Starting phenix.real_space_refine on Thu Mar 14 10:37:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1s_15086/03_2024/8a1s_15086_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1s_15086/03_2024/8a1s_15086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1s_15086/03_2024/8a1s_15086.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1s_15086/03_2024/8a1s_15086.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1s_15086/03_2024/8a1s_15086_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1s_15086/03_2024/8a1s_15086_updated.pdb" } resolution = 4.0 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= 0.005 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-5265/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: 25.02, per 1000 atoms: 0.37 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: 18.26 Conformation dependent library (CDL) restraints added in 8.5 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: 9.72 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: 22.68 Time building geometry restraints manager: 20.34 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 group one per residue 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 11.450 Check model and map are aligned: 0.720 Set scattering table: 0.460 Process input model: 129.180 Find NCS groups from input model: 3.820 Set up NCS constraints: 0.590 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0024 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 761 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 688 time to evaluate : 5.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.1922 (mtm) cc_final: 0.1158 (ptt) REVERT: A 106 ASN cc_start: 0.5456 (t0) cc_final: 0.5039 (t0) REVERT: B 304 ASP cc_start: 0.4766 (t0) cc_final: 0.4419 (t0) REVERT: C 193 LEU cc_start: 0.8555 (tp) cc_final: 0.8180 (mm) REVERT: D 247 ILE cc_start: -0.2509 (OUTLIER) cc_final: -0.2867 (tp) REVERT: E 105 MET cc_start: -0.3613 (ttm) cc_final: -0.4346 (mmt) REVERT: G 176 MET cc_start: 0.6586 (mtt) cc_final: 0.6306 (mtt) REVERT: G 406 ASP cc_start: 0.6261 (t0) cc_final: 0.5473 (m-30) REVERT: G 533 MET cc_start: -0.3595 (ptp) cc_final: -0.5450 (mmt) REVERT: H 47 PRO cc_start: 0.2973 (Cg_endo) cc_final: 0.2763 (Cg_exo) REVERT: H 176 MET cc_start: 0.7337 (mtt) cc_final: 0.7029 (mmp) REVERT: H 196 LEU cc_start: 0.7370 (mm) cc_final: 0.6914 (tp) REVERT: H 205 VAL cc_start: 0.7166 (t) cc_final: 0.6881 (t) REVERT: H 529 PHE cc_start: 0.5513 (p90) cc_final: 0.5124 (p90) REVERT: H 599 MET cc_start: -0.0446 (mmp) cc_final: -0.0795 (tpt) REVERT: I 154 ASN cc_start: 0.5363 (m-40) cc_final: 0.4800 (p0) REVERT: I 599 MET cc_start: 0.4755 (mmt) cc_final: 0.1540 (mtm) REVERT: J 180 ASP cc_start: 0.5855 (m-30) cc_final: 0.5192 (t0) REVERT: K 153 ARG cc_start: 0.1519 (ttt-90) cc_final: 0.0716 (mtt180) REVERT: K 176 MET cc_start: 0.3980 (mtt) cc_final: 0.3469 (ttp) REVERT: K 196 LEU cc_start: -0.0659 (OUTLIER) cc_final: -0.1001 (tt) REVERT: K 442 CYS cc_start: 0.1497 (m) cc_final: 0.1184 (m) REVERT: K 599 MET cc_start: 0.1760 (mmt) cc_final: 0.0176 (mtt) REVERT: L 136 MET cc_start: 0.2996 (ptt) cc_final: 0.2590 (ptm) REVERT: L 304 ASP cc_start: 0.0847 (t0) cc_final: 0.0112 (t0) REVERT: L 322 LEU cc_start: -0.0118 (mt) cc_final: -0.0686 (mm) REVERT: L 443 LYS cc_start: 0.0376 (pttt) cc_final: -0.0211 (mttp) REVERT: M 181 GLN cc_start: -0.4238 (OUTLIER) cc_final: -0.4775 (tt0) REVERT: M 528 PHE cc_start: 0.3284 (m-80) cc_final: 0.2189 (m-80) REVERT: M 529 PHE cc_start: 0.6328 (p90) cc_final: 0.6120 (p90) REVERT: M 576 LYS cc_start: -0.0515 (mttt) cc_final: -0.0789 (tttt) REVERT: N 116 ASN cc_start: 0.5302 (m-40) cc_final: 0.5102 (t0) REVERT: N 171 PHE cc_start: 0.2157 (t80) cc_final: 0.1623 (t80) REVERT: N 233 GLN cc_start: 0.6883 (tt0) cc_final: 0.6260 (mp10) REVERT: N 408 SER cc_start: 0.2190 (p) cc_final: 0.1917 (t) REVERT: N 585 LEU cc_start: -0.1191 (OUTLIER) cc_final: -0.1667 (mt) REVERT: O 154 ASN cc_start: 0.1213 (m-40) cc_final: 0.0304 (m-40) REVERT: O 160 LYS cc_start: 0.3507 (mttm) cc_final: 0.3264 (tptm) REVERT: O 176 MET cc_start: 0.4309 (mtt) cc_final: 0.3697 (tpt) REVERT: O 406 ASP cc_start: 0.2565 (t0) cc_final: 0.2072 (m-30) REVERT: O 407 PHE cc_start: 0.2639 (m-80) cc_final: 0.1814 (m-10) REVERT: O 488 MET cc_start: -0.0280 (tmt) cc_final: -0.1699 (ttm) REVERT: P 96 MET cc_start: -0.1935 (mtt) cc_final: -0.3621 (ttt) outliers start: 73 outliers final: 17 residues processed: 752 average time/residue: 0.6297 time to fit residues: 804.2437 Evaluate side-chains 460 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 439 time to evaluate : 5.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 242 ILE Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain M residue 181 GLN Chi-restraints excluded: chain N residue 45 VAL 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 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=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 716 optimal weight: 0.5980 chunk 642 optimal weight: 0.5980 chunk 356 optimal weight: 0.4980 chunk 219 optimal weight: 20.0000 chunk 433 optimal weight: 30.0000 chunk 343 optimal weight: 6.9990 chunk 664 optimal weight: 0.0270 chunk 257 optimal weight: 40.0000 chunk 404 optimal weight: 3.9990 chunk 494 optimal weight: 0.1980 chunk 770 optimal weight: 4.9990 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN A 276 GLN ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN B 234 ASN B 467 GLN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN C 311 HIS C 467 GLN C 570 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 GLN D 467 GLN D 570 GLN E 32 GLN E 276 GLN E 467 GLN E 570 GLN F 220 HIS F 259 GLN F 276 GLN F 340 HIS F 383 GLN ** F 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 467 GLN F 561 HIS F 570 GLN ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 276 GLN G 383 GLN G 401 ASN G 467 GLN H 134 GLN H 181 GLN ** H 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 