Starting phenix.real_space_refine on Fri Feb 16 07:07:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1d_15072/02_2024/8a1d_15072_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1d_15072/02_2024/8a1d_15072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1d_15072/02_2024/8a1d_15072.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1d_15072/02_2024/8a1d_15072.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1d_15072/02_2024/8a1d_15072_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1d_15072/02_2024/8a1d_15072_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 432 5.16 5 C 42912 2.51 5 N 11008 2.21 5 O 12800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 95": "OE1" <-> "OE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C ASP 304": "OD1" <-> "OD2" Residue "C PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 448": "OD1" <-> "OD2" Residue "C PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "E ASP 219": "OD1" <-> "OD2" Residue "E TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 448": "OD1" <-> "OD2" Residue "E PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 166": "OE1" <-> "OE2" Residue "F PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 219": "OD1" <-> "OD2" Residue "G TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 304": "OD1" <-> "OD2" Residue "G PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 456": "OE1" <-> "OE2" Residue "G PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 95": "OE1" <-> "OE2" Residue "H PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 228": "OD1" <-> "OD2" Residue "I PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 95": "OE1" <-> "OE2" Residue "J TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 95": "OE1" <-> "OE2" Residue "K PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 448": "OD1" <-> "OD2" Residue "K TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 102": "OE1" <-> "OE2" Residue "M PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 218": "OE1" <-> "OE2" Residue "M ASP 219": "OD1" <-> "OD2" Residue "M ASP 304": "OD1" <-> "OD2" Residue "M PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 448": "OD1" <-> "OD2" Residue "N PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 166": "OE1" <-> "OE2" Residue "N PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 219": "OD1" <-> "OD2" Residue "O ASP 304": "OD1" <-> "OD2" Residue "O PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 95": "OE1" <-> "OE2" Residue "P PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 448": "OD1" <-> "OD2" Residue "P TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 67152 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "B" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "C" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "D" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "E" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "F" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "G" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "H" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "I" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "J" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "K" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "L" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "M" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "N" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "O" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "P" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 26.52, per 1000 atoms: 0.39 Number of scatterers: 67152 At special positions: 0 Unit cell: (212.541, 214.635, 157.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 432 16.00 O 12800 8.00 N 11008 7.00 C 42912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=128, symmetry=0 Simple disulfide: pdb=" SG CYS A 34 " - pdb=" SG CYS A 70 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 409 " - pdb=" SG CYS A 462 " distance=2.03 Simple disulfide: pdb=" SG CYS A 432 " - pdb=" SG CYS A 446 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 442 " distance=2.03 Simple disulfide: pdb=" SG CYS A 494 " - pdb=" SG CYS A 510 " distance=2.03 Simple disulfide: pdb=" SG CYS A 531 " - pdb=" SG CYS A 569 " distance=2.03 Simple disulfide: pdb=" SG CYS A 554 " - pdb=" SG CYS A 574 " distance=2.03 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 70 " distance=2.04 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 409 " - pdb=" SG CYS B 462 " distance=2.03 Simple disulfide: pdb=" SG CYS B 432 " - pdb=" SG CYS B 446 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 442 " distance=2.03 Simple disulfide: pdb=" SG CYS B 494 " - pdb=" SG CYS B 510 " distance=2.03 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 569 " distance=2.03 Simple disulfide: pdb=" SG CYS B 554 " - pdb=" SG CYS B 574 " distance=2.03 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 70 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 394 " distance=2.03 Simple disulfide: pdb=" SG CYS C 409 " - pdb=" SG CYS C 462 " distance=2.03 Simple disulfide: pdb=" SG CYS C 432 " - pdb=" SG CYS C 446 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 442 " distance=2.03 Simple disulfide: pdb=" SG CYS C 494 " - pdb=" SG CYS C 510 " distance=2.03 Simple disulfide: pdb=" SG CYS C 531 " - pdb=" SG CYS C 569 " distance=2.03 Simple disulfide: pdb=" SG CYS C 554 " - pdb=" SG CYS C 574 " distance=2.03 Simple disulfide: pdb=" SG CYS D 34 " - pdb=" SG CYS D 70 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 394 " distance=2.03 Simple disulfide: pdb=" SG CYS D 409 " - pdb=" SG CYS D 462 " distance=2.03 Simple disulfide: pdb=" SG CYS D 432 " - pdb=" SG CYS D 446 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 442 " distance=2.03 Simple disulfide: pdb=" SG CYS D 494 " - pdb=" SG CYS D 510 " distance=2.03 Simple disulfide: pdb=" SG CYS D 531 " - pdb=" SG CYS D 569 " distance=2.03 Simple disulfide: pdb=" SG CYS D 554 " - pdb=" SG CYS D 574 " distance=2.03 Simple disulfide: pdb=" SG CYS E 34 " - pdb=" SG CYS E 70 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 394 " distance=2.03 Simple disulfide: pdb=" SG CYS E 409 " - pdb=" SG CYS E 462 " distance=2.03 Simple disulfide: pdb=" SG CYS E 432 " - pdb=" SG CYS E 446 " distance=2.03 Simple disulfide: pdb=" SG CYS E 436 " - pdb=" SG CYS E 442 " distance=2.03 Simple disulfide: pdb=" SG CYS E 494 " - pdb=" SG CYS E 510 " distance=2.03 Simple disulfide: pdb=" SG CYS E 531 " - pdb=" SG CYS E 569 " distance=2.03 Simple disulfide: pdb=" SG CYS E 554 " - pdb=" SG CYS E 574 " distance=2.03 Simple disulfide: pdb=" SG CYS F 34 " - pdb=" SG CYS F 70 " distance=2.04 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 394 " distance=2.03 Simple disulfide: pdb=" SG CYS F 409 " - pdb=" SG CYS F 462 " distance=2.03 Simple disulfide: pdb=" SG CYS F 432 " - pdb=" SG CYS F 446 " distance=2.03 Simple disulfide: pdb=" SG CYS F 436 " - pdb=" SG CYS F 442 " distance=2.03 Simple disulfide: pdb=" SG CYS F 494 " - pdb=" SG CYS F 510 " distance=2.03 Simple disulfide: pdb=" SG CYS F 531 " - pdb=" SG CYS F 569 " distance=2.03 Simple disulfide: pdb=" SG CYS F 554 " - pdb=" SG CYS F 574 " distance=2.03 Simple disulfide: pdb=" SG CYS G 34 " - pdb=" SG CYS G 70 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 394 " distance=2.03 Simple disulfide: pdb=" SG CYS G 409 " - pdb=" SG CYS G 462 " distance=2.03 Simple disulfide: pdb=" SG CYS G 432 " - pdb=" SG CYS G 446 " distance=2.03 Simple disulfide: pdb=" SG CYS G 436 " - pdb=" SG CYS G 442 " distance=2.03 Simple disulfide: pdb=" SG CYS G 494 " - pdb=" SG CYS G 510 " distance=2.03 Simple disulfide: pdb=" SG CYS G 531 " - pdb=" SG CYS G 569 " distance=2.03 Simple disulfide: pdb=" SG CYS G 554 " - pdb=" SG CYS G 574 " distance=2.03 Simple disulfide: pdb=" SG CYS H 34 " - pdb=" SG CYS H 70 " distance=2.03 Simple disulfide: pdb=" SG CYS H 385 " - pdb=" SG CYS H 394 " distance=2.03 Simple disulfide: pdb=" SG CYS H 409 " - pdb=" SG CYS H 462 " distance=2.03 Simple disulfide: pdb=" SG CYS H 432 " - pdb=" SG CYS H 446 " distance=2.03 Simple disulfide: pdb=" SG CYS H 436 " - pdb=" SG CYS H 442 " distance=2.03 Simple disulfide: pdb=" SG CYS H 494 " - pdb=" SG CYS H 510 " distance=2.03 Simple disulfide: pdb=" SG CYS H 531 " - pdb=" SG CYS H 569 " distance=2.03 Simple disulfide: pdb=" SG CYS H 554 " - pdb=" SG CYS H 574 " distance=2.03 Simple disulfide: pdb=" SG CYS I 34 " - pdb=" SG CYS I 70 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 394 " distance=2.03 Simple disulfide: pdb=" SG CYS I 409 " - pdb=" SG CYS I 462 " distance=2.03 Simple disulfide: pdb=" SG CYS I 432 " - pdb=" SG CYS I 446 " distance=2.03 Simple disulfide: pdb=" SG CYS I 436 " - pdb=" SG CYS I 442 " distance=2.03 Simple disulfide: pdb=" SG CYS I 494 " - pdb=" SG CYS I 510 " distance=2.03 Simple disulfide: pdb=" SG CYS I 531 " - pdb=" SG CYS I 569 " distance=2.03 Simple disulfide: pdb=" SG CYS I 554 " - pdb=" SG CYS I 574 " distance=2.03 Simple disulfide: pdb=" SG CYS J 34 " - pdb=" SG CYS J 70 " distance=2.04 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 394 " distance=2.03 Simple disulfide: pdb=" SG CYS J 409 " - pdb=" SG CYS J 462 " distance=2.03 Simple disulfide: pdb=" SG CYS J 432 " - pdb=" SG CYS J 446 " distance=2.03 Simple disulfide: pdb=" SG CYS J 436 " - pdb=" SG CYS J 442 " distance=2.03 Simple disulfide: pdb=" SG CYS J 494 " - pdb=" SG CYS J 510 " distance=2.03 Simple disulfide: pdb=" SG CYS J 531 " - pdb=" SG CYS J 569 " distance=2.03 Simple disulfide: pdb=" SG CYS J 554 " - pdb=" SG CYS J 574 " distance=2.03 Simple disulfide: pdb=" SG CYS K 34 " - pdb=" SG CYS K 70 " distance=2.03 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 394 " distance=2.03 Simple disulfide: pdb=" SG CYS K 409 " - pdb=" SG CYS K 462 " distance=2.03 Simple disulfide: pdb=" SG CYS K 432 " - pdb=" SG CYS K 446 " distance=2.03 Simple disulfide: pdb=" SG CYS K 436 " - pdb=" SG CYS K 442 " distance=2.03 Simple disulfide: pdb=" SG CYS K 494 " - pdb=" SG CYS K 510 " distance=2.03 Simple disulfide: pdb=" SG CYS K 531 " - pdb=" SG CYS K 569 " distance=2.03 Simple disulfide: pdb=" SG CYS K 554 " - pdb=" SG CYS K 574 " distance=2.03 Simple disulfide: pdb=" SG CYS L 34 " - pdb=" SG CYS L 70 " distance=2.03 Simple disulfide: pdb=" SG CYS L 385 " - pdb=" SG CYS L 394 " distance=2.03 Simple disulfide: pdb=" SG CYS L 409 " - pdb=" SG CYS L 462 " distance=2.03 Simple disulfide: pdb=" SG CYS L 432 " - pdb=" SG CYS L 446 " distance=2.03 Simple disulfide: pdb=" SG CYS L 436 " - pdb=" SG CYS L 442 " distance=2.03 Simple disulfide: pdb=" SG CYS L 494 " - pdb=" SG CYS L 510 " distance=2.03 Simple disulfide: pdb=" SG CYS L 531 " - pdb=" SG CYS L 569 " distance=2.03 Simple disulfide: pdb=" SG CYS L 554 " - pdb=" SG CYS L 574 " distance=2.03 Simple disulfide: pdb=" SG CYS M 34 " - pdb=" SG CYS M 70 " distance=2.03 Simple disulfide: pdb=" SG CYS M 385 " - pdb=" SG CYS M 394 " distance=2.03 Simple disulfide: pdb=" SG CYS M 409 " - pdb=" SG CYS M 462 " distance=2.03 Simple disulfide: pdb=" SG CYS M 432 " - pdb=" SG CYS M 446 " distance=2.03 Simple disulfide: pdb=" SG CYS M 436 " - pdb=" SG CYS M 442 " distance=2.03 Simple disulfide: pdb=" SG CYS M 494 " - pdb=" SG CYS M 510 " distance=2.03 Simple disulfide: pdb=" SG CYS M 531 " - pdb=" SG CYS M 569 " distance=2.03 Simple disulfide: pdb=" SG CYS M 554 " - pdb=" SG CYS M 574 " distance=2.03 Simple disulfide: pdb=" SG CYS N 34 " - pdb=" SG CYS N 70 " distance=2.04 Simple disulfide: pdb=" SG CYS N 385 " - pdb=" SG CYS N 394 " distance=2.03 Simple disulfide: pdb=" SG CYS N 409 " - pdb=" SG CYS N 462 " distance=2.03 Simple disulfide: pdb=" SG CYS N 432 " - pdb=" SG CYS N 446 " distance=2.03 Simple disulfide: pdb=" SG CYS N 436 " - pdb=" SG CYS N 442 " distance=2.03 Simple disulfide: pdb=" SG CYS N 494 " - pdb=" SG CYS N 510 " distance=2.03 Simple disulfide: pdb=" SG CYS N 531 " - pdb=" SG CYS N 569 " distance=2.03 Simple disulfide: pdb=" SG CYS N 554 " - pdb=" SG CYS N 574 " distance=2.03 Simple disulfide: pdb=" SG CYS O 34 " - pdb=" SG CYS O 70 " distance=2.03 Simple disulfide: pdb=" SG CYS O 385 " - pdb=" SG CYS O 394 " distance=2.03 Simple disulfide: pdb=" SG CYS O 409 " - pdb=" SG CYS O 462 " distance=2.03 Simple disulfide: pdb=" SG CYS O 432 " - pdb=" SG CYS O 446 " distance=2.03 Simple disulfide: pdb=" SG CYS O 436 " - pdb=" SG CYS O 442 " distance=2.03 Simple disulfide: pdb=" SG CYS O 494 " - pdb=" SG CYS O 510 " distance=2.03 Simple disulfide: pdb=" SG CYS O 531 " - pdb=" SG CYS O 569 " distance=2.03 Simple disulfide: pdb=" SG CYS O 554 " - pdb=" SG CYS O 574 " distance=2.03 Simple disulfide: pdb=" SG CYS P 34 " - pdb=" SG CYS P 70 " distance=2.03 Simple disulfide: pdb=" SG CYS P 385 " - pdb=" SG CYS P 394 " distance=2.03 Simple disulfide: pdb=" SG CYS P 409 " - pdb=" SG CYS P 462 " distance=2.03 Simple disulfide: pdb=" SG CYS P 432 " - pdb=" SG CYS P 446 " distance=2.03 Simple disulfide: pdb=" SG CYS P 436 " - pdb=" SG CYS P 442 " distance=2.03 Simple disulfide: pdb=" SG CYS P 494 " - pdb=" SG CYS P 510 " distance=2.03 Simple disulfide: pdb=" SG CYS P 531 " - pdb=" SG CYS P 569 " distance=2.03 Simple disulfide: pdb=" SG CYS P 554 " - pdb=" SG CYS P 574 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 269 " " NAG B 701 " - " ASN B 269 " " NAG C 701 " - " ASN C 269 " " NAG D 701 " - " ASN D 269 " " NAG E 701 " - " ASN E 269 " " NAG F 701 " - " ASN F 269 " " NAG G 701 " - " ASN G 269 " " NAG H 701 " - " ASN H 269 " " NAG I 701 " - " ASN I 269 " " NAG J 701 " - " ASN J 269 " " NAG K 701 " - " ASN K 269 " " NAG L 701 " - " ASN L 269 " " NAG M 701 " - " ASN M 269 " " NAG N 701 " - " ASN N 269 " " NAG O 701 " - " ASN O 269 " " NAG P 701 " - " ASN P 269 " Time building additional restraints: 19.76 Conformation dependent library (CDL) restraints added in 9.0 seconds 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15808 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 146 helices and 97 sheets defined 15.4% alpha, 48.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.79 Creating SS restraints... Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 169 through 183 Processing helix chain 'A' and resid 187 through 201 Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 310 through 313 Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 324 through 344 Processing helix chain 'A' and resid 394 through 397 No H-bonds generated for 'chain 'A' and resid 394 through 397' Processing helix chain 'A' and resid 515 through 520 Processing helix chain 'B' and resid 32 through 38 Processing helix chain 'B' and resid 169 through 183 Processing helix chain 'B' and resid 187 through 201 Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 310 through 312 No H-bonds generated for 'chain 'B' and resid 310 through 312' Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'B' and resid 324 through 344 Processing helix chain 'B' and resid 394 through 397 No H-bonds generated for 'chain 'B' and resid 394 through 397' Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 515 through 520 Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 169 through 183 Processing helix chain 'C' and resid 187 through 201 removed outlier: 3.702A pdb=" N THR C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR C 192 " --> pdb=" O LYS C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 310 through 313 Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 324 through 344 Processing helix chain 'C' and resid 393 through 395 No H-bonds generated for 'chain 'C' and resid 393 through 395' Processing helix chain 'C' and resid 515 through 521 Processing helix chain 'D' and resid 32 through 38 Processing helix chain 'D' and resid 169 through 183 Processing helix chain 'D' and resid 187 through 201 removed outlier: 3.738A pdb=" N THR D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 310 through 313 Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 324 through 344 Processing helix chain 'D' and resid 393 through 395 No H-bonds generated for 'chain 'D' and resid 393 through 395' Processing helix chain 'D' and resid 515 through 521 Processing helix chain 'E' and resid 32 through 38 Processing helix chain 'E' and resid 169 through 183 Processing helix chain 'E' and resid 187 through 201 Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 310 through 313 No H-bonds generated for 'chain 'E' and resid 310 through 313' Processing helix chain 'E' and resid 324 through 344 Processing helix chain 'E' and resid 393 through 397 removed outlier: 3.992A pdb=" N ASN E 396 " --> pdb=" O LEU E 393 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU E 397 " --> pdb=" O CYS E 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 393 through 397' Processing helix chain 'E' and resid 515 through 521 Processing helix chain 'F' and resid 32 through 38 Processing helix chain 'F' and resid 169 through 183 Processing helix chain 'F' and resid 187 through 201 removed outlier: 3.541A pdb=" N THR F 191 " --> pdb=" O THR F 187 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR F 192 " --> pdb=" O LYS F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 295 Processing helix chain 'F' and resid 310 through 313 Processing helix chain 'F' and resid 316 through 318 No H-bonds generated for 'chain 'F' and resid 316 through 318' Processing helix chain 'F' and resid 324 through 344 Processing helix chain 'F' and resid 393 through 395 No H-bonds generated for 'chain 'F' and resid 393 through 395' Processing helix chain 'F' and resid 515 through 520 Processing helix chain 'G' and resid 32 through 38 Processing helix chain 'G' and resid 169 through 183 Processing helix chain 'G' and resid 187 through 201 removed outlier: 3.554A pdb=" N THR G 191 " --> pdb=" O THR G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 295 Processing helix chain 'G' and resid 310 through 313 Processing helix chain 'G' and resid 316 through 318 No H-bonds generated for 'chain 'G' and resid 316 through 318' Processing helix chain 'G' and resid 324 through 344 Processing helix chain 'G' and resid 394 through 397 No H-bonds generated for 'chain 'G' and resid 394 through 397' Processing helix chain 'G' and resid 437 through 439 No H-bonds generated for 'chain 'G' and resid 437 through 439' Processing helix chain 'G' and resid 515 through 521 Processing helix chain 'H' and resid 32 through 38 Processing helix chain 'H' and resid 169 through 183 Processing helix chain 'H' and resid 187 through 201 Processing helix chain 'H' and resid 289 through 295 Processing helix chain 'H' and resid 310 through 313 Processing helix chain 'H' and resid 316 through 318 No H-bonds generated for 'chain 'H' and resid 316 through 318' Processing helix chain 'H' and resid 324 through 344 Processing helix chain 'H' and resid 393 through 395 No H-bonds generated for 'chain 'H' and resid 393 through 395' Processing helix chain 'H' and resid 515 through 520 Processing helix chain 'I' and resid 32 through 38 Processing helix chain 'I' and resid 169 through 183 Processing helix chain 'I' and resid 187 through 201 removed outlier: 3.587A pdb=" N THR I 191 " --> pdb=" O THR I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 289 through 295 Processing helix chain 'I' and resid 310 through 313 Processing helix chain 'I' and resid 316 through 318 No H-bonds generated for 'chain 'I' and resid 316 through 318' Processing helix chain 'I' and resid 324 through 344 Processing helix chain 'I' and resid 394 through 397 No H-bonds generated for 'chain 'I' and resid 394 through 397' Processing helix chain 'I' and resid 515 through 519 Processing helix chain 'J' and resid 32 through 38 Processing helix chain 'J' and resid 169 through 183 Processing helix chain 'J' and resid 187 through 201 removed outlier: 3.624A pdb=" N THR J 191 " --> pdb=" O THR J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 295 Processing helix chain 'J' and resid 310 through 312 No H-bonds generated for 'chain 'J' and resid 310 through 312' Processing helix chain 'J' and resid 316 through 318 No H-bonds generated for 'chain 'J' and resid 316 through 318' Processing helix chain 'J' and resid 324 through 344 Processing helix chain 'J' and resid 394 through 397 No H-bonds generated for 'chain 'J' and resid 394 through 397' Processing helix chain 'J' and resid 437 through 439 No H-bonds generated for 'chain 'J' and resid 437 through 439' Processing helix chain 'J' and resid 515 through 520 Processing helix chain 'K' and resid 32 through 38 Processing helix chain 'K' and resid 169 through 183 Processing helix chain 'K' and resid 187 through 201 removed outlier: 3.761A pdb=" N THR K 191 " --> pdb=" O THR K 187 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR K 192 " --> pdb=" O LYS K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 289 through 295 Processing helix chain 'K' and resid 310 through 313 Processing helix chain 'K' and resid 316 through 318 No H-bonds generated for 'chain 'K' and resid 316 through 318' Processing helix chain 'K' and resid 324 through 344 Processing helix chain 'K' and resid 393 through 395 No H-bonds generated for 'chain 'K' and resid 393 through 395' Processing helix chain 'K' and resid 515 through 521 Processing helix chain 'L' and resid 32 through 38 Processing helix chain 'L' and resid 169 through 183 Processing helix chain 'L' and resid 187 through 201 removed outlier: 3.676A pdb=" N THR L 191 " --> pdb=" O THR L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 289 through 295 Processing helix chain 'L' and resid 310 through 313 Processing helix chain 'L' and resid 316 through 318 No H-bonds generated for 'chain 'L' and resid 316 through 318' Processing helix chain 'L' and resid 324 through 344 Processing helix chain 'L' and resid 393 through 395 No H-bonds generated for 'chain 'L' and resid 393 through 395' Processing helix chain 'L' and resid 515 through 521 Processing helix chain 'M' and resid 32 through 38 Processing helix chain 'M' and resid 169 through 183 Processing helix chain 'M' and resid 187 through 201 removed outlier: 3.588A pdb=" N TYR M 192 " --> pdb=" O LYS M 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 289 through 295 Processing helix chain 'M' and resid 310 through 313 Processing helix chain 'M' and resid 324 through 344 Processing helix chain 'M' and resid 393 through 397 removed outlier: 4.019A pdb=" N ASN M 396 " --> pdb=" O LEU M 393 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU M 397 " --> pdb=" O CYS M 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 393 through 397' Processing helix chain 'M' and resid 515 through 520 Processing helix chain 'N' and resid 32 through 38 Processing helix chain 'N' and resid 169 through 183 Processing helix chain 'N' and resid 187 through 201 removed outlier: 3.557A pdb=" N TYR N 192 " --> pdb=" O LYS N 188 " (cutoff:3.500A) Processing helix chain 'N' and resid 289 through 295 Processing helix chain 'N' and resid 310 through 313 Processing helix chain 'N' and resid 316 through 318 No H-bonds generated for 'chain 'N' and resid 316 through 318' Processing helix chain 'N' and resid 324 through 344 Processing helix chain 'N' and resid 393 through 395 No H-bonds generated for 'chain 'N' and resid 393 through 395' Processing helix chain 'N' and resid 437 through 439 No H-bonds generated for 'chain 'N' and resid 437 through 439' Processing helix chain 'N' and resid 515 through 520 Processing helix chain 'O' and resid 32 through 38 Processing helix chain 'O' and resid 169 through 183 Processing helix chain 'O' and resid 187 through 201 removed outlier: 3.527A pdb=" N THR O 191 " --> pdb=" O THR O 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 289 through 295 Processing helix chain 'O' and resid 310 through 313 Processing helix chain 'O' and resid 324 through 344 Processing helix chain 'O' and resid 394 through 397 No H-bonds generated for 'chain 'O' and resid 394 through 397' Processing helix chain 'O' and resid 437 through 439 No H-bonds generated for 'chain 'O' and resid 437 through 439' Processing helix chain 'O' and resid 515 through 521 Processing helix chain 'P' and resid 32 through 38 Processing helix chain 'P' and resid 169 through 183 Processing helix chain 'P' and resid 187 through 201 Processing helix chain 'P' and resid 289 through 295 Processing helix chain 'P' and resid 310 through 313 Processing helix chain 'P' and resid 316 through 318 No H-bonds generated for 'chain 'P' and resid 316 through 318' Processing helix chain 'P' and resid 324 through 344 Processing helix chain 'P' and resid 393 through 395 No H-bonds generated for 'chain 'P' and resid 393 through 395' Processing helix chain 'P' and resid 515 through 521 Processing sheet with id= A, first strand: chain 'A' and resid 84 through 88 removed outlier: 6.708A pdb=" N ALA A 211 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR A 158 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A 209 " --> pdb=" O THR A 158 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 91 through 121 Processing sheet with id= C, first strand: chain 'A' and resid 479 through 481 Processing sheet with id= D, first strand: chain 'A' and resid 528 through 530 removed outlier: 3.520A pdb=" N PHE A 529 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR A 573 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU A 562 " --> pdb=" O TYR A 573 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL A 575 " --> pdb=" O GLN A 560 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLN A 560 " --> pdb=" O VAL A 575 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 204 through 209 removed outlier: 6.768A pdb=" N ALA A 306 " --> pdb=" O THR A 207 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 378 through 387 removed outlier: 5.631A pdb=" N CYS A 462 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL A 381 " --> pdb=" O TYR A 460 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TYR A 460 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLN A 383 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ARG A 458 " --> pdb=" O GLN A 383 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N CYS A 385 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU A 456 " --> pdb=" O CYS A 385 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLU A 387 " --> pdb=" O LYS A 454 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LYS A 454 " --> pdb=" O GLU A 387 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TRP A 461 " --> pdb=" O HIS A 417 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N HIS A 417 " --> pdb=" O TRP A 461 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL A 463 " --> pdb=" O PRO A 415 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 84 through 88 removed outlier: 6.626A pdb=" N ALA B 211 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR B 158 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL B 209 " --> pdb=" O THR B 158 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 91 through 121 Processing sheet with id= I, first strand: chain 'B' and resid 479 through 481 Processing sheet with id= J, first strand: chain 'B' and resid 204 through 209 removed outlier: 6.764A pdb=" N ALA B 306 " --> pdb=" O THR B 207 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 378 through 387 removed outlier: 5.704A pdb=" N CYS B 462 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N VAL B 381 " --> pdb=" O TYR B 460 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR B 460 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLN B 383 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ARG B 458 " --> pdb=" O GLN B 383 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N CYS B 385 " --> pdb=" O GLU B 456 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU B 456 " --> pdb=" O CYS B 385 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLU B 387 " --> pdb=" O LYS B 454 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LYS B 454 " --> pdb=" O GLU B 387 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N TRP B 461 " --> pdb=" O HIS B 417 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N HIS B 417 " --> pdb=" O TRP B 461 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL B 463 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 525 through 529 removed outlier: 6.349A pdb=" N CYS B 574 " --> pdb=" O GLY B 526 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE B 528 " --> pdb=" O SER B 572 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER B 572 " --> pdb=" O PHE B 528 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N TYR B 573 " --> pdb=" O LEU B 562 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU B 562 " --> pdb=" O TYR B 573 