: 0.8754 (tttm) cc_final: 0.8473 (tptt) REVERT: V 80 LYS cc_start: 0.8840 (tptm) cc_final: 0.8217 (tptt) REVERT: V 87 ASP cc_start: 0.7265 (m-30) cc_final: 0.6819 (m-30) REVERT: V 93 ASP cc_start: 0.8287 (t0) cc_final: 0.7829 (t0) REVERT: 1 32 MET cc_start: 0.7377 (mtm) cc_final: 0.7088 (ptp) outliers start: 106 outliers final: 56 residues processed: 952 average time/residue: 1.4015 time to fit residues: 1752.0768 Evaluate side-chains 935 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 865 time to evaluate : 5.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 264 ARG Chi-restraints excluded: chain G residue 311 VAL Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain G residue 362 GLU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 223 LYS Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 350 GLU Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 362 GLU Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 LYS Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain J residue 266 LYS Chi-restraints excluded: chain J residue 350 GLU Chi-restraints excluded: chain J residue 362 GLU Chi-restraints excluded: chain J residue 392 LYS Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 264 ARG Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain I residue 350 GLU Chi-restraints excluded: chain I residue 362 GLU Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain H residue 362 GLU Chi-restraints excluded: chain N residue 246 VAL Chi-restraints excluded: chain N residue 350 GLU Chi-restraints excluded: chain Y residue 223 LYS Chi-restraints excluded: chain Y residue 246 VAL Chi-restraints excluded: chain Y residue 402 THR Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 322 VAL Chi-restraints excluded: chain L residue 350 GLU Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain K residue 246 VAL Chi-restraints excluded: chain K residue 266 LYS Chi-restraints excluded: chain K residue 311 VAL Chi-restraints excluded: chain K residue 350 GLU Chi-restraints excluded: chain K residue 362 GLU Chi-restraints excluded: chain K residue 522 GLU Chi-restraints excluded: chain U residue 19 GLU Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain P residue 19 GLU Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain W residue 19 GLU Chi-restraints excluded: chain 2 residue 73 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 761 optimal weight: 1.9990 chunk 801 optimal weight: 0.0020 chunk 731 optimal weight: 8.9990 chunk 779 optimal weight: 8.9990 chunk 469 optimal weight: 0.9980 chunk 339 optimal weight: 6.9990 chunk 612 optimal weight: 0.6980 chunk 239 optimal weight: 10.0000 chunk 704 optimal weight: 0.8980 chunk 737 optimal weight: 6.9990 chunk 776 optimal weight: 9.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- 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 40 GLN F 239 ASN E 239 ASN D 214 GLN D 239 ASN C 214 GLN C 239 ASN J 239 ASN I 239 ASN H 239 ASN N 239 ASN Y 40 GLN Y 239 ASN L 214 GLN L 239 ASN K 214 GLN K 239 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 66710 Z= 0.143 Angle : 0.468 9.517 90034 Z= 0.249 Chirality : 0.042 0.163 10850 Planarity : 0.004 0.040 11522 Dihedral : 6.479 63.301 9660 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.27 % Allowed : 14.38 % Favored : 84.35 % 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: 1.21 (0.09), residues: 8722 helix: 1.95 (0.08), residues: 3934 sheet: 0.99 (0.15), residues: 1106 loop : -0.52 (0.09), residues: 3682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 42 HIS 0.002 0.001 HIS B 241 PHE 0.007 0.001 PHE H 213 TYR 0.008 0.001 TYR 2 88 ARG 0.008 0.000 ARG H 264 *********************** 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 980 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 890 time to evaluate : 5.