ASN H 234 ASN H 276 GLN H 345 ASN ** H 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 467 GLN I 276 GLN J 89 GLN J 220 HIS J 311 HIS J 340 HIS J 467 GLN K 204 HIS K 276 GLN K 311 HIS K 383 GLN K 467 GLN K 560 GLN K 570 GLN L 181 GLN L 186 GLN ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 276 GLN L 467 GLN L 570 GLN M 32 GLN M 276 GLN M 311 HIS ** M 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 570 GLN N 204 HIS N 276 GLN N 467 GLN N 570 GLN O 69 ASN O 108 GLN ** O 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 276 GLN O 383 GLN O 467 GLN P 77 GLN ** P 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 276 GLN P 467 GLN P 490 ASN Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0136 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 68624 Z= 0.156 Angle : 0.609 15.928 93136 Z= 0.292 Chirality : 0.045 0.219 10816 Planarity : 0.004 0.054 11792 Dihedral : 10.782 94.682 10484 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.45 % Favored : 97.37 % Rotamer: Outliers : 1.92 % Allowed : 9.05 % Favored : 89.03 % 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: -0.14 (0.09), residues: 8432 helix: 1.14 (0.14), residues: 1376 sheet: 0.22 (0.09), residues: 3744 loop : -0.90 (0.11), residues: 3312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 51 HIS 0.007 0.001 HIS G 340 PHE 0.035 0.001 PHE P 225 TYR 0.022 0.001 TYR C 593 ARG 0.006 0.000 ARG E 153 *********************** 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 623 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 479 time to evaluate : 5.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.1711 (mtm) cc_final: 0.1003 (ptt) REVERT: A 503 LEU cc_start: 0.1446 (OUTLIER) cc_final: 0.1166 (mm) REVERT: B 488 MET cc_start: -0.3409 (mmt) cc_final: -0.4138 (mmt) REVERT: C 99 GLU cc_start: -0.4548 (OUTLIER) cc_final: -0.5381 (tt0) REVERT: C 533 MET cc_start: 0.3945 (ppp) cc_final: 0.3606 (ppp) REVERT: D 63 MET cc_start: -0.5441 (mmt) cc_final: -0.6374 (mmt) REVERT: D 105 MET cc_start: 0.1072 (ppp) cc_final: 0.0245 (ppp) REVERT: E 59 MET cc_start: -0.3781 (mmp) cc_final: -0.4068 (mmt) REVERT: E 105 MET cc_start: -0.4144 (ttm) cc_final: -0.4654 (mpp) REVERT: F 533 MET cc_start: -0.0297 (OUTLIER) cc_final: -0.1175 (tmm) REVERT: G 176 MET cc_start: 0.6494 (mtt) cc_final: 0.6213 (mtt) REVERT: G 394 CYS cc_start: 0.3253 (OUTLIER) cc_final: 0.2851 (m) REVERT: G 406 ASP cc_start: 0.6378 (t0) cc_final: 0.5659 (m-30) REVERT: G 430 LEU cc_start: -0.1254 (OUTLIER) cc_final: -0.3077 (pp) REVERT: G 533 MET cc_start: -0.4546 (ptp) cc_final: -0.5607 (mmt) REVERT: H 176 MET cc_start: 0.7492 (mtt) cc_final: 0.7101 (mmp) REVERT: H 503 LEU cc_start: -0.4895 (OUTLIER) cc_final: -0.5118 (tt) REVERT: H 529 PHE cc_start: 0.5575 (p90) cc_final: 0.5147 (p90) REVERT: I 63 MET cc_start: 0.0966 (ttt) cc_final: 0.0664 (ttm) REVERT: I 488 MET cc_start: 0.0817 (mmp) cc_final: 0.0224 (mtp) REVERT: I 599 MET cc_start: 0.3942 (mmt) cc_final: 0.1933 (mtm) REVERT: J 155 ARG cc_start: 0.1410 (ttp-170) cc_final: 0.1151 (ttp-170) REVERT: J 180 ASP cc_start: 0.5661 (m-30) cc_final: 0.5240 (t0) REVERT: J 488 MET cc_start: 0.3633 (mmt) cc_final: 0.2828 (mmt) REVERT: J 525 PHE cc_start: 0.2552 (t80) cc_final: 0.2056 (p90) REVERT: J 580 PHE cc_start: -0.1901 (OUTLIER) cc_final: -0.4325 (m-80) REVERT: K 97 ASN cc_start: 0.3465 (m110) cc_final: 0.2533 (t0) REVERT: K 153 ARG cc_start: 0.1809 (ttt-90) cc_final: 0.1021 (ptm160) REVERT: K 442 CYS cc_start: 0.1668 (m) cc_final: 0.1267 (m) REVERT: K 570 GLN cc_start: -0.1799 (OUTLIER) cc_final: -0.2391 (pm20) REVERT: K 599 MET cc_start: 0.1654 (mmt) cc_final: 0.0439 (mtt) REVERT: L 189 MET cc_start: -0.3098 (tpt) cc_final: -0.3489 (tpt) REVERT: L 423 HIS cc_start: 0.5184 (t70) cc_final: 0.4963 (p90) REVERT: L 443 LYS cc_start: 0.0555 (pttt) cc_final: 0.0022 (mttp) REVERT: M 59 MET cc_start: 0.2155 (mmm) cc_final: 0.1668 (mmm) REVERT: M 96 MET cc_start: 0.3636 (mmm) cc_final: 0.3266 (mmt) REVERT: M 188 LYS cc_start: 0.1846 (mppt) cc_final: 0.0741 (tptt) REVERT: M 196 LEU cc_start: -0.4547 (OUTLIER) cc_final: -0.4817 (tt) REVERT: M 528 PHE cc_start: 0.3208 (m-80) cc_final: 0.2273 (m-10) REVERT: M 576 LYS cc_start: -0.0761 (mttt) cc_final: -0.1075 (tttt) REVERT: N 119 LEU cc_start: 0.4728 (OUTLIER) cc_final: 0.4445 (mp) REVERT: N 275 VAL cc_start: -0.0631 (t) cc_final: -0.1228 (m) REVERT: N 462 CYS cc_start: 0.4263 (m) cc_final: 0.3689 (p) REVERT: O 136 MET cc_start: 0.8192 (mpp) cc_final: 0.7689 (mpp) REVERT: O 154 ASN cc_start: 0.1553 (m-40) cc_final: 0.1079 (t0) REVERT: O 160 LYS cc_start: 0.3597 (mttm) cc_final: 0.2925 (tptm) REVERT: O 179 CYS cc_start: 0.5604 (t) cc_final: 0.5274 (m) REVERT: O 488 MET cc_start: -0.0309 (tmt) cc_final: -0.1609 (ttm) REVERT: P 105 MET cc_start: -0.0081 (OUTLIER) cc_final: -0.0499 (tpt) REVERT: P 176 MET cc_start: 0.5763 (mmp) cc_final: 0.5538 (mmp) REVERT: P 181 GLN cc_start: -0.6608 (OUTLIER) cc_final: -0.7429 (mt0) REVERT: P 394 CYS cc_start: 0.3795 (OUTLIER) cc_final: 0.3098 (p) REVERT: P 430 LEU cc_start: 0.2627 (OUTLIER) cc_final: 0.2392 (tp) REVERT: P 461 TRP cc_start: -0.3267 (p-90) cc_final: -0.3940 (p-90) REVERT: P 488 MET cc_start: 0.1470 (mmt) cc_final: -0.0522 (mtp) REVERT: P 523 VAL cc_start: -0.0973 (OUTLIER) cc_final: -0.1865 (t) REVERT: P 580 PHE cc_start: 0.2343 (OUTLIER) cc_final: 0.2071 (t80) outliers start: 144 outliers final: 52 residues processed: 597 average time/residue: 0.6056 time to fit residues: 625.0108 Evaluate side-chains 476 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 408 time to evaluate : 5.