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL B 575 " --> pdb=" O GLN B 560 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLN B 560 " --> pdb=" O VAL B 575 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 84 through 88 removed outlier: 6.615A pdb=" N ALA C 211 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR C 158 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL C 209 " --> pdb=" O THR C 158 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 91 through 121 Processing sheet with id= O, first strand: chain 'C' and resid 498 through 502 Processing sheet with id= P, first strand: chain 'C' and resid 49 through 52 removed outlier: 5.194A pdb=" N GLY C 60 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ASP C 52 " --> pdb=" O ASP C 58 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ASP C 58 " --> pdb=" O ASP C 52 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 204 through 210 removed outlier: 6.837A pdb=" N ALA C 306 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL C 209 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASP C 304 " --> pdb=" O VAL C 209 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 378 through 387 removed outlier: 5.954A pdb=" N CYS C 462 " --> pdb=" O GLY C 379 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N VAL C 381 " --> pdb=" O TYR C 460 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TYR C 460 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLN C 383 " --> pdb=" O ARG C 458 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ARG C 458 " --> pdb=" O GLN C 383 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N CYS C 385 " --> pdb=" O GLU C 456 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU C 456 " --> pdb=" O CYS C 385 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N GLU C 387 " --> pdb=" O LYS C 454 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LYS C 454 " --> pdb=" O GLU C 387 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TRP C 461 " --> pdb=" O HIS C 417 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N HIS C 417 " --> pdb=" O TRP C 461 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL C 463 " --> pdb=" O PRO C 415 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 525 through 529 removed outlier: 6.365A pdb=" N CYS C 574 " --> pdb=" O GLY C 526 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N PHE C 528 " --> pdb=" O SER C 572 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N SER C 572 " --> pdb=" O PHE C 528 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TYR C 573 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LEU C 562 " --> pdb=" O TYR C 573 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL C 575 " --> pdb=" O GLN C 560 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLN C 560 " --> pdb=" O VAL C 575 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 84 through 88 removed outlier: 6.642A pdb=" N ALA D 211 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR D 158 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL D 209 " --> pdb=" O THR D 158 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 91 through 121 Processing sheet with id= V, first strand: chain 'D' and resid 498 through 502 Processing sheet with id= W, first strand: chain 'D' and resid 204 through 210 removed outlier: 6.824A pdb=" N ALA D 306 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL D 209 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP D 304 " --> pdb=" O VAL D 209 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 378 through 387 removed outlier: 5.810A pdb=" N CYS D 462 " --> pdb=" O GLY D 379 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N VAL D 381 " --> pdb=" O TYR D 460 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N TYR D 460 " --> pdb=" O VAL D 381 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLN D 383 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ARG D 458 " --> pdb=" O GLN D 383 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N CYS D 385 " --> pdb=" O GLU D 456 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU D 456 " --> pdb=" O CYS D 385 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLU D 387 " --> pdb=" O LYS D 454 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LYS D 454 " --> pdb=" O GLU D 387 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TRP D 461 " --> pdb=" O HIS D 417 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N HIS D 417 " --> pdb=" O TRP D 461 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL D 463 " --> pdb=" O PRO D 415 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 558 through 566 removed outlier: 3.559A pdb=" N HIS D 561 " --> pdb=" O TYR D 573 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL D 571 " --> pdb=" O ALA D 563 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE D 565 " --> pdb=" O CYS D 569 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N CYS D 569 " --> pdb=" O ILE D 565 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 84 through 88 removed outlier: 6.690A pdb=" N ALA E 211 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR E 158 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL E 209 " --> pdb=" O THR E 158 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 91 through 121 Processing sheet with id= AB, first strand: chain 'E' and resid 498 through 502 Processing sheet with id= AC, first strand: chain 'E' and resid 204 through 209 removed outlier: 6.745A pdb=" N ALA E 306 " --> pdb=" O THR E 207 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 378 through 387 removed outlier: 6.020A pdb=" N CYS E 462 " --> pdb=" O GLY E 379 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL E 381 " --> pdb=" O TYR E 460 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TYR E 460 " --> pdb=" O VAL E 381 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLN E 383 " --> pdb=" O ARG E 458 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ARG E 458 " --> pdb=" O GLN E 383 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N CYS E 385 " --> pdb=" O GLU E 456 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLU E 456 " --> pdb=" O CYS E 385 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLU E 387 " --> pdb=" O LYS E 454 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LYS E 454 " --> pdb=" O GLU E 387 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TRP E 461 " --> pdb=" O HIS E 417 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N HIS E 417 " --> pdb=" O TRP E 461 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL E 463 " --> pdb=" O PRO E 415 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 558 through 566 removed outlier: 3.711A pdb=" N HIS E 561 " --> pdb=" O TYR E 573 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR E 573 " --> pdb=" O HIS E 561 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL E 571 " --> pdb=" O ALA E 563 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE E 565 " --> pdb=" O CYS E 569 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N CYS E 569 " --> pdb=" O ILE E 565 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 84 through 88 removed outlier: 6.720A pdb=" N ALA F 211 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR F 158 " --> pdb=" O VAL F 209 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL F 209 " --> pdb=" O THR F 158 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 91 through 121 Processing sheet with id= AH, first strand: chain 'F' and resid 383 through 387 removed outlier: 6.520A pdb=" N TRP F 461 " --> pdb=" O HIS F 417 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N HIS F 417 " --> pdb=" O TRP F 461 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL F 463 " --> pdb=" O PRO F 415 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 498 through 502 Processing sheet with id= AJ, first strand: chain 'F' and resid 204 through 209 removed outlier: 6.750A pdb=" N ALA F 306 " --> pdb=" O THR F 207 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'F' and resid 558 through 566 removed outlier: 3.644A pdb=" N HIS F 561 " --> pdb=" O TYR F 573 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR F 573 " --> pdb=" O HIS F 561 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL F 571 " --> pdb=" O ALA F 563 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE F 565 " --> pdb=" O CYS F 569 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N CYS F 569 " --> pdb=" O ILE F 565 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'G' and resid 84 through 88 removed outlier: 6.643A pdb=" N ALA G 211 " --> pdb=" O ILE G 156 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR G 158 " --> pdb=" O VAL G 209 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL G 209 " --> pdb=" O THR G 158 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'G' and resid 91 through 121 Processing sheet with id= AN, first strand: chain 'G' and resid 498 through 502 Processing sheet with id= AO, first strand: chain 'G' and resid 204 through 209 removed outlier: 6.829A pdb=" N ALA G 306 " --> pdb=" O THR G 207 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'G' and resid 378 through 387 removed outlier: 5.642A pdb=" N CYS G 462 " --> pdb=" O GLY G 379 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL G 381 " --> pdb=" O TYR G 460 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYR G 460 " --> pdb=" O VAL G 381 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN G 383 " --> pdb=" O ARG G 458 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ARG G 458 " --> pdb=" O GLN G 383 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N CYS G 385 " --> pdb=" O GLU G 456 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU G 456 " --> pdb=" O CYS G 385 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLU G 387 " --> pdb=" O LYS G 454 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LYS G 454 " --> pdb=" O GLU G 387 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TRP G 461 " --> pdb=" O HIS G 417 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N HIS G 417 " --> pdb=" O TRP G 461 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL G 463 " --> pdb=" O PRO G 415 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'G' and resid 525 through 529 removed outlier: 6.562A pdb=" N CYS G 574 " --> pdb=" O GLY G 526 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE G 528 " --> pdb=" O SER G 572 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER G 572 " --> pdb=" O PHE G 528 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N TYR G 573 " --> pdb=" O LEU G 562 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LEU G 562 " --> pdb=" O TYR G 573 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL G 575 " --> pdb=" O GLN G 560 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLN G 560 " --> pdb=" O VAL G 575 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'H' and resid 84 through 88 removed outlier: 6.704A pdb=" N ALA H 211 " --> pdb=" O ILE H 156 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR H 158 " --> pdb=" O VAL H 209 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL H 209 " --> pdb=" O THR H 158 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'H' and resid 91 through 121 Processing sheet with id= AT, first strand: chain 'H' and resid 479 through 481 Processing sheet with id= AU, first strand: chain 'H' and resid 204 through 209 removed outlier: 6.813A pdb=" N ALA H 306 " --> pdb=" O THR H 207 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'H' and resid 378 through 387 removed outlier: 5.762A pdb=" N CYS H 462 " --> pdb=" O GLY H 379 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL H 381 " --> pdb=" O TYR H 460 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N TYR H 460 " --> pdb=" O VAL H 381 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLN H 383 " --> pdb=" O ARG H 458 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG H 458 " --> pdb=" O GLN H 383 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N CYS H 385 " --> pdb=" O GLU H 456 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLU H 456 " --> pdb=" O CYS H 385 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLU H 387 " --> pdb=" O LYS H 454 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LYS H 454 " --> pdb=" O GLU H 387 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TRP H 461 " --> pdb=" O HIS H 417 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N HIS H 417 " --> pdb=" O TRP H 461 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL H 463 " --> pdb=" O PRO H 415 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'H' and resid 525 through 530 removed outlier: 6.381A pdb=" N CYS H 574 " --> pdb=" O GLY H 526 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE H 528 " --> pdb=" O SER H 572 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N SER H 572 " --> pdb=" O PHE H 528 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER H 530 " --> pdb=" O GLN H 570 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLN H 570 " --> pdb=" O SER H 530 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N TYR H 573 " --> pdb=" O LEU H 562 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU H 562 " --> pdb=" O TYR H 573 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL H 575 " --> pdb=" O GLN H 560 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLN H 560 " --> pdb=" O VAL H 575 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'I' and resid 84 through 88 removed outlier: 6.662A pdb=" N ALA I 211 " --> pdb=" O ILE I 156 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR I 158 " --> pdb=" O VAL I 209 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL I 209 " --> pdb=" O THR I 158 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'I' and resid 91 through 121 Processing sheet with id= AZ, first strand: chain 'I' and resid 479 through 481 Processing sheet with id= BA, first strand: chain 'I' and resid 204 through 209 removed outlier: 6.778A pdb=" N ALA I 306 " --> pdb=" O THR I 207 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'I' and resid 378 through 387 removed outlier: 5.602A pdb=" N CYS I 462 " --> pdb=" O GLY I 379 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL I 381 " --> pdb=" O TYR I 460 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N TYR I 460 " --> pdb=" O VAL I 381 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLN I 383 " --> pdb=" O ARG I 458 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ARG I 458 " --> pdb=" O GLN I 383 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N CYS I 385 " --> pdb=" O GLU I 456 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU I 456 " --> pdb=" O CYS I 385 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N GLU I 387 " --> pdb=" O LYS I 454 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LYS I 454 " --> pdb=" O GLU I 387 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N TRP I 461 " --> pdb=" O HIS I 417 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N HIS I 417 " --> pdb=" O TRP I 461 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL I 463 " --> pdb=" O PRO I 415 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'I' and resid 525 through 530 removed outlier: 6.279A pdb=" N CYS I 574 " --> pdb=" O GLY I 526 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE I 528 " --> pdb=" O SER I 572 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N SER I 572 " --> pdb=" O PHE I 528 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER I 530 " --> pdb=" O GLN I 570 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLN I 570 " --> pdb=" O SER I 530 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N TYR I 573 " --> pdb=" O LEU I 562 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU I 562 " --> pdb=" O TYR I 573 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL I 575 " --> pdb=" O GLN I 560 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLN I 560 " --> pdb=" O VAL I 575 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'J' and resid 84 through 88 removed outlier: 6.651A pdb=" N ALA J 211 " --> pdb=" O ILE J 156 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR J 158 " --> pdb=" O VAL J 209 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL J 209 " --> pdb=" O THR J 158 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'J' and resid 91 through 121 Processing sheet with id= BF, first strand: chain 'J' and resid 479 through 481 Processing sheet with id= BG, first strand: chain 'J' and resid 204 through 210 removed outlier: 6.743A pdb=" N ALA J 306 " --> pdb=" O THR J 207 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL J 209 " --> pdb=" O ASP J 304 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASP J 304 " --> pdb=" O VAL J 209 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'J' and resid 378 through 387 removed outlier: 5.716A pdb=" N CYS J 462 " --> pdb=" O GLY J 379 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL J 381 " --> pdb=" O TYR J 460 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N TYR J 460 " --> pdb=" O VAL J 381 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN J 383 " --> pdb=" O ARG J 458 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG J 458 " --> pdb=" O GLN J 383 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N CYS J 385 " --> pdb=" O GLU J 456 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU J 456 " --> pdb=" O CYS J 385 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLU J 387 " --> pdb=" O LYS J 454 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LYS J 454 " --> pdb=" O GLU J 387 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TRP J 461 " --> pdb=" O HIS J 417 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N HIS J 417 " --> pdb=" O TRP J 461 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL J 463 " --> pdb=" O PRO J 415 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'J' and resid 525 through 529 removed outlier: 6.349A pdb=" N CYS J 574 " --> pdb=" O GLY J 526 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE J 528 " --> pdb=" O SER J 572 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER J 572 " --> pdb=" O PHE J 528 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TYR J 573 " --> pdb=" O LEU J 562 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LEU J 562 " --> pdb=" O TYR J 573 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL J 575 " --> pdb=" O GLN J 560 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLN J 560 " --> pdb=" O VAL J 575 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'K' and resid 84 through 88 removed outlier: 6.623A pdb=" N ALA K 211 " --> pdb=" O ILE K 156 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR K 158 " --> pdb=" O VAL K 209 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL K 209 " --> pdb=" O THR K 158 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'K' and resid 91 through 121 Processing sheet with id= BL, first strand: chain 'K' and resid 498 through 502 Processing sheet with id= BM, first strand: chain 'K' and resid 204 through 210 removed outlier: 6.881A pdb=" N ALA K 306 " --> pdb=" O THR K 207 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL K 209 " --> pdb=" O ASP K 304 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP K 304 " --> pdb=" O VAL K 209 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'K' and resid 378 through 387 removed outlier: 5.914A pdb=" N CYS K 462 " --> pdb=" O GLY K 379 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL K 381 " --> pdb=" O TYR K 460 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TYR K 460 " --> pdb=" O VAL K 381 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLN K 383 " --> pdb=" O ARG K 458 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ARG K 458 " --> pdb=" O GLN K 383 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N CYS K 385 " --> pdb=" O GLU K 456 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU K 456 " --> pdb=" O CYS K 385 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLU K 387 " --> pdb=" O LYS K 454 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LYS K 454 " --> pdb=" O GLU K 387 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N TRP K 461 " --> pdb=" O HIS K 417 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N HIS K 417 " --> pdb=" O TRP K 461 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL K 463 " --> pdb=" O PRO K 415 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'K' and resid 525 through 529 removed outlier: 6.353A pdb=" N CYS K 574 " --> pdb=" O GLY K 526 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE K 528 " --> pdb=" O SER K 572 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER K 572 " --> pdb=" O PHE K 528 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N TYR K 573 " --> pdb=" O LEU K 562 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU K 562 " --> pdb=" O TYR K 573 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL K 575 " --> pdb=" O GLN K 560 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLN K 560 " --> pdb=" O VAL K 575 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'L' and resid 84 through 87 removed outlier: 6.676A pdb=" N ALA L 211 " --> pdb=" O ILE L 156 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR L 158 " --> pdb=" O VAL L 209 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL L 209 " --> pdb=" O THR L 158 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'L' and resid 91 through 121 Processing sheet with id= BR, first strand: chain 'L' and resid 498 through 502 Processing sheet with id= BS, first strand: chain 'L' and resid 204 through 210 removed outlier: 6.814A pdb=" N ALA L 306 " --> pdb=" O THR L 207 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL L 209 " --> pdb=" O ASP L 304 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP L 304 " --> pdb=" O VAL L 209 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'L' and resid 378 through 387 removed outlier: 5.795A pdb=" N CYS L 462 " --> pdb=" O GLY L 379 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N VAL L 381 " --> pdb=" O TYR L 460 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N TYR L 460 " --> pdb=" O VAL L 381 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN L 383 " --> pdb=" O ARG L 458 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ARG L 458 " --> pdb=" O GLN L 383 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N CYS L 385 " --> pdb=" O GLU L 456 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU L 456 " --> pdb=" O CYS L 385 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N GLU L 387 " --> pdb=" O LYS L 454 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LYS L 454 " --> pdb=" O GLU L 387 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TRP L 461 " --> pdb=" O HIS L 417 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N HIS L 417 " --> pdb=" O TRP L 461 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL L 463 " --> pdb=" O PRO L 415 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'L' and resid 558 through 566 removed outlier: 3.592A pdb=" N HIS L 561 " --> pdb=" O TYR L 573 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL L 571 " --> pdb=" O ALA L 563 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE L 565 " --> pdb=" O CYS L 569 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N CYS L 569 " --> pdb=" O ILE L 565 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'M' and resid 84 through 88 removed outlier: 6.720A pdb=" N ALA M 211 " --> pdb=" O ILE M 156 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR M 158 " --> pdb=" O VAL M 209 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL M 209 " --> pdb=" O THR M 158 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'M' and resid 91 through 121 Processing sheet with id= BX, first strand: chain 'M' and resid 498 through 502 Processing sheet with id= BY, first strand: chain 'M' and resid 204 through 210 removed outlier: 6.761A pdb=" N ALA M 306 " --> pdb=" O THR M 207 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL M 209 " --> pdb=" O ASP M 304 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASP M 304 " --> pdb=" O VAL M 209 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'M' and resid 378 through 387 removed outlier: 6.023A pdb=" N CYS M 462 " --> pdb=" O GLY M 379 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL M 381 " --> pdb=" O TYR M 460 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR M 460 " --> pdb=" O VAL M 381 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLN M 383 " --> pdb=" O ARG M 458 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ARG M 458 " --> pdb=" O GLN M 383 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N CYS M 385 " --> pdb=" O GLU M 456 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLU M 456 " --> pdb=" O CYS M 385 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLU M 387 " --> pdb=" O LYS M 454 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LYS M 454 " --> pdb=" O GLU M 387 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP M 461 " --> pdb=" O HIS M 417 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N HIS M 417 " --> pdb=" O TRP M 461 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL M 463 " --> pdb=" O PRO M 415 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'M' and resid 558 through 566 removed outlier: 3.747A pdb=" N HIS M 561 " --> pdb=" O TYR M 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR M 573 " --> pdb=" O HIS M 561 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL M 571 " --> pdb=" O ALA M 563 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE M 565 " --> pdb=" O CYS M 569 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N CYS M 569 " --> pdb=" O ILE M 565 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'N' and resid 84 through 88 removed outlier: 6.720A pdb=" N ALA N 211 " --> pdb=" O ILE N 156 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR N 158 " --> pdb=" O VAL N 209 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL N 209 " --> pdb=" O THR N 158 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'N' and resid 91 through 121 Processing sheet with id= CD, first strand: chain 'N' and resid 383 through 387 removed outlier: 6.500A pdb=" N TRP N 461 " --> pdb=" O HIS N 417 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N HIS N 417 " --> pdb=" O TRP N 461 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL N 463 " --> pdb=" O PRO N 415 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'N' and resid 498 through 502 Processing sheet with id= CF, first strand: chain 'N' and resid 204 through 209 removed outlier: 6.727A pdb=" N ALA N 306 " --> pdb=" O THR N 207 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'N' and resid 558 through 566 removed outlier: 3.945A pdb=" N HIS N 561 " --> pdb=" O TYR N 573 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR N 573 " --> pdb=" O HIS N 561 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL N 571 " --> pdb=" O ALA N 563 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE N 565 " --> pdb=" O CYS N 569 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N CYS N 569 " --> pdb=" O ILE N 565 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'O' and resid 84 through 88 removed outlier: 6.654A pdb=" N ALA O 211 " --> pdb=" O ILE O 156 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR O 158 " --> pdb=" O VAL O 209 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL O 209 " --> pdb=" O THR O 158 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'O' and resid 91 through 121 Processing sheet with id= CJ, first strand: chain 'O' and resid 499 through 502 Processing sheet with id= CK, first strand: chain 'O' and resid 204 through 210 removed outlier: 6.823A pdb=" N ALA O 306 " --> pdb=" O THR O 207 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL O 209 " --> pdb=" O ASP O 304 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASP O 304 " --> pdb=" O VAL O 209 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain 'O' and resid 378 through 387 removed outlier: 5.661A pdb=" N CYS O 462 " --> pdb=" O GLY O 379 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL O 381 " --> pdb=" O TYR O 460 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR O 460 " --> pdb=" O VAL O 381 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN O 383 " --> pdb=" O ARG O 458 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ARG O 458 " --> pdb=" O GLN O 383 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N CYS O 385 " --> pdb=" O GLU O 456 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU O 456 " --> pdb=" O CYS O 385 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLU O 387 " --> pdb=" O LYS O 454 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LYS O 454 " --> pdb=" O GLU O 387 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N TRP O 461 " --> pdb=" O HIS O 417 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N HIS O 417 " --> pdb=" O TRP O 461 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL O 463 " --> pdb=" O PRO O 415 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'O' and resid 525 through 529 removed outlier: 6.547A pdb=" N CYS O 574 " --> pdb=" O GLY O 526 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N PHE O 528 " --> pdb=" O SER O 572 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N SER O 572 " --> pdb=" O PHE O 528 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N TYR O 573 " --> pdb=" O LEU O 562 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU O 562 " --> pdb=" O TYR O 573 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL O 575 " --> pdb=" O GLN O 560 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLN O 560 " --> pdb=" O VAL O 575 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'P' and resid 84 through 88 removed outlier: 6.733A pdb=" N ALA P 211 " --> pdb=" O ILE P 156 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR P 158 " --> pdb=" O VAL P 209 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL P 209 " --> pdb=" O THR P 158 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'P' and resid 91 through 121 Processing sheet with id= CP, first strand: chain 'P' and resid 479 through 481 Processing sheet with id= CQ, first strand: chain 'P' and resid 204 through 210 removed outlier: 6.802A pdb=" N ALA P 306 " --> pdb=" O THR P 207 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL P 209 " --> pdb=" O ASP P 304 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASP P 304 " --> pdb=" O VAL P 209 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'P' and resid 378 through 387 removed outlier: 5.757A pdb=" N CYS P 462 " --> pdb=" O GLY P 379 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N VAL P 381 " --> pdb=" O TYR P 460 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TYR P 460 " --> pdb=" O VAL P 381 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLN P 383 " --> pdb=" O ARG P 458 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ARG P 458 " --> pdb=" O GLN P 383 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N CYS P 385 " --> pdb=" O GLU P 456 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLU P 456 " --> pdb=" O CYS P 385 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLU P 387 " --> pdb=" O LYS P 454 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LYS P 454 " --> pdb=" O GLU P 387 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TRP P 461 " --> pdb=" O HIS P 417 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N HIS P 417 " --> pdb=" O TRP P 461 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL P 463 " --> pdb=" O PRO P 415 " (cutoff:3.500A) Processing sheet with id= CS, first strand: chain 'P' and resid 525 through 530 removed outlier: 6.370A pdb=" N CYS P 574 " --> pdb=" O GLY P 526 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N PHE P 528 " --> pdb=" O SER P 572 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N SER P 572 " --> pdb=" O PHE P 528 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER P 530 " --> pdb=" O GLN P 570 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLN P 570 " --> pdb=" O SER P 530 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N TYR P 573 " --> pdb=" O LEU P 562 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU P 562 " --> pdb=" O TYR P 573 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL P 575 " --> pdb=" O GLN P 560 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLN P 560 " --> pdb=" O VAL P 575 " (cutoff:3.500A) 2847 hydrogen bonds defined for protein. 