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6859 (mm-30) REVERT: A 312 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7352 (mm-40) REVERT: A 392 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8420 (mtmm) REVERT: A 469 MET cc_start: 0.8621 (mtp) cc_final: 0.8311 (mtp) REVERT: G 212 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6551 (mm-30) REVERT: G 312 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7470 (mm-40) REVERT: G 321 GLU cc_start: 0.7122 (tp30) cc_final: 0.6905 (tp30) REVERT: F 212 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6650 (mm-30) REVERT: F 220 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8445 (mt) REVERT: F 264 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.6258 (tpt90) REVERT: F 312 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7558 (mm110) REVERT: F 362 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6709 (tt0) REVERT: E 212 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6770 (mm-30) REVERT: D 212 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6773 (mm-30) REVERT: D 284 LYS cc_start: 0.7462 (mtmm) cc_final: 0.7204 (tttp) REVERT: D 312 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7376 (mm-40) REVERT: D 340 GLN cc_start: 0.7570 (mm110) cc_final: 0.7192 (mm110) REVERT: C 212 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6987 (mt-10) REVERT: C 312 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7398 (mm-40) REVERT: C 343 LYS cc_start: 0.8037 (mtpp) cc_final: 0.7499 (mttp) REVERT: B 212 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6546 (mm-30) REVERT: B 312 GLN cc_start: 0.8035 (mm110) cc_final: 0.7665 (mm110) REVERT: B 321 GLU cc_start: 0.7335 (tp30) cc_final: 0.7090 (tp30) REVERT: B 362 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6689 (tt0) REVERT: J 212 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6856 (mm-30) REVERT: J 312 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7353 (mm-40) REVERT: J 392 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8420 (mtmm) REVERT: J 469 MET cc_start: 0.8619 (mtp) cc_final: 0.8301 (mtp) REVERT: I 212 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6542 (mm-30) REVERT: I 217 TYR cc_start: 0.8301 (m-80) cc_final: 0.8073 (m-80) REVERT: I 312 GLN cc_start: 0.7795 (mm-40) cc_final: 0.7434 (mm-40) REVERT: H 212 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6613 (mm-30) REVERT: H 220 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8458 (mt) REVERT: H 308 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8049 (mt) REVERT: H 312 GLN cc_start: 0.7795 (mm-40) cc_final: 0.7563 (mm110) REVERT: H 362 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6724 (tt0) REVERT: N 212 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6815 (mm-30) REVERT: N 262 LEU cc_start: 0.8403 (tt) cc_final: 0.8203 (tm) REVERT: N 264 ARG cc_start: 0.8150 (tpt90) cc_final: 0.7883 (tpt90) REVERT: Y 284 LYS cc_start: 0.7422 (mtmm) cc_final: 0.7193 (tttt) REVERT: Y 312 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7376 (mm-40) REVERT: L 212 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6798 (mm-30) REVERT: L 312 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7397 (mm-40) REVERT: L 342 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7229 (mm-30) REVERT: L 343 LYS cc_start: 0.8028 (mttp) cc_final: 0.7747 (mtpp) REVERT: K 312 GLN cc_start: 0.8032 (mm110) cc_final: 0.7690 (mm110) REVERT: K 362 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6691 (tt0) REVERT: O 80 LYS cc_start: 0.8683 (tptp) cc_final: 0.8336 (tptt) REVERT: T 93 ASP cc_start: 0.8254 (t0) cc_final: 0.7783 (t0) REVERT: R 73 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8312 (mt) REVERT: P 32 MET cc_start: 0.7447 (mtm) cc_final: 0.7136 (ptp) REVERT: X 80 LYS cc_start: 0.8679 (tptp) cc_final: 0.8329 (tptt) REVERT: W 80 LYS cc_start: 0.8709 (tttm) cc_final: 0.8373 (tptt) REVERT: V 80 LYS cc_start: 0.8839 (tptm) cc_final: 0.8225 (tptt) REVERT: V 87 ASP cc_start: 0.7216 (m-30) cc_final: 0.6795 (m-30) REVERT: V 93 ASP cc_start: 0.8260 (t0) cc_final: 0.7790 (t0) REVERT: 1 32 MET cc_start: 0.7335 (mtm) cc_final: 0.7099 (ptp) REVERT: 1 73 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8313 (mt) outliers start: 90 outliers final: 54 residues processed: 954 average time/residue: 1.3754 time to fit residues: 1728.9618 Evaluate side-chains 938 residues out of total 7098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 872 time to evaluate : 5.