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain G residue 394 CYS Chi-restraints excluded: chain G residue 430 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 229 ASN Chi-restraints excluded: chain H residue 378 PHE Chi-restraints excluded: chain H residue 409 CYS Chi-restraints excluded: chain H residue 420 SER Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 565 ILE Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 580 PHE Chi-restraints excluded: chain J residue 588 VAL Chi-restraints excluded: chain J residue 594 THR Chi-restraints excluded: chain J residue 599 MET Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 570 GLN Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 189 MET Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 310 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 128 LYS Chi-restraints excluded: chain N residue 326 LEU Chi-restraints excluded: chain N residue 437 THR Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 69 ASN Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 105 MET Chi-restraints excluded: chain P residue 175 LEU Chi-restraints excluded: chain P residue 181 GLN Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain P residue 247 ILE Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain P residue 394 CYS Chi-restraints excluded: chain P residue 430 LEU Chi-restraints excluded: chain P residue 484 THR Chi-restraints excluded: chain P residue 523 VAL Chi-restraints excluded: chain P residue 574 CYS Chi-restraints excluded: chain P residue 580 PHE Chi-restraints excluded: chain P residue 599 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 427 optimal weight: 20.0000 chunk 238 optimal weight: 50.0000 chunk 640 optimal weight: 2.9990 chunk 524 optimal weight: 3.9990 chunk 212 optimal weight: 620.0000 chunk 771 optimal weight: 0.9990 chunk 833 optimal weight: 6.9990 chunk 687 optimal weight: 6.9990 chunk 765 optimal weight: 6.9990 chunk 263 optimal weight: 0.5980 chunk 618 optimal weight: 0.0170 overall best weight: 1.7224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN A 383 GLN A 401 ASN A 490 ASN B 186 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 HIS F 217 GLN ** F 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 570 GLN H 144 GLN H 154 ASN ** H 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 293 GLN H 383 GLN H 401 ASN I 144 GLN ** I 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 217 GLN J 234 ASN ** J 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 217 GLN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 97 ASN L 108 GLN ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 234 ASN ** L 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 311 HIS L 383 GLN L 561 HIS M 217 GLN M 220 HIS M 272 ASN ** M 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 144 GLN ** N 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 217 GLN N 220 HIS N 234 ASN N 299 HIS ** N 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 399 GLN O 217 GLN ** O 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 144 GLN P 154 ASN P 233 GLN P 293 GLN P 399 GLN P 539 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0595 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 68624 Z= 0.214 Angle : 0.677 13.987 93136 Z= 0.333 Chirality : 0.047 0.341 10816 Planarity : 0.005 0.074 11792 Dihedral : 8.433 100.645 10468 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.06 % Favored : 96.77 % Rotamer: Outliers : 2.15 % Allowed : 9.54 % Favored : 88.31 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % Twisted Proline : 0.22 % 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: 0.81 (0.14), residues: 1360 sheet: 0.28 (0.09), residues: 3616 loop : -0.95 (0.11), residues: 3456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP L 461 HIS 0.016 0.001 HIS L 220 PHE 0.034 0.002 PHE L 278 TYR 0.029 0.002 TYR J 573 ARG 0.016 0.001 ARG K 270 *********************** 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 659 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 498 time to evaluate : 5.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.0857 (mtm) cc_final: 0.0440 (ptt) REVERT: B 488 MET cc_start: -0.4275 (mmt) cc_final: -0.4546 (mmt) REVERT: C 99 GLU cc_start: -0.4255 (OUTLIER) cc_final: -0.5344 (tt0) REVERT: D 63 MET cc_start: -0.5623 (mmt) cc_final: -0.6470 (mmt) REVERT: E 105 MET cc_start: -0.3892 (ttm) cc_final: -0.4512 (mpp) REVERT: F 59 MET cc_start: -0.1993 (mmm) cc_final: -0.2439 (mmm) REVERT: F 593 TYR cc_start: -0.2360 (OUTLIER) cc_final: -0.3013 (t80) REVERT: G 176 MET cc_start: 0.6628 (mtt) cc_final: 0.6322 (mtt) REVERT: G 406 ASP cc_start: 0.6518 (t0) cc_final: 0.5768 (m-30) REVERT: G 533 MET cc_start: -0.4844 (ptp) cc_final: -0.5724 (mmt) REVERT: G 589 ARG cc_start: -0.2203 (OUTLIER) cc_final: -0.2820 (ppt170) REVERT: H 176 MET cc_start: 0.7452 (mtt) cc_final: 0.7087 (mmp) REVERT: H 503 LEU cc_start: -0.4123 (OUTLIER) cc_final: -0.4604 (tp) REVERT: H 529 PHE cc_start: 0.5691 (p90) cc_final: 0.5364 (p90) REVERT: H 533 MET cc_start: -0.5663 (mtp) cc_final: -0.6373 (mmm) REVERT: I 227 LEU cc_start: 0.1359 (tp) cc_final: 0.1158 (tt) REVERT: I 488 MET cc_start: 0.1233 (mmp) cc_final: 0.0732 (mtm) REVERT: I 599 MET cc_start: 0.4005 (mmt) cc_final: 0.1639 (mtm) REVERT: J 180 ASP cc_start: 0.5866 (m-30) cc_final: 0.5348 (t0) REVERT: J 525 PHE cc_start: 0.3319 (t80) cc_final: 0.2894 (p90) REVERT: J 535 ASN cc_start: 0.5970 (t0) cc_final: 0.5592 (m-40) REVERT: J 580 PHE cc_start: -0.1761 (OUTLIER) cc_final: -0.2276 (m-80) REVERT: K 70 CYS cc_start: 0.3088 (m) cc_final: 0.2645 (m) REVERT: K 97 ASN cc_start: 0.3766 (m110) cc_final: 0.3529 (m110) REVERT: K 217 GLN cc_start: 0.1971 (OUTLIER) cc_final: 0.0519 (tm-30) REVERT: K 599 MET cc_start: 0.1680 (mmt) cc_final: -0.0203 (mtt) REVERT: L 272 ASN cc_start: -0.0967 (OUTLIER) cc_final: -0.3454 (t0) REVERT: L 430 LEU cc_start: -0.3827 (OUTLIER) cc_final: -0.5229 (tp) REVERT: L 443 LYS cc_start: 0.0833 (pttt) cc_final: 0.0179 (mptt) REVERT: L 480 PHE cc_start: 0.2227 (p90) cc_final: 0.1739 (p90) REVERT: M 96 MET cc_start: 0.5157 (mmm) cc_final: 0.4948 (mtp) REVERT: M 196 LEU cc_start: -0.4998 (OUTLIER) cc_final: -0.5304 (tt) REVERT: M 528 PHE cc_start: 0.3962 (m-80) cc_final: 0.2972 (m-10) REVERT: M 529 PHE cc_start: 0.5742 (p90) cc_final: 0.5450 (p90) REVERT: M 576 LYS cc_start: -0.1408 (mttt) cc_final: -0.1758 (tttt) REVERT: M 599 MET cc_start: 0.7271 (mmp) cc_final: 0.7037 (mmm) REVERT: N 176 MET cc_start: -0.2012 (mmt) cc_final: -0.2220 (mmt) REVERT: N 234 ASN cc_start: 0.6697 (m-40) cc_final: 0.5527 (t0) REVERT: N 391 ASP cc_start: 0.4734 (p0) cc_final: 0.3924 (t70) REVERT: N 525 PHE cc_start: 0.1974 (t80) cc_final: 0.1279 (t80) REVERT: O 63 MET cc_start: 0.1668 (mtt) cc_final: 0.1270 (ptp) REVERT: O 136 MET cc_start: 0.8725 (mpp) cc_final: 0.6144 (tmm) REVERT: O 179 CYS cc_start: 0.6068 (t) cc_final: 0.5648 (m) REVERT: O 274 ARG cc_start: 0.1116 (ttp-170) cc_final: 0.0607 (mtt180) REVERT: O 488 MET cc_start: -0.0845 (tmt) cc_final: -0.2151 (ttm) REVERT: P 95 GLU cc_start: -0.2829 (OUTLIER) cc_final: -0.4434 (tt0) REVERT: P 96 MET cc_start: -0.1050 (mpp) cc_final: -0.2552 (ttt) REVERT: P 105 MET cc_start: 0.0741 (OUTLIER) cc_final: -0.0600 (tpt) REVERT: P 159 VAL cc_start: 0.0424 (OUTLIER) cc_final: 0.0142 (p) REVERT: P 181 GLN cc_start: -0.6724 (OUTLIER) cc_final: -0.7577 (mt0) REVERT: P 385 CYS cc_start: 0.3210 (OUTLIER) cc_final: -0.0110 (p) REVERT: P 394 CYS cc_start: 0.4173 (OUTLIER) cc_final: 0.3025 (p) REVERT: P 396 ASN cc_start: 0.6306 (OUTLIER) cc_final: 0.5168 (t0) REVERT: P 418 LEU cc_start: 0.2295 (mt) cc_final: 0.1726 (mt) REVERT: P 461 TRP cc_start: -0.2965 (p-90) cc_final: -0.3596 (p-90) REVERT: P 488 MET cc_start: 0.1158 (mmt) cc_final: -0.0977 (mtp) REVERT: P 533 MET cc_start: 0.6425 (mtp) cc_final: 0.6103 (ttt) outliers start: 161 outliers final: 74 residues processed: 624 average time/residue: 0.6239 time to fit residues: 672.1559 Evaluate side-chains 517 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 427 time to evaluate : 5.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 394 CYS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 593 TYR Chi-restraints excluded: chain G residue 417 HIS Chi-restraints excluded: chain G residue 589 ARG Chi-restraints excluded: chain G residue 590 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 378 PHE Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 512 SER Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 594 THR Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 400 LYS Chi-restraints excluded: chain J residue 402 LEU Chi-restraints excluded: chain J residue 580 PHE Chi-restraints excluded: chain J residue 599 MET Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 217 GLN Chi-restraints excluded: chain K residue 386 THR Chi-restraints excluded: chain L residue 31 PHE Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 272 ASN Chi-restraints excluded: chain L residue 403 LEU Chi-restraints excluded: chain L residue 430 LEU Chi-restraints excluded: chain L residue 462 CYS Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 189 MET Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 303 ILE Chi-restraints excluded: chain M residue 574 CYS Chi-restraints excluded: chain M residue 588 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 251 LYS Chi-restraints excluded: chain N residue 303 ILE Chi-restraints excluded: chain N residue 437 THR Chi-restraints excluded: chain N residue 445 VAL Chi-restraints excluded: chain N residue 533 MET Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 172 THR Chi-restraints excluded: chain O residue 376 PHE Chi-restraints excluded: chain O residue 392 VAL Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 105 MET Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain P residue 175 LEU Chi-restraints excluded: chain P residue 181 GLN 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 385 CYS Chi-restraints excluded: chain P residue 394 CYS Chi-restraints excluded: chain P residue 396 ASN Chi-restraints excluded: chain P residue 484 THR Chi-restraints excluded: chain P residue 574 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 762 optimal weight: 30.0000 chunk 580 optimal weight: 3.9990 chunk 400 optimal weight: 8.9990 chunk 85 optimal weight: 30.0000 chunk 368 optimal weight: 9.9990 chunk 518 optimal weight: 1.9990 chunk 774 optimal weight: 0.9990 chunk 819 optimal weight: 4.9990 chunk 404 optimal weight: 20.0000 chunk 733 optimal weight: 6.9990 chunk 220 optimal weight: 40.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 186 GLN A 340 HIS B 299 HIS ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 ASN E 217 GLN E 561 HIS F 401 ASN G 401 ASN ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 229 ASN H 401 ASN I 144 GLN ** J 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 GLN J 401 ASN ** J 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 GLN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 293 GLN K 401 ASN ** K 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 234 ASN ** L 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 399 GLN ** L 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 417 HIS L 423 HIS L 561 HIS M 32 GLN ** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN ** M 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 93 ASN N 144 GLN ** N 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 535 ASN ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 539 ASN ** O 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 134 GLN P 217 GLN ** P 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 234 ASN ** P 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1132 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.190 68624 Z= 0.361 Angle : 0.899 18.511 93136 Z= 0.458 Chirality : 0.054 0.447 10816 Planarity : 0.008 0.165 11792 Dihedral : 8.517 104.233 10467 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.45 % Favored : 95.36 % Rotamer: Outliers : 3.22 % Allowed : 10.33 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.00 (0.09), residues: 8432 helix: -0.07 (0.13), residues: 1403 sheet: 0.04 (0.09), residues: 3428 loop : -1.56 (0.10), residues: 3601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP H 51 HIS 0.023 0.003 HIS K 220 PHE 0.078 0.003 PHE K 278 TYR 0.040 0.003 TYR L 107 ARG 0.040 0.001 ARG J 305 *********************** 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 755 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 513 time to evaluate : 5.