8325 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: 23.70 Time building geometry restraints manager: 21.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 20981 1.33 - 1.46: 12946 1.46 - 1.58: 34101 1.58 - 1.70: 4 1.70 - 1.82: 592 Bond restraints: 68624 Sorted by residual: bond pdb=" CB PRO E 500 " pdb=" CG PRO E 500 " ideal model delta sigma weight residual 1.492 1.634 -0.142 5.00e-02 4.00e+02 8.07e+00 bond pdb=" CB PRO M 500 " pdb=" CG PRO M 500 " ideal model delta sigma weight residual 1.492 1.634 -0.142 5.00e-02 4.00e+02 8.02e+00 bond pdb=" CA ILE E 499 " pdb=" C ILE E 499 " ideal model delta sigma weight residual 1.524 1.543 -0.019 8.30e-03 1.45e+04 5.27e+00 bond pdb=" CB PRO H 592 " pdb=" CG PRO H 592 " ideal model delta sigma weight residual 1.506 1.586 -0.080 3.90e-02 6.57e+02 4.22e+00 bond pdb=" CB PRO P 592 " pdb=" CG PRO P 592 " ideal model delta sigma weight residual 1.506 1.586 -0.080 3.90e-02 6.57e+02 4.19e+00 ... (remaining 68619 not shown) Histogram of bond angle deviations from ideal: 98.87 - 105.89: 1703 105.89 - 112.91: 38039 112.91 - 119.93: 21695 119.93 - 126.95: 30981 126.95 - 133.97: 718 Bond angle restraints: 93136 Sorted by residual: angle pdb=" N VAL O 588 " pdb=" CA VAL O 588 " pdb=" C VAL O 588 " ideal model delta sigma weight residual 111.91 103.63 8.28 8.90e-01 1.26e+00 8.65e+01 angle pdb=" CA PRO E 500 " pdb=" N PRO E 500 " pdb=" CD PRO E 500 " ideal model delta sigma weight residual 112.00 100.43 11.57 1.40e+00 5.10e-01 6.83e+01 angle pdb=" CA PRO M 500 " pdb=" N PRO M 500 " pdb=" CD PRO M 500 " ideal model delta sigma weight residual 112.00 100.74 11.26 1.40e+00 5.10e-01 6.47e+01 angle pdb=" CA PRO P 592 " pdb=" N PRO P 592 " pdb=" CD PRO P 592 " ideal model delta sigma weight residual 111.50 103.16 8.34 1.40e+00 5.10e-01 3.55e+01 angle pdb=" CA PRO H 592 " pdb=" N PRO H 592 " pdb=" CD PRO H 592 " ideal model delta sigma weight residual 111.50 103.18 8.32 1.40e+00 5.10e-01 3.53e+01 ... (remaining 93131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.69: 40800 24.69 - 49.38: 1079 49.38 - 74.07: 293 74.07 - 98.76: 22 98.76 - 123.46: 174 Dihedral angle restraints: 42368 sinusoidal: 17760 harmonic: 24608 Sorted by residual: dihedral pdb=" CA MET F 533 " pdb=" C MET F 533 " pdb=" N GLY F 534 " pdb=" CA GLY F 534 " ideal model delta harmonic sigma weight residual 180.00 151.19 28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA MET N 533 " pdb=" C MET N 533 " pdb=" N GLY N 534 " pdb=" CA GLY N 534 " ideal model delta harmonic sigma weight residual 180.00 153.77 26.23 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA LEU G 590 " pdb=" C LEU G 590 " pdb=" N PRO G 591 " pdb=" CA PRO G 591 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 42365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 8336 0.049 - 0.099: 1944 0.099 - 0.148: 500 0.148 - 0.197: 5 0.197 - 0.247: 31 Chirality restraints: 10816 Sorted by residual: chirality pdb=" C1 NAG I 701 " pdb=" ND2 ASN I 269 " pdb=" C2 NAG I 701 " pdb=" O5 NAG I 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 269 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C1 NAG D 701 " pdb=" ND2 ASN D 269 " pdb=" C2 NAG D 701 " pdb=" O5 NAG D 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 10813 not shown) Planarity restraints: 11808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE M 499 " 0.071 5.00e-02 4.00e+02 9.95e-02 1.58e+01 pdb=" N PRO M 500 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO M 500 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO M 500 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 499 " 0.071 5.00e-02 4.00e+02 9.94e-02 1.58e+01 pdb=" N PRO E 500 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO E 500 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO E 500 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 590 " 0.044 5.00e-02 4.00e+02 6.60e-02 6.97e+00 pdb=" N PRO D 591 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 591 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 591 " 0.037 5.00e-02 4.00e+02 ... (remaining 11805 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 728 2.57 - 3.15: 53431 3.15 - 3.74: 100650 3.74 - 4.32: 144760 4.32 - 4.90: 245515 Nonbonded interactions: 545084 Sorted by model distance: nonbonded pdb=" OD1 ASN M 345 " pdb=" OH TYR M 593 " model vdw 1.988 2.440 nonbonded pdb=" O MET A 59 " pdb=" OH TYR B 85 " model vdw 1.999 2.440 nonbonded pdb=" OD1 ASN E 345 " pdb=" OH TYR E 593 " model vdw 2.001 2.440 nonbonded pdb=" O MET J 59 " pdb=" OH TYR K 85 " model vdw 2.005 2.440 nonbonded pdb=" O MET N 59 " pdb=" OH TYR O 85 " model vdw 2.013 2.440 ... (remaining 545079 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 11.530 Check model and map are aligned: 0.740 Set scattering table: 0.500 Process input model: 137.410 Find NCS groups from input model: 3.960 Set up NCS constraints: 0.600 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:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 169.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 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 : 0.008 0.142 68624 Z= 0.493 Angle : 0.739 12.560 93136 Z= 0.392 Chirality : 0.046 0.247 10816 Planarity : 0.004 0.100 11792 Dihedral : 14.734 123.456 26176 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.87 % Favored : 95.96 % Rotamer: Outliers : 0.97 % Allowed : 8.93 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % 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: -0.24 (0.09), residues: 8432 helix: 1.59 (0.15), residues: 1232 sheet: -0.02 (0.09), residues: 3744 loop : -0.85 (0.11), residues: 3456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 104 HIS 0.006 0.001 HIS A 220 PHE 0.020 0.002 PHE L 313 TYR 0.037 0.002 TYR C 593 ARG 0.004 0.001 ARG G 589 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 876 time to evaluate : 5.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.6918 (tttt) cc_final: 0.6678 (ttmm) REVERT: A 176 MET cc_start: 0.6508 (mmt) cc_final: 0.6304 (mtt) REVERT: A 218 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7749 (mt-10) REVERT: A 222 ARG cc_start: 0.7076 (mtt180) cc_final: 0.6424 (mtp180) REVERT: A 344 PHE cc_start: 0.7504 (t80) cc_final: 0.7298 (t80) REVERT: A 401 ASN cc_start: 0.6255 (t0) cc_final: 0.5706 (t0) REVERT: A 599 MET cc_start: 0.3673 (mmt) cc_final: 0.3240 (mmt) REVERT: B 63 MET cc_start: 0.8191 (mmm) cc_final: 0.7638 (mmm) REVERT: B 91 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7596 (mt-10) REVERT: B 104 TRP cc_start: 0.6527 (t60) cc_final: 0.5792 (t-100) REVERT: B 105 MET cc_start: 0.6972 (ttm) cc_final: 0.6481 (ttt) REVERT: B 144 GLN cc_start: 0.7724 (mt0) cc_final: 0.6968 (mt0) REVERT: B 166 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6213 (pm20) REVERT: B 222 ARG cc_start: 0.6952 (mtt180) cc_final: 0.6361 (mpt180) REVERT: B 270 ARG cc_start: 0.6986 (mtp-110) cc_final: 0.6297 (mtp180) REVERT: B 274 ARG cc_start: 0.7515 (ttp-170) cc_final: 0.6409 (ttt-90) REVERT: B 276 GLN cc_start: 0.8509 (tt0) cc_final: 0.8235 (tt0) REVERT: B 524 PRO cc_start: 0.7746 (Cg_exo) cc_final: 0.7533 (Cg_endo) REVERT: B 599 MET cc_start: 0.1332 (mmp) cc_final: 0.0259 (mmp) REVERT: C 95 GLU cc_start: 0.8254 (mp0) cc_final: 0.7968 (mp0) REVERT: C 104 TRP cc_start: 0.6348 (t60) cc_final: 0.5641 (t-100) REVERT: C 144 GLN cc_start: 0.7785 (mt0) cc_final: 0.7438 (tt0) REVERT: C 210 ASP cc_start: 0.8692 (m-30) cc_final: 0.8479 (m-30) REVERT: C 218 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7209 (mm-30) REVERT: C 274 ARG cc_start: 0.7222 (ttp-170) cc_final: 0.6888 (ttm-80) REVERT: C 454 LYS cc_start: 0.8785 (tttt) cc_final: 0.8541 (tttp) REVERT: C 524 PRO cc_start: 0.6663 (Cg_exo) cc_final: 0.6349 (Cg_endo) REVERT: C 599 MET cc_start: 0.3436 (OUTLIER) cc_final: 0.2553 (mmp) REVERT: D 59 MET cc_start: 0.7110 (mmm) cc_final: 0.6710 (mmm) REVERT: D 105 MET cc_start: 0.7413 (ttp) cc_final: 0.6980 (ttt) REVERT: D 136 MET cc_start: 0.6366 (OUTLIER) cc_final: 0.5976 (mpp) REVERT: D 219 ASP cc_start: 0.7913 (t0) cc_final: 0.7585 (t70) REVERT: D 222 ARG cc_start: 0.6940 (mtt180) cc_final: 0.6264 (mtp180) REVERT: D 230 GLN cc_start: 0.7569 (mt0) cc_final: 0.7323 (mt0) REVERT: D 270 ARG cc_start: 0.7317 (mtp-110) cc_final: 0.6889 (mtp85) REVERT: D 274 ARG cc_start: 0.7552 (ttp-170) cc_final: 0.6948 (ttt90) REVERT: D 297 THR cc_start: 0.8378 (t) cc_final: 0.7973 (m) REVERT: D 304 ASP cc_start: 0.8271 (t0) cc_final: 0.8064 (t70) REVERT: D 331 SER cc_start: 0.7941 (t) cc_final: 0.7691 (m) REVERT: D 340 HIS cc_start: 0.8058 (t-90) cc_final: 0.7116 (t70) REVERT: D 488 MET cc_start: 0.5393 (tmm) cc_final: 0.4887 (tpt) REVERT: D 533 MET cc_start: 0.3237 (ptp) cc_final: 0.2852 (ppp) REVERT: E 53 ASN cc_start: 0.8174 (t0) cc_final: 0.7858 (t0) REVERT: E 126 ASN cc_start: 0.6222 (m-40) cc_final: 0.5938 (t0) REVERT: E 166 GLU cc_start: 0.6565 (mt-10) cc_final: 0.5797 (mm-30) REVERT: E 189 MET cc_start: 0.5898 (mtt) cc_final: 0.5580 (ttt) REVERT: E 219 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7522 (m-30) REVERT: E 222 ARG cc_start: 0.7206 (mtp180) cc_final: 0.6209 (mtt90) REVERT: E 230 GLN cc_start: 0.7776 (mt0) cc_final: 0.7523 (mt0) REVERT: E 270 ARG cc_start: 0.7376 (mtp-110) cc_final: 0.6722 (ttm110) REVERT: E 274 ARG cc_start: 0.7334 (ttp-170) cc_final: 0.6907 (ttt90) REVERT: E 332 LYS cc_start: 0.8739 (mttt) cc_final: 0.8289 (mmtm) REVERT: E 340 HIS cc_start: 0.7688 (t-90) cc_final: 0.7436 (t-170) REVERT: E 488 MET cc_start: 0.3410 (tmm) cc_final: 0.2591 (tmt) REVERT: E 599 MET cc_start: 0.2556 (mmp) cc_final: 0.1834 (mmp) REVERT: F 39 LYS cc_start: 0.7759 (mmtp) cc_final: 0.7169 (mmtt) REVERT: F 57 VAL cc_start: 0.7819 (p) cc_final: 0.7537 (m) REVERT: F 105 MET cc_start: 0.7488 (ttm) cc_final: 0.6139 (tmm) REVERT: F 118 GLU cc_start: 0.5953 (mt-10) cc_final: 0.5649 (tt0) REVERT: F 160 LYS cc_start: 0.7889 (mttm) cc_final: 0.7586 (mttt) REVERT: F 189 MET cc_start: 0.5751 (mtt) cc_final: 0.5154 (ttm) REVERT: F 210 ASP cc_start: 0.8416 (m-30) cc_final: 0.8189 (m-30) REVERT: F 218 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7319 (mt-10) REVERT: F 222 ARG cc_start: 0.7228 (mtt180) cc_final: 0.6547 (mpt90) REVERT: F 247 ILE cc_start: 0.4393 (OUTLIER) cc_final: 0.4109 (mp) REVERT: F 253 GLU cc_start: 0.6595 (pt0) cc_final: 0.5897 (pm20) REVERT: F 270 ARG cc_start: 0.7363 (mtp-110) cc_final: 0.6752 (ttm170) REVERT: F 274 ARG cc_start: 0.7468 (ttp-170) cc_final: 0.6960 (tmm160) REVERT: F 301 VAL cc_start: 0.8442 (t) cc_final: 0.8223 (m) REVERT: F 340 HIS cc_start: 0.8246 (t-90) cc_final: 0.7767 (t70) REVERT: F 488 MET cc_start: 0.3010 (tmm) cc_final: 0.2671 (ppp) REVERT: F 599 MET cc_start: 0.3478 (mmp) cc_final: 0.1901 (mmp) REVERT: G 95 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7937 (mt-10) REVERT: G 166 GLU cc_start: 0.6620 (mt-10) cc_final: 0.6234 (mp0) REVERT: G 218 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7100 (mm-30) REVERT: G 222 ARG cc_start: 0.6970 (mtt180) cc_final: 0.6353 (mpt90) REVERT: G 270 ARG cc_start: 0.6960 (mtp-110) cc_final: 0.6657 (mtp180) REVERT: G 274 ARG cc_start: 0.7557 (ttp-170) cc_final: 0.6715 (ttt-90) REVERT: G 447 GLU cc_start: 0.6198 (pt0) cc_final: 0.5902 (pm20) REVERT: G 488 MET cc_start: 0.5202 (tmt) cc_final: 0.4795 (tmm) REVERT: G 586 LEU cc_start: 0.7430 (tm) cc_final: 0.7136 (pp) REVERT: G 599 MET cc_start: 0.2570 (mmt) cc_final: 0.2022 (mpt) REVERT: H 95 GLU cc_start: 0.8097 (mp0) cc_final: 0.7677 (mt-10) REVERT: H 96 MET cc_start: 0.7445 (mtt) cc_final: 0.7142 (mtm) REVERT: H 104 TRP cc_start: 0.6808 (t60) cc_final: 0.6499 (t60) REVERT: H 105 MET cc_start: 0.7462 (ttm) cc_final: 0.7192 (ttm) REVERT: H 218 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7425 (mt-10) REVERT: H 253 GLU cc_start: 0.5975 (pt0) cc_final: 0.5773 (tm-30) REVERT: H 274 ARG cc_start: 0.7411 (ttp-170) cc_final: 0.7009 (ttt90) REVERT: H 339 ARG cc_start: 0.8013 (mtp85) cc_final: 0.7752 (ttm-80) REVERT: H 340 HIS cc_start: 0.7601 (t-90) cc_final: 0.7189 (t-170) REVERT: H 344 PHE cc_start: 0.7392 (t80) cc_final: 0.6992 (t80) REVERT: H 475 LEU cc_start: 0.6511 (mt) cc_final: 0.6162 (mp) REVERT: H 592 PRO cc_start: 0.6758 (Cg_endo) cc_final: 0.6408 (Cg_exo) REVERT: I 55 ARG cc_start: 0.7515 (mtm110) cc_final: 0.6970 (mtp180) REVERT: I 173 LYS cc_start: 0.6907 (tttt) cc_final: 0.6668 (ttmm) REVERT: I 188 LYS cc_start: 0.8361 (mmmt) cc_final: 0.8078 (mmmt) REVERT: I 218 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7690 (mt-10) REVERT: I 222 ARG cc_start: 0.6999 (mtt180) cc_final: 0.6372 (mtp180) REVERT: I 301 VAL cc_start: 0.8127 (t) cc_final: 0.7893 (m) REVERT: I 344 PHE cc_start: 0.7551 (t80) cc_final: 0.7172 (t80) REVERT: I 401 ASN cc_start: 0.6168 (t0) cc_final: 0.5608 (t0) REVERT: I 524 PRO cc_start: 0.7870 (Cg_exo) cc_final: 0.7657 (Cg_endo) REVERT: J 63 MET cc_start: 0.8258 (mmm) cc_final: 0.7799 (mmm) REVERT: J 91 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7682 (mt-10) REVERT: J 144 GLN cc_start: 0.7638 (mt0) cc_final: 0.6903 (mt0) REVERT: J 166 GLU cc_start: 0.6809 (mt-10) cc_final: 0.6228 (pm20) REVERT: J 195 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6927 (tt0) REVERT: J 270 ARG cc_start: 0.6869 (mtp-110) cc_final: 0.6344 (mtp180) REVERT: J 274 ARG cc_start: 0.7453 (ttp-170) cc_final: 0.6382 (ttt-90) REVERT: J 276 GLN cc_start: 0.8505 (tt0) cc_final: 0.8244 (tt0) REVERT: J 461 TRP cc_start: 0.6961 (p-90) cc_final: 0.6434 (p-90) REVERT: J 524 PRO cc_start: 0.7530 (Cg_exo) cc_final: 0.7316 (Cg_endo) REVERT: J 589 ARG cc_start: 0.2578 (OUTLIER) cc_final: 0.0612 (ttm110) REVERT: J 594 THR cc_start: 0.4826 (OUTLIER) cc_final: 0.4528 (t) REVERT: J 599 MET cc_start: 0.0971 (mpt) cc_final: 0.0729 (mmt) REVERT: K 77 GLN cc_start: 0.7617 (mt0) cc_final: 0.6891 (mm-40) REVERT: K 95 GLU cc_start: 0.8164 (mp0) cc_final: 0.7859 (mp0) REVERT: K 104 TRP cc_start: 0.6401 (t60) cc_final: 0.5635 (t-100) REVERT: K 144 GLN cc_start: 0.7756 (mt0) cc_final: 0.7374 (tt0) REVERT: K 189 MET cc_start: 0.4910 (tpt) cc_final: 0.4567 (tpp) REVERT: K 210 ASP cc_start: 0.8791 (m-30) cc_final: 0.8589 (m-30) REVERT: K 218 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7414 (mm-30) REVERT: K 222 ARG cc_start: 0.6830 (mtt180) cc_final: 0.6279 (mmm160) REVERT: K 270 ARG cc_start: 0.7411 (mtt-85) cc_final: 0.7166 (mmm160) REVERT: K 274 ARG cc_start: 0.7205 (ttp-170) cc_final: 0.6940 (ttm-80) REVERT: K 454 LYS cc_start: 0.8721 (tttt) cc_final: 0.8495 (tttp) REVERT: K 586 LEU cc_start: 0.6707 (mt) cc_final: 0.6485 (mm) REVERT: K 599 MET cc_start: 0.4368 (mmt) cc_final: 0.3603 (mmp) REVERT: L 59 MET cc_start: 0.7243 (mmm) cc_final: 0.6925 (mmm) REVERT: L 96 MET cc_start: 0.7404 (mtt) cc_final: 0.6914 (mtm) REVERT: L 104 TRP cc_start: 0.6629 (t60) cc_final: 0.5769 (t-100) REVERT: L 105 MET cc_start: 0.7274 (ttp) cc_final: 0.6887 (ttt) REVERT: L 136 MET cc_start: 0.6733 (ptt) cc_final: 0.6419 (mpp) REVERT: L 144 GLN cc_start: 0.7596 (mt0) cc_final: 0.7287 (tt0) REVERT: L 219 ASP cc_start: 0.7735 (t0) cc_final: 0.7424 (t70) REVERT: L 222 ARG cc_start: 0.6916 (mtt180) cc_final: 0.6265 (mtp180) REVERT: L 230 GLN cc_start: 0.7496 (mt0) cc_final: 0.7199 (mt0) REVERT: L 270 ARG cc_start: 0.7265 (mtp-110) cc_final: 0.6780 (mtp85) REVERT: L 274 ARG cc_start: 0.7469 (ttp-170) cc_final: 0.6832 (ttt90) REVERT: L 297 THR cc_start: 0.8200 (t) cc_final: 0.7828 (m) REVERT: L 304 ASP cc_start: 0.8318 (t0) cc_final: 0.8039 (t70) REVERT: L 331 SER cc_start: 0.7886 (t) cc_final: 0.7630 (m) REVERT: L 340 HIS cc_start: 0.7917 (t-90) cc_final: 0.7054 (t70) REVERT: L 488 MET cc_start: 0.5381 (tmm) cc_final: 0.4863 (tpt) REVERT: M 53 ASN cc_start: 0.8325 (t0) cc_final: 0.7968 (t0) REVERT: M 99 GLU cc_start: 0.8057 (tt0) cc_final: 0.7831 (tt0) REVERT: M 136 MET cc_start: 0.7251 (mtp) cc_final: 0.6735 (mtm) REVERT: M 166 GLU cc_start: 0.6515 (mt-10) cc_final: 0.6259 (pt0) REVERT: M 173 LYS cc_start: 0.6726 (tttt) cc_final: 0.6525 (mtmm) REVERT: M 188 LYS cc_start: 0.8702 (mppt) cc_final: 0.8411 (mppt) REVERT: M 189 MET cc_start: 0.6036 (mtt) cc_final: 0.5535 (ttt) REVERT: M 222 ARG cc_start: 0.7259 (mtt180) cc_final: 0.6607 (mtt90) REVERT: M 230 GLN cc_start: 0.7995 (mt0) cc_final: 0.7711 (mt0) REVERT: M 270 ARG cc_start: 0.7429 (mtp-110) cc_final: 0.6790 (ttm110) REVERT: M 274 ARG cc_start: 0.7451 (ttp-170) cc_final: 0.7140 (ttt90) REVERT: M 332 LYS cc_start: 0.8778 (mttt) cc_final: 0.8362 (mmtm) REVERT: M 488 MET cc_start: 0.3562 (tmm) cc_final: 0.2700 (tmt) REVERT: M 599 MET cc_start: 0.1758 (mmp) cc_final: 0.1114 (mmp) REVERT: N 39 LYS cc_start: 0.7883 (mmtp) cc_final: 0.7535 (mmtt) REVERT: N 57 VAL cc_start: 0.7863 (p) cc_final: 0.7638 (m) REVERT: N 105 MET cc_start: 0.7670 (ttm) cc_final: 0.6295 (tmm) REVERT: N 153 ARG cc_start: 0.8279 (ttt-90) cc_final: 0.8063 (ttt90) REVERT: N 160 LYS cc_start: 0.7923 (mttm) cc_final: 0.7483 (mttt) REVERT: N 189 MET cc_start: 0.5519 (mtt) cc_final: 0.5153 (ttm) REVERT: N 210 ASP cc_start: 0.8487 (m-30) cc_final: 0.8214 (m-30) REVERT: N 218 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7555 (mt-10) REVERT: N 253 GLU cc_start: 0.6648 (pt0) cc_final: 0.5929 (pm20) REVERT: N 274 ARG cc_start: 0.7545 (ttp-170) cc_final: 0.7010 (tmm160) REVERT: N 301 VAL cc_start: 0.8461 (t) cc_final: 0.8232 (m) REVERT: N 340 HIS cc_start: 0.8103 (t-90) cc_final: 0.7512 (t70) REVERT: N 488 MET cc_start: 0.2963 (tmm) cc_final: 0.0999 (ptp) REVERT: N 599 MET cc_start: 0.3604 (mmp) cc_final: 0.3362 (mmt) REVERT: O 33 ILE cc_start: 0.8106 (mt) cc_final: 0.7741 (mm) REVERT: O 95 GLU cc_start: 0.8216 (mt-10) cc_final: 0.8010 (mt-10) REVERT: O 164 THR cc_start: 0.8534 (p) cc_final: 0.8241 (p) REVERT: O 166 GLU cc_start: 0.6811 (mt-10) cc_final: 0.6367 (mp0) REVERT: O 218 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7056 (mm-30) REVERT: O 222 ARG cc_start: 0.7034 (mtt180) cc_final: 0.6381 (mpt90) REVERT: O 270 ARG cc_start: 0.6920 (mtp-110) cc_final: 0.6598 (mtp180) REVERT: O 274 ARG cc_start: 0.7412 (ttp-170) cc_final: 0.6716 (ttt90) REVERT: O 447 GLU cc_start: 0.6077 (pt0) cc_final: 0.5787 (pm20) REVERT: O 488 MET cc_start: 0.5009 (tmt) cc_final: 0.4680 (tmm) REVERT: O 533 MET cc_start: 0.3075 (mtp) cc_final: 0.2556 (ppp) REVERT: P 57 VAL cc_start: 0.8081 (p) cc_final: 0.7859 (m) REVERT: P 96 MET cc_start: 0.7410 (mtt) cc_final: 0.7179 (mtm) REVERT: P 105 MET cc_start: 0.7542 (ttm) cc_final: 0.7312 (ttm) REVERT: P 130 SER cc_start: 0.6651 (m) cc_final: 0.6313 (t) REVERT: P 187 THR cc_start: 0.8644 (p) cc_final: 0.8370 (t) REVERT: P 218 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7469 (mt-10) REVERT: P 253 GLU cc_start: 0.6068 (pt0) cc_final: 0.5857 (tm-30) REVERT: P 270 ARG cc_start: 0.7315 (mtp-110) cc_final: 0.7064 (mtp180) REVERT: P 274 ARG cc_start: 0.7475 (ttp-170) cc_final: 0.7101 (ttt90) REVERT: P 340 HIS cc_start: 0.7523 (t-90) cc_final: 0.7106 (t-170) REVERT: P 344 PHE cc_start: 0.7430 (t80) cc_final: 0.7066 (t80) REVERT: P 447 GLU cc_start: 0.6457 (pt0) cc_final: 0.6100 (pm20) REVERT: P 475 LEU cc_start: 0.6577 (mt) cc_final: 0.6208 (mp) outliers start: 73 outliers final: 41 residues processed: 937 average time/residue: 1.3571 time to fit residues: 1685.2951 Evaluate side-chains 616 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 569 time to evaluate : 5.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 599 MET Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 515 TYR Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 310 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 242 ILE Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 310 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 297 THR Chi-restraints excluded: chain J residue 589 ARG Chi-restraints excluded: chain J residue 594 THR Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain L residue 247 ILE Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 247 ILE Chi-restraints excluded: chain N residue 430 LEU Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain N residue 586 LEU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain P residue 247 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 716 optimal weight: 0.9980 chunk 642 optimal weight: 1.9990 chunk 356 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 433 optimal weight: 2.9990 chunk 343 optimal weight: 0.9980 chunk 664 optimal weight: 0.8980 chunk 257 optimal weight: 20.0000 chunk 404 optimal weight: 30.0000 chunk 494 optimal weight: 0.9980 chunk 770 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 234 ASN A 259 GLN A 276 GLN A 467 GLN A 490 ASN B 32 GLN B 311 HIS B 467 GLN B 561 HIS C 181 GLN C 276 GLN C 311 HIS C 417 HIS C 467 GLN D 181 GLN D 276 GLN D 311 HIS D 417 HIS D 467 GLN D 570 GLN E 32 GLN E 234 ASN E 276 GLN E 467 GLN E 570 GLN F 234 ASN F 259 GLN F 272 ASN F 276 GLN F 311 HIS F 340 HIS F 383 GLN ** F 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 467 GLN F 570 GLN G 234 ASN G 276 GLN G 467 GLN G 570 GLN H 181 GLN H 276 GLN H 311 HIS ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 467 GLN I 276 GLN I 467 GLN I 490 ASN J 32 GLN J 89 GLN J 181 GLN J 311 HIS J 467 GLN K 276 GLN K 311 HIS K 417 HIS K 467 GLN K 570 GLN L 89 GLN L 181 GLN L 276 GLN L 311 HIS L 417 HIS L 467 GLN L 570 GLN M 32 GLN M 234 ASN M 276 GLN M 340 HIS M 467 GLN M 570 GLN N 234 ASN N 272 ASN N 276 GLN ** N 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 467 GLN N 570 GLN O 234 ASN O 276 GLN O 467 GLN O 570 GLN P 77 GLN P 276 GLN ** P 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 467 GLN Total number of N/Q/H flips: 81 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 68624 Z= 0.198 Angle : 0.598 10.453 93136 Z= 0.286 Chirality : 0.045 0.257 10816 Planarity : 0.004 0.062 11792 Dihedral : 11.687 98.958 10529 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.63 % Favored : 97.19 % Rotamer: Outliers : 2.84 % Allowed : 10.51 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.09), residues: 8432 helix: 1.45 (0.15), residues: 1280 sheet: 0.12 (0.09), residues: 3680 loop : -0.87 (0.11), residues: 3472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 292 HIS 0.004 0.001 HIS M 340 PHE 0.034 0.001 PHE K 528 TYR 0.022 0.001 TYR C 593 ARG 0.007 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 647 time to evaluate : 5.