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 264 ARG Chi-restraints excluded: chain G residue 311 VAL Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 350 GLU Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 362 GLU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain J residue 266 LYS Chi-restraints excluded: chain J residue 350 GLU Chi-restraints excluded: chain J residue 392 LYS Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 264 ARG Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain I residue 350 GLU Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 308 LEU Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain H residue 362 GLU Chi-restraints excluded: chain N residue 246 VAL Chi-restraints excluded: chain N residue 350 GLU Chi-restraints excluded: chain Y residue 9 ASP Chi-restraints excluded: chain Y residue 223 LYS Chi-restraints excluded: chain Y residue 246 VAL Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 350 GLU Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain K residue 214 GLN Chi-restraints excluded: chain K residue 246 VAL Chi-restraints excluded: chain K residue 311 VAL Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 350 GLU Chi-restraints excluded: chain K residue 362 GLU Chi-restraints excluded: chain K residue 522 GLU Chi-restraints excluded: chain U residue 19 GLU Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain P residue 19 GLU Chi-restraints excluded: chain 2 residue 73 LEU Chi-restraints excluded: chain 1 residue 73 LEU Chi-restraints excluded: chain M residue 19 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.5618 > 50: distance: 38 - 43: 29.662 distance: 43 - 44: 27.194 distance: 43 - 188: 26.579 distance: 44 - 45: 58.479 distance: 44 - 47: 41.260 distance: 45 - 46: 43.933 distance: 45 - 51: 46.104 distance: 46 - 185: 34.620 distance: 47 - 48: 34.509 distance: 48 - 50: 37.022 distance: 51 - 52: 28.900 distance: 52 - 53: 13.466 distance: 52 - 55: 34.403 distance: 53 - 54: 37.050 distance: 53 - 59: 15.797 distance: 55 - 56: 6.594 distance: 56 - 57: 18.280 distance: 56 - 58: 31.555 distance: 59 - 60: 9.488 distance: 59 - 65: 42.951 distance: 60 - 61: 43.469 distance: 60 - 63: 30.735 distance: 61 - 62: 38.965 distance: 61 - 66: 37.015 distance: 63 - 64: 37.452 distance: 64 - 65: 15.866 distance: 66 - 67: 34.736 distance: 67 - 68: 14.111 distance: 67 - 70: 13.411 distance: 68 - 69: 16.001 distance: 68 - 75: 22.037 distance: 70 - 71: 3.940 distance: 71 - 72: 9.903 distance: 72 - 73: 9.723 distance: 72 - 74: 15.489 distance: 75 - 76: 42.257 distance: 76 - 77: 52.906 distance: 76 - 79: 16.383 distance: 77 - 78: 56.174 distance: 77 - 87: 4.256 distance: 79 - 80: 23.895 distance: 80 - 81: 44.996 distance: 80 - 82: 37.165 distance: 81 - 83: 42.623 distance: 82 - 84: 12.811 distance: 83 - 85: 26.490 distance: 84 - 85: 13.674 distance: 85 - 86: 20.744 distance: 88 - 89: 6.322 distance: 89 - 90: 34.145 distance: 89 - 91: 22.469 distance: 91 - 92: 25.257 distance: 92 - 93: 37.128 distance: 93 - 94: 35.526 distance: 93 - 95: 20.658 distance: 95 - 96: 31.445 distance: 95 - 157: 26.485 distance: 96 - 97: 17.243 distance: 96 - 99: 14.121 distance: 97 - 98: 15.500 distance: 97 - 102: 41.579 distance: 98 - 154: 31.247 distance: 99 - 100: 34.620 distance: 99 - 101: 11.651 distance: 102 - 103: 27.488 distance: 103 - 104: 41.654 distance: 103 - 106: 13.255 distance: 104 - 105: 42.510 distance: 104 - 111: 62.207 distance: 106 - 107: 56.022 distance: 107 - 108: 42.933 distance: 108 - 109: 15.593 distance: 109 - 110: 37.227 distance: 111 - 112: 18.871 distance: 111 - 141: 28.816 distance: 112 - 113: 24.849 distance: 112 - 115: 34.296 distance: 113 - 114: 29.944 distance: 113 - 118: 15.038 distance: 114 - 138: 34.398 distance: 115 - 116: 47.761 distance: 115 - 117: 41.379