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.0363 (mtm) cc_final: 0.0046 (ptp) REVERT: A 209 VAL cc_start: 0.5325 (m) cc_final: 0.5038 (m) REVERT: A 431 GLU cc_start: 0.0183 (pp20) cc_final: -0.0072 (pp20) REVERT: A 503 LEU cc_start: 0.2046 (OUTLIER) cc_final: 0.1529 (mm) REVERT: B 95 GLU cc_start: -0.3657 (OUTLIER) cc_final: -0.4085 (tt0) REVERT: B 209 VAL cc_start: 0.0023 (m) cc_final: -0.0608 (p) REVERT: B 488 MET cc_start: -0.4332 (mmt) cc_final: -0.4682 (mmt) REVERT: C 99 GLU cc_start: -0.4364 (OUTLIER) cc_final: -0.5078 (tt0) REVERT: D 63 MET cc_start: -0.5673 (mmt) cc_final: -0.6199 (mmt) REVERT: E 105 MET cc_start: -0.3734 (ttm) cc_final: -0.4087 (mpp) REVERT: F 59 MET cc_start: -0.1190 (mmm) cc_final: -0.1574 (mmm) REVERT: F 593 TYR cc_start: -0.2030 (OUTLIER) cc_final: -0.2442 (t80) REVERT: G 176 MET cc_start: 0.6648 (mtt) cc_final: 0.6337 (mtt) REVERT: G 533 MET cc_start: -0.5065 (ptp) cc_final: -0.5887 (mmt) REVERT: G 589 ARG cc_start: -0.3089 (OUTLIER) cc_final: -0.3985 (ppt170) REVERT: H 95 GLU cc_start: 0.1830 (OUTLIER) cc_final: 0.1554 (mt-10) REVERT: H 105 MET cc_start: 0.0642 (ptp) cc_final: 0.0425 (ptp) REVERT: H 153 ARG cc_start: 0.3507 (ttt-90) cc_final: 0.1699 (mtp180) REVERT: H 176 MET cc_start: 0.7545 (mtt) cc_final: 0.7039 (mmp) REVERT: H 430 LEU cc_start: -0.0913 (OUTLIER) cc_final: -0.2939 (mp) REVERT: H 503 LEU cc_start: -0.2943 (OUTLIER) cc_final: -0.3407 (tp) REVERT: H 533 MET cc_start: -0.4800 (mtp) cc_final: -0.5991 (mmm) REVERT: H 592 PRO cc_start: 0.5009 (Cg_exo) cc_final: 0.4766 (Cg_endo) REVERT: I 96 MET cc_start: -0.0500 (OUTLIER) cc_final: -0.1959 (tpt) REVERT: I 181 GLN cc_start: 0.4584 (mm-40) cc_final: 0.3905 (pt0) REVERT: I 189 MET cc_start: 0.1867 (mmm) cc_final: 0.0643 (mmm) REVERT: I 488 MET cc_start: 0.1633 (mmp) cc_final: 0.1283 (mtm) REVERT: I 599 MET cc_start: 0.3873 (mmt) cc_final: 0.1473 (mtm) REVERT: J 54 LEU cc_start: -0.0692 (OUTLIER) cc_final: -0.0940 (tt) REVERT: J 95 GLU cc_start: 0.0729 (OUTLIER) cc_final: 0.0367 (mt-10) REVERT: J 189 MET cc_start: 0.4301 (mmm) cc_final: 0.3767 (mmm) REVERT: J 220 HIS cc_start: -0.1574 (OUTLIER) cc_final: -0.4057 (p-80) REVERT: J 222 ARG cc_start: -0.0898 (OUTLIER) cc_final: -0.5353 (ptp-170) REVERT: J 304 ASP cc_start: 0.6280 (t0) cc_final: 0.5530 (m-30) REVERT: J 448 ASP cc_start: -0.0840 (OUTLIER) cc_final: -0.1682 (t0) REVERT: J 488 MET cc_start: 0.2890 (OUTLIER) cc_final: 0.2621 (mmm) REVERT: J 599 MET cc_start: 0.1198 (mpt) cc_final: -0.1980 (mtt) REVERT: K 176 MET cc_start: 0.3031 (mmp) cc_final: 0.0206 (tmm) REVERT: K 303 ILE cc_start: -0.2021 (OUTLIER) cc_final: -0.2582 (tt) REVERT: K 589 ARG cc_start: 0.2145 (ptp90) cc_final: 0.1085 (ptt-90) REVERT: K 599 MET cc_start: 0.0938 (mmp) cc_final: -0.0620 (mtt) REVERT: L 63 MET cc_start: 0.1850 (mmt) cc_final: 0.1345 (tpp) REVERT: L 97 ASN cc_start: 0.2413 (OUTLIER) cc_final: -0.0712 (t0) REVERT: L 136 MET cc_start: 0.3893 (ttp) cc_final: 0.3615 (ttt) REVERT: L 143 ASP cc_start: -0.0978 (OUTLIER) cc_final: -0.1413 (m-30) REVERT: L 234 ASN cc_start: 0.0473 (OUTLIER) cc_final: 0.0226 (m-40) REVERT: L 272 ASN cc_start: -0.1393 (OUTLIER) cc_final: -0.3653 (t0) REVERT: L 418 LEU cc_start: -0.3089 (OUTLIER) cc_final: -0.3574 (tt) REVERT: L 533 MET cc_start: -0.3991 (ppp) cc_final: -0.5255 (ptp) REVERT: L 599 MET cc_start: 0.0515 (mpp) cc_final: 0.0272 (mpp) REVERT: M 51 TRP cc_start: 0.5482 (t-100) cc_final: 0.5095 (t-100) REVERT: M 96 MET cc_start: 0.3705 (OUTLIER) cc_final: 0.3224 (mmt) REVERT: M 101 LEU cc_start: -0.0481 (OUTLIER) cc_final: -0.0805 (mt) REVERT: M 176 MET cc_start: -0.4357 (mmt) cc_final: -0.4803 (mmp) REVERT: M 186 GLN cc_start: 0.4916 (tt0) cc_final: 0.4103 (mt0) REVERT: M 226 LEU cc_start: 0.1883 (OUTLIER) cc_final: 0.0581 (mp) REVERT: M 513 LEU cc_start: 0.6492 (OUTLIER) cc_final: 0.6243 (tm) REVERT: M 528 PHE cc_start: 0.4302 (m-80) cc_final: 0.3350 (m-10) REVERT: M 529 PHE cc_start: 0.6238 (p90) cc_final: 0.5900 (p90) REVERT: M 570 GLN cc_start: -0.1905 (OUTLIER) cc_final: -0.2126 (pt0) REVERT: M 598 LEU cc_start: 0.3958 (mt) cc_final: 0.3250 (pp) REVERT: N 126 ASN cc_start: 0.6277 (p0) cc_final: 0.5417 (p0) REVERT: N 234 ASN cc_start: 0.7053 (m-40) cc_final: 0.5678 (t0) REVERT: N 391 ASP cc_start: 0.5226 (p0) cc_final: 0.4197 (t70) REVERT: N 430 LEU cc_start: 0.2615 (OUTLIER) cc_final: 0.2278 (tp) REVERT: O 63 MET cc_start: 0.0736 (mtt) cc_final: 0.0438 (ptt) REVERT: O 72 THR cc_start: 0.0269 (OUTLIER) cc_final: -0.0181 (p) REVERT: O 93 ASN cc_start: 0.0825 (OUTLIER) cc_final: -0.2866 (t0) REVERT: O 94 LEU cc_start: 0.0316 (OUTLIER) cc_final: -0.0852 (mt) REVERT: O 136 MET cc_start: 0.8906 (mpp) cc_final: 0.6285 (tmm) REVERT: O 167 LEU cc_start: 0.1331 (OUTLIER) cc_final: 0.1119 (mt) REVERT: O 431 GLU cc_start: 0.1712 (mm-30) cc_final: 0.1356 (mm-30) REVERT: O 488 MET cc_start: -0.1790 (tmt) cc_final: -0.2504 (ttm) REVERT: P 59 MET cc_start: 0.2148 (mmm) cc_final: 0.1592 (mmm) REVERT: P 95 GLU cc_start: -0.1174 (OUTLIER) cc_final: -0.3484 (tt0) REVERT: P 96 MET cc_start: 0.0989 (mpp) cc_final: -0.0200 (ttt) REVERT: P 196 LEU cc_start: 0.1183 (OUTLIER) cc_final: 0.0930 (tp) REVERT: P 272 ASN cc_start: -0.0053 (OUTLIER) cc_final: -0.3554 (t0) REVERT: P 385 CYS cc_start: 0.3445 (OUTLIER) cc_final: 0.1512 (p) REVERT: P 394 CYS cc_start: 0.4808 (OUTLIER) cc_final: 0.3530 (p) REVERT: P 418 LEU cc_start: 0.4132 (mt) cc_final: 0.3596 (mt) REVERT: P 447 GLU cc_start: -0.4224 (pt0) cc_final: -0.4470 (mp0) outliers start: 242 outliers final: 124 residues processed: 706 average time/residue: 0.6149 time to fit residues: 744.1745 Evaluate side-chains 593 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 433 time to evaluate : 5.