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8163 (m-30) cc_final: 0.7948 (m-30) REVERT: A 75 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7428 (p0) REVERT: A 173 LYS cc_start: 0.6882 (tttt) cc_final: 0.6611 (ttmm) REVERT: A 196 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7530 (mm) REVERT: A 218 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7744 (mt-10) REVERT: A 222 ARG cc_start: 0.7042 (mtt180) cc_final: 0.6474 (mtp180) REVERT: A 344 PHE cc_start: 0.7372 (t80) cc_final: 0.7135 (t80) REVERT: A 401 ASN cc_start: 0.6493 (t0) cc_final: 0.5885 (t0) REVERT: A 488 MET cc_start: 0.7520 (tmt) cc_final: 0.7242 (tmt) REVERT: A 599 MET cc_start: 0.3304 (mmt) cc_final: 0.3041 (mmt) REVERT: B 63 MET cc_start: 0.8196 (mmm) cc_final: 0.7392 (mmm) REVERT: B 91 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7663 (mt-10) REVERT: B 104 TRP cc_start: 0.6539 (t60) cc_final: 0.5809 (t-100) REVERT: B 105 MET cc_start: 0.6983 (ttm) cc_final: 0.6512 (ttt) REVERT: B 144 GLN cc_start: 0.7681 (mt0) cc_final: 0.7021 (mt0) REVERT: B 166 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6204 (pm20) REVERT: B 222 ARG cc_start: 0.6939 (mtt180) cc_final: 0.6341 (mpt90) REVERT: B 270 ARG cc_start: 0.6939 (mtp-110) cc_final: 0.6250 (mtp180) REVERT: B 274 ARG cc_start: 0.7557 (ttp-170) cc_final: 0.6466 (ttt-90) REVERT: B 276 GLN cc_start: 0.8422 (tt0) cc_final: 0.8193 (tt0) REVERT: B 524 PRO cc_start: 0.7640 (Cg_exo) cc_final: 0.7408 (Cg_endo) REVERT: B 599 MET cc_start: 0.1380 (mmp) cc_final: 0.0688 (mmp) REVERT: C 95 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: C 104 TRP cc_start: 0.6235 (t60) cc_final: 0.5620 (t-100) REVERT: C 136 MET cc_start: 0.7145 (mtt) cc_final: 0.6703 (mtp) REVERT: C 144 GLN cc_start: 0.7701 (mt0) cc_final: 0.7362 (tt0) REVERT: C 210 ASP cc_start: 0.8854 (m-30) cc_final: 0.8621 (m-30) REVERT: C 218 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7188 (mm-30) REVERT: C 222 ARG cc_start: 0.6780 (mtt180) cc_final: 0.6331 (mmm160) REVERT: C 274 ARG cc_start: 0.7269 (ttp-170) cc_final: 0.6861 (ttm-80) REVERT: C 454 LYS cc_start: 0.8789 (tttt) cc_final: 0.8562 (tttp) REVERT: C 524 PRO cc_start: 0.6837 (Cg_exo) cc_final: 0.6362 (Cg_endo) REVERT: C 599 MET cc_start: 0.3003 (mmt) cc_final: 0.2554 (mmp) REVERT: D 59 MET cc_start: 0.7277 (mmm) cc_final: 0.6868 (mmm) REVERT: D 63 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.5803 (mpt) REVERT: D 104 TRP cc_start: 0.6433 (t60) cc_final: 0.5913 (t-100) REVERT: D 105 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.6958 (ttt) REVERT: D 181 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.7126 (tp40) REVERT: D 222 ARG cc_start: 0.6989 (mtt180) cc_final: 0.6334 (mtp180) REVERT: D 270 ARG cc_start: 0.7217 (mtp-110) cc_final: 0.6823 (mtp180) REVERT: D 274 ARG cc_start: 0.7461 (ttp-170) cc_final: 0.6952 (ttt90) REVERT: D 297 THR cc_start: 0.8238 (t) cc_final: 0.7859 (m) REVERT: D 331 SER cc_start: 0.8008 (t) cc_final: 0.7653 (m) REVERT: D 332 LYS cc_start: 0.8734 (mmtm) cc_final: 0.8486 (mmtm) REVERT: D 417 HIS cc_start: 0.7912 (t-90) cc_final: 0.7577 (t70) REVERT: D 488 MET cc_start: 0.5151 (tmm) cc_final: 0.4660 (tpt) REVERT: D 533 MET cc_start: 0.4180 (ptp) cc_final: 0.3680 (ppp) REVERT: D 589 ARG cc_start: 0.0509 (OUTLIER) cc_final: 0.0010 (tpm170) REVERT: D 599 MET cc_start: 0.2319 (OUTLIER) cc_final: 0.0501 (mmt) REVERT: E 53 ASN cc_start: 0.8262 (t0) cc_final: 0.7576 (t0) REVERT: E 136 MET cc_start: 0.7273 (mtp) cc_final: 0.6848 (mtm) REVERT: E 166 GLU cc_start: 0.6596 (mt-10) cc_final: 0.5889 (mm-30) REVERT: E 189 MET cc_start: 0.5740 (mtt) cc_final: 0.5298 (ttm) REVERT: E 203 THR cc_start: 0.8969 (m) cc_final: 0.8333 (p) REVERT: E 222 ARG cc_start: 0.7223 (mtp180) cc_final: 0.6227 (mtm180) REVERT: E 270 ARG cc_start: 0.7242 (mtp-110) cc_final: 0.6589 (ttm110) REVERT: E 274 ARG cc_start: 0.7338 (ttp-170) cc_final: 0.6997 (ttt90) REVERT: E 332 LYS cc_start: 0.8695 (mttt) cc_final: 0.8258 (mmtm) REVERT: E 340 HIS cc_start: 0.7608 (t-90) cc_final: 0.7392 (t-170) REVERT: E 488 MET cc_start: 0.3352 (tmm) cc_final: 0.2630 (tmt) REVERT: E 599 MET cc_start: 0.2447 (mmp) cc_final: 0.1775 (mmp) REVERT: F 39 LYS cc_start: 0.7857 (mmtp) cc_final: 0.7480 (mmtt) REVERT: F 57 VAL cc_start: 0.7815 (p) cc_final: 0.7605 (m) REVERT: F 105 MET cc_start: 0.7480 (ttm) cc_final: 0.6169 (tmm) REVERT: F 160 LYS cc_start: 0.7945 (mttm) cc_final: 0.7523 (mttt) REVERT: F 189 MET cc_start: 0.5751 (OUTLIER) cc_final: 0.5419 (ttm) REVERT: F 218 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7434 (mt-10) REVERT: F 222 ARG cc_start: 0.7189 (mtt180) cc_final: 0.6530 (mpt90) REVERT: F 247 ILE cc_start: 0.4457 (OUTLIER) cc_final: 0.4173 (mp) REVERT: F 253 GLU cc_start: 0.6520 (pt0) cc_final: 0.5825 (pm20) REVERT: F 266 TYR cc_start: 0.7296 (t80) cc_final: 0.6495 (m-80) REVERT: F 270 ARG cc_start: 0.7288 (mtp-110) cc_final: 0.6794 (ttm170) REVERT: F 274 ARG cc_start: 0.7487 (ttp-170) cc_final: 0.6928 (tmm160) REVERT: F 340 HIS cc_start: 0.8293 (t70) cc_final: 0.7840 (t70) REVERT: F 599 MET cc_start: 0.3334 (mmp) cc_final: 0.1971 (mmp) REVERT: G 95 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7385 (mt-10) REVERT: G 188 LYS cc_start: 0.8118 (mttt) cc_final: 0.7900 (ptpt) REVERT: G 218 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7383 (mm-30) REVERT: G 222 ARG cc_start: 0.7015 (mtt180) cc_final: 0.6447 (mpt90) REVERT: G 270 ARG cc_start: 0.6999 (mtp-110) cc_final: 0.6717 (mtp180) REVERT: G 447 GLU cc_start: 0.6181 (pt0) cc_final: 0.5965 (pm20) REVERT: G 488 MET cc_start: 0.5077 (tmt) cc_final: 0.4633 (tmm) REVERT: G 586 LEU cc_start: 0.7600 (tm) cc_final: 0.7356 (pp) REVERT: G 599 MET cc_start: 0.2036 (OUTLIER) cc_final: 0.1790 (mpt) REVERT: H 95 GLU cc_start: 0.8106 (mp0) cc_final: 0.7661 (mt-10) REVERT: H 96 MET cc_start: 0.7342 (mtt) cc_final: 0.7046 (mtm) REVERT: H 130 SER cc_start: 0.6600 (m) cc_final: 0.6033 (p) REVERT: H 218 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7438 (mt-10) REVERT: H 270 ARG cc_start: 0.7006 (mtt180) cc_final: 0.6566 (mmm160) REVERT: H 274 ARG cc_start: 0.7415 (ttp-170) cc_final: 0.7198 (ttm170) REVERT: H 339 ARG cc_start: 0.7989 (mtp85) cc_final: 0.7777 (mtt90) REVERT: H 340 HIS cc_start: 0.7492 (t-90) cc_final: 0.6956 (t-170) REVERT: H 344 PHE cc_start: 0.7344 (t80) cc_final: 0.6942 (t80) REVERT: H 475 LEU cc_start: 0.6459 (mt) cc_final: 0.6148 (mp) REVERT: H 521 PHE cc_start: 0.5903 (OUTLIER) cc_final: 0.5554 (t80) REVERT: H 592 PRO cc_start: 0.6885 (Cg_endo) cc_final: 0.6647 (Cg_exo) REVERT: I 55 ARG cc_start: 0.7436 (mtm110) cc_final: 0.6950 (mtp180) REVERT: I 196 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7489 (mm) REVERT: I 218 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7672 (mt-10) REVERT: I 222 ARG cc_start: 0.7008 (mtt180) cc_final: 0.6317 (mpt-90) REVERT: I 301 VAL cc_start: 0.8084 (t) cc_final: 0.7882 (m) REVERT: I 344 PHE cc_start: 0.7517 (t80) cc_final: 0.7183 (OUTLIER) REVERT: I 401 ASN cc_start: 0.6378 (t0) cc_final: 0.5758 (t0) REVERT: I 425 GLU cc_start: 0.7135 (tt0) cc_final: 0.6935 (tm-30) REVERT: J 91 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7748 (mt-10) REVERT: J 144 GLN cc_start: 0.7612 (mt0) cc_final: 0.6908 (tp40) REVERT: J 166 GLU cc_start: 0.6758 (mt-10) cc_final: 0.6188 (pm20) REVERT: J 195 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6930 (tt0) REVERT: J 270 ARG cc_start: 0.6872 (mtp-110) cc_final: 0.6329 (mtp180) REVERT: J 274 ARG cc_start: 0.7470 (ttp-170) cc_final: 0.6412 (ttt-90) REVERT: J 276 GLN cc_start: 0.8424 (tt0) cc_final: 0.8205 (tt0) REVERT: J 524 PRO cc_start: 0.7314 (Cg_exo) cc_final: 0.7095 (Cg_endo) REVERT: J 599 MET cc_start: 0.0924 (OUTLIER) cc_final: 0.0528 (mmt) REVERT: K 77 GLN cc_start: 0.7704 (mt0) cc_final: 0.6983 (mm-40) REVERT: K 95 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: K 104 TRP cc_start: 0.6233 (t60) cc_final: 0.5561 (t-100) REVERT: K 144 GLN cc_start: 0.7759 (mt0) cc_final: 0.7449 (tt0) REVERT: K 189 MET cc_start: 0.4994 (tpt) cc_final: 0.4577 (tpp) REVERT: K 218 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7452 (mm-30) REVERT: K 222 ARG cc_start: 0.6853 (mtt180) cc_final: 0.6282 (mmt-90) REVERT: K 270 ARG cc_start: 0.7340 (mtt-85) cc_final: 0.7094 (mmm160) REVERT: K 274 ARG cc_start: 0.7203 (ttp-170) cc_final: 0.6872 (ttm-80) REVERT: K 454 LYS cc_start: 0.8702 (tttt) cc_final: 0.8496 (tttp) REVERT: K 488 MET cc_start: 0.7097 (tmm) cc_final: 0.6885 (tmm) REVERT: K 586 LEU cc_start: 0.6829 (mt) cc_final: 0.6580 (mm) REVERT: K 599 MET cc_start: 0.4160 (mmt) cc_final: 0.3469 (mmp) REVERT: L 59 MET cc_start: 0.7190 (mmm) cc_final: 0.6966 (mmm) REVERT: L 63 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.7160 (mpm) REVERT: L 75 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7659 (p0) REVERT: L 89 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7313 (mt0) REVERT: L 96 MET cc_start: 0.7110 (mtm) cc_final: 0.6598 (mtm) REVERT: L 104 TRP cc_start: 0.6454 (t60) cc_final: 0.5782 (t-100) REVERT: L 105 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6783 (ttt) REVERT: L 136 MET cc_start: 0.6612 (OUTLIER) cc_final: 0.6362 (mpp) REVERT: L 144 GLN cc_start: 0.7597 (mt0) cc_final: 0.7295 (tt0) REVERT: L 219 ASP cc_start: 0.7790 (t0) cc_final: 0.7556 (t70) REVERT: L 222 ARG cc_start: 0.6869 (mtt180) cc_final: 0.6242 (mtp180) REVERT: L 270 ARG cc_start: 0.7251 (mtp-110) cc_final: 0.6789 (mtp180) REVERT: L 274 ARG cc_start: 0.7350 (ttp-170) cc_final: 0.6822 (ttt90) REVERT: L 297 THR cc_start: 0.8167 (t) cc_final: 0.7770 (m) REVERT: L 304 ASP cc_start: 0.8281 (t0) cc_final: 0.7991 (t0) REVERT: L 331 SER cc_start: 0.8044 (t) cc_final: 0.7684 (m) REVERT: M 53 ASN cc_start: 0.8404 (t0) cc_final: 0.8009 (t0) REVERT: M 99 GLU cc_start: 0.8115 (tt0) cc_final: 0.7850 (tt0) REVERT: M 136 MET cc_start: 0.7238 (mtp) cc_final: 0.6730 (mtm) REVERT: M 189 MET cc_start: 0.5988 (OUTLIER) cc_final: 0.5504 (ttt) REVERT: M 203 THR cc_start: 0.9030 (m) cc_final: 0.8444 (p) REVERT: M 222 ARG cc_start: 0.7309 (mtt180) cc_final: 0.6731 (mtp180) REVERT: M 270 ARG cc_start: 0.7358 (mtp-110) cc_final: 0.6811 (ttm110) REVERT: M 274 ARG cc_start: 0.7459 (ttp-170) cc_final: 0.7152 (ttt90) REVERT: M 332 LYS cc_start: 0.8738 (mttt) cc_final: 0.8319 (mmtm) REVERT: M 488 MET cc_start: 0.3422 (tmm) cc_final: 0.2539 (tmt) REVERT: M 599 MET cc_start: 0.1720 (mmp) cc_final: 0.1219 (mmp) REVERT: N 39 LYS cc_start: 0.7986 (mmtp) cc_final: 0.7669 (mmtt) REVERT: N 57 VAL cc_start: 0.7810 (p) cc_final: 0.7608 (m) REVERT: N 105 MET cc_start: 0.7629 (ttm) cc_final: 0.6259 (tmm) REVERT: N 160 LYS cc_start: 0.7868 (mttm) cc_final: 0.7651 (mttt) REVERT: N 195 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7846 (mm-30) REVERT: N 218 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7577 (mt-10) REVERT: N 253 GLU cc_start: 0.6548 (pt0) cc_final: 0.5891 (pm20) REVERT: N 266 TYR cc_start: 0.7255 (t80) cc_final: 0.6453 (m-80) REVERT: N 274 ARG cc_start: 0.7509 (ttp-170) cc_final: 0.7017 (tmm160) REVERT: N 340 HIS cc_start: 0.8079 (t-90) cc_final: 0.7395 (t70) REVERT: N 344 PHE cc_start: 0.7766 (t80) cc_final: 0.7442 (t80) REVERT: N 345 ASN cc_start: 0.8181 (OUTLIER) cc_final: 0.7967 (m110) REVERT: N 599 MET cc_start: 0.3251 (mmp) cc_final: 0.3041 (mmp) REVERT: O 95 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7438 (mt-10) REVERT: O 166 GLU cc_start: 0.6833 (mt-10) cc_final: 0.6315 (mp0) REVERT: O 188 LYS cc_start: 0.8249 (mttt) cc_final: 0.8007 (ptpt) REVERT: O 218 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7021 (mm-30) REVERT: O 222 ARG cc_start: 0.7007 (mtt180) cc_final: 0.6452 (mpt90) REVERT: O 270 ARG cc_start: 0.6921 (mtp-110) cc_final: 0.6578 (mtp180) REVERT: O 274 ARG cc_start: 0.7368 (ttp-170) cc_final: 0.6680 (ttt90) REVERT: O 332 LYS cc_start: 0.9074 (pptt) cc_final: 0.8808 (pttm) REVERT: O 417 HIS cc_start: 0.6500 (t-90) cc_final: 0.4918 (t-90) REVERT: O 488 MET cc_start: 0.4967 (tmt) cc_final: 0.4610 (tmm) REVERT: O 533 MET cc_start: 0.4139 (mtp) cc_final: 0.3462 (pmm) REVERT: O 599 MET cc_start: 0.2028 (mmt) cc_final: 0.1554 (mpt) REVERT: P 130 SER cc_start: 0.6774 (m) cc_final: 0.6344 (t) REVERT: P 218 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7505 (mt-10) REVERT: P 270 ARG cc_start: 0.7246 (mtp-110) cc_final: 0.6914 (mtm180) REVERT: P 339 ARG cc_start: 0.8264 (mtt90) cc_final: 0.7685 (ttm-80) REVERT: P 344 PHE cc_start: 0.7414 (t80) cc_final: 0.7007 (t80) REVERT: P 475 LEU cc_start: 0.6613 (mt) cc_final: 0.6312 (mp) outliers start: 213 outliers final: 84 residues processed: 815 average time/residue: 1.2939 time to fit residues: 1410.3584 Evaluate side-chains 654 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 548 time to evaluate : 5.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain D residue 515 TYR Chi-restraints excluded: chain D residue 589 ARG Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 189 MET Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 310 LEU Chi-restraints excluded: chain G residue 599 MET Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 521 PHE Chi-restraints excluded: chain H residue 584 SER Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain I residue 503 LEU Chi-restraints excluded: chain I residue 564 VAL Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 187 THR Chi-restraints excluded: chain J residue 189 MET Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 418 LEU Chi-restraints excluded: chain J residue 475 LEU Chi-restraints excluded: chain J residue 564 VAL Chi-restraints excluded: chain J residue 599 MET Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain K residue 99 GLU Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 523 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 63 MET Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 136 MET Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 247 ILE Chi-restraints excluded: chain L residue 263 THR Chi-restraints excluded: chain L residue 281 VAL Chi-restraints excluded: chain L residue 444 THR Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 181 GLN Chi-restraints excluded: chain M residue 189 MET Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 590 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 195 GLU Chi-restraints excluded: chain N residue 247 ILE Chi-restraints excluded: chain N residue 345 ASN Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 136 MET Chi-restraints excluded: chain O residue 165 SER Chi-restraints excluded: chain O residue 209 VAL Chi-restraints excluded: chain O residue 254 THR Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 445 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain P residue 247 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 427 optimal weight: 5.9990 chunk 238 optimal weight: 0.0970 chunk 640 optimal weight: 3.9990 chunk 524 optimal weight: 10.0000 chunk 212 optimal weight: 5.9990 chunk 771 optimal weight: 6.9990 chunk 833 optimal weight: 10.0000 chunk 687 optimal weight: 7.9990 chunk 765 optimal weight: 3.9990 chunk 263 optimal weight: 10.0000 chunk 618 optimal weight: 0.2980 overall best weight: 2.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 HIS B 53 ASN B 204 HIS B 234 ASN B 561 HIS C 181 GLN C 234 ASN ** C 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN D 234 ASN D 401 ASN ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 GLN F 486 ASN G 383 GLN H 181 GLN H 234 ASN ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 234 ASN I 340 HIS J 234 ASN K 234 ASN ** K 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN L 181 GLN L 234 ASN L 401 ASN L 417 HIS L 561 HIS M 340 HIS ** M 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 486 ASN O 97 ASN P 234 ASN ** P 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 68624 Z= 0.370 Angle : 0.627 10.444 93136 Z= 0.310 Chirality : 0.046 0.296 10816 Planarity : 0.005 0.063 11792 Dihedral : 9.650 101.190 10495 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.49 % Favored : 96.35 % Rotamer: Outliers : 3.58 % Allowed : 11.10 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % 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: -0.33 (0.09), residues: 8432 helix: 1.41 (0.15), residues: 1248 sheet: -0.13 (0.09), residues: 3760 loop : -0.81 (0.11), residues: 3424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 461 HIS 0.007 0.001 HIS D 299 PHE 0.032 0.002 PHE C 344 TYR 0.032 0.002 TYR C 593 ARG 0.006 0.001 ARG J 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 528 time to evaluate : 6.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8239 (m-30) cc_final: 0.7962 (m-30) REVERT: A 182 LEU cc_start: 0.8606 (mt) cc_final: 0.8261 (mt) REVERT: A 196 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7643 (mm) REVERT: A 218 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7856 (mt-10) REVERT: A 222 ARG cc_start: 0.7094 (mtt180) cc_final: 0.6467 (mtp180) REVERT: A 344 PHE cc_start: 0.7448 (t80) cc_final: 0.7098 (OUTLIER) REVERT: A 401 ASN cc_start: 0.6754 (t0) cc_final: 0.5977 (t0) REVERT: A 488 MET cc_start: 0.7531 (tmt) cc_final: 0.7146 (tmt) REVERT: A 524 PRO cc_start: 0.8065 (Cg_exo) cc_final: 0.7838 (Cg_endo) REVERT: B 104 TRP cc_start: 0.6783 (t60) cc_final: 0.6031 (t-100) REVERT: B 105 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6516 (ttt) REVERT: B 166 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6100 (pm20) REVERT: B 222 ARG cc_start: 0.6996 (mtt180) cc_final: 0.6314 (mpt90) REVERT: B 270 ARG cc_start: 0.7027 (mtp-110) cc_final: 0.6331 (mtp180) REVERT: B 274 ARG cc_start: 0.7581 (ttp-170) cc_final: 0.6379 (ttt-90) REVERT: B 276 GLN cc_start: 0.8451 (tt0) cc_final: 0.8196 (tt0) REVERT: B 344 PHE cc_start: 0.7883 (t80) cc_final: 0.7676 (t80) REVERT: B 431 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6545 (pm20) REVERT: B 599 MET cc_start: 0.1449 (mmp) cc_final: 0.0534 (mmp) REVERT: C 95 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: C 104 TRP cc_start: 0.6475 (t60) cc_final: 0.5789 (t-100) REVERT: C 136 MET cc_start: 0.7096 (mtt) cc_final: 0.6695 (mtp) REVERT: C 210 ASP cc_start: 0.8905 (m-30) cc_final: 0.8646 (m-30) REVERT: C 218 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7280 (mm-30) REVERT: C 274 ARG cc_start: 0.7427 (ttp-170) cc_final: 0.6899 (ttm-80) REVERT: C 454 LYS cc_start: 0.8785 (tttt) cc_final: 0.8560 (tttp) REVERT: D 59 MET cc_start: 0.7741 (mmm) cc_final: 0.7486 (mmm) REVERT: D 63 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.5698 (mpt) REVERT: D 104 TRP cc_start: 0.6602 (t60) cc_final: 0.6168 (t-100) REVERT: D 105 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.6797 (ttt) REVERT: D 270 ARG cc_start: 0.7268 (mtp-110) cc_final: 0.6887 (mtm180) REVERT: D 274 ARG cc_start: 0.7461 (ttp-170) cc_final: 0.6949 (ttt90) REVERT: D 331 SER cc_start: 0.8137 (t) cc_final: 0.7773 (m) REVERT: D 332 LYS cc_start: 0.8811 (mmtm) cc_final: 0.8599 (mmtm) REVERT: D 417 HIS cc_start: 0.7530 (t-90) cc_final: 0.7242 (t70) REVERT: D 533 MET cc_start: 0.4161 (ptp) cc_final: 0.3516 (ppp) REVERT: D 589 ARG cc_start: 0.0537 (OUTLIER) cc_final: 0.0150 (tpm170) REVERT: D 599 MET cc_start: 0.2298 (OUTLIER) cc_final: 0.0669 (mmt) REVERT: E 53 ASN cc_start: 0.8478 (t0) cc_final: 0.8263 (t0) REVERT: E 126 ASN cc_start: 0.6313 (m-40) cc_final: 0.6012 (t0) REVERT: E 136 MET cc_start: 0.7326 (mtp) cc_final: 0.6842 (mtm) REVERT: E 166 GLU cc_start: 0.6746 (mt-10) cc_final: 0.5983 (mm-30) REVERT: E 188 LYS cc_start: 0.8514 (mppt) cc_final: 0.8297 (mmtt) REVERT: E 189 MET cc_start: 0.5598 (OUTLIER) cc_final: 0.5172 (ttm) REVERT: E 222 ARG cc_start: 0.7329 (mtp180) cc_final: 0.6175 (mtt90) REVERT: E 230 GLN cc_start: 0.7742 (mt0) cc_final: 0.7449 (mt0) REVERT: E 270 ARG cc_start: 0.7356 (mtp-110) cc_final: 0.6669 (ttm110) REVERT: E 274 ARG cc_start: 0.7414 (ttp-170) cc_final: 0.7128 (ttt90) REVERT: E 332 LYS cc_start: 0.8722 (mttt) cc_final: 0.8318 (mmtm) REVERT: E 340 HIS cc_start: 0.7619 (t-90) cc_final: 0.7405 (t-170) REVERT: E 488 MET cc_start: 0.3386 (tmm) cc_final: 0.2581 (tmt) REVERT: E 599 MET cc_start: 0.2631 (mmp) cc_final: 0.1337 (mmp) REVERT: F 39 LYS cc_start: 0.7903 (mmtp) cc_final: 0.7573 (mmtt) REVERT: F 57 VAL cc_start: 0.7841 (p) cc_final: 0.7609 (m) REVERT: F 95 GLU cc_start: 0.7923 (mp0) cc_final: 0.7691 (mt-10) REVERT: F 105 MET cc_start: 0.7378 (ttm) cc_final: 0.6115 (tmm) REVERT: F 160 LYS cc_start: 0.8068 (mttm) cc_final: 0.7829 (mmmm) REVERT: F 189 MET cc_start: 0.5920 (OUTLIER) cc_final: 0.5300 (ttm) REVERT: F 195 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7616 (mt-10) REVERT: F 218 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7381 (mt-10) REVERT: F 222 ARG cc_start: 0.7110 (mtt180) cc_final: 0.6498 (mpt90) REVERT: F 253 GLU cc_start: 0.6650 (pt0) cc_final: 0.5871 (pm20) REVERT: F 270 ARG cc_start: 0.7382 (mtp-110) cc_final: 0.6747 (ttm170) REVERT: F 274 ARG cc_start: 0.7570 (ttp-170) cc_final: 0.6926 (tmm160) REVERT: F 340 HIS cc_start: 0.8302 (t70) cc_final: 0.7812 (t70) REVERT: F 599 MET cc_start: 0.3391 (mmp) cc_final: 0.2025 (mmp) REVERT: G 105 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.5748 (tmm) REVERT: G 188 LYS cc_start: 0.8219 (mttt) cc_final: 0.8007 (tptm) REVERT: G 218 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7480 (mm-30) REVERT: G 222 ARG cc_start: 0.7004 (mtt180) cc_final: 0.6354 (mpt90) REVERT: G 270 ARG cc_start: 0.6931 (mtp-110) cc_final: 0.6543 (mtp180) REVERT: G 488 MET cc_start: 0.4851 (tmt) cc_final: 0.4399 (tmm) REVERT: G 533 MET cc_start: 0.3644 (ptp) cc_final: 0.3385 (pmm) REVERT: G 586 LEU cc_start: 0.7548 (tm) cc_final: 0.7187 (pp) REVERT: G 599 MET cc_start: 0.1877 (OUTLIER) cc_final: 0.1645 (mpt) REVERT: H 95 GLU cc_start: 0.8159 (mp0) cc_final: 0.7615 (mt-10) REVERT: H 96 MET cc_start: 0.7654 (mtt) cc_final: 0.7318 (mtm) REVERT: H 218 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7619 (mt-10) REVERT: H 270 ARG cc_start: 0.7019 (mtt180) cc_final: 0.6617 (mmm160) REVERT: H 274 ARG cc_start: 0.7473 (ttp-170) cc_final: 0.7203 (ttm170) REVERT: H 339 ARG cc_start: 0.8019 (mtp85) cc_final: 0.7750 (ttm-80) REVERT: H 344 PHE cc_start: 0.7290 (t80) cc_final: 0.6930 (t80) REVERT: I 58 ASP cc_start: 0.7915 (m-30) cc_final: 0.7578 (m-30) REVERT: I 182 LEU cc_start: 0.8570 (mt) cc_final: 0.8232 (mt) REVERT: I 196 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7552 (mm) REVERT: I 218 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7840 (mt-10) REVERT: I 222 ARG cc_start: 0.7051 (mtt180) cc_final: 0.6377 (mpt-90) REVERT: I 344 PHE cc_start: 0.7462 (t80) cc_final: 0.7100 (OUTLIER) REVERT: I 401 ASN cc_start: 0.6562 (t0) cc_final: 0.5780 (t0) REVERT: I 425 GLU cc_start: 0.7107 (tt0) cc_final: 0.6860 (tm-30) REVERT: I 434 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7053 (tppp) REVERT: J 91 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7686 (mt-10) REVERT: J 105 MET cc_start: 0.6861 (OUTLIER) cc_final: 0.6352 (ttt) REVERT: J 166 GLU cc_start: 0.6802 (mt-10) cc_final: 0.6140 (pm20) REVERT: J 195 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6840 (tt0) REVERT: J 270 ARG cc_start: 0.6886 (mtp-110) cc_final: 0.6322 (mtp180) REVERT: J 274 ARG cc_start: 0.7470 (ttp-170) cc_final: 0.6335 (ttt-90) REVERT: J 276 GLN cc_start: 0.8460 (tt0) cc_final: 0.8222 (tt0) REVERT: J 344 PHE cc_start: 0.7660 (t80) cc_final: 0.7434 (t80) REVERT: J 524 PRO cc_start: 0.7500 (Cg_exo) cc_final: 0.7268 (Cg_endo) REVERT: J 561 HIS cc_start: 0.6452 (m-70) cc_final: 0.6252 (m90) REVERT: J 570 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.7089 (pp30) REVERT: J 599 MET cc_start: 0.1094 (OUTLIER) cc_final: 0.0832 (mmt) REVERT: K 77 GLN cc_start: 0.7732 (mt0) cc_final: 0.7003 (mm-40) REVERT: K 95 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: K 104 TRP cc_start: 0.6370 (t60) cc_final: 0.5666 (t-100) REVERT: K 189 MET cc_start: 0.4943 (tpt) cc_final: 0.4586 (tpp) REVERT: K 218 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7500 (mm-30) REVERT: K 222 ARG cc_start: 0.6856 (mtt180) cc_final: 0.6464 (mmm160) REVERT: K 274 ARG cc_start: 0.7427 (ttp-170) cc_final: 0.6905 (ttm-80) REVERT: K 586 LEU cc_start: 0.6651 (mt) cc_final: 0.6397 (mm) REVERT: K 599 MET cc_start: 0.3938 (mmp) cc_final: 0.3305 (mmp) REVERT: L 59 MET cc_start: 0.7541 (mmm) cc_final: 0.7273 (mmm) REVERT: L 63 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.5723 (mpt) REVERT: L 75 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7582 (p0) REVERT: L 96 MET cc_start: 0.7116 (mtm) cc_final: 0.6584 (mtm) REVERT: L 104 TRP cc_start: 0.6662 (t60) cc_final: 0.6143 (t-100) REVERT: L 105 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6757 (ttt) REVERT: L 136 MET cc_start: 0.6542 (OUTLIER) cc_final: 0.6308 (mpp) REVERT: L 188 LYS cc_start: 0.8029 (mppt) cc_final: 0.7741 (pmmt) REVERT: L 219 ASP cc_start: 0.7742 (t0) cc_final: 0.7477 (t70) REVERT: L 222 ARG cc_start: 0.6889 (mtt180) cc_final: 0.6247 (mtp180) REVERT: L 270 ARG cc_start: 0.7197 (mtp-110) cc_final: 0.6738 (mtp180) REVERT: L 274 ARG cc_start: 0.7358 (ttp-170) cc_final: 0.6806 (ttt90) REVERT: L 304 ASP cc_start: 0.8287 (t0) cc_final: 0.7960 (t0) REVERT: L 331 SER cc_start: 0.8099 (t) cc_final: 0.7730 (m) REVERT: L 457 PHE cc_start: 0.7528 (p90) cc_final: 0.7106 (p90) REVERT: M 53 ASN cc_start: 0.8613 (t0) cc_final: 0.8212 (t0) REVERT: M 99 GLU cc_start: 0.8148 (tt0) cc_final: 0.7879 (tt0) REVERT: M 136 MET cc_start: 0.7246 (mtp) cc_final: 0.6674 (mtm) REVERT: M 166 GLU cc_start: 0.6774 (mt-10) cc_final: 0.5982 (mm-30) REVERT: M 188 LYS cc_start: 0.8900 (mppt) cc_final: 0.8619 (mppt) REVERT: M 189 MET cc_start: 0.5994 (OUTLIER) cc_final: 0.5691 (ttm) REVERT: M 203 THR cc_start: 0.8978 (m) cc_final: 0.8376 (p) REVERT: M 222 ARG cc_start: 0.7238 (mtt180) cc_final: 0.6707 (mtp180) REVERT: M 230 GLN cc_start: 0.7954 (mt0) cc_final: 0.7629 (mt0) REVERT: M 270 ARG cc_start: 0.7490 (mtp-110) cc_final: 0.6811 (ttm110) REVERT: M 274 ARG cc_start: 0.7518 (ttp-170) cc_final: 0.7274 (ttt90) REVERT: M 332 LYS cc_start: 0.8704 (mttt) cc_final: 0.8317 (mmtm) REVERT: M 488 MET cc_start: 0.3370 (tmm) cc_final: 0.2575 (tmt) REVERT: M 599 MET cc_start: 0.1754 (mmp) cc_final: 0.1256 (mmp) REVERT: N 39 LYS cc_start: 0.8024 (mmtp) cc_final: 0.7709 (mmtt) REVERT: N 57 VAL cc_start: 0.7842 (p) cc_final: 0.7625 (m) REVERT: N 105 MET cc_start: 0.7646 (ttm) cc_final: 0.6271 (tmm) REVERT: N 160 LYS cc_start: 0.8097 (mttm) cc_final: 0.7723 (mttt) REVERT: N 218 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7621 (mt-10) REVERT: N 253 GLU cc_start: 0.6452 (pt0) cc_final: 0.5967 (pm20) REVERT: N 274 ARG cc_start: 0.7636 (ttp-170) cc_final: 0.7053 (ttp-170) REVERT: N 340 HIS cc_start: 0.8129 (t-90) cc_final: 0.7454 (t70) REVERT: N 344 PHE cc_start: 0.7970 (t80) cc_final: 0.7545 (t80) REVERT: N 345 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7555 (m-40) REVERT: N 599 MET cc_start: 0.3653 (mmp) cc_final: 0.2807 (mmp) REVERT: O 105 MET cc_start: 0.6903 (OUTLIER) cc_final: 0.5717 (tmm) REVERT: O 166 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6343 (mp0) REVERT: O 188 LYS cc_start: 0.8324 (mttt) cc_final: 0.8065 (ptpt) REVERT: O 218 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7480 (mm-30) REVERT: O 222 ARG cc_start: 0.7026 (mtt180) cc_final: 0.6361 (mpt90) REVERT: O 270 ARG cc_start: 0.6876 (mtp-110) cc_final: 0.6472 (mtp180) REVERT: O 332 LYS cc_start: 0.9076 (pptt) cc_final: 0.8797 (pttt) REVERT: O 417 HIS cc_start: 0.6577 (t-90) cc_final: 0.5000 (t-90) REVERT: O 488 MET cc_start: 0.4870 (tmt) cc_final: 0.4458 (tmm) REVERT: O 533 MET cc_start: 0.4084 (mtp) cc_final: 0.3408 (pmm) REVERT: P 61 ARG cc_start: 0.7595 (tpp-160) cc_final: 0.7194 (tpp-160) REVERT: P 218 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7557 (mt-10) REVERT: P 219 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7768 (m-30) REVERT: P 270 ARG cc_start: 0.7319 (mtp-110) cc_final: 0.7051 (mtm180) REVERT: P 339 ARG cc_start: 0.8262 (mtt90) cc_final: 0.7718 (ttm-80) REVERT: P 340 HIS cc_start: 0.7820 (OUTLIER) cc_final: 0.7261 (t70) REVERT: P 344 PHE cc_start: 0.7350 (t80) cc_final: 0.7001 (t80) outliers start: 269 outliers final: 145 residues processed: 749 average time/residue: 1.2776 time to fit residues: 1288.5415 Evaluate side-chains 675 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 504 time to evaluate : 5.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 515 TYR Chi-restraints excluded: chain D residue 523 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 589 ARG Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 189 MET Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 189 MET Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 310 LEU Chi-restraints excluded: chain G residue 599 MET Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 310 LEU Chi-restraints excluded: chain H residue 428 SER Chi-restraints excluded: chain H residue 584 SER Chi-restraints excluded: chain H residue 594 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 434 LYS Chi-restraints excluded: chain I residue 564 VAL Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 105 MET Chi-restraints excluded: chain J residue 187 THR Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 418 LEU Chi-restraints excluded: chain J residue 511 VAL Chi-restraints excluded: chain J residue 564 VAL Chi-restraints excluded: chain J residue 570 GLN Chi-restraints excluded: chain J residue 599 MET Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain K residue 99 GLU Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 523 VAL Chi-restraints excluded: chain K residue 590 LEU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 63 MET Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 136 MET Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 247 ILE Chi-restraints excluded: chain L residue 263 THR Chi-restraints excluded: chain L residue 281 VAL Chi-restraints excluded: chain L residue 444 THR Chi-restraints excluded: chain L residue 445 VAL Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain L residue 523 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 181 GLN Chi-restraints excluded: chain M residue 189 MET Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 219 ASP Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 586 LEU Chi-restraints excluded: chain M residue 590 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 181 GLN Chi-restraints excluded: chain N residue 247 ILE Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 345 ASN Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain N residue 594 THR Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 105 MET Chi-restraints excluded: chain O residue 136 MET Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 165 SER Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 209 VAL Chi-restraints excluded: chain O residue 254 THR Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 271 THR Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 96 MET Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 187 THR Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain P residue 219 ASP Chi-restraints excluded: chain P residue 247 ILE Chi-restraints excluded: chain P residue 271 THR Chi-restraints excluded: chain P residue 340 HIS Chi-restraints excluded: chain P residue 428 SER Chi-restraints excluded: chain P residue 584 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 762 optimal weight: 7.9990 chunk 580 optimal weight: 9.9990 chunk 400 optimal weight: 3.9990 chunk 85 optimal weight: 30.0000 chunk 368 optimal weight: 30.0000 chunk 518 optimal weight: 20.0000 chunk 774 optimal weight: 30.0000 chunk 819 optimal weight: 4.9990 chunk 404 optimal weight: 10.0000 chunk 733 optimal weight: 20.0000 chunk 220 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS B 401 ASN ** B 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 HIS D 89 GLN D 97 ASN D 181 GLN D 345 ASN ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN F 383 GLN ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 311 HIS H 181 GLN ** I 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN J 181 GLN J 204 HIS J 502 ASN J 561 HIS K 417 HIS K 539 ASN ** K 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN L 417 HIS M 97 ASN M 311 HIS ** M 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 383 GLN P 97 ASN P 181 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.128 68624 Z= 0.830 Angle : 0.836 14.411 93136 Z= 0.426 Chirality : 0.056 0.451 10816 Planarity : 0.007 0.096 11792 Dihedral : 10.177 106.271 10493 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.40 % Favored : 94.44 % Rotamer: Outliers : 5.00 % Allowed : 11.46 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % 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: -1.19 (0.09), residues: 8432 helix: 0.62 (0.14), residues: 1344 sheet: -0.80 (0.08), residues: 3744 loop : -1.20 (0.11), residues: 3344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP E 292 HIS 0.017 0.002 HIS L 299 PHE 0.033 0.002 PHE F 312 TYR 0.026 0.003 TYR L 593 ARG 0.009 0.001 ARG J 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 375 poor density : 530 time to evaluate : 6.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8264 (m-30) cc_final: 0.7939 (m-30) REVERT: A 104 TRP cc_start: 0.6605 (t60) cc_final: 0.6117 (t-100) REVERT: A 344 PHE cc_start: 0.7493 (t80) cc_final: 0.7153 (t80) REVERT: A 401 ASN cc_start: 0.7188 (t0) cc_final: 0.6216 (t0) REVERT: A 425 GLU cc_start: 0.7023 (tt0) cc_final: 0.6787 (tm-30) REVERT: A 488 MET cc_start: 0.7588 (tmt) cc_final: 0.7227 (tmt) REVERT: A 599 MET cc_start: 0.1692 (mmt) cc_final: 0.1354 (mmt) REVERT: B 104 TRP cc_start: 0.7039 (t60) cc_final: 0.6301 (t-100) REVERT: B 105 MET cc_start: 0.6786 (OUTLIER) cc_final: 0.6286 (ttt) REVERT: B 166 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6262 (pm20) REVERT: B 183 GLU cc_start: 0.7970 (tt0) cc_final: 0.7711 (mp0) REVERT: B 222 ARG cc_start: 0.6957 (mtt180) cc_final: 0.6277 (mtt90) REVERT: B 270 ARG cc_start: 0.7085 (mtp-110) cc_final: 0.6334 (mtp180) REVERT: B 274 ARG cc_start: 0.7659 (ttp-170) cc_final: 0.6523 (ttt-90) REVERT: B 276 GLN cc_start: 0.8335 (tt0) cc_final: 0.8074 (tt0) REVERT: B 340 HIS cc_start: 0.6764 (t-90) cc_final: 0.6435 (t-90) REVERT: B 342 TYR cc_start: 0.7458 (m-80) cc_final: 0.7228 (m-80) REVERT: B 344 PHE cc_start: 0.7940 (t80) cc_final: 0.7583 (t80) REVERT: B 431 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6412 (pm20) REVERT: B 524 PRO cc_start: 0.7596 (Cg_exo) cc_final: 0.7336 (Cg_endo) REVERT: B 570 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.7252 (pp30) REVERT: B 599 MET cc_start: 0.1284 (mmp) cc_final: 0.0438 (mmp) REVERT: C 95 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: C 104 TRP cc_start: 0.6675 (t60) cc_final: 0.5986 (t-100) REVERT: C 136 MET cc_start: 0.7148 (mtt) cc_final: 0.6727 (mtp) REVERT: C 218 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7275 (mm-30) REVERT: C 222 ARG cc_start: 0.6872 (mtt180) cc_final: 0.6463 (mmm160) REVERT: C 274 ARG cc_start: 0.7727 (ttp-170) cc_final: 0.7091 (ttm170) REVERT: C 447 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6214 (pp20) REVERT: C 454 LYS cc_start: 0.8762 (tttt) cc_final: 0.8518 (tttp) REVERT: C 599 MET cc_start: 0.3298 (mmt) cc_final: 0.2515 (mmp) REVERT: D 39 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7829 (mtpt) REVERT: D 63 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.5894 (mpt) REVERT: D 75 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7700 (p0) REVERT: D 104 TRP cc_start: 0.6983 (t60) cc_final: 0.6545 (t-100) REVERT: D 105 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.6754 (ttt) REVERT: D 181 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.7192 (tp40) REVERT: D 274 ARG cc_start: 0.7490 (ttp-170) cc_final: 0.6889 (ttt90) REVERT: D 314 ILE cc_start: 0.8601 (mt) cc_final: 0.8364 (mt) REVERT: D 331 SER cc_start: 0.8176 (t) cc_final: 0.7721 (m) REVERT: D 332 LYS cc_start: 0.8770 (mmtm) cc_final: 0.8496 (tppt) REVERT: D 417 HIS cc_start: 0.7451 (t-90) cc_final: 0.7171 (t70) REVERT: D 533 MET cc_start: 0.3922 (ptp) cc_final: 0.3271 (ppp) REVERT: D 589 ARG cc_start: 0.0443 (OUTLIER) cc_final: 0.0025 (tpm170) REVERT: D 599 MET cc_start: 0.1884 (OUTLIER) cc_final: 0.0279 (mmt) REVERT: E 104 TRP cc_start: 0.6498 (t60) cc_final: 0.5999 (t-100) REVERT: E 126 ASN cc_start: 0.6151 (m-40) cc_final: 0.5928 (t0) REVERT: E 136 MET cc_start: 0.7308 (mtp) cc_final: 0.6718 (mtm) REVERT: E 166 GLU cc_start: 0.6790 (mt-10) cc_final: 0.6029 (mm-30) REVERT: E 218 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7226 (mt-10) REVERT: E 219 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7627 (m-30) REVERT: E 230 GLN cc_start: 0.7915 (mt0) cc_final: 0.7677 (mt0) REVERT: E 270 ARG cc_start: 0.7442 (mtp-110) cc_final: 0.6781 (mtt-85) REVERT: E 274 ARG cc_start: 0.7610 (ttp-170) cc_final: 0.7101 (ttt90) REVERT: E 332 LYS cc_start: 0.8752 (mttt) cc_final: 0.8385 (mmtm) REVERT: E 340 HIS cc_start: 0.7766 (t-90) cc_final: 0.7449 (t-170) REVERT: E 488 MET cc_start: 0.3269 (tmm) cc_final: 0.2470 (tmt) REVERT: E 599 MET cc_start: 0.2525 (mmp) cc_final: 0.1555 (mmp) REVERT: F 39 LYS cc_start: 0.7935 (mmtp) cc_final: 0.7621 (mmtt) REVERT: F 95 GLU cc_start: 0.7976 (mp0) cc_final: 0.7764 (mt-10) REVERT: F 105 MET cc_start: 0.7441 (ttm) cc_final: 0.6166 (tmm) REVERT: F 132 GLU cc_start: 0.7492 (tm-30) cc_final: 0.7112 (tm-30) REVERT: F 160 LYS cc_start: 0.8127 (mttm) cc_final: 0.7909 (mttp) REVERT: F 189 MET cc_start: 0.6036 (OUTLIER) cc_final: 0.5396 (ttm) REVERT: F 218 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7526 (mt-10) REVERT: F 222 ARG cc_start: 0.7104 (mtt180) cc_final: 0.6454 (mpt90) REVERT: F 253 GLU cc_start: 0.6854 (pt0) cc_final: 0.6194 (pm20) REVERT: F 270 ARG cc_start: 0.7380 (mtp-110) cc_final: 0.6613 (mtt90) REVERT: F 274 ARG cc_start: 0.7566 (ttp-170) cc_final: 0.6975 (ttp-170) REVERT: F 340 HIS cc_start: 0.8290 (t70) cc_final: 0.7741 (t70) REVERT: F 599 MET cc_start: 0.2958 (mmp) cc_final: 0.1844 (mmp) REVERT: G 57 VAL cc_start: 0.7579 (p) cc_final: 0.7347 (m) REVERT: G 104 TRP cc_start: 0.6681 (t60) cc_final: 0.6302 (t60) REVERT: G 105 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.5830 (tmm) REVERT: G 169 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7699 (tp) REVERT: G 218 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7456 (mm-30) REVERT: G 222 ARG cc_start: 0.7062 (mtt180) cc_final: 0.6404 (mpt90) REVERT: G 270 ARG cc_start: 0.7122 (mtp-110) cc_final: 0.6659 (mtp180) REVERT: G 454 LYS cc_start: 0.8202 (tttt) cc_final: 0.7824 (tptt) REVERT: G 488 MET cc_start: 0.4995 (tmt) cc_final: 0.4475 (tmm) REVERT: G 586 LEU cc_start: 0.7480 (tm) cc_final: 0.7006 (pp) REVERT: G 599 MET cc_start: 0.1859 (OUTLIER) cc_final: 0.1486 (mpt) REVERT: H 95 GLU cc_start: 0.8221 (mp0) cc_final: 0.7705 (mt-10) REVERT: H 96 MET cc_start: 0.8073 (mtt) cc_final: 0.7752 (mtm) REVERT: H 104 TRP cc_start: 0.6811 (t60) cc_final: 0.6533 (t60) REVERT: H 218 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7558 (mt-10) REVERT: H 219 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7754 (m-30) REVERT: H 222 ARG cc_start: 0.6955 (mtt180) cc_final: 0.6340 (mtp180) REVERT: H 270 ARG cc_start: 0.7151 (mtt180) cc_final: 0.6640 (mmm160) REVERT: H 274 ARG cc_start: 0.7511 (ttp-170) cc_final: 0.7069 (ttm-80) REVERT: H 336 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8358 (p) REVERT: H 339 ARG cc_start: 0.7985 (mtp85) cc_final: 0.7650 (ttm-80) REVERT: H 340 HIS cc_start: 0.7791 (OUTLIER) cc_final: 0.7285 (t70) REVERT: H 344 PHE cc_start: 0.7196 (t80) cc_final: 0.6816 (t80) REVERT: H 594 THR cc_start: 0.5725 (OUTLIER) cc_final: 0.5244 (t) REVERT: I 58 ASP cc_start: 0.7980 (m-30) cc_final: 0.7642 (m-30) REVERT: I 189 MET cc_start: 0.5346 (mmm) cc_final: 0.4915 (mmt) REVERT: I 344 PHE cc_start: 0.7513 (t80) cc_final: 0.7172 (t80) REVERT: I 401 ASN cc_start: 0.7187 (t0) cc_final: 0.6867 (t0) REVERT: I 425 GLU cc_start: 0.7061 (tt0) cc_final: 0.6736 (tm-30) REVERT: I 447 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.6011 (pm20) REVERT: J 166 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6318 (pm20) REVERT: J 195 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6886 (tt0) REVERT: J 270 ARG cc_start: 0.6989 (mtp-110) cc_final: 0.6400 (mtp180) REVERT: J 274 ARG cc_start: 0.7596 (ttp-170) cc_final: 0.6509 (ttt-90) REVERT: J 276 GLN cc_start: 0.8349 (tt0) cc_final: 0.8105 (tt0) REVERT: J 336 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8712 (p) REVERT: J 431 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6925 (pm20) REVERT: J 524 PRO cc_start: 0.7441 (Cg_exo) cc_final: 0.7189 (Cg_endo) REVERT: J 570 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.7066 (pp30) REVERT: J 599 MET cc_start: 0.0846 (OUTLIER) cc_final: -0.0269 (mmt) REVERT: K 77 GLN cc_start: 0.7913 (mt0) cc_final: 0.7658 (tt0) REVERT: K 95 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: K 104 TRP cc_start: 0.6588 (t60) cc_final: 0.5876 (t-100) REVERT: K 189 MET cc_start: 0.5064 (tpt) cc_final: 0.4690 (tpp) REVERT: K 218 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7841 (mm-30) REVERT: K 222 ARG cc_start: 0.6968 (mtt180) cc_final: 0.6542 (mmm160) REVERT: K 274 ARG cc_start: 0.7639 (ttp-170) cc_final: 0.7079 (ttm-80) REVERT: K 599 MET cc_start: 0.3397 (mmp) cc_final: 0.2538 (mmp) REVERT: L 39 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7834 (mtpt) REVERT: L 63 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.5785 (mpt) REVERT: L 75 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7684 (p0) REVERT: L 77 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7388 (tp40) REVERT: L 96 MET cc_start: 0.7415 (mtm) cc_final: 0.6875 (mtm) REVERT: L 104 TRP cc_start: 0.6913 (t60) cc_final: 0.6425 (t-100) REVERT: L 136 MET cc_start: 0.6443 (OUTLIER) cc_final: 0.6174 (mpp) REVERT: L 274 ARG cc_start: 0.7370 (ttp-170) cc_final: 0.6789 (ttt90) REVERT: L 314 ILE cc_start: 0.8575 (mt) cc_final: 0.8354 (mt) REVERT: L 331 SER cc_start: 0.8140 (t) cc_final: 0.7677 (m) REVERT: L 332 LYS cc_start: 0.8756 (mmtm) cc_final: 0.8466 (tppt) REVERT: L 418 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7765 (tp) REVERT: L 457 PHE cc_start: 0.7563 (p90) cc_final: 0.7175 (p90) REVERT: L 589 ARG cc_start: 0.1125 (OUTLIER) cc_final: 0.0435 (tpm170) REVERT: L 599 MET cc_start: 0.2015 (OUTLIER) cc_final: 0.0378 (mmt) REVERT: M 104 TRP cc_start: 0.6717 (t60) cc_final: 0.6225 (t-100) REVERT: M 136 MET cc_start: 0.7332 (mtp) cc_final: 0.6593 (mtm) REVERT: M 166 GLU cc_start: 0.6747 (mt-10) cc_final: 0.5956 (mm-30) REVERT: M 188 LYS cc_start: 0.8943 (mppt) cc_final: 0.8648 (mppt) REVERT: M 218 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7373 (mt-10) REVERT: M 219 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7743 (m-30) REVERT: M 222 ARG cc_start: 0.7328 (mtt180) cc_final: 0.6758 (mtp180) REVERT: M 230 GLN cc_start: 0.8113 (mt0) cc_final: 0.7822 (mt0) REVERT: M 270 ARG cc_start: 0.7566 (mtp-110) cc_final: 0.6853 (mtt-85) REVERT: M 274 ARG cc_start: 0.7684 (ttp-170) cc_final: 0.7253 (ttt90) REVERT: M 332 LYS cc_start: 0.8779 (mttt) cc_final: 0.8438 (mmtm) REVERT: M 488 MET cc_start: 0.3301 (tmm) cc_final: 0.2490 (tmt) REVERT: M 599 MET cc_start: 0.2203 (mmp) cc_final: 0.1779 (mmp) REVERT: N 57 VAL cc_start: 0.7829 (p) cc_final: 0.7618 (m) REVERT: N 95 GLU cc_start: 0.8131 (mp0) cc_final: 0.7903 (mt-10) REVERT: N 105 MET cc_start: 0.7649 (ttm) cc_final: 0.6186 (tmm) REVERT: N 218 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7651 (mt-10) REVERT: N 253 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6179 (pm20) REVERT: N 274 ARG cc_start: 0.7561 (ttp-170) cc_final: 0.7017 (ttp-170) REVERT: N 340 HIS cc_start: 0.8147 (t-90) cc_final: 0.7308 (t70) REVERT: N 344 PHE cc_start: 0.8112 (t80) cc_final: 0.7589 (t80) REVERT: N 345 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.8009 (m110) REVERT: N 599 MET cc_start: 0.3181 (mmp) cc_final: 0.2621 (mmt) REVERT: O 57 VAL cc_start: 0.7542 (p) cc_final: 0.7291 (m) REVERT: O 104 TRP cc_start: 0.6502 (t60) cc_final: 0.6137 (t60) REVERT: O 105 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.5825 (tmm) REVERT: O 166 GLU cc_start: 0.6834 (mt-10) cc_final: 0.6508 (mp0) REVERT: O 218 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7458 (mm-30) REVERT: O 222 ARG cc_start: 0.7051 (mtt180) cc_final: 0.6401 (mpt90) REVERT: O 270 ARG cc_start: 0.7064 (mtp-110) cc_final: 0.6628 (mtp180) REVERT: O 488 MET cc_start: 0.4730 (tmt) cc_final: 0.4286 (tmm) REVERT: O 533 MET cc_start: 0.4102 (mtp) cc_final: 0.3341 (pmm) REVERT: P 63 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7192 (mmm) REVERT: P 94 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8621 (mm) REVERT: P 104 TRP cc_start: 0.6887 (t60) cc_final: 0.6602 (t60) REVERT: P 218 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7627 (mt-10) REVERT: P 219 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7866 (m-30) REVERT: P 270 ARG cc_start: 0.7394 (mtp-110) cc_final: 0.7109 (mtm180) REVERT: P 339 ARG cc_start: 0.8192 (mtt90) cc_final: 0.7685 (ttm-80) REVERT: P 340 HIS cc_start: 0.7830 (OUTLIER) cc_final: 0.7276 (t70) REVERT: P 344 PHE cc_start: 0.7239 (t80) cc_final: 0.6890 (t80) REVERT: P 594 THR cc_start: 0.5947 (OUTLIER) cc_final: 0.5259 (m) outliers start: 375 outliers final: 202 residues processed: 836 average time/residue: 1.2099 time to fit residues: 1379.4013 Evaluate side-chains 746 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 500 time to evaluate : 5.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain D residue 515 TYR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 589 ARG Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 189 MET Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 523 VAL Chi-restraints excluded: chain G residue 588 VAL Chi-restraints excluded: chain G residue 599 MET Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 219 ASP Chi-restraints excluded: chain H residue 242 ILE Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 310 LEU Chi-restraints excluded: chain H residue 336 THR Chi-restraints excluded: chain H residue 340 HIS Chi-restraints excluded: chain H residue 428 SER Chi-restraints excluded: chain H residue 594 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 254 THR Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 301 VAL Chi-restraints excluded: chain I residue 447 GLU Chi-restraints excluded: chain I residue 503 LEU Chi-restraints excluded: chain I residue 533 MET Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 187 THR Chi-restraints excluded: chain J residue 191 THR Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 271 THR Chi-restraints excluded: chain J residue 336 THR Chi-restraints excluded: chain J residue 431 GLU Chi-restraints excluded: chain J residue 511 VAL Chi-restraints excluded: chain J residue 564 VAL Chi-restraints excluded: chain J residue 570 GLN Chi-restraints excluded: chain J residue 586 LEU Chi-restraints excluded: chain J residue 599 MET Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 206 ILE Chi-restraints excluded: chain K residue 247 ILE Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 310 LEU Chi-restraints excluded: chain K residue 523 VAL Chi-restraints excluded: chain K residue 564 VAL Chi-restraints excluded: chain K residue 588 VAL Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 63 MET Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 77 GLN Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain L residue 97 ASN Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 136 MET Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 247 ILE Chi-restraints excluded: chain L residue 263 THR Chi-restraints excluded: chain L residue 281 VAL Chi-restraints excluded: chain L residue 418 LEU Chi-restraints excluded: chain L residue 444 THR Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain L residue 523 VAL Chi-restraints excluded: chain L residue 589 ARG Chi-restraints excluded: chain L residue 599 MET Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 181 GLN Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 219 ASP Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 418 LEU Chi-restraints excluded: chain M residue 586 LEU Chi-restraints excluded: chain M residue 590 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 247 ILE Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 271 THR Chi-restraints excluded: chain N residue 345 ASN Chi-restraints excluded: chain N residue 430 LEU Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 94 LEU Chi-restraints excluded: chain O residue 105 MET Chi-restraints excluded: chain O residue 136 MET Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 165 SER Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 209 VAL Chi-restraints excluded: chain O residue 254 THR Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 271 THR Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain O residue 523 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 63 MET Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 96 MET Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 187 THR Chi-restraints excluded: chain P residue 189 MET Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain P residue 219 ASP Chi-restraints excluded: chain P residue 242 ILE Chi-restraints excluded: chain P residue 247 ILE Chi-restraints excluded: chain P residue 254 THR Chi-restraints excluded: chain P residue 263 THR Chi-restraints excluded: chain P residue 271 THR Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain P residue 336 THR Chi-restraints excluded: chain P residue 340 HIS Chi-restraints excluded: chain P residue 428 SER Chi-restraints excluded: chain P residue 594 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 682 optimal weight: 40.0000 chunk 465 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 610 optimal weight: 2.9990 chunk 338 optimal weight: 2.9990 chunk 699 optimal weight: 1.9990 chunk 566 optimal weight: 20.0000 chunk 0 optimal weight: 0.6980 chunk 418 optimal weight: 0.9990 chunk 735 optimal weight: 30.0000 chunk 206 optimal weight: 20.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 561 HIS C 181 GLN C 417 HIS D 345 ASN E 181 GLN E 204 HIS ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN H 181 GLN H 401 ASN ** I 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN J 204 HIS J 401 ASN K 144 GLN K 259 GLN K 417 HIS ** K 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN L 417 HIS M 204 HIS M 340 HIS ** N 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 340 HIS O 490 ASN P 181 GLN ** P 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 401 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 68624 Z= 0.268 Angle : 0.598 13.294 93136 Z= 0.297 Chirality : 0.045 0.329 10816 Planarity : 0.005 0.064 11792 Dihedral : 8.829 100.754 10485 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.89 % Favored : 96.93 % Rotamer: Outliers : 3.69 % Allowed : 13.34 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.80 (0.09), residues: 8432 helix: 0.78 (0.14), residues: 1344 sheet: -0.51 (0.08), residues: 3760 loop : -0.94 (0.11), residues: 3328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 292 HIS 0.006 0.001 HIS L 340 PHE 0.031 0.001 PHE E 450 TYR 0.026 0.001 TYR C 593 ARG 0.003 0.000 ARG F 589 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 503 time to evaluate : 5.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8208 (m-30) cc_final: 0.7753 (m-30) REVERT: A 209 VAL cc_start: 0.8432 (OUTLIER) cc_final: 0.8090 (p) REVERT: A 218 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7892 (mt-10) REVERT: A 222 ARG cc_start: 0.7106 (mtt180) cc_final: 0.6467 (mtp180) REVERT: A 326 LEU cc_start: 0.8460 (mt) cc_final: 0.8241 (pt) REVERT: A 344 PHE cc_start: 0.7447 (t80) cc_final: 0.7229 (OUTLIER) REVERT: A 401 ASN cc_start: 0.7157 (t0) cc_final: 0.6174 (t0) REVERT: A 425 GLU cc_start: 0.6918 (tt0) cc_final: 0.6714 (tm-30) REVERT: A 488 MET cc_start: 0.7618 (tmt) cc_final: 0.7232 (tmt) REVERT: B 104 TRP cc_start: 0.6896 (t60) cc_final: 0.6158 (t-100) REVERT: B 105 MET cc_start: 0.6654 (OUTLIER) cc_final: 0.6214 (ttt) REVERT: B 166 GLU cc_start: 0.6752 (mt-10) cc_final: 0.6152 (pm20) REVERT: B 222 ARG cc_start: 0.6944 (mtt180) cc_final: 0.6085 (mtt90) REVERT: B 270 ARG cc_start: 0.6995 (mtp-110) cc_final: 0.6078 (mtm180) REVERT: B 274 ARG cc_start: 0.7703 (ttp-170) cc_final: 0.6605 (ttt-90) REVERT: B 276 GLN cc_start: 0.8389 (tt0) cc_final: 0.8158 (tt0) REVERT: B 344 PHE cc_start: 0.7977 (t80) cc_final: 0.7471 (t80) REVERT: B 431 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6434 (pm20) REVERT: B 524 PRO cc_start: 0.7531 (Cg_exo) cc_final: 0.7279 (Cg_endo) REVERT: B 570 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7219 (pp30) REVERT: B 599 MET cc_start: 0.1019 (mmp) cc_final: 0.0143 (mmp) REVERT: C 95 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: C 104 TRP cc_start: 0.6547 (t60) cc_final: 0.5926 (t-100) REVERT: C 136 MET cc_start: 0.7065 (mtt) cc_final: 0.6655 (mtp) REVERT: C 218 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7310 (mm-30) REVERT: C 222 ARG cc_start: 0.6815 (mtt180) cc_final: 0.6367 (mmm160) REVERT: C 274 ARG cc_start: 0.7583 (ttp-170) cc_final: 0.7016 (ttm-80) REVERT: C 461 TRP cc_start: 0.7688 (p-90) cc_final: 0.7484 (p-90) REVERT: C 590 LEU cc_start: 0.3741 (OUTLIER) cc_final: 0.3397 (mp) REVERT: C 599 MET cc_start: 0.2651 (mmt) cc_final: 0.1953 (mmp) REVERT: D 75 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7687 (p0) REVERT: D 89 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7553 (mt0) REVERT: D 104 TRP cc_start: 0.6839 (t60) cc_final: 0.6382 (t-100) REVERT: D 274 ARG cc_start: 0.7414 (ttp-170) cc_final: 0.6815 (ttt90) REVERT: D 314 ILE cc_start: 0.8511 (mt) cc_final: 0.8310 (mt) REVERT: D 331 SER cc_start: 0.8156 (t) cc_final: 0.7750 (m) REVERT: D 332 LYS cc_start: 0.8816 (mmtm) cc_final: 0.8466 (tppt) REVERT: D 417 HIS cc_start: 0.7278 (t-90) cc_final: 0.6972 (t70) REVERT: D 529 PHE cc_start: 0.6267 (p90) cc_final: 0.6066 (p90) REVERT: D 533 MET cc_start: 0.3803 (ptp) cc_final: 0.3258 (ppp) REVERT: D 589 ARG cc_start: 0.0540 (OUTLIER) cc_final: 0.0124 (tpm170) REVERT: E 53 ASN cc_start: 0.8588 (t0) cc_final: 0.8322 (t0) REVERT: E 126 ASN cc_start: 0.6098 (OUTLIER) cc_final: 0.5859 (t0) REVERT: E 136 MET cc_start: 0.7288 (mtp) cc_final: 0.6771 (mtm) REVERT: E 166 GLU cc_start: 0.6587 (mt-10) cc_final: 0.5805 (mm-30) REVERT: E 188 LYS cc_start: 0.8419 (mppt) cc_final: 0.8132 (mmtt) REVERT: E 230 GLN cc_start: 0.7834 (mt0) cc_final: 0.7536 (mt0) REVERT: E 270 ARG cc_start: 0.7329 (mtp-110) cc_final: 0.6660 (ttm110) REVERT: E 274 ARG cc_start: 0.7478 (ttp-170) cc_final: 0.7008 (ttt90) REVERT: E 332 LYS cc_start: 0.8743 (mttt) cc_final: 0.8363 (mmtm) REVERT: E 340 HIS cc_start: 0.7639 (t-90) cc_final: 0.7299 (t-170) REVERT: E 488 MET cc_start: 0.3634 (tmm) cc_final: 0.2909 (tmt) REVERT: E 599 MET cc_start: 0.2620 (mmp) cc_final: 0.1774 (mmp) REVERT: F 39 LYS cc_start: 0.7938 (mmtp) cc_final: 0.7591 (mmpt) REVERT: F 57 VAL cc_start: 0.7722 (p) cc_final: 0.7507 (m) REVERT: F 105 MET cc_start: 0.7320 (ttm) cc_final: 0.5992 (tmt) REVERT: F 160 LYS cc_start: 0.8037 (mttm) cc_final: 0.7793 (mmmm) REVERT: F 189 MET cc_start: 0.6011 (OUTLIER) cc_final: 0.5634 (ttm) REVERT: F 218 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7553 (mt-10) REVERT: F 222 ARG cc_start: 0.7150 (mtt180) cc_final: 0.6442 (mpt90) REVERT: F 253 GLU cc_start: 0.6664 (pt0) cc_final: 0.6002 (pm20) REVERT: F 270 ARG cc_start: 0.7308 (mtp-110) cc_final: 0.6740 (ttm170) REVERT: F 274 ARG cc_start: 0.7504 (ttp-170) cc_final: 0.6848 (tmm160) REVERT: F 340 HIS cc_start: 0.8265 (t70) cc_final: 0.7707 (t70) REVERT: F 599 MET cc_start: 0.2958 (mmp) cc_final: 0.2551 (mmp) REVERT: G 105 MET cc_start: 0.6848 (OUTLIER) cc_final: 0.5690 (tmm) REVERT: G 218 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7306 (mm-30) REVERT: G 222 ARG cc_start: 0.6973 (mtt180) cc_final: 0.6328 (mpt90) REVERT: G 270 ARG cc_start: 0.6991 (mtp-110) cc_final: 0.6531 (mpp-170) REVERT: G 454 LYS cc_start: 0.8148 (tttt) cc_final: 0.7749 (tptt) REVERT: G 488 MET cc_start: 0.4970 (tmt) cc_final: 0.4477 (tmm) REVERT: G 586 LEU cc_start: 0.7305 (tm) cc_final: 0.6953 (pp) REVERT: G 599 MET cc_start: 0.1860 (OUTLIER) cc_final: 0.1562 (mpt) REVERT: H 95 GLU cc_start: 0.8132 (mp0) cc_final: 0.7615 (mt-10) REVERT: H 96 MET cc_start: 0.7879 (mtt) cc_final: 0.7616 (mtm) REVERT: H 218 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7392 (mt-10) REVERT: H 270 ARG cc_start: 0.6989 (mtt180) cc_final: 0.6454 (mmm160) REVERT: H 274 ARG cc_start: 0.7586 (ttp-170) cc_final: 0.7214 (ttm170) REVERT: H 336 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8363 (p) REVERT: H 339 ARG cc_start: 0.7925 (mtp85) cc_final: 0.7651 (ttm-80) REVERT: H 340 HIS cc_start: 0.7842 (OUTLIER) cc_final: 0.7243 (t70) REVERT: H 344 PHE cc_start: 0.7135 (t80) cc_final: 0.6785 (t80) REVERT: H 594 THR cc_start: 0.5660 (OUTLIER) cc_final: 0.5198 (t) REVERT: I 58 ASP cc_start: 0.8078 (m-30) cc_final: 0.7694 (m-30) REVERT: I 209 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.8053 (p) REVERT: I 218 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7840 (mt-10) REVERT: I 222 ARG cc_start: 0.7079 (mtt180) cc_final: 0.6415 (mtp180) REVERT: I 263 THR cc_start: 0.7404 (OUTLIER) cc_final: 0.7087 (t) REVERT: I 344 PHE cc_start: 0.7488 (t80) cc_final: 0.7222 (OUTLIER) REVERT: I 425 GLU cc_start: 0.7051 (tt0) cc_final: 0.6732 (tm-30) REVERT: J 105 MET cc_start: 0.6829 (OUTLIER) cc_final: 0.6297 (ttt) REVERT: J 166 GLU cc_start: 0.6745 (mt-10) cc_final: 0.6205 (pm20) REVERT: J 187 THR cc_start: 0.7963 (OUTLIER) cc_final: 0.7455 (m) REVERT: J 188 LYS cc_start: 0.8517 (mmpt) cc_final: 0.7995 (pptt) REVERT: J 195 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6932 (tt0) REVERT: J 270 ARG cc_start: 0.6725 (mtp-110) cc_final: 0.5970 (mtm180) REVERT: J 274 ARG cc_start: 0.7630 (ttp-170) cc_final: 0.6582 (ttt-90) REVERT: J 276 GLN cc_start: 0.8440 (tt0) cc_final: 0.8212 (tt0) REVERT: J 336 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8703 (p) REVERT: J 461 TRP cc_start: 0.7506 (p-90) cc_final: 0.6185 (p-90) REVERT: J 524 PRO cc_start: 0.7351 (Cg_exo) cc_final: 0.7093 (Cg_endo) REVERT: J 570 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.7026 (pp30) REVERT: K 77 GLN cc_start: 0.7900 (mt0) cc_final: 0.7153 (mm-40) REVERT: K 95 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: K 104 TRP cc_start: 0.6478 (t60) cc_final: 0.5855 (t-100) REVERT: K 218 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7581 (mm-30) REVERT: K 222 ARG cc_start: 0.6894 (mtt180) cc_final: 0.6426 (mmm160) REVERT: K 274 ARG cc_start: 0.7558 (ttp-170) cc_final: 0.6991 (ttm-80) REVERT: K 417 HIS cc_start: 0.7958 (OUTLIER) cc_final: 0.7402 (t70) REVERT: K 599 MET cc_start: 0.3328 (mmp) cc_final: 0.2407 (mmp) REVERT: L 57 VAL cc_start: 0.7607 (p) cc_final: 0.7399 (m) REVERT: L 63 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7492 (mpt) REVERT: L 75 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7707 (p0) REVERT: L 96 MET cc_start: 0.7178 (mtm) cc_final: 0.6632 (mtm) REVERT: L 104 TRP cc_start: 0.6747 (t60) cc_final: 0.6280 (t-100) REVERT: L 136 MET cc_start: 0.6601 (OUTLIER) cc_final: 0.6290 (mpp) REVERT: L 188 LYS cc_start: 0.7988 (mppt) cc_final: 0.7646 (pmmt) REVERT: L 219 ASP cc_start: 0.7957 (t0) cc_final: 0.7597 (t70) REVERT: L 274 ARG cc_start: 0.7349 (ttp-170) cc_final: 0.6804 (ttt90) REVERT: L 331 SER cc_start: 0.8155 (t) cc_final: 0.7775 (m) REVERT: L 457 PHE cc_start: 0.7391 (p90) cc_final: 0.7089 (p90) REVERT: L 503 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7580 (tm) REVERT: L 589 ARG cc_start: 0.1418 (OUTLIER) cc_final: 0.0702 (tpm170) REVERT: L 599 MET cc_start: 0.2512 (OUTLIER) cc_final: 0.0571 (mmt) REVERT: M 53 ASN cc_start: 0.8675 (t0) cc_final: 0.8310 (t0) REVERT: M 104 TRP cc_start: 0.6545 (t60) cc_final: 0.6089 (t-100) REVERT: M 136 MET cc_start: 0.7343 (mtp) cc_final: 0.6644 (mtm) REVERT: M 166 GLU cc_start: 0.6559 (mt-10) cc_final: 0.5820 (mm-30) REVERT: M 188 LYS cc_start: 0.8896 (mppt) cc_final: 0.8611 (mppt) REVERT: M 222 ARG cc_start: 0.7245 (mtt180) cc_final: 0.6734 (mtp180) REVERT: M 230 GLN cc_start: 0.8104 (mt0) cc_final: 0.7741 (mt0) REVERT: M 270 ARG cc_start: 0.7386 (mtp-110) cc_final: 0.6707 (ttm110) REVERT: M 274 ARG cc_start: 0.7566 (ttp-170) cc_final: 0.7208 (ttt90) REVERT: M 332 LYS cc_start: 0.8730 (mttt) cc_final: 0.8382 (mmtm) REVERT: M 488 MET cc_start: 0.3620 (tmm) cc_final: 0.2885 (tmt) REVERT: M 586 LEU cc_start: 0.5648 (OUTLIER) cc_final: 0.4829 (pp) REVERT: M 599 MET cc_start: 0.2060 (mmp) cc_final: 0.1610 (mmp) REVERT: N 94 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8598 (mm) REVERT: N 105 MET cc_start: 0.7688 (ttm) cc_final: 0.6250 (tmm) REVERT: N 160 LYS cc_start: 0.8075 (mttm) cc_final: 0.7839 (mmmm) REVERT: N 218 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7396 (mt-10) REVERT: N 253 GLU cc_start: 0.6666 (pt0) cc_final: 0.6138 (pm20) REVERT: N 266 TYR cc_start: 0.7270 (t80) cc_final: 0.6558 (m-80) REVERT: N 274 ARG cc_start: 0.7469 (ttp-170) cc_final: 0.6942 (ttp-170) REVERT: N 340 HIS cc_start: 0.8190 (t-90) cc_final: 0.7379 (t70) REVERT: N 344 PHE cc_start: 0.8022 (t80) cc_final: 0.7521 (t80) REVERT: N 345 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.7955 (m-40) REVERT: N 599 MET cc_start: 0.3083 (mmp) cc_final: 0.2428 (mmt) REVERT: O 105 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.5714 (tmm) REVERT: O 166 GLU cc_start: 0.6745 (mt-10) cc_final: 0.6393 (mp0) REVERT: O 218 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7365 (mm-30) REVERT: O 222 ARG cc_start: 0.7008 (mtt180) cc_final: 0.6255 (mpt90) REVERT: O 270 ARG cc_start: 0.6933 (mtp-110) cc_final: 0.6475 (mpp-170) REVERT: O 454 LYS cc_start: 0.8091 (tttt) cc_final: 0.7664 (tptp) REVERT: O 488 MET cc_start: 0.4704 (tmt) cc_final: 0.4312 (tmm) REVERT: O 533 MET cc_start: 0.3941 (mtp) cc_final: 0.3418 (pmm) REVERT: P 61 ARG cc_start: 0.7572 (tpp-160) cc_final: 0.7172 (tpp-160) REVERT: P 63 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.7080 (mmm) REVERT: P 218 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7441 (mt-10) REVERT: P 270 ARG cc_start: 0.7393 (mtp-110) cc_final: 0.7164 (mtm180) REVERT: P 336 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8437 (p) REVERT: P 339 ARG cc_start: 0.8174 (mtt90) cc_final: 0.7693 (ttm-80) REVERT: P 340 HIS cc_start: 0.7920 (OUTLIER) cc_final: 0.7311 (t70) REVERT: P 344 PHE cc_start: 0.7228 (t80) cc_final: 0.6898 (t80) outliers start: 277 outliers final: 140 residues processed: 721 average time/residue: 1.3019 time to fit residues: 1266.0884 Evaluate side-chains 662 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 487 time to evaluate : 5.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 521 PHE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 515 TYR Chi-restraints excluded: chain D residue 523 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 589 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 126 ASN Chi-restraints excluded: chain E residue 189 MET Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 189 MET Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 599 MET Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 310 LEU Chi-restraints excluded: chain H residue 336 THR Chi-restraints excluded: chain H residue 340 HIS Chi-restraints excluded: chain H residue 428 SER Chi-restraints excluded: chain H residue 594 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 503 LEU Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 53 ASN Chi-restraints excluded: chain J residue 105 MET Chi-restraints excluded: chain J residue 187 THR Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 297 THR Chi-restraints excluded: chain J residue 336 THR Chi-restraints excluded: chain J residue 418 LEU Chi-restraints excluded: chain J residue 511 VAL Chi-restraints excluded: chain J residue 564 VAL Chi-restraints excluded: chain J residue 570 GLN Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 417 HIS Chi-restraints excluded: chain K residue 523 VAL Chi-restraints excluded: chain K residue 564 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 63 MET Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 136 MET Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain L residue 247 ILE Chi-restraints excluded: chain L residue 263 THR Chi-restraints excluded: chain L residue 281 VAL Chi-restraints excluded: chain L residue 444 THR Chi-restraints excluded: chain L residue 445 VAL Chi-restraints excluded: chain L residue 503 LEU Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain L residue 523 VAL Chi-restraints excluded: chain L residue 589 ARG Chi-restraints excluded: chain L residue 599 MET Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 181 GLN Chi-restraints excluded: chain M residue 189 MET Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 586 LEU Chi-restraints excluded: chain M residue 590 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 247 ILE Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 345 ASN Chi-restraints excluded: chain N residue 430 LEU Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain N residue 594 THR Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 105 MET Chi-restraints excluded: chain O residue 136 MET Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 165 SER Chi-restraints excluded: chain O residue 209 VAL Chi-restraints excluded: chain O residue 254 THR Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 523 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 63 MET Chi-restraints excluded: chain P residue 96 MET Chi-restraints excluded: chain P residue 162 THR Chi-restraints excluded: chain P residue 187 THR Chi-restraints excluded: chain P residue 189 MET Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain P residue 247 ILE Chi-restraints excluded: chain P residue 260 THR Chi-restraints excluded: chain P residue 271 THR Chi-restraints excluded: chain P residue 336 THR Chi-restraints excluded: chain P residue 340 HIS Chi-restraints excluded: chain P residue 428 SER Chi-restraints excluded: chain P residue 523 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 275 optimal weight: 8.9990 chunk 738 optimal weight: 40.0000 chunk 162 optimal weight: 5.9990 chunk 481 optimal weight: 4.9990 chunk 202 optimal weight: 20.0000 chunk 820 optimal weight: 0.9990 chunk 681 optimal weight: 50.0000 chunk 379 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 271 optimal weight: 1.9990 chunk 430 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 561 HIS ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN D 89 GLN D 181 GLN D 561 HIS E 181 GLN ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 GLN G 181 GLN H 181 GLN H 401 ASN ** I 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 401 ASN J 204 HIS J 561 HIS K 417 HIS ** K 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN L 417 HIS ** M 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 181 GLN ** P 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 383 GLN P 401 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 68624 Z= 0.379 Angle : 0.618 12.044 93136 Z= 0.308 Chirality : 0.046 0.350 10816 Planarity : 0.005 0.061 11792 Dihedral : 8.183 101.021 10485 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.27 % Favored : 95.56 % Rotamer: Outliers : 3.81 % Allowed : 13.46 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % 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: -0.83 (0.09), residues: 8432 helix: 0.77 (0.14), residues: 1344 sheet: -0.53 (0.08), residues: 3744 loop : -0.97 (0.11), residues: 3344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 292 HIS 0.013 0.001 HIS K 417 PHE 0.029 0.002 PHE D 528 TYR 0.021 0.001 TYR C 593 ARG 0.005 0.000 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 492 time to evaluate : 5.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8263 (m-30) cc_final: 0.8039 (m-30) REVERT: A 59 MET cc_start: 0.7422 (mmp) cc_final: 0.7196 (mmm) REVERT: A 95 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: A 222 ARG cc_start: 0.7096 (mtt180) cc_final: 0.6446 (mtp180) REVERT: A 344 PHE cc_start: 0.7496 (t80) cc_final: 0.7249 (OUTLIER) REVERT: A 401 ASN cc_start: 0.7124 (t0) cc_final: 0.6059 (t0) REVERT: A 425 GLU cc_start: 0.6853 (tt0) cc_final: 0.6650 (tm-30) REVERT: A 488 MET cc_start: 0.7606 (tmt) cc_final: 0.7279 (tmt) REVERT: B 104 TRP cc_start: 0.6955 (t60) cc_final: 0.6234 (t-100) REVERT: B 105 MET cc_start: 0.6693 (OUTLIER) cc_final: 0.6240 (ttt) REVERT: B 166 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6220 (pm20) REVERT: B 222 ARG cc_start: 0.7028 (mtt180) cc_final: 0.6103 (mtt90) REVERT: B 270 ARG cc_start: 0.7071 (mtp-110) cc_final: 0.6164 (mtm180) REVERT: B 274 ARG cc_start: 0.7659 (ttp-170) cc_final: 0.6578 (ttt-90) REVERT: B 276 GLN cc_start: 0.8372 (tt0) cc_final: 0.8103 (tt0) REVERT: B 344 PHE cc_start: 0.7888 (t80) cc_final: 0.7471 (t80) REVERT: B 431 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6410 (pm20) REVERT: B 524 PRO cc_start: 0.7557 (Cg_exo) cc_final: 0.7308 (Cg_endo) REVERT: B 570 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.7223 (pp30) REVERT: B 599 MET cc_start: 0.1194 (mmp) cc_final: 0.0036 (mmp) REVERT: C 95 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: C 104 TRP cc_start: 0.6574 (t60) cc_final: 0.5947 (t-100) REVERT: C 136 MET cc_start: 0.7031 (mtt) cc_final: 0.6624 (mtp) REVERT: C 218 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7307 (mm-30) REVERT: C 222 ARG cc_start: 0.6840 (mtt180) cc_final: 0.6381 (mmm160) REVERT: C 274 ARG cc_start: 0.7605 (ttp-170) cc_final: 0.7048 (ttm-80) REVERT: C 461 TRP cc_start: 0.7742 (p-90) cc_final: 0.7432 (p-90) REVERT: C 599 MET cc_start: 0.2733 (mmt) cc_final: 0.2079 (mmp) REVERT: D 75 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7692 (p0) REVERT: D 104 TRP cc_start: 0.6919 (t60) cc_final: 0.6461 (t-100) REVERT: D 105 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6781 (ttt) REVERT: D 136 MET cc_start: 0.6796 (mtp) cc_final: 0.6343 (mtt) REVERT: D 274 ARG cc_start: 0.7447 (ttp-170) cc_final: 0.6834 (ttt90) REVERT: D 314 ILE cc_start: 0.8564 (mt) cc_final: 0.8344 (mt) REVERT: D 331 SER cc_start: 0.8111 (t) cc_final: 0.7682 (m) REVERT: D 332 LYS cc_start: 0.8815 (mmtm) cc_final: 0.8466 (tppt) REVERT: D 417 HIS cc_start: 0.7259 (t-90) cc_final: 0.7022 (t70) REVERT: D 533 MET cc_start: 0.3718 (ptp) cc_final: 0.3166 (ppp) REVERT: E 53 ASN cc_start: 0.8584 (t0) cc_final: 0.8343 (t0) REVERT: E 136 MET cc_start: 0.7304 (mtp) cc_final: 0.6768 (mtm) REVERT: E 166 GLU cc_start: 0.6518 (mt-10) cc_final: 0.5773 (mm-30) REVERT: E 188 LYS cc_start: 0.8436 (mppt) cc_final: 0.8130 (mmmt) REVERT: E 189 MET cc_start: 0.5546 (OUTLIER) cc_final: 0.5090 (ttm) REVERT: E 230 GLN cc_start: 0.7882 (mt0) cc_final: 0.7574 (mt0) REVERT: E 270 ARG cc_start: 0.7308 (mtp-110) cc_final: 0.6715 (ttm110) REVERT: E 274 ARG cc_start: 0.7568 (ttp-170) cc_final: 0.7129 (ttt90) REVERT: E 332 LYS cc_start: 0.8749 (mttt) cc_final: 0.8355 (mmtm) REVERT: E 340 HIS cc_start: 0.7581 (t-90) cc_final: 0.7220 (t-170) REVERT: E 488 MET cc_start: 0.3187 (tmm) cc_final: 0.2510 (tmt) REVERT: E 586 LEU cc_start: 0.5551 (mp) cc_final: 0.4740 (pp) REVERT: E 599 MET cc_start: 0.2700 (mmp) cc_final: 0.1512 (mmp) REVERT: F 39 LYS cc_start: 0.7918 (mmtp) cc_final: 0.7629 (mmtt) REVERT: F 105 MET cc_start: 0.7379 (ttm) cc_final: 0.5975 (tmt) REVERT: F 160 LYS cc_start: 0.8069 (mttm) cc_final: 0.7800 (mmmm) REVERT: F 189 MET cc_start: 0.5933 (OUTLIER) cc_final: 0.5729 (ttm) REVERT: F 218 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7586 (mt-10) REVERT: F 222 ARG cc_start: 0.7063 (mtt180) cc_final: 0.6422 (mpt90) REVERT: F 253 GLU cc_start: 0.6676 (pt0) cc_final: 0.5990 (pm20) REVERT: F 270 ARG cc_start: 0.7309 (mtp-110) cc_final: 0.6741 (ttm170) REVERT: F 274 ARG cc_start: 0.7556 (ttp-170) cc_final: 0.6862 (tmm160) REVERT: F 340 HIS cc_start: 0.8270 (t70) cc_final: 0.7731 (t70) REVERT: F 599 MET cc_start: 0.2967 (mmp) cc_final: 0.2558 (mmp) REVERT: G 59 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7203 (mmp) REVERT: G 104 TRP cc_start: 0.6252 (t60) cc_final: 0.5846 (t60) REVERT: G 105 MET cc_start: 0.6869 (OUTLIER) cc_final: 0.5730 (tmm) REVERT: G 218 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7293 (mm-30) REVERT: G 222 ARG cc_start: 0.6979 (mtt180) cc_final: 0.6330 (mpt90) REVERT: G 270 ARG cc_start: 0.7064 (mtp-110) cc_final: 0.6507 (mpp-170) REVERT: G 454 LYS cc_start: 0.8174 (tttt) cc_final: 0.7705 (tptp) REVERT: G 488 MET cc_start: 0.4967 (tmt) cc_final: 0.4511 (tmm) REVERT: G 586 LEU cc_start: 0.7281 (tm) cc_final: 0.6920 (pp) REVERT: G 599 MET cc_start: 0.2021 (OUTLIER) cc_final: 0.1711 (mpt) REVERT: H 95 GLU cc_start: 0.8011 (mp0) cc_final: 0.7517 (mt-10) REVERT: H 104 TRP cc_start: 0.6699 (t60) cc_final: 0.6375 (t60) REVERT: H 218 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7467 (mt-10) REVERT: H 270 ARG cc_start: 0.7006 (mtt180) cc_final: 0.6451 (mmm160) REVERT: H 274 ARG cc_start: 0.7563 (ttp-170) cc_final: 0.7149 (ttm-80) REVERT: H 336 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8352 (p) REVERT: H 339 ARG cc_start: 0.7931 (mtp85) cc_final: 0.7644 (ttm-80) REVERT: H 340 HIS cc_start: 0.7866 (OUTLIER) cc_final: 0.7316 (t70) REVERT: H 344 PHE cc_start: 0.7135 (t80) cc_final: 0.6772 (t80) REVERT: H 594 THR cc_start: 0.5922 (OUTLIER) cc_final: 0.5531 (t) REVERT: I 95 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7465 (mp0) REVERT: I 222 ARG cc_start: 0.7048 (mtt180) cc_final: 0.6395 (mtp180) REVERT: I 344 PHE cc_start: 0.7571 (t80) cc_final: 0.7286 (OUTLIER) REVERT: I 425 GLU cc_start: 0.7059 (tt0) cc_final: 0.6729 (tm-30) REVERT: J 105 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.6272 (ttt) REVERT: J 166 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6268 (pm20) REVERT: J 188 LYS cc_start: 0.8297 (mmpt) cc_final: 0.8012 (pptt) REVERT: J 195 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6916 (tt0) REVERT: J 270 ARG cc_start: 0.6800 (mtp-110) cc_final: 0.6082 (mtm180) REVERT: J 274 ARG cc_start: 0.7590 (ttp-170) cc_final: 0.6560 (ttt-90) REVERT: J 276 GLN cc_start: 0.8394 (tt0) cc_final: 0.8126 (tt0) REVERT: J 336 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8700 (p) REVERT: J 461 TRP cc_start: 0.7616 (p-90) cc_final: 0.6308 (p-90) REVERT: J 524 PRO cc_start: 0.7363 (Cg_exo) cc_final: 0.7108 (Cg_endo) REVERT: J 570 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.7051 (pp30) REVERT: J 589 ARG cc_start: 0.2323 (OUTLIER) cc_final: 0.0538 (ttm110) REVERT: K 77 GLN cc_start: 0.7888 (mt0) cc_final: 0.7186 (mm-40) REVERT: K 95 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: K 104 TRP cc_start: 0.6564 (t60) cc_final: 0.5929 (t-100) REVERT: K 218 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7635 (mm-30) REVERT: K 222 ARG cc_start: 0.6972 (mtt180) cc_final: 0.6561 (mmm160) REVERT: K 274 ARG cc_start: 0.7591 (ttp-170) cc_final: 0.7028 (ttm-80) REVERT: K 599 MET cc_start: 0.3144 (mmp) cc_final: 0.2521 (mmp) REVERT: L 57 VAL cc_start: 0.7679 (p) cc_final: 0.7439 (m) REVERT: L 75 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7707 (p0) REVERT: L 96 MET cc_start: 0.7120 (mtm) cc_final: 0.6568 (mtm) REVERT: L 104 TRP cc_start: 0.6829 (t60) cc_final: 0.6344 (t-100) REVERT: L 108 GLN cc_start: 0.7102 (tm-30) cc_final: 0.6827 (tt0) REVERT: L 136 MET cc_start: 0.6539 (OUTLIER) cc_final: 0.6302 (mpp) REVERT: L 219 ASP cc_start: 0.7922 (t0) cc_final: 0.7594 (t70) REVERT: L 274 ARG cc_start: 0.7330 (ttp-170) cc_final: 0.6791 (ttt90) REVERT: L 331 SER cc_start: 0.8089 (t) cc_final: 0.7647 (m) REVERT: L 332 LYS cc_start: 0.8799 (mmtm) cc_final: 0.8443 (tppt) REVERT: L 418 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7807 (tp) REVERT: L 457 PHE cc_start: 0.7534 (p90) cc_final: 0.7259 (p90) REVERT: L 503 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7648 (tm) REVERT: L 589 ARG cc_start: 0.1516 (OUTLIER) cc_final: 0.0775 (tpm170) REVERT: L 599 MET cc_start: 0.2630 (OUTLIER) cc_final: 0.0866 (mmt) REVERT: M 53 ASN cc_start: 0.8691 (t0) cc_final: 0.8332 (t0) REVERT: M 104 TRP cc_start: 0.6607 (t60) cc_final: 0.6145 (t-100) REVERT: M 136 MET cc_start: 0.7375 (mtp) cc_final: 0.6666 (mtm) REVERT: M 166 GLU cc_start: 0.6634 (mt-10) cc_final: 0.5839 (mm-30) REVERT: M 188 LYS cc_start: 0.8907 (mppt) cc_final: 0.8609 (mppt) REVERT: M 203 THR cc_start: 0.8907 (m) cc_final: 0.8341 (p) REVERT: M 222 ARG cc_start: 0.7232 (mtt180) cc_final: 0.6695 (mtp180) REVERT: M 230 GLN cc_start: 0.8164 (mt0) cc_final: 0.7814 (mt0) REVERT: M 270 ARG cc_start: 0.7445 (mtp-110) cc_final: 0.6762 (ttm110) REVERT: M 274 ARG cc_start: 0.7614 (ttp-170) cc_final: 0.7259 (ttt90) REVERT: M 332 LYS cc_start: 0.8728 (mttt) cc_final: 0.8372 (mmtm) REVERT: M 488 MET cc_start: 0.3667 (tmm) cc_final: 0.3012 (tmt) REVERT: M 586 LEU cc_start: 0.5902 (OUTLIER) cc_final: 0.5104 (pp) REVERT: M 599 MET cc_start: 0.2412 (mmp) cc_final: 0.1811 (mmp) REVERT: N 105 MET cc_start: 0.7678 (ttm) cc_final: 0.6207 (tmm) REVERT: N 160 LYS cc_start: 0.8108 (mttm) cc_final: 0.7789 (mmmm) REVERT: N 218 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7591 (mt-10) REVERT: N 253 GLU cc_start: 0.6730 (pt0) cc_final: 0.6183 (pm20) REVERT: N 274 ARG cc_start: 0.7528 (ttp-170) cc_final: 0.6957 (ttp-170) REVERT: N 340 HIS cc_start: 0.8185 (t-90) cc_final: 0.7344 (t70) REVERT: N 344 PHE cc_start: 0.8029 (t80) cc_final: 0.7514 (t80) REVERT: N 345 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.7949 (m-40) REVERT: N 599 MET cc_start: 0.2982 (mmp) cc_final: 0.2435 (mmt) REVERT: O 59 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.7237 (mmp) REVERT: O 104 TRP cc_start: 0.6178 (t60) cc_final: 0.5846 (t60) REVERT: O 105 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.5669 (tmm) REVERT: O 166 GLU cc_start: 0.6809 (mt-10) cc_final: 0.6579 (pm20) REVERT: O 218 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7361 (mm-30) REVERT: O 222 ARG cc_start: 0.6996 (mtt180) cc_final: 0.6344 (mpt90) REVERT: O 270 ARG cc_start: 0.6951 (mtp-110) cc_final: 0.6449 (mpp-170) REVERT: O 488 MET cc_start: 0.4601 (tmt) cc_final: 0.4172 (tmm) REVERT: P 63 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7168 (mmm) REVERT: P 94 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8552 (mm) REVERT: P 218 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7470 (mt-10) REVERT: P 270 ARG cc_start: 0.7400 (mtp-110) cc_final: 0.7169 (mtm180) REVERT: P 336 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8429 (p) REVERT: P 339 ARG cc_start: 0.8175 (mtt90) cc_final: 0.7675 (ttm-80) REVERT: P 340 HIS cc_start: 0.7974 (OUTLIER) cc_final: 0.7413 (t70) REVERT: P 344 PHE cc_start: 0.7210 (t80) cc_final: 0.6858 (t80) outliers start: 286 outliers final: 167 residues processed: 718 average time/residue: 1.2317 time to fit residues: 1201.1165 Evaluate side-chains 677 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 477 time to evaluate : 5.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 521 PHE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 515 TYR Chi-restraints excluded: chain D residue 523 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 189 MET Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 189 MET Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 392 VAL Chi-restraints excluded: chain G residue 523 VAL Chi-restraints excluded: chain G residue 599 MET Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 310 LEU Chi-restraints excluded: chain H residue 336 THR Chi-restraints excluded: chain H residue 340 HIS Chi-restraints excluded: chain H residue 428 SER Chi-restraints excluded: chain H residue 594 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 345 ASN Chi-restraints excluded: chain I residue 503 LEU Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 105 MET Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 271 THR Chi-restraints excluded: chain J residue 297 THR Chi-restraints excluded: chain J residue 336 THR Chi-restraints excluded: chain J residue 511 VAL Chi-restraints excluded: chain J residue 564 VAL Chi-restraints excluded: chain J residue 570 GLN Chi-restraints excluded: chain J residue 586 LEU Chi-restraints excluded: chain J residue 589 ARG Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 523 VAL Chi-restraints excluded: chain K residue 564 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 136 MET Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain L residue 247 ILE Chi-restraints excluded: chain L residue 263 THR Chi-restraints excluded: chain L residue 281 VAL Chi-restraints excluded: chain L residue 403 LEU Chi-restraints excluded: chain L residue 418 LEU Chi-restraints excluded: chain L residue 444 THR Chi-restraints excluded: chain L residue 445 VAL Chi-restraints excluded: chain L residue 503 LEU Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain L residue 523 VAL Chi-restraints excluded: chain L residue 589 ARG Chi-restraints excluded: chain L residue 599 MET Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 181 GLN Chi-restraints excluded: chain M residue 189 MET Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 586 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 247 ILE Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 345 ASN Chi-restraints excluded: chain N residue 430 LEU Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain N residue 594 THR Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 59 MET Chi-restraints excluded: chain O residue 105 MET Chi-restraints excluded: chain O residue 136 MET Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 165 SER Chi-restraints excluded: chain O residue 188 LYS Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 209 VAL Chi-restraints excluded: chain O residue 254 THR Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 271 THR Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain O residue 392 VAL Chi-restraints excluded: chain O residue 523 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 63 MET Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 96 MET Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 187 THR Chi-restraints excluded: chain P residue 189 MET Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain P residue 247 ILE Chi-restraints excluded: chain P residue 260 THR Chi-restraints excluded: chain P residue 271 THR Chi-restraints excluded: chain P residue 336 THR Chi-restraints excluded: chain P residue 340 HIS Chi-restraints excluded: chain P residue 428 SER Chi-restraints excluded: chain P residue 523 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 791 optimal weight: 40.0000 chunk 92 optimal weight: 9.9990 chunk 467 optimal weight: 0.0070 chunk 599 optimal weight: 6.9990 chunk 464 optimal weight: 30.0000 chunk 690 optimal weight: 0.8980 chunk 458 optimal weight: 20.0000 chunk 817 optimal weight: 9.9990 chunk 511 optimal weight: 20.0000 chunk 498 optimal weight: 20.0000 chunk 377 optimal weight: 2.9990 overall best weight: 4.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 HIS C 417 HIS D 181 GLN ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN F 181 GLN F 345 ASN G 181 GLN H 383 GLN ** I 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 401 ASN K 144 GLN K 417 HIS ** K 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN L 417 HIS M 340 HIS M 399 GLN ** N 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 181 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 68624 Z= 0.514 Angle : 0.674 11.187 93136 Z= 0.339 Chirality : 0.048 0.376 10816 Planarity : 0.005 0.068 11792 Dihedral : 7.862 102.969 10485 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.79 % Favored : 95.07 % Rotamer: Outliers : 4.33 % Allowed : 13.34 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.06 (0.09), residues: 8432 helix: 0.65 (0.14), residues: 1344 sheet: -0.74 (0.08), residues: 3744 loop : -1.05 (0.11), residues: 3344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 292 HIS 0.010 0.002 HIS D 299 PHE 0.060 0.002 PHE C 525 TYR 0.025 0.002 TYR M 593 ARG 0.005 0.001 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 325 poor density : 486 time to evaluate : 5.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: A 326 LEU cc_start: 0.8527 (mt) cc_final: 0.8298 (pt) REVERT: A 344 PHE cc_start: 0.7520 (t80) cc_final: 0.7261 (OUTLIER) REVERT: A 401 ASN cc_start: 0.7325 (t0) cc_final: 0.6804 (t0) REVERT: A 488 MET cc_start: 0.7546 (tmt) cc_final: 0.7223 (tmt) REVERT: B 104 TRP cc_start: 0.6989 (t60) cc_final: 0.6321 (t-100) REVERT: B 105 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.6300 (ttt) REVERT: B 166 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6234 (pm20) REVERT: B 222 ARG cc_start: 0.7067 (mtt180) cc_final: 0.6429 (mtt90) REVERT: B 274 ARG cc_start: 0.7702 (ttp-170) cc_final: 0.6607 (ttt-90) REVERT: B 276 GLN cc_start: 0.8381 (tt0) cc_final: 0.8096 (tt0) REVERT: B 344 PHE cc_start: 0.7926 (t80) cc_final: 0.7537 (t80) REVERT: B 431 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6382 (pm20) REVERT: B 524 PRO cc_start: 0.7527 (Cg_exo) cc_final: 0.7274 (Cg_endo) REVERT: B 570 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7265 (pp30) REVERT: B 599 MET cc_start: 0.1160 (mmp) cc_final: 0.0015 (mmp) REVERT: C 95 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: C 99 GLU cc_start: 0.7820 (tt0) cc_final: 0.7611 (tt0) REVERT: C 104 TRP cc_start: 0.6665 (t60) cc_final: 0.6038 (t-100) REVERT: C 136 MET cc_start: 0.7024 (mtt) cc_final: 0.6619 (mtp) REVERT: C 218 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7388 (mm-30) REVERT: C 222 ARG cc_start: 0.6962 (mtt180) cc_final: 0.6465 (mmm160) REVERT: C 274 ARG cc_start: 0.7598 (ttp-170) cc_final: 0.7038 (ttm-80) REVERT: C 461 TRP cc_start: 0.7721 (p-90) cc_final: 0.7475 (p-90) REVERT: C 599 MET cc_start: 0.3172 (mmt) cc_final: 0.2358 (mmp) REVERT: D 39 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7798 (mtpt) REVERT: D 75 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7674 (p0) REVERT: D 89 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7616 (mt0) REVERT: D 104 TRP cc_start: 0.6997 (t60) cc_final: 0.6547 (t-100) REVERT: D 105 MET cc_start: 0.7211 (OUTLIER) cc_final: 0.6777 (ttt) REVERT: D 136 MET cc_start: 0.6805 (mtp) cc_final: 0.6359 (mtt) REVERT: D 274 ARG cc_start: 0.7468 (ttp-170) cc_final: 0.6859 (ttt90) REVERT: D 331 SER cc_start: 0.8089 (t) cc_final: 0.7649 (m) REVERT: D 332 LYS cc_start: 0.8797 (mmtm) cc_final: 0.8475 (tppt) REVERT: D 417 HIS cc_start: 0.7216 (t-90) cc_final: 0.6956 (t70) REVERT: D 529 PHE cc_start: 0.6590 (p90) cc_final: 0.6340 (p90) REVERT: D 533 MET cc_start: 0.3660 (ptp) cc_final: 0.2960 (ppp) REVERT: E 53 ASN cc_start: 0.8593 (t0) cc_final: 0.8374 (t0) REVERT: E 136 MET cc_start: 0.7233 (mtp) cc_final: 0.6621 (mtm) REVERT: E 166 GLU cc_start: 0.6667 (mt-10) cc_final: 0.5944 (mm-30) REVERT: E 189 MET cc_start: 0.5411 (OUTLIER) cc_final: 0.5004 (ttm) REVERT: E 218 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7312 (mt-10) REVERT: E 230 GLN cc_start: 0.7882 (mt0) cc_final: 0.7582 (mt0) REVERT: E 270 ARG cc_start: 0.7332 (mtp-110) cc_final: 0.6724 (ttm110) REVERT: E 274 ARG cc_start: 0.7586 (ttp-170) cc_final: 0.7109 (ttt90) REVERT: E 332 LYS cc_start: 0.8754 (mttt) cc_final: 0.8384 (mmtm) REVERT: E 340 HIS cc_start: 0.7716 (t-90) cc_final: 0.7329 (t-170) REVERT: E 488 MET cc_start: 0.2921 (tmm) cc_final: 0.1694 (tpt) REVERT: E 586 LEU cc_start: 0.5540 (mp) cc_final: 0.4712 (pp) REVERT: E 599 MET cc_start: 0.2931 (mmp) cc_final: 0.1881 (mmp) REVERT: F 39 LYS cc_start: 0.7886 (mmtp) cc_final: 0.7600 (mmtt) REVERT: F 105 MET cc_start: 0.7418 (ttm) cc_final: 0.6147 (tmm) REVERT: F 160 LYS cc_start: 0.8093 (mttm) cc_final: 0.7808 (mmmm) REVERT: F 195 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: F 218 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7580 (mt-10) REVERT: F 222 ARG cc_start: 0.7166 (mtt180) cc_final: 0.6448 (mpt90) REVERT: F 253 GLU cc_start: 0.6589 (pt0) cc_final: 0.6062 (pm20) REVERT: F 270 ARG cc_start: 0.7348 (mtp-110) cc_final: 0.6713 (ttm170) REVERT: F 274 ARG cc_start: 0.7469 (ttp-170) cc_final: 0.6920 (ttp-170) REVERT: F 340 HIS cc_start: 0.8293 (t70) cc_final: 0.7760 (t70) REVERT: G 59 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7180 (mmp) REVERT: G 104 TRP cc_start: 0.6311 (t60) cc_final: 0.6040 (t60) REVERT: G 105 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.5729 (tmm) REVERT: G 218 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7319 (mm-30) REVERT: G 222 ARG cc_start: 0.6992 (mtt180) cc_final: 0.6372 (mpt90) REVERT: G 270 ARG cc_start: 0.6997 (mtp-110) cc_final: 0.6619 (mtp180) REVERT: G 454 LYS cc_start: 0.8203 (tttt) cc_final: 0.7800 (tptp) REVERT: G 488 MET cc_start: 0.5199 (tmt) cc_final: 0.4647 (tmm) REVERT: G 586 LEU cc_start: 0.7304 (tm) cc_final: 0.6951 (pp) REVERT: G 599 MET cc_start: 0.2109 (OUTLIER) cc_final: 0.1826 (mpt) REVERT: H 63 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.6112 (mpt) REVERT: H 95 GLU cc_start: 0.8034 (mp0) cc_final: 0.7544 (mt-10) REVERT: H 104 TRP cc_start: 0.6777 (t60) cc_final: 0.6477 (t60) REVERT: H 218 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7515 (mt-10) REVERT: H 222 ARG cc_start: 0.6749 (mtt180) cc_final: 0.6149 (mtp180) REVERT: H 270 ARG cc_start: 0.7075 (mtt180) cc_final: 0.6476 (mmm160) REVERT: H 274 ARG cc_start: 0.7427 (ttp-170) cc_final: 0.7020 (ttm-80) REVERT: H 336 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8350 (p) REVERT: H 339 ARG cc_start: 0.7944 (mtp85) cc_final: 0.7629 (ttm-80) REVERT: H 344 PHE cc_start: 0.7179 (t80) cc_final: 0.6811 (t80) REVERT: H 594 THR cc_start: 0.5879 (OUTLIER) cc_final: 0.5519 (t) REVERT: I 95 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7477 (mp0) REVERT: I 189 MET cc_start: 0.5092 (tpt) cc_final: 0.4803 (tpt) REVERT: I 326 LEU cc_start: 0.8467 (mt) cc_final: 0.8123 (pp) REVERT: I 344 PHE cc_start: 0.7627 (t80) cc_final: 0.7350 (OUTLIER) REVERT: I 425 GLU cc_start: 0.7065 (tt0) cc_final: 0.6701 (tm-30) REVERT: J 105 MET cc_start: 0.6712 (OUTLIER) cc_final: 0.6150 (ttt) REVERT: J 166 GLU cc_start: 0.6833 (mt-10) cc_final: 0.6278 (pm20) REVERT: J 181 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.6316 (mp10) REVERT: J 195 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6921 (tt0) REVERT: J 270 ARG cc_start: 0.6933 (mtp-110) cc_final: 0.6322 (mtp180) REVERT: J 274 ARG cc_start: 0.7628 (ttp-170) cc_final: 0.6588 (ttt-90) REVERT: J 276 GLN cc_start: 0.8403 (tt0) cc_final: 0.8143 (tt0) REVERT: J 336 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8699 (p) REVERT: J 461 TRP cc_start: 0.7695 (p-90) cc_final: 0.6488 (p-90) REVERT: J 524 PRO cc_start: 0.7355 (Cg_exo) cc_final: 0.7098 (Cg_endo) REVERT: J 570 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6995 (pp30) REVERT: J 589 ARG cc_start: 0.2240 (OUTLIER) cc_final: 0.0243 (ttm110) REVERT: K 77 GLN cc_start: 0.7800 (mt0) cc_final: 0.7171 (mm-40) REVERT: K 95 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: K 104 TRP cc_start: 0.6625 (t60) cc_final: 0.5969 (t-100) REVERT: K 218 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7673 (mm-30) REVERT: K 222 ARG cc_start: 0.6980 (mtt180) cc_final: 0.6546 (mmm160) REVERT: K 274 ARG cc_start: 0.7594 (ttp-170) cc_final: 0.7021 (ttm-80) REVERT: K 599 MET cc_start: 0.3050 (mmp) cc_final: 0.2321 (mmp) REVERT: L 75 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7716 (p0) REVERT: L 96 MET cc_start: 0.7172 (mtm) cc_final: 0.6623 (mtm) REVERT: L 104 TRP cc_start: 0.6883 (t60) cc_final: 0.6383 (t-100) REVERT: L 136 MET cc_start: 0.6399 (OUTLIER) cc_final: 0.6175 (mpp) REVERT: L 274 ARG cc_start: 0.7324 (ttp-170) cc_final: 0.6784 (ttt90) REVERT: L 331 SER cc_start: 0.8132 (t) cc_final: 0.7674 (m) REVERT: L 332 LYS cc_start: 0.8803 (mmtm) cc_final: 0.8474 (tppt) REVERT: L 418 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7728 (tp) REVERT: L 457 PHE cc_start: 0.7496 (p90) cc_final: 0.7196 (p90) REVERT: L 503 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7596 (tm) REVERT: M 53 ASN cc_start: 0.8718 (t0) cc_final: 0.8418 (t0) REVERT: M 104 TRP cc_start: 0.6708 (t60) cc_final: 0.6166 (t-100) REVERT: M 136 MET cc_start: 0.7320 (mtp) cc_final: 0.6591 (mtm) REVERT: M 166 GLU cc_start: 0.6667 (mt-10) cc_final: 0.5857 (mm-30) REVERT: M 188 LYS cc_start: 0.8908 (mppt) cc_final: 0.8597 (mppt) REVERT: M 203 THR cc_start: 0.8931 (m) cc_final: 0.8362 (p) REVERT: M 222 ARG cc_start: 0.7273 (mtt180) cc_final: 0.6746 (mtp180) REVERT: M 230 GLN cc_start: 0.8145 (mt0) cc_final: 0.7785 (mt0) REVERT: M 270 ARG cc_start: 0.7482 (mtp-110) cc_final: 0.6785 (ttm110) REVERT: M 274 ARG cc_start: 0.7705 (ttp-170) cc_final: 0.7275 (ttt90) REVERT: M 332 LYS cc_start: 0.8761 (mttt) cc_final: 0.8420 (mmtm) REVERT: M 586 LEU cc_start: 0.5810 (OUTLIER) cc_final: 0.4922 (pp) REVERT: M 599 MET cc_start: 0.2456 (mmp) cc_final: 0.1651 (mmp) REVERT: N 94 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8652 (mm) REVERT: N 105 MET cc_start: 0.7609 (ttm) cc_final: 0.6138 (tmm) REVERT: N 218 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7605 (mt-10) REVERT: N 253 GLU cc_start: 0.6891 (pt0) cc_final: 0.6323 (pm20) REVERT: N 274 ARG cc_start: 0.7569 (ttp-170) cc_final: 0.6966 (ttp-170) REVERT: N 340 HIS cc_start: 0.8209 (t-90) cc_final: 0.7333 (t70) REVERT: N 344 PHE cc_start: 0.8040 (t80) cc_final: 0.7528 (t80) REVERT: N 345 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.7850 (m-40) REVERT: N 599 MET cc_start: 0.2882 (mmp) cc_final: 0.2339 (mmp) REVERT: O 55 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7366 (mtm180) REVERT: O 59 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7231 (mmp) REVERT: O 104 TRP cc_start: 0.6202 (t60) cc_final: 0.5914 (t60) REVERT: O 105 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.5836 (tmm) REVERT: O 166 GLU cc_start: 0.6780 (mt-10) cc_final: 0.6547 (pm20) REVERT: O 218 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7380 (mm-30) REVERT: O 222 ARG cc_start: 0.7033 (mtt180) cc_final: 0.6352 (mpt90) REVERT: O 270 ARG cc_start: 0.6958 (mtp-110) cc_final: 0.6602 (mtp180) REVERT: O 454 LYS cc_start: 0.8164 (tttt) cc_final: 0.7800 (ptpp) REVERT: O 488 MET cc_start: 0.4614 (tmt) cc_final: 0.4138 (tmm) REVERT: P 63 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7243 (mmm) REVERT: P 94 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8574 (mm) REVERT: P 104 TRP cc_start: 0.6761 (t60) cc_final: 0.6429 (t60) REVERT: P 218 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7526 (mt-10) REVERT: P 270 ARG cc_start: 0.7448 (mtp-110) cc_final: 0.7236 (mtm180) REVERT: P 336 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8402 (p) REVERT: P 339 ARG cc_start: 0.8175 (mtt90) cc_final: 0.7728 (ttm-80) REVERT: P 340 HIS cc_start: 0.7922 (OUTLIER) cc_final: 0.7371 (t70) REVERT: P 344 PHE cc_start: 0.7236 (t80) cc_final: 0.6899 (t80) outliers start: 325 outliers final: 189 residues processed: 756 average time/residue: 1.2007 time to fit residues: 1245.2271 Evaluate side-chains 700 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 475 time to evaluate : 5.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 521 PHE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 417 HIS Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 515 TYR Chi-restraints excluded: chain D residue 523 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 189 MET Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 392 VAL Chi-restraints excluded: chain G residue 523 VAL Chi-restraints excluded: chain G residue 599 MET Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 310 LEU Chi-restraints excluded: chain H residue 336 THR Chi-restraints excluded: chain H residue 428 SER Chi-restraints excluded: chain H residue 594 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 126 ASN Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 254 THR Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 503 LEU Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 105 MET Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 181 GLN Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 271 THR Chi-restraints excluded: chain J residue 297 THR Chi-restraints excluded: chain J residue 336 THR Chi-restraints excluded: chain J residue 511 VAL Chi-restraints excluded: chain J residue 564 VAL Chi-restraints excluded: chain J residue 570 GLN Chi-restraints excluded: chain J residue 586 LEU Chi-restraints excluded: chain J residue 589 ARG Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 523 VAL Chi-restraints excluded: chain K residue 564 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 136 MET Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain L residue 247 ILE Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 263 THR Chi-restraints excluded: chain L residue 281 VAL Chi-restraints excluded: chain L residue 403 LEU Chi-restraints excluded: chain L residue 418 LEU Chi-restraints excluded: chain L residue 444 THR Chi-restraints excluded: chain L residue 445 VAL Chi-restraints excluded: chain L residue 503 LEU Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain L residue 523 VAL Chi-restraints excluded: chain L residue 589 ARG Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 181 GLN Chi-restraints excluded: chain M residue 189 MET Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 219 ASP Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 345 ASN Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 586 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 247 ILE Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 271 THR Chi-restraints excluded: chain N residue 345 ASN Chi-restraints excluded: chain N residue 430 LEU Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain N residue 594 THR Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 59 MET Chi-restraints excluded: chain O residue 105 MET Chi-restraints excluded: chain O residue 136 MET Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 165 SER Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 209 VAL Chi-restraints excluded: chain O residue 254 THR Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 271 THR Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain O residue 392 VAL Chi-restraints excluded: chain O residue 523 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 63 MET Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 96 MET Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 162 THR Chi-restraints excluded: chain P residue 181 GLN Chi-restraints excluded: chain P residue 187 THR Chi-restraints excluded: chain P residue 189 MET Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain P residue 247 ILE Chi-restraints excluded: chain P residue 254 THR Chi-restraints excluded: chain P residue 260 THR Chi-restraints excluded: chain P residue 271 THR Chi-restraints excluded: chain P residue 336 THR Chi-restraints excluded: chain P residue 340 HIS Chi-restraints excluded: chain P residue 428 SER Chi-restraints excluded: chain P residue 523 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 505 optimal weight: 0.8980 chunk 326 optimal weight: 2.9990 chunk 488 optimal weight: 0.6980 chunk 246 optimal weight: 30.0000 chunk 160 optimal weight: 1.9990 chunk 158 optimal weight: 0.0370 chunk 519 optimal weight: 5.9990 chunk 556 optimal weight: 0.8980 chunk 404 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 642 optimal weight: 0.8980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 HIS ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN F 181 GLN ** F 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN H 401 ASN ** I 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 401 ASN J 299 HIS ** K 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 417 HIS ** M 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN P 181 GLN ** P 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 401 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 68624 Z= 0.153 Angle : 0.532 9.996 93136 Z= 0.264 Chirality : 0.043 0.289 10816 Planarity : 0.004 0.065 11792 Dihedral : 6.792 93.907 10485 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.81 % Favored : 97.04 % Rotamer: Outliers : 2.57 % Allowed : 15.19 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % 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: -0.58 (0.09), residues: 8432 helix: 0.80 (0.14), residues: 1344 sheet: -0.33 (0.09), residues: 3760 loop : -0.77 (0.11), residues: 3328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 461 HIS 0.009 0.001 HIS B 417 PHE 0.035 0.001 PHE C 525 TYR 0.022 0.001 TYR C 593 ARG 0.003 0.000 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 506 time to evaluate : 5.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8224 (m-30) cc_final: 0.7898 (m-30) REVERT: A 209 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8152 (p) REVERT: A 222 ARG cc_start: 0.7083 (mtt180) cc_final: 0.6429 (mtp180) REVERT: A 401 ASN cc_start: 0.7086 (t0) cc_final: 0.6037 (t0) REVERT: A 488 MET cc_start: 0.7540 (tmt) cc_final: 0.7181 (tmt) REVERT: A 524 PRO cc_start: 0.7740 (Cg_exo) cc_final: 0.7438 (Cg_endo) REVERT: B 104 TRP cc_start: 0.6794 (t60) cc_final: 0.6150 (t-100) REVERT: B 166 GLU cc_start: 0.6653 (mt-10) cc_final: 0.6113 (pm20) REVERT: B 222 ARG cc_start: 0.7030 (mtt180) cc_final: 0.6158 (mpt90) REVERT: B 270 ARG cc_start: 0.6950 (mtp-110) cc_final: 0.6056 (mtm180) REVERT: B 274 ARG cc_start: 0.7632 (ttp-170) cc_final: 0.6563 (ttt-90) REVERT: B 276 GLN cc_start: 0.8438 (tt0) cc_final: 0.8168 (tt0) REVERT: B 344 PHE cc_start: 0.7858 (t80) cc_final: 0.7457 (t80) REVERT: B 524 PRO cc_start: 0.7447 (Cg_exo) cc_final: 0.7199 (Cg_endo) REVERT: B 533 MET cc_start: 0.4424 (pmm) cc_final: 0.4212 (pmm) REVERT: B 570 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.7210 (pp30) REVERT: B 599 MET cc_start: 0.0870 (mmp) cc_final: -0.0417 (mmp) REVERT: C 95 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: C 104 TRP cc_start: 0.6430 (t60) cc_final: 0.5866 (t-100) REVERT: C 136 MET cc_start: 0.7022 (mtt) cc_final: 0.6634 (mtp) REVERT: C 218 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7287 (mm-30) REVERT: C 222 ARG cc_start: 0.6828 (mtt180) cc_final: 0.6333 (mmm160) REVERT: C 274 ARG cc_start: 0.7529 (ttp-170) cc_final: 0.6992 (ttm-80) REVERT: C 461 TRP cc_start: 0.7703 (p-90) cc_final: 0.7471 (p-90) REVERT: C 599 MET cc_start: 0.2799 (mmt) cc_final: 0.1983 (mmp) REVERT: D 75 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7678 (p0) REVERT: D 89 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7443 (mt0) REVERT: D 96 MET cc_start: 0.7407 (mtm) cc_final: 0.7044 (mtm) REVERT: D 104 TRP cc_start: 0.6780 (t60) cc_final: 0.6303 (t-100) REVERT: D 105 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6787 (ttt) REVERT: D 136 MET cc_start: 0.6605 (mtp) cc_final: 0.6262 (mtt) REVERT: D 188 LYS cc_start: 0.7885 (mppt) cc_final: 0.7662 (pmmt) REVERT: D 274 ARG cc_start: 0.7440 (ttp-170) cc_final: 0.7067 (ttt90) REVERT: D 314 ILE cc_start: 0.8485 (mt) cc_final: 0.8270 (mt) REVERT: D 331 SER cc_start: 0.8147 (t) cc_final: 0.7799 (m) REVERT: D 332 LYS cc_start: 0.8879 (mmtm) cc_final: 0.8608 (mmtm) REVERT: D 417 HIS cc_start: 0.7163 (t-90) cc_final: 0.6937 (t70) REVERT: D 529 PHE cc_start: 0.6514 (p90) cc_final: 0.6290 (p90) REVERT: D 533 MET cc_start: 0.3571 (ptp) cc_final: 0.2861 (ppp) REVERT: D 599 MET cc_start: 0.2451 (OUTLIER) cc_final: 0.0569 (mmt) REVERT: E 53 ASN cc_start: 0.8500 (t0) cc_final: 0.8179 (t0) REVERT: E 136 MET cc_start: 0.7245 (mtp) cc_final: 0.6741 (mtm) REVERT: E 166 GLU cc_start: 0.6481 (mt-10) cc_final: 0.5720 (mm-30) REVERT: E 188 LYS cc_start: 0.8307 (mppt) cc_final: 0.8005 (mmmt) REVERT: E 189 MET cc_start: 0.5364 (OUTLIER) cc_final: 0.4998 (ttm) REVERT: E 230 GLN cc_start: 0.7802 (mt0) cc_final: 0.7520 (mt0) REVERT: E 270 ARG cc_start: 0.7239 (mtp-110) cc_final: 0.6641 (ttm110) REVERT: E 274 ARG cc_start: 0.7433 (ttp-170) cc_final: 0.7033 (ttt90) REVERT: E 332 LYS cc_start: 0.8725 (mttt) cc_final: 0.8338 (mmtm) REVERT: E 340 HIS cc_start: 0.7650 (t-90) cc_final: 0.7309 (t-170) REVERT: E 488 MET cc_start: 0.3330 (tmm) cc_final: 0.2874 (ttp) REVERT: E 599 MET cc_start: 0.3230 (mmp) cc_final: 0.1776 (mmp) REVERT: F 39 LYS cc_start: 0.7913 (mmtp) cc_final: 0.7600 (mmpt) REVERT: F 105 MET cc_start: 0.7353 (ttm) cc_final: 0.5984 (tmt) REVERT: F 160 LYS cc_start: 0.7919 (mttm) cc_final: 0.7699 (mmmm) REVERT: F 181 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.7149 (tt0) REVERT: F 195 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: F 218 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7577 (mt-10) REVERT: F 222 ARG cc_start: 0.7177 (mtt180) cc_final: 0.6451 (mpt90) REVERT: F 253 GLU cc_start: 0.6320 (pt0) cc_final: 0.5768 (pm20) REVERT: F 266 TYR cc_start: 0.7338 (t80) cc_final: 0.6612 (m-80) REVERT: F 270 ARG cc_start: 0.7260 (mtp-110) cc_final: 0.6714 (ttm170) REVERT: F 274 ARG cc_start: 0.7406 (ttp-170) cc_final: 0.6787 (tmm160) REVERT: F 340 HIS cc_start: 0.8229 (t70) cc_final: 0.7712 (t70) REVERT: G 105 MET cc_start: 0.6757 (OUTLIER) cc_final: 0.5654 (tmm) REVERT: G 218 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7166 (mm-30) REVERT: G 222 ARG cc_start: 0.6925 (mtt180) cc_final: 0.6287 (mpt90) REVERT: G 266 TYR cc_start: 0.6913 (t80) cc_final: 0.6471 (m-80) REVERT: G 270 ARG cc_start: 0.7097 (mtp-110) cc_final: 0.6707 (mpp-170) REVERT: G 454 LYS cc_start: 0.8181 (tttt) cc_final: 0.7734 (tptp) REVERT: G 488 MET cc_start: 0.4932 (tmt) cc_final: 0.4439 (tmm) REVERT: G 586 LEU cc_start: 0.7227 (tm) cc_final: 0.6881 (pp) REVERT: G 599 MET cc_start: 0.2127 (OUTLIER) cc_final: 0.1777 (mpt) REVERT: H 61 ARG cc_start: 0.7516 (tpp-160) cc_final: 0.7299 (tpp-160) REVERT: H 63 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.7087 (mmm) REVERT: H 95 GLU cc_start: 0.7974 (mp0) cc_final: 0.7483 (mt-10) REVERT: H 203 THR cc_start: 0.8635 (m) cc_final: 0.8098 (p) REVERT: H 218 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7435 (mt-10) REVERT: H 270 ARG cc_start: 0.7016 (mtt180) cc_final: 0.6452 (mmm160) REVERT: H 274 ARG cc_start: 0.7463 (ttp-170) cc_final: 0.7206 (ttm-80) REVERT: H 336 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8378 (p) REVERT: H 339 ARG cc_start: 0.7982 (mtp85) cc_final: 0.7679 (ttm-80) REVERT: H 594 THR cc_start: 0.5916 (OUTLIER) cc_final: 0.5489 (t) REVERT: I 209 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.8182 (p) REVERT: I 218 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7867 (mt-10) REVERT: I 222 ARG cc_start: 0.7035 (mtt180) cc_final: 0.6369 (mtp180) REVERT: I 344 PHE cc_start: 0.7592 (t80) cc_final: 0.7389 (t80) REVERT: I 401 ASN cc_start: 0.7183 (OUTLIER) cc_final: 0.6544 (t0) REVERT: I 425 GLU cc_start: 0.7041 (tt0) cc_final: 0.6696 (tm-30) REVERT: J 166 GLU cc_start: 0.6719 (mt-10) cc_final: 0.6221 (pm20) REVERT: J 195 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6961 (tt0) REVERT: J 270 ARG cc_start: 0.6729 (mtp-110) cc_final: 0.5999 (mtm180) REVERT: J 274 ARG cc_start: 0.7604 (ttp-170) cc_final: 0.6551 (ttt-90) REVERT: J 276 GLN cc_start: 0.8339 (tt0) cc_final: 0.8085 (tt0) REVERT: J 336 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8686 (p) REVERT: J 461 TRP cc_start: 0.7715 (p-90) cc_final: 0.6431 (p-90) REVERT: J 524 PRO cc_start: 0.7241 (Cg_exo) cc_final: 0.6994 (Cg_endo) REVERT: J 570 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.7042 (pp30) REVERT: J 589 ARG cc_start: 0.2394 (OUTLIER) cc_final: 0.0632 (ttm110) REVERT: J 599 MET cc_start: 0.0376 (mmt) cc_final: -0.0052 (mmp) REVERT: K 77 GLN cc_start: 0.7877 (mt0) cc_final: 0.7180 (mm-40) REVERT: K 95 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: K 104 TRP cc_start: 0.6420 (t60) cc_final: 0.5829 (t-100) REVERT: K 218 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7544 (mm-30) REVERT: K 222 ARG cc_start: 0.6907 (mtt180) cc_final: 0.6443 (mmm160) REVERT: K 274 ARG cc_start: 0.7544 (ttp-170) cc_final: 0.7006 (ttm-80) REVERT: K 528 PHE cc_start: 0.8231 (m-80) cc_final: 0.7950 (m-80) REVERT: K 599 MET cc_start: 0.3021 (mmp) cc_final: 0.2329 (mmp) REVERT: L 63 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7332 (mpm) REVERT: L 75 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7712 (p0) REVERT: L 96 MET cc_start: 0.6984 (mtm) cc_final: 0.6452 (mtm) REVERT: L 104 TRP cc_start: 0.6674 (t60) cc_final: 0.6189 (t-100) REVERT: L 136 MET cc_start: 0.6574 (OUTLIER) cc_final: 0.6306 (mpp) REVERT: L 219 ASP cc_start: 0.7871 (t0) cc_final: 0.7575 (t70) REVERT: L 274 ARG cc_start: 0.7271 (ttp-170) cc_final: 0.6935 (ttt90) REVERT: L 331 SER cc_start: 0.8124 (t) cc_final: 0.7759 (m) REVERT: L 332 LYS cc_start: 0.8860 (mmtm) cc_final: 0.8587 (mmtm) REVERT: L 457 PHE cc_start: 0.7324 (p90) cc_final: 0.7120 (p90) REVERT: L 503 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7673 (tm) REVERT: L 589 ARG cc_start: 0.1885 (OUTLIER) cc_final: 0.1181 (tpm170) REVERT: M 53 ASN cc_start: 0.8594 (t0) cc_final: 0.8210 (t0) REVERT: M 104 TRP cc_start: 0.6510 (t60) cc_final: 0.6036 (t-100) REVERT: M 136 MET cc_start: 0.7294 (mtp) cc_final: 0.6672 (mtm) REVERT: M 166 GLU cc_start: 0.6550 (mt-10) cc_final: 0.5726 (mm-30) REVERT: M 188 LYS cc_start: 0.8884 (mppt) cc_final: 0.8568 (mppt) REVERT: M 203 THR cc_start: 0.8912 (m) cc_final: 0.8358 (p) REVERT: M 222 ARG cc_start: 0.7286 (mtt180) cc_final: 0.6588 (mpt180) REVERT: M 230 GLN cc_start: 0.8113 (mt0) cc_final: 0.7770 (mt0) REVERT: M 270 ARG cc_start: 0.7379 (mtp-110) cc_final: 0.6689 (ttm110) REVERT: M 274 ARG cc_start: 0.7548 (ttp-170) cc_final: 0.7235 (ttt90) REVERT: M 332 LYS cc_start: 0.8712 (mttt) cc_final: 0.8343 (mmtm) REVERT: M 586 LEU cc_start: 0.6239 (OUTLIER) cc_final: 0.5091 (pp) REVERT: M 599 MET cc_start: 0.2572 (mmp) cc_final: 0.1644 (mmp) REVERT: N 94 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8460 (mm) REVERT: N 105 MET cc_start: 0.7596 (ttm) cc_final: 0.6243 (tmm) REVERT: N 136 MET cc_start: 0.6968 (ttm) cc_final: 0.6612 (ttm) REVERT: N 160 LYS cc_start: 0.8047 (mttm) cc_final: 0.7778 (mmmt) REVERT: N 218 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7589 (mt-10) REVERT: N 253 GLU cc_start: 0.6675 (pt0) cc_final: 0.6184 (pm20) REVERT: N 266 TYR cc_start: 0.7223 (t80) cc_final: 0.6538 (m-80) REVERT: N 274 ARG cc_start: 0.7543 (ttp-170) cc_final: 0.6846 (tmm160) REVERT: N 340 HIS cc_start: 0.8206 (t-90) cc_final: 0.7363 (t70) REVERT: N 344 PHE cc_start: 0.8148 (t80) cc_final: 0.7711 (t80) REVERT: N 599 MET cc_start: 0.2665 (mmp) cc_final: 0.2271 (mmt) REVERT: O 105 MET cc_start: 0.6745 (OUTLIER) cc_final: 0.5676 (tmm) REVERT: O 218 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7266 (mm-30) REVERT: O 222 ARG cc_start: 0.7043 (mtt180) cc_final: 0.6307 (mpt90) REVERT: O 270 ARG cc_start: 0.7041 (mtp-110) cc_final: 0.6578 (mpp-170) REVERT: O 454 LYS cc_start: 0.8111 (tttt) cc_final: 0.7807 (ptpp) REVERT: O 488 MET cc_start: 0.4590 (tmt) cc_final: 0.4149 (tmm) REVERT: O 533 MET cc_start: 0.4389 (mtp) cc_final: 0.3949 (pmm) REVERT: P 53 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8479 (t0) REVERT: P 63 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7264 (mmm) REVERT: P 203 THR cc_start: 0.8660 (m) cc_final: 0.8140 (p) REVERT: P 218 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7534 (mt-10) REVERT: P 270 ARG cc_start: 0.7410 (mtp-110) cc_final: 0.7190 (mtm180) REVERT: P 336 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8448 (p) REVERT: P 339 ARG cc_start: 0.8223 (mtt90) cc_final: 0.7709 (ttm-80) REVERT: P 340 HIS cc_start: 0.7971 (OUTLIER) cc_final: 0.7414 (t70) outliers start: 193 outliers final: 99 residues processed: 657 average time/residue: 1.3264 time to fit residues: 1162.8096 Evaluate side-chains 608 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 476 time to evaluate : 5.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 521 PHE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 417 HIS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 515 TYR Chi-restraints excluded: chain D residue 523 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 189 MET Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 392 VAL Chi-restraints excluded: chain G residue 523 VAL Chi-restraints excluded: chain G residue 599 MET Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 336 THR Chi-restraints excluded: chain H residue 594 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 401 ASN Chi-restraints excluded: chain I residue 503 LEU Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 271 THR Chi-restraints excluded: chain J residue 297 THR Chi-restraints excluded: chain J residue 336 THR Chi-restraints excluded: chain J residue 418 LEU Chi-restraints excluded: chain J residue 511 VAL Chi-restraints excluded: chain J residue 570 GLN Chi-restraints excluded: chain J residue 589 ARG Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain K residue 523 VAL Chi-restraints excluded: chain K residue 564 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 63 MET Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 136 MET Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 247 ILE Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 444 THR Chi-restraints excluded: chain L residue 445 VAL Chi-restraints excluded: chain L residue 503 LEU Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain L residue 523 VAL Chi-restraints excluded: chain L residue 589 ARG Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 189 MET Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 586 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 247 ILE Chi-restraints excluded: chain N residue 430 LEU Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain N residue 594 THR Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 105 MET Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 209 VAL Chi-restraints excluded: chain O residue 392 VAL Chi-restraints excluded: chain O residue 523 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain P residue 63 MET Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain P residue 247 ILE Chi-restraints excluded: chain P residue 260 THR Chi-restraints excluded: chain P residue 336 THR Chi-restraints excluded: chain P residue 340 HIS Chi-restraints excluded: chain P residue 428 SER Chi-restraints excluded: chain P residue 523 VAL Chi-restraints excluded: chain P residue 590 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 743 optimal weight: 2.9990 chunk 783 optimal weight: 30.0000 chunk 714 optimal weight: 0.0000 chunk 761 optimal weight: 5.9990 chunk 782 optimal weight: 30.0000 chunk 458 optimal weight: 20.0000 chunk 331 optimal weight: 0.8980 chunk 598 optimal weight: 5.9990 chunk 233 optimal weight: 7.9990 chunk 688 optimal weight: 5.9990 chunk 720 optimal weight: 6.9990 overall best weight: 3.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 417 HIS ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN E 399 GLN ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN F 181 GLN ** F 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN ** K 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN L 417 HIS M 181 GLN ** M 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 345 ASN ** N 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 181 GLN ** P 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 401 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 68624 Z= 0.403 Angle : 0.619 11.943 93136 Z= 0.308 Chirality : 0.046 0.347 10816 Planarity : 0.005 0.061 11792 Dihedral : 7.013 96.471 10483 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.25 % Favored : 95.60 % Rotamer: Outliers : 2.77 % Allowed : 15.31 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % 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: -0.75 (0.09), residues: 8432 helix: 0.75 (0.14), residues: 1344 sheet: -0.47 (0.08), residues: 3744 loop : -0.88 (0.11), residues: 3344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 461 HIS 0.010 0.001 HIS M 340 PHE 0.036 0.002 PHE K 528 TYR 0.025 0.002 TYR M 593 ARG 0.006 0.001 ARG O 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 481 time to evaluate : 5.524 Fit side-chains revert: symmetry clash REVERT: A 222 ARG cc_start: 0.7140 (mtt180) cc_final: 0.6445 (mtp180) REVERT: A 401 ASN cc_start: 0.7133 (t0) cc_final: 0.6641 (t0) REVERT: A 402 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8672 (tt) REVERT: A 425 GLU cc_start: 0.6784 (tm-30) cc_final: 0.6554 (tm-30) REVERT: A 488 MET cc_start: 0.7534 (tmt) cc_final: 0.7161 (tmt) REVERT: B 104 TRP cc_start: 0.6904 (t60) cc_final: 0.6242 (t-100) REVERT: B 166 GLU cc_start: 0.6732 (mt-10) cc_final: 0.6225 (pm20) REVERT: B 222 ARG cc_start: 0.7032 (mtt180) cc_final: 0.6127 (mpt90) REVERT: B 270 ARG cc_start: 0.7020 (mtp-110) cc_final: 0.6131 (mtm180) REVERT: B 274 ARG cc_start: 0.7665 (ttp-170) cc_final: 0.6579 (ttt-90) REVERT: B 276 GLN cc_start: 0.8407 (tt0) cc_final: 0.8117 (tt0) REVERT: B 344 PHE cc_start: 0.7875 (t80) cc_final: 0.7475 (t80) REVERT: B 524 PRO cc_start: 0.7460 (Cg_exo) cc_final: 0.7214 (Cg_endo) REVERT: B 570 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.7225 (pp30) REVERT: B 599 MET cc_start: 0.0902 (mmp) cc_final: -0.0378 (mmp) REVERT: C 95 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: C 104 TRP cc_start: 0.6602 (t60) cc_final: 0.6048 (t-100) REVERT: C 136 MET cc_start: 0.6971 (mtt) cc_final: 0.6578 (mtp) REVERT: C 218 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7275 (mm-30) REVERT: C 222 ARG cc_start: 0.6958 (mtt180) cc_final: 0.6462 (mmm160) REVERT: C 274 ARG cc_start: 0.7565 (ttp-170) cc_final: 0.7030 (ttm-80) REVERT: C 461 TRP cc_start: 0.7745 (p-90) cc_final: 0.7488 (p-90) REVERT: C 599 MET cc_start: 0.3246 (mmt) cc_final: 0.2424 (mmp) REVERT: D 75 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7661 (p0) REVERT: D 104 TRP cc_start: 0.6957 (t60) cc_final: 0.6492 (t-100) REVERT: D 105 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6766 (ttt) REVERT: D 136 MET cc_start: 0.6827 (mtp) cc_final: 0.6363 (mtt) REVERT: D 188 LYS cc_start: 0.7904 (mppt) cc_final: 0.7651 (pmmt) REVERT: D 274 ARG cc_start: 0.7504 (ttp-170) cc_final: 0.6965 (ttt90) REVERT: D 331 SER cc_start: 0.8081 (t) cc_final: 0.7658 (m) REVERT: D 332 LYS cc_start: 0.8803 (mmtm) cc_final: 0.8444 (tppt) REVERT: D 417 HIS cc_start: 0.7183 (t-90) cc_final: 0.6925 (t70) REVERT: D 529 PHE cc_start: 0.6532 (p90) cc_final: 0.6310 (p90) REVERT: D 533 MET cc_start: 0.3596 (ptp) cc_final: 0.2566 (ppp) REVERT: E 53 ASN cc_start: 0.8526 (t0) cc_final: 0.8259 (t0) REVERT: E 136 MET cc_start: 0.7298 (mtp) cc_final: 0.6758 (mtm) REVERT: E 166 GLU cc_start: 0.6669 (mt-10) cc_final: 0.5900 (mm-30) REVERT: E 188 LYS cc_start: 0.8347 (mppt) cc_final: 0.8079 (mmmt) REVERT: E 189 MET cc_start: 0.5343 (OUTLIER) cc_final: 0.4932 (ttm) REVERT: E 230 GLN cc_start: 0.7870 (mt0) cc_final: 0.7579 (mt0) REVERT: E 270 ARG cc_start: 0.7296 (mtp-110) cc_final: 0.6700 (ttm110) REVERT: E 274 ARG cc_start: 0.7570 (ttp-170) cc_final: 0.7115 (ttt90) REVERT: E 332 LYS cc_start: 0.8744 (mttt) cc_final: 0.8354 (mmtm) REVERT: E 340 HIS cc_start: 0.7666 (t-90) cc_final: 0.7332 (t-170) REVERT: E 488 MET cc_start: 0.3398 (tmm) cc_final: 0.2968 (ttp) REVERT: E 599 MET cc_start: 0.3323 (mmp) cc_final: 0.1822 (mmp) REVERT: F 39 LYS cc_start: 0.7911 (mmtp) cc_final: 0.7592 (mmpt) REVERT: F 105 MET cc_start: 0.7424 (ttm) cc_final: 0.6168 (tmm) REVERT: F 149 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7761 (ttt180) REVERT: F 160 LYS cc_start: 0.8088 (mttm) cc_final: 0.7820 (mmmm) REVERT: F 195 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7488 (mp0) REVERT: F 218 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7612 (mt-10) REVERT: F 222 ARG cc_start: 0.7193 (mtt180) cc_final: 0.6413 (mpt90) REVERT: F 253 GLU cc_start: 0.6442 (pt0) cc_final: 0.5854 (pm20) REVERT: F 270 ARG cc_start: 0.7335 (mtp-110) cc_final: 0.6729 (ttm170) REVERT: F 274 ARG cc_start: 0.7407 (ttp-170) cc_final: 0.6793 (tmm160) REVERT: F 340 HIS cc_start: 0.8237 (t70) cc_final: 0.7724 (t70) REVERT: G 104 TRP cc_start: 0.6210 (t60) cc_final: 0.5887 (t60) REVERT: G 105 MET cc_start: 0.6811 (OUTLIER) cc_final: 0.5684 (tmm) REVERT: G 218 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7197 (mm-30) REVERT: G 222 ARG cc_start: 0.6992 (mtt180) cc_final: 0.6341 (mpt90) REVERT: G 270 ARG cc_start: 0.7116 (mtp-110) cc_final: 0.6622 (mpp-170) REVERT: G 454 LYS cc_start: 0.8169 (tttt) cc_final: 0.7716 (tptp) REVERT: G 488 MET cc_start: 0.5012 (tmt) cc_final: 0.4494 (tmm) REVERT: G 586 LEU cc_start: 0.7188 (tm) cc_final: 0.6846 (pp) REVERT: G 599 MET cc_start: 0.2229 (OUTLIER) cc_final: 0.2005 (mpt) REVERT: H 61 ARG cc_start: 0.7571 (tpp-160) cc_final: 0.7283 (tpp-160) REVERT: H 63 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.6077 (mpt) REVERT: H 95 GLU cc_start: 0.7995 (mp0) cc_final: 0.7492 (mt-10) REVERT: H 218 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7441 (mt-10) REVERT: H 222 ARG cc_start: 0.6814 (mtt180) cc_final: 0.6272 (mtp180) REVERT: H 270 ARG cc_start: 0.7033 (mtt180) cc_final: 0.6452 (mmm160) REVERT: H 274 ARG cc_start: 0.7502 (ttp-170) cc_final: 0.7124 (ttm-80) REVERT: H 336 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8378 (p) REVERT: H 339 ARG cc_start: 0.7901 (mtp85) cc_final: 0.7601 (ttm-80) REVERT: H 594 THR cc_start: 0.6040 (OUTLIER) cc_final: 0.5681 (t) REVERT: I 135 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6580 (mmt180) REVERT: I 218 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7866 (mt-10) REVERT: I 344 PHE cc_start: 0.7601 (t80) cc_final: 0.7314 (OUTLIER) REVERT: I 425 GLU cc_start: 0.7045 (tt0) cc_final: 0.6680 (tm-30) REVERT: J 105 MET cc_start: 0.6812 (OUTLIER) cc_final: 0.6240 (ttt) REVERT: J 166 GLU cc_start: 0.6719 (mt-10) cc_final: 0.6224 (pm20) REVERT: J 195 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6957 (tt0) REVERT: J 270 ARG cc_start: 0.6812 (mtp-110) cc_final: 0.6096 (mtm180) REVERT: J 274 ARG cc_start: 0.7597 (ttp-170) cc_final: 0.6560 (ttt-90) REVERT: J 276 GLN cc_start: 0.8377 (tt0) cc_final: 0.8116 (tt0) REVERT: J 336 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8693 (p) REVERT: J 461 TRP cc_start: 0.7746 (p-90) cc_final: 0.6519 (p-90) REVERT: J 524 PRO cc_start: 0.7224 (Cg_exo) cc_final: 0.6981 (Cg_endo) REVERT: J 570 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.7065 (pp30) REVERT: J 589 ARG cc_start: 0.2509 (OUTLIER) cc_final: 0.0683 (ttm110) REVERT: J 599 MET cc_start: 0.0655 (mmt) cc_final: 0.0137 (mmt) REVERT: K 77 GLN cc_start: 0.7847 (mt0) cc_final: 0.7183 (mm-40) REVERT: K 95 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: K 104 TRP cc_start: 0.6588 (t60) cc_final: 0.5964 (t-100) REVERT: K 218 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7614 (mm-30) REVERT: K 222 ARG cc_start: 0.6962 (mtt180) cc_final: 0.6525 (mmm160) REVERT: K 274 ARG cc_start: 0.7602 (ttp-170) cc_final: 0.7019 (ttm-80) REVERT: K 599 MET cc_start: 0.3184 (mmp) cc_final: 0.2449 (mmp) REVERT: L 75 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7710 (p0) REVERT: L 96 MET cc_start: 0.7125 (mtm) cc_final: 0.6584 (mtm) REVERT: L 104 TRP cc_start: 0.6820 (t60) cc_final: 0.6341 (t-100) REVERT: L 108 GLN cc_start: 0.7095 (tm-30) cc_final: 0.6838 (tt0) REVERT: L 136 MET cc_start: 0.6525 (OUTLIER) cc_final: 0.6286 (mpp) REVERT: L 219 ASP cc_start: 0.7896 (t0) cc_final: 0.7586 (t70) REVERT: L 274 ARG cc_start: 0.7355 (ttp-170) cc_final: 0.6878 (ttt90) REVERT: L 331 SER cc_start: 0.8060 (t) cc_final: 0.7622 (m) REVERT: L 332 LYS cc_start: 0.8857 (mmtm) cc_final: 0.8493 (tppt) REVERT: L 457 PHE cc_start: 0.7549 (p90) cc_final: 0.7276 (p90) REVERT: L 503 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7653 (tm) REVERT: M 53 ASN cc_start: 0.8606 (t0) cc_final: 0.8314 (t0) REVERT: M 104 TRP cc_start: 0.6710 (t60) cc_final: 0.6163 (t-100) REVERT: M 136 MET cc_start: 0.7385 (mtp) cc_final: 0.6656 (mtm) REVERT: M 166 GLU cc_start: 0.6750 (mt-10) cc_final: 0.5992 (mm-30) REVERT: M 188 LYS cc_start: 0.8892 (mppt) cc_final: 0.8574 (mppt) REVERT: M 222 ARG cc_start: 0.7305 (mtt180) cc_final: 0.6666 (mtm180) REVERT: M 230 GLN cc_start: 0.8178 (mt0) cc_final: 0.7827 (mt0) REVERT: M 270 ARG cc_start: 0.7425 (mtp-110) cc_final: 0.6689 (ttm110) REVERT: M 274 ARG cc_start: 0.7655 (ttp-170) cc_final: 0.7265 (ttt90) REVERT: M 332 LYS cc_start: 0.8726 (mttt) cc_final: 0.8362 (mmtm) REVERT: M 586 LEU cc_start: 0.6152 (OUTLIER) cc_final: 0.5362 (pp) REVERT: M 599 MET cc_start: 0.2604 (mmp) cc_final: 0.1635 (mmp) REVERT: N 94 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8610 (mm) REVERT: N 105 MET cc_start: 0.7655 (ttm) cc_final: 0.6197 (tmm) REVERT: N 160 LYS cc_start: 0.8071 (mttm) cc_final: 0.7850 (mmmt) REVERT: N 218 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7539 (mt-10) REVERT: N 253 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6251 (pm20) REVERT: N 266 TYR cc_start: 0.7320 (t80) cc_final: 0.6608 (m-80) REVERT: N 274 ARG cc_start: 0.7609 (ttp-170) cc_final: 0.7016 (ttp-170) REVERT: N 340 HIS cc_start: 0.8265 (t-90) cc_final: 0.7423 (t70) REVERT: N 344 PHE cc_start: 0.8075 (t80) cc_final: 0.7612 (t80) REVERT: N 599 MET cc_start: 0.2821 (mmp) cc_final: 0.2350 (mmp) REVERT: O 104 TRP cc_start: 0.6081 (t60) cc_final: 0.5751 (t60) REVERT: O 105 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.5662 (tmm) REVERT: O 218 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7067 (mm-30) REVERT: O 222 ARG cc_start: 0.7042 (mtt180) cc_final: 0.6330 (mpt90) REVERT: O 270 ARG cc_start: 0.7057 (mtp-110) cc_final: 0.6557 (mpp-170) REVERT: O 274 ARG cc_start: 0.7363 (ttp-170) cc_final: 0.6662 (ttt90) REVERT: O 454 LYS cc_start: 0.8154 (tttt) cc_final: 0.7850 (ptpp) REVERT: O 488 MET cc_start: 0.4616 (tmt) cc_final: 0.4158 (tmm) REVERT: O 533 MET cc_start: 0.4558 (mtp) cc_final: 0.3572 (pmm) REVERT: P 218 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7481 (mt-10) REVERT: P 270 ARG cc_start: 0.7420 (mtp-110) cc_final: 0.7159 (mtm180) REVERT: P 336 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8418 (p) REVERT: P 339 ARG cc_start: 0.8132 (mtt90) cc_final: 0.7639 (ttm-80) REVERT: P 344 PHE cc_start: 0.7194 (t80) cc_final: 0.6786 (t80) outliers start: 208 outliers final: 133 residues processed: 650 average time/residue: 1.3009 time to fit residues: 1131.8215 Evaluate side-chains 631 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 472 time to evaluate : 5.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 521 PHE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 515 TYR Chi-restraints excluded: chain D residue 523 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 189 MET Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 345 ASN Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 149 ARG Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 392 VAL Chi-restraints excluded: chain G residue 523 VAL Chi-restraints excluded: chain G residue 599 MET Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 310 LEU Chi-restraints excluded: chain H residue 336 THR Chi-restraints excluded: chain H residue 428 SER Chi-restraints excluded: chain H residue 594 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 135 ARG Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 301 VAL Chi-restraints excluded: chain I residue 503 LEU Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 105 MET Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 271 THR Chi-restraints excluded: chain J residue 297 THR Chi-restraints excluded: chain J residue 336 THR Chi-restraints excluded: chain J residue 378 PHE Chi-restraints excluded: chain J residue 511 VAL Chi-restraints excluded: chain J residue 570 GLN Chi-restraints excluded: chain J residue 589 ARG Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain K residue 523 VAL Chi-restraints excluded: chain K residue 564 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 136 MET Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain L residue 247 ILE Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 444 THR Chi-restraints excluded: chain L residue 445 VAL Chi-restraints excluded: chain L residue 503 LEU Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain L residue 523 VAL Chi-restraints excluded: chain L residue 589 ARG Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 189 MET Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 586 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 247 ILE Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 430 LEU Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 105 MET Chi-restraints excluded: chain O residue 136 MET Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 165 SER Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 254 THR Chi-restraints excluded: chain O residue 392 VAL Chi-restraints excluded: chain O residue 523 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 111 THR Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain P residue 247 ILE Chi-restraints excluded: chain P residue 254 THR Chi-restraints excluded: chain P residue 260 THR Chi-restraints excluded: chain P residue 336 THR Chi-restraints excluded: chain P residue 428 SER Chi-restraints excluded: chain P residue 502 ASN Chi-restraints excluded: chain P residue 523 VAL Chi-restraints excluded: chain P residue 590 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 758 optimal weight: 7.9990 chunk 500 optimal weight: 5.9990 chunk 805 optimal weight: 2.9990 chunk 491 optimal weight: 4.9990 chunk 382 optimal weight: 0.8980 chunk 559 optimal weight: 9.9990 chunk 844 optimal weight: 3.9990 chunk 777 optimal weight: 10.0000 chunk 672 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 chunk 519 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 GLN ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN D 340 HIS ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN I 186 GLN I 401 ASN ** K 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** L 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 417 HIS M 181 GLN ** M 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN P 181 GLN ** P 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 401 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 68624 Z= 0.270 Angle : 0.577 13.053 93136 Z= 0.286 Chirality : 0.045 0.327 10816 Planarity : 0.005 0.077 11792 Dihedral : 6.771 93.937 10483 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.02 % Favored : 96.82 % Rotamer: Outliers : 2.35 % Allowed : 15.75 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.64 (0.09), residues: 8432 helix: 0.89 (0.14), residues: 1312 sheet: -0.40 (0.09), residues: 3760 loop : -0.82 (0.11), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP M 461 HIS 0.011 0.001 HIS M 340 PHE 0.030 0.001 PHE D 528 TYR 0.022 0.001 TYR M 593 ARG 0.006 0.000 ARG O 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 474 time to evaluate : 5.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 VAL cc_start: 0.8435 (OUTLIER) cc_final: 0.8086 (p) REVERT: A 222 ARG cc_start: 0.7109 (mtt180) cc_final: 0.6423 (mtp180) REVERT: A 401 ASN cc_start: 0.7028 (t0) cc_final: 0.6572 (t0) REVERT: A 402 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8670 (tt) REVERT: A 425 GLU cc_start: 0.6852 (tm-30) cc_final: 0.6481 (tm-30) REVERT: A 488 MET cc_start: 0.7519 (tmt) cc_final: 0.7143 (tmt) REVERT: A 599 MET cc_start: 0.3196 (mmt) cc_final: 0.2976 (mmt) REVERT: B 104 TRP cc_start: 0.6867 (t60) cc_final: 0.6235 (t-100) REVERT: B 166 GLU cc_start: 0.6704 (mt-10) cc_final: 0.6222 (pm20) REVERT: B 222 ARG cc_start: 0.7039 (mtt180) cc_final: 0.6140 (mpt90) REVERT: B 270 ARG cc_start: 0.7012 (mtp-110) cc_final: 0.6139 (mtm180) REVERT: B 274 ARG cc_start: 0.7654 (ttp-170) cc_final: 0.6575 (ttt-90) REVERT: B 276 GLN cc_start: 0.8403 (tt0) cc_final: 0.8107 (tt0) REVERT: B 344 PHE cc_start: 0.7854 (t80) cc_final: 0.7442 (t80) REVERT: B 524 PRO cc_start: 0.7406 (Cg_exo) cc_final: 0.7146 (Cg_endo) REVERT: B 570 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7288 (pp30) REVERT: B 599 MET cc_start: 0.0882 (mmp) cc_final: -0.0221 (mmp) REVERT: C 95 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: C 104 TRP cc_start: 0.6555 (t60) cc_final: 0.6017 (t-100) REVERT: C 136 MET cc_start: 0.6972 (mtt) cc_final: 0.6585 (mtp) REVERT: C 218 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7278 (mm-30) REVERT: C 222 ARG cc_start: 0.6850 (mtt180) cc_final: 0.6338 (mmm160) REVERT: C 274 ARG cc_start: 0.7559 (ttp-170) cc_final: 0.7013 (ttm-80) REVERT: C 461 TRP cc_start: 0.7758 (p-90) cc_final: 0.7450 (p-90) REVERT: C 599 MET cc_start: 0.3180 (mmt) cc_final: 0.2342 (mmp) REVERT: D 75 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7682 (p0) REVERT: D 104 TRP cc_start: 0.6897 (t60) cc_final: 0.6437 (t-100) REVERT: D 105 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.6851 (ttt) REVERT: D 136 MET cc_start: 0.6732 (mtp) cc_final: 0.6348 (mtt) REVERT: D 189 MET cc_start: 0.4259 (ttm) cc_final: 0.3921 (ttm) REVERT: D 274 ARG cc_start: 0.7498 (ttp-170) cc_final: 0.7028 (ttt90) REVERT: D 331 SER cc_start: 0.8122 (t) cc_final: 0.7764 (m) REVERT: D 417 HIS cc_start: 0.7144 (t-90) cc_final: 0.6888 (t70) REVERT: D 529 PHE cc_start: 0.6508 (p90) cc_final: 0.6296 (p90) REVERT: D 533 MET cc_start: 0.3205 (ptp) cc_final: 0.2137 (ppp) REVERT: E 53 ASN cc_start: 0.8489 (t0) cc_final: 0.8194 (t0) REVERT: E 136 MET cc_start: 0.7238 (mtp) cc_final: 0.6691 (mtm) REVERT: E 166 GLU cc_start: 0.6627 (mt-10) cc_final: 0.5894 (mm-30) REVERT: E 188 LYS cc_start: 0.8292 (mppt) cc_final: 0.8013 (mmmt) REVERT: E 189 MET cc_start: 0.5362 (OUTLIER) cc_final: 0.4992 (ttm) REVERT: E 230 GLN cc_start: 0.7859 (mt0) cc_final: 0.7570 (mt0) REVERT: E 270 ARG cc_start: 0.7283 (mtp-110) cc_final: 0.6678 (ttm110) REVERT: E 274 ARG cc_start: 0.7547 (ttp-170) cc_final: 0.7095 (ttt90) REVERT: E 332 LYS cc_start: 0.8736 (mttt) cc_final: 0.8343 (mmtm) REVERT: E 340 HIS cc_start: 0.7557 (t-90) cc_final: 0.7265 (t-170) REVERT: E 488 MET cc_start: 0.3406 (tmm) cc_final: 0.2976 (ttp) REVERT: E 599 MET cc_start: 0.3465 (mmp) cc_final: 0.1946 (mmp) REVERT: F 39 LYS cc_start: 0.7926 (mmtp) cc_final: 0.7612 (mmpt) REVERT: F 105 MET cc_start: 0.7369 (ttm) cc_final: 0.6152 (tmm) REVERT: F 149 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7688 (ttt180) REVERT: F 160 LYS cc_start: 0.8026 (mttm) cc_final: 0.7717 (mmmm) REVERT: F 195 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: F 218 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7600 (mt-10) REVERT: F 222 ARG cc_start: 0.7191 (mtt180) cc_final: 0.6391 (mpt90) REVERT: F 253 GLU cc_start: 0.6379 (pt0) cc_final: 0.5830 (pm20) REVERT: F 266 TYR cc_start: 0.7374 (t80) cc_final: 0.6574 (m-80) REVERT: F 270 ARG cc_start: 0.7285 (mtp-110) cc_final: 0.6760 (ttm170) REVERT: F 274 ARG cc_start: 0.7471 (ttp-170) cc_final: 0.6835 (tmm160) REVERT: F 340 HIS cc_start: 0.8246 (t70) cc_final: 0.7741 (t70) REVERT: G 105 MET cc_start: 0.6757 (OUTLIER) cc_final: 0.5654 (tmm) REVERT: G 218 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7168 (mm-30) REVERT: G 222 ARG cc_start: 0.6980 (mtt180) cc_final: 0.6340 (mpt90) REVERT: G 270 ARG cc_start: 0.7081 (mtp-110) cc_final: 0.6615 (mpp-170) REVERT: G 454 LYS cc_start: 0.8167 (tttt) cc_final: 0.7712 (tptp) REVERT: G 488 MET cc_start: 0.4999 (tmt) cc_final: 0.4482 (tmm) REVERT: G 586 LEU cc_start: 0.7124 (tm) cc_final: 0.6801 (pp) REVERT: G 599 MET cc_start: 0.2267 (OUTLIER) cc_final: 0.1972 (mpt) REVERT: H 61 ARG cc_start: 0.7560 (tpp-160) cc_final: 0.7275 (tpp-160) REVERT: H 95 GLU cc_start: 0.8003 (mp0) cc_final: 0.7473 (mt-10) REVERT: H 218 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7404 (mt-10) REVERT: H 270 ARG cc_start: 0.7000 (mtt180) cc_final: 0.6427 (mmm160) REVERT: H 274 ARG cc_start: 0.7509 (ttp-170) cc_final: 0.7193 (ttm-80) REVERT: H 336 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8379 (p) REVERT: H 339 ARG cc_start: 0.7888 (mtp85) cc_final: 0.7591 (ttm-80) REVERT: H 594 THR cc_start: 0.6094 (OUTLIER) cc_final: 0.5753 (t) REVERT: I 135 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.6564 (mmt180) REVERT: I 218 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7828 (mt-10) REVERT: I 222 ARG cc_start: 0.7018 (mtt180) cc_final: 0.6345 (mtp180) REVERT: I 344 PHE cc_start: 0.7620 (t80) cc_final: 0.7414 (t80) REVERT: I 425 GLU cc_start: 0.7043 (tt0) cc_final: 0.6672 (tm-30) REVERT: J 105 MET cc_start: 0.6733 (OUTLIER) cc_final: 0.6235 (ttt) REVERT: J 166 GLU cc_start: 0.6687 (mt-10) cc_final: 0.6216 (pm20) REVERT: J 195 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6981 (tt0) REVERT: J 270 ARG cc_start: 0.6814 (mtp-110) cc_final: 0.6112 (mtm180) REVERT: J 274 ARG cc_start: 0.7586 (ttp-170) cc_final: 0.6555 (ttt-90) REVERT: J 276 GLN cc_start: 0.8358 (tt0) cc_final: 0.8106 (tt0) REVERT: J 336 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8684 (p) REVERT: J 461 TRP cc_start: 0.7760 (p-90) cc_final: 0.6484 (p-90) REVERT: J 524 PRO cc_start: 0.7186 (Cg_exo) cc_final: 0.6942 (Cg_endo) REVERT: J 570 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.7119 (pp30) REVERT: J 589 ARG cc_start: 0.2456 (OUTLIER) cc_final: 0.0656 (ttm110) REVERT: J 599 MET cc_start: 0.0516 (mmt) cc_final: -0.0050 (mmt) REVERT: K 77 GLN cc_start: 0.7874 (mt0) cc_final: 0.7185 (mm-40) REVERT: K 95 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: K 104 TRP cc_start: 0.6541 (t60) cc_final: 0.5929 (t-100) REVERT: K 218 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7570 (mm-30) REVERT: K 222 ARG cc_start: 0.6955 (mtt180) cc_final: 0.6526 (mmm160) REVERT: K 274 ARG cc_start: 0.7562 (ttp-170) cc_final: 0.7000 (ttm-80) REVERT: K 599 MET cc_start: 0.3309 (mmp) cc_final: 0.2553 (mmp) REVERT: L 75 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7736 (p0) REVERT: L 96 MET cc_start: 0.7093 (mtm) cc_final: 0.6563 (mtm) REVERT: L 104 TRP cc_start: 0.6773 (t60) cc_final: 0.6300 (t-100) REVERT: L 126 ASN cc_start: 0.6998 (m-40) cc_final: 0.6677 (t0) REVERT: L 136 MET cc_start: 0.6523 (OUTLIER) cc_final: 0.6288 (mpp) REVERT: L 219 ASP cc_start: 0.7886 (t0) cc_final: 0.7596 (t70) REVERT: L 274 ARG cc_start: 0.7318 (ttp-170) cc_final: 0.6911 (ttt90) REVERT: L 331 SER cc_start: 0.8103 (t) cc_final: 0.7726 (m) REVERT: L 457 PHE cc_start: 0.7490 (p90) cc_final: 0.7249 (p90) REVERT: L 503 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7601 (tm) REVERT: M 53 ASN cc_start: 0.8604 (t0) cc_final: 0.8264 (t0) REVERT: M 104 TRP cc_start: 0.6678 (t60) cc_final: 0.6153 (t-100) REVERT: M 136 MET cc_start: 0.7358 (mtp) cc_final: 0.6650 (mtm) REVERT: M 166 GLU cc_start: 0.6592 (mt-10) cc_final: 0.5808 (mm-30) REVERT: M 188 LYS cc_start: 0.8847 (mppt) cc_final: 0.8537 (mppt) REVERT: M 222 ARG cc_start: 0.7273 (mtt180) cc_final: 0.6590 (mpt180) REVERT: M 230 GLN cc_start: 0.8143 (mt0) cc_final: 0.7802 (mt0) REVERT: M 270 ARG cc_start: 0.7405 (mtp-110) cc_final: 0.6745 (ttm110) REVERT: M 274 ARG cc_start: 0.7618 (ttp-170) cc_final: 0.7241 (ttt90) REVERT: M 332 LYS cc_start: 0.8720 (mttt) cc_final: 0.8352 (mmtm) REVERT: M 586 LEU cc_start: 0.6161 (OUTLIER) cc_final: 0.5384 (pp) REVERT: M 599 MET cc_start: 0.2568 (mmp) cc_final: 0.1545 (mmp) REVERT: N 94 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8492 (mm) REVERT: N 105 MET cc_start: 0.7639 (ttm) cc_final: 0.6235 (tmm) REVERT: N 160 LYS cc_start: 0.8027 (mttm) cc_final: 0.7814 (mmmt) REVERT: N 218 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7571 (mt-10) REVERT: N 253 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6211 (pm20) REVERT: N 266 TYR cc_start: 0.7292 (t80) cc_final: 0.6574 (m-80) REVERT: N 274 ARG cc_start: 0.7559 (ttp-170) cc_final: 0.6988 (ttp-170) REVERT: N 340 HIS cc_start: 0.8261 (t-90) cc_final: 0.7421 (t70) REVERT: N 344 PHE cc_start: 0.8029 (t80) cc_final: 0.7768 (t80) REVERT: N 599 MET cc_start: 0.2786 (mmp) cc_final: 0.2425 (mmt) REVERT: O 105 MET cc_start: 0.6717 (OUTLIER) cc_final: 0.5618 (tmm) REVERT: O 218 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7093 (mm-30) REVERT: O 222 ARG cc_start: 0.7015 (mtt180) cc_final: 0.6292 (mpt90) REVERT: O 270 ARG cc_start: 0.7050 (mtp-110) cc_final: 0.6607 (mpp-170) REVERT: O 274 ARG cc_start: 0.7456 (ttp-170) cc_final: 0.6775 (ttt90) REVERT: O 454 LYS cc_start: 0.8113 (tttt) cc_final: 0.7809 (ptpp) REVERT: O 488 MET cc_start: 0.4588 (tmt) cc_final: 0.4178 (tmm) REVERT: O 533 MET cc_start: 0.4669 (mtp) cc_final: 0.4100 (pmm) REVERT: P 218 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7516 (mt-10) REVERT: P 270 ARG cc_start: 0.7395 (mtp-110) cc_final: 0.7155 (mtm180) REVERT: P 336 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8440 (p) REVERT: P 339 ARG cc_start: 0.8125 (mtt90) cc_final: 0.7627 (ttm-80) outliers start: 176 outliers final: 127 residues processed: 621 average time/residue: 1.3147 time to fit residues: 1092.5952 Evaluate side-chains 619 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 465 time to evaluate : 5.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 521 PHE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 515 TYR Chi-restraints excluded: chain D residue 523 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 189 MET Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 149 ARG Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 392 VAL Chi-restraints excluded: chain G residue 523 VAL Chi-restraints excluded: chain G residue 599 MET Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 310 LEU Chi-restraints excluded: chain H residue 336 THR Chi-restraints excluded: chain H residue 428 SER Chi-restraints excluded: chain H residue 594 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 126 ASN Chi-restraints excluded: chain I residue 135 ARG Chi-restraints excluded: chain I residue 254 THR Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 499 ILE Chi-restraints excluded: chain I residue 503 LEU Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 105 MET Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 271 THR Chi-restraints excluded: chain J residue 297 THR Chi-restraints excluded: chain J residue 336 THR Chi-restraints excluded: chain J residue 511 VAL Chi-restraints excluded: chain J residue 570 GLN Chi-restraints excluded: chain J residue 589 ARG Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain K residue 523 VAL Chi-restraints excluded: chain K residue 564 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 136 MET Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 247 ILE Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 403 LEU Chi-restraints excluded: chain L residue 444 THR Chi-restraints excluded: chain L residue 445 VAL Chi-restraints excluded: chain L residue 503 LEU Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain L residue 523 VAL Chi-restraints excluded: chain L residue 589 ARG Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 189 MET Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 586 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 247 ILE Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 430 LEU Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 105 MET Chi-restraints excluded: chain O residue 136 MET Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 165 SER Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 209 VAL Chi-restraints excluded: chain O residue 392 VAL Chi-restraints excluded: chain O residue 523 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 111 THR Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain P residue 247 ILE Chi-restraints excluded: chain P residue 254 THR Chi-restraints excluded: chain P residue 260 THR Chi-restraints excluded: chain P residue 336 THR Chi-restraints excluded: chain P residue 428 SER Chi-restraints excluded: chain P residue 502 ASN Chi-restraints excluded: chain P residue 523 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 412 optimal weight: 9.9990 chunk 534 optimal weight: 1.9990 chunk 716 optimal weight: 0.7980 chunk 206 optimal weight: 4.9990 chunk 620 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 186 optimal weight: 1.9990 chunk 673 optimal weight: 6.9990 chunk 281 optimal weight: 2.9990 chunk 691 optimal weight: 0.9990 chunk 85 optimal weight: 30.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 HIS ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN D 340 HIS F 89 GLN ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 401 ASN G 181 GLN ** K 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN L 181 GLN ** L 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 417 HIS ** M 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN P 181 GLN ** P 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.249879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.188465 restraints weight = 60476.498| |-----------------------------------------------------------------------------| r_work (start): 0.4273 rms_B_bonded: 1.45 r_work: 0.4019 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 68624 Z= 0.246 Angle : 0.561 12.040 93136 Z= 0.277 Chirality : 0.044 0.316 10816 Planarity : 0.005 0.060 11792 Dihedral : 6.596 89.803 10483 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.32 % Favored : 96.53 % Rotamer: Outliers : 2.52 % Allowed : 15.64 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.55 (0.09), residues: 8432 helix: 0.93 (0.14), residues: 1312 sheet: -0.32 (0.09), residues: 3760 loop : -0.79 (0.11), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 461 HIS 0.010 0.001 HIS M 340 PHE 0.031 0.001 PHE K 528 TYR 0.020 0.001 TYR C 593 ARG 0.005 0.000 ARG O 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19326.08 seconds wall clock time: 338 minutes 31.82 seconds (20311.82 seconds total)