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 570 GLN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 394 CYS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 593 TYR Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 585 LEU Chi-restraints excluded: chain G residue 589 ARG Chi-restraints excluded: chain G residue 590 LEU Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 229 ASN Chi-restraints excluded: chain H residue 378 PHE Chi-restraints excluded: chain H residue 396 ASN Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 512 SER Chi-restraints excluded: chain I residue 96 MET Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 463 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 220 HIS Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 271 THR Chi-restraints excluded: chain J residue 402 LEU Chi-restraints excluded: chain J residue 430 LEU Chi-restraints excluded: chain J residue 431 GLU Chi-restraints excluded: chain J residue 448 ASP Chi-restraints excluded: chain J residue 488 MET Chi-restraints excluded: chain J residue 516 GLU Chi-restraints excluded: chain J residue 570 GLN Chi-restraints excluded: chain J residue 585 LEU Chi-restraints excluded: chain J residue 586 LEU Chi-restraints excluded: chain J residue 594 THR Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain K residue 93 ASN Chi-restraints excluded: chain K residue 217 GLN Chi-restraints excluded: chain K residue 278 PHE Chi-restraints excluded: chain K residue 299 HIS Chi-restraints excluded: chain K residue 303 ILE Chi-restraints excluded: chain K residue 386 THR Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain K residue 512 SER Chi-restraints excluded: chain L residue 31 PHE Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 85 TYR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain L residue 97 ASN Chi-restraints excluded: chain L residue 143 ASP Chi-restraints excluded: chain L residue 155 ARG Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 193 LEU Chi-restraints excluded: chain L residue 204 HIS Chi-restraints excluded: chain L residue 234 ASN Chi-restraints excluded: chain L residue 272 ASN Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 403 LEU Chi-restraints excluded: chain L residue 418 LEU Chi-restraints excluded: chain L residue 440 ILE Chi-restraints excluded: chain L residue 589 ARG Chi-restraints excluded: chain L residue 590 LEU Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 96 MET Chi-restraints excluded: chain M residue 101 LEU Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 167 LEU Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 266 TYR Chi-restraints excluded: chain M residue 299 HIS Chi-restraints excluded: chain M residue 303 ILE Chi-restraints excluded: chain M residue 445 VAL Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain M residue 539 ASN Chi-restraints excluded: chain M residue 570 GLN Chi-restraints excluded: chain M residue 574 CYS Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 68 THR Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 87 ILE Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 303 ILE Chi-restraints excluded: chain N residue 406 ASP Chi-restraints excluded: chain N residue 430 LEU Chi-restraints excluded: chain N residue 437 THR Chi-restraints excluded: chain N residue 445 VAL Chi-restraints excluded: chain N residue 533 MET Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 93 ASN Chi-restraints excluded: chain O residue 94 LEU Chi-restraints excluded: chain O residue 105 MET Chi-restraints excluded: chain O residue 167 LEU Chi-restraints excluded: chain O residue 172 THR Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 206 ILE Chi-restraints excluded: chain O residue 226 LEU Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 303 ILE Chi-restraints excluded: chain O residue 312 PHE Chi-restraints excluded: chain O residue 376 PHE Chi-restraints excluded: chain O residue 392 VAL Chi-restraints excluded: chain O residue 393 LEU Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 95 GLU 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 256 TYR Chi-restraints excluded: chain P residue 272 ASN Chi-restraints excluded: chain P residue 299 HIS Chi-restraints excluded: chain P residue 338 VAL Chi-restraints excluded: chain P residue 385 CYS Chi-restraints excluded: chain P residue 394 CYS Chi-restraints excluded: chain P residue 417 HIS Chi-restraints excluded: chain P residue 423 HIS Chi-restraints excluded: chain P residue 484 THR Chi-restraints excluded: chain P residue 574 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 682 optimal weight: 7.9990 chunk 465 optimal weight: 0.1980 chunk 11 optimal weight: 20.0000 chunk 610 optimal weight: 3.9990 chunk 338 optimal weight: 10.0000 chunk 699 optimal weight: 3.9990 chunk 566 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 418 optimal weight: 6.9990 chunk 735 optimal weight: 0.8980 chunk 206 optimal weight: 10.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN A 230 GLN ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 GLN ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN J 134 GLN ** J 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 276 GLN J 401 ASN ** J 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN ** K 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 401 ASN L 421 GLN M 97 ASN ** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 259 GLN ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 93 ASN N 399 GLN ** O 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 311 HIS ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 217 GLN P 560 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1102 moved from start: 0.5989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 68624 Z= 0.210 Angle : 0.659 13.223 93136 Z= 0.335 Chirality : 0.046 0.402 10816 Planarity : 0.005 0.091 11792 Dihedral : 7.309 100.178 10463 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.56 % Favored : 96.26 % Rotamer: Outliers : 2.40 % Allowed : 12.05 % Favored : 85.55 % 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: -0.77 (0.09), residues: 8432 helix: 0.29 (0.14), residues: 1346 sheet: 0.12 (0.09), residues: 3356 loop : -1.37 (0.10), residues: 3730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP M 104 HIS 0.010 0.001 HIS L 204 PHE 0.069 0.002 PHE D 344 TYR 0.023 0.002 TYR L 341 ARG 0.006 0.001 ARG D 339 *********************** 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 635 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 455 time to evaluate : 6.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.0653 (mtm) cc_final: -0.0263 (ptt) REVERT: A 503 LEU cc_start: 0.1907 (OUTLIER) cc_final: 0.1263 (mm) REVERT: A 533 MET cc_start: 0.6486 (ppp) cc_final: 0.6233 (ppp) REVERT: B 304 ASP cc_start: 0.5245 (t0) cc_final: 0.4902 (p0) REVERT: B 488 MET cc_start: -0.4469 (mmt) cc_final: -0.4764 (mmt) REVERT: C 99 GLU cc_start: -0.4706 (OUTLIER) cc_final: -0.5252 (tt0) REVERT: C 488 MET cc_start: -0.3006 (mtt) cc_final: -0.5001 (mmt) REVERT: D 63 MET cc_start: -0.5750 (mmt) cc_final: -0.6791 (mmt) REVERT: E 105 MET cc_start: -0.3660 (ttm) cc_final: -0.4038 (mpp) REVERT: E 599 MET cc_start: 0.1247 (mmp) cc_final: -0.0059 (mmp) REVERT: F 59 MET cc_start: -0.1467 (mmm) cc_final: -0.1777 (mmm) REVERT: F 593 TYR cc_start: -0.1810 (OUTLIER) cc_final: -0.2218 (t80) REVERT: G 176 MET cc_start: 0.6648 (mtt) cc_final: 0.6356 (mtt) REVERT: G 533 MET cc_start: -0.5448 (ptp) cc_final: -0.6314 (mmt) REVERT: G 589 ARG cc_start: -0.3002 (OUTLIER) cc_final: -0.4078 (ppt170) REVERT: H 104 TRP cc_start: 0.4439 (t60) cc_final: 0.2623 (m-90) REVERT: H 176 MET cc_start: 0.7550 (mtt) cc_final: 0.7030 (mmp) REVERT: H 430 LEU cc_start: -0.0944 (OUTLIER) cc_final: -0.1962 (tp) REVERT: H 462 CYS cc_start: 0.3566 (m) cc_final: 0.2778 (m) REVERT: H 503 LEU cc_start: -0.3245 (OUTLIER) cc_final: -0.3704 (tp) REVERT: H 533 MET cc_start: -0.4780 (mtp) cc_final: -0.6053 (mmm) REVERT: I 96 MET cc_start: -0.0083 (OUTLIER) cc_final: -0.1296 (tpt) REVERT: I 105 MET cc_start: -0.1385 (OUTLIER) cc_final: -0.1744 (mpp) REVERT: I 181 GLN cc_start: 0.4238 (mm-40) cc_final: 0.3992 (pt0) REVERT: I 189 MET cc_start: 0.2203 (mmm) cc_final: 0.1053 (mmm) REVERT: I 329 LYS cc_start: 0.2176 (OUTLIER) cc_final: 0.1551 (tmtt) REVERT: I 488 MET cc_start: 0.1808 (mmp) cc_final: 0.1517 (mmm) REVERT: I 553 LYS cc_start: -0.0369 (tptt) cc_final: -0.0720 (mtpt) REVERT: I 599 MET cc_start: 0.3936 (mmt) cc_final: 0.1512 (mtm) REVERT: J 52 ASP cc_start: 0.4169 (t0) cc_final: 0.3959 (t0) REVERT: J 54 LEU cc_start: -0.1148 (OUTLIER) cc_final: -0.1362 (tt) REVERT: J 95 GLU cc_start: 0.0681 (OUTLIER) cc_final: 0.0361 (mt-10) REVERT: J 189 MET cc_start: 0.4262 (mmm) cc_final: 0.3581 (mmm) REVERT: J 222 ARG cc_start: -0.1206 (OUTLIER) cc_final: -0.4829 (ptt180) REVERT: J 304 ASP cc_start: 0.5829 (t0) cc_final: 0.5074 (m-30) REVERT: J 488 MET cc_start: 0.2856 (mmm) cc_final: 0.2640 (mmm) REVERT: J 599 MET cc_start: 0.1051 (mpt) cc_final: -0.2039 (mtt) REVERT: K 342 TYR cc_start: 0.1833 (OUTLIER) cc_final: 0.0497 (t80) REVERT: K 516 GLU cc_start: -0.0890 (tt0) cc_final: -0.1292 (tt0) REVERT: K 551 LEU cc_start: 0.0044 (mt) cc_final: -0.0174 (tp) REVERT: K 589 ARG cc_start: 0.1743 (ptp90) cc_final: 0.0874 (ptt-90) REVERT: K 599 MET cc_start: 0.0901 (mmp) cc_final: -0.0952 (mtt) REVERT: L 63 MET cc_start: 0.1685 (mmt) cc_final: 0.1114 (tpp) REVERT: L 303 ILE cc_start: 0.2761 (OUTLIER) cc_final: 0.2350 (tt) REVERT: L 480 PHE cc_start: 0.2648 (p90) cc_final: 0.2236 (p90) REVERT: M 51 TRP cc_start: 0.5103 (t-100) cc_final: 0.4803 (t-100) REVERT: M 176 MET cc_start: -0.4646 (OUTLIER) cc_final: -0.5085 (mmp) REVERT: M 529 PHE cc_start: 0.6105 (p90) cc_final: 0.5888 (p90) REVERT: M 598 LEU cc_start: 0.4133 (mt) cc_final: 0.3597 (pp) REVERT: N 97 ASN cc_start: -0.3575 (OUTLIER) cc_final: -0.4245 (t0) REVERT: N 391 ASP cc_start: 0.4947 (p0) cc_final: 0.3926 (t70) REVERT: N 599 MET cc_start: -0.1633 (ptp) cc_final: -0.2173 (ptm) REVERT: O 63 MET cc_start: 0.0699 (mtt) cc_final: 0.0391 (ptt) REVERT: O 72 THR cc_start: 0.1011 (OUTLIER) cc_final: 0.0458 (p) REVERT: O 94 LEU cc_start: -0.0158 (OUTLIER) cc_final: -0.0393 (mt) REVERT: O 136 MET cc_start: 0.8870 (mpp) cc_final: 0.8254 (mpp) REVERT: O 167 LEU cc_start: 0.1000 (OUTLIER) cc_final: 0.0790 (mt) REVERT: O 431 GLU cc_start: 0.1412 (mm-30) cc_final: 0.0663 (mm-30) REVERT: O 488 MET cc_start: -0.1846 (tmt) cc_final: -0.2520 (ttm) REVERT: P 59 MET cc_start: 0.1892 (mmm) cc_final: 0.1653 (mmm) REVERT: P 95 GLU cc_start: -0.0891 (OUTLIER) cc_final: -0.3151 (tt0) REVERT: P 96 MET cc_start: 0.1146 (mpp) cc_final: 0.0297 (ttt) REVERT: P 176 MET cc_start: 0.6171 (OUTLIER) cc_final: 0.5859 (mmp) REVERT: P 196 LEU cc_start: 0.0791 (OUTLIER) cc_final: 0.0449 (tp) REVERT: P 385 CYS cc_start: 0.3616 (OUTLIER) cc_final: 0.1671 (p) REVERT: P 394 CYS cc_start: 0.5000 (OUTLIER) cc_final: 0.4005 (p) REVERT: P 396 ASN cc_start: 0.6191 (OUTLIER) cc_final: 0.5195 (t0) REVERT: P 417 HIS cc_start: 0.6410 (OUTLIER) cc_final: 0.5391 (t70) REVERT: P 418 LEU cc_start: 0.3312 (mt) cc_final: 0.2928 (mt) REVERT: P 447 GLU cc_start: -0.4040 (pt0) cc_final: -0.4491 (mp0) outliers start: 180 outliers final: 99 residues processed: 598 average time/residue: 0.6135 time to fit residues: 635.6844 Evaluate side-chains 546 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 421 time to evaluate : 5.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 570 GLN Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 394 CYS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 189 MET Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 593 TYR Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain G residue 589 ARG Chi-restraints excluded: chain G residue 590 LEU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 378 PHE Chi-restraints excluded: chain H residue 396 ASN Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 512 SER Chi-restraints excluded: chain I residue 96 MET Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 329 LYS Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 276 GLN Chi-restraints excluded: chain J residue 402 LEU Chi-restraints excluded: chain J residue 533 MET Chi-restraints excluded: chain J residue 570 GLN Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 93 ASN Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 192 TYR Chi-restraints excluded: chain K residue 305 ARG Chi-restraints excluded: chain K residue 341 TYR Chi-restraints excluded: chain K residue 342 TYR Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain K residue 461 TRP Chi-restraints excluded: chain K residue 512 SER Chi-restraints excluded: chain L residue 31 PHE Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain L residue 155 ARG Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 193 LEU Chi-restraints excluded: chain L residue 234 ASN Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 377 THR Chi-restraints excluded: chain L residue 403 LEU Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 590 LEU Chi-restraints excluded: chain M residue 176 MET Chi-restraints excluded: chain M residue 301 VAL Chi-restraints excluded: chain M residue 303 ILE Chi-restraints excluded: chain M residue 436 CYS Chi-restraints excluded: chain M residue 523 VAL Chi-restraints excluded: chain M residue 574 CYS Chi-restraints excluded: chain M residue 581 THR Chi-restraints excluded: chain N residue 68 THR Chi-restraints excluded: chain N residue 87 ILE Chi-restraints excluded: chain N residue 97 ASN Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 206 ILE Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 210 ASP Chi-restraints excluded: chain N residue 242 ILE Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 265 ASP Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 303 ILE Chi-restraints excluded: chain N residue 437 THR Chi-restraints excluded: chain N residue 445 VAL Chi-restraints excluded: chain N residue 533 MET Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 94 LEU Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 167 LEU Chi-restraints excluded: chain O residue 172 THR Chi-restraints excluded: chain O residue 376 PHE Chi-restraints excluded: chain O residue 588 VAL Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain P residue 176 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 255 ASP Chi-restraints excluded: chain P residue 264 LYS Chi-restraints excluded: chain P residue 385 CYS Chi-restraints excluded: chain P residue 394 CYS Chi-restraints excluded: chain P residue 396 ASN Chi-restraints excluded: chain P residue 417 HIS Chi-restraints excluded: chain P residue 423 HIS Chi-restraints excluded: chain P residue 484 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 275 optimal weight: 30.0000 chunk 738 optimal weight: 10.0000 chunk 162 optimal weight: 20.0000 chunk 481 optimal weight: 8.9990 chunk 202 optimal weight: 5.9990 chunk 820 optimal weight: 4.9990 chunk 681 optimal weight: 4.9990 chunk 379 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 271 optimal weight: 30.0000 chunk 430 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN A 217 GLN ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 154 ASN B 230 GLN ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 ASN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 HIS D 108 GLN D 234 ASN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 ASN F 53 ASN G 234 ASN ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 ASN H 144 GLN H 229 ASN H 231 ASN I 77 GLN I 108 GLN I 154 ASN ** I 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 HIS I 231 ASN I 259 GLN ** I 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 423 HIS ** I 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 GLN J 134 GLN J 401 ASN ** J 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 490 ASN J 539 ASN ** J 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 56 ASN ** K 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 217 GLN ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 421 GLN L 490 ASN ** L 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 ASN M 151 GLN M 220 HIS M 423 HIS ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 539 ASN O 144 GLN ** O 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 230 GLN ** P 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 560 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1611 moved from start: 0.8263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.136 68624 Z= 0.510 Angle : 1.121 25.763 93136 Z= 0.575 Chirality : 0.061 0.507 10816 Planarity : 0.010 0.419 11792 Dihedral : 8.839 62.917 10461 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 27.51 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.26 % Favored : 92.47 % Rotamer: Outliers : 3.66 % Allowed : 12.86 % Favored : 83.48 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % Twisted Proline : 0.89 % Twisted General : 0.35 % 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: -1.69 (0.09), residues: 8432 helix: -0.42 (0.14), residues: 1240 sheet: -0.28 (0.09), residues: 3164 loop : -2.06 (0.09), residues: 4028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP J 51 HIS 0.023 0.003 HIS K 220 PHE 0.072 0.003 PHE N 278 TYR 0.061 0.004 TYR K 256 ARG 0.037 0.002 ARG J 305 *********************** 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 798 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 523 time to evaluate : 5.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.0969 (mtm) cc_final: 0.0132 (ptp) REVERT: A 158 THR cc_start: 0.2478 (OUTLIER) cc_final: 0.2104 (m) REVERT: A 341 TYR cc_start: 0.1108 (OUTLIER) cc_final: 0.0764 (t80) REVERT: A 431 GLU cc_start: 0.0459 (pp20) cc_final: 0.0184 (pp20) REVERT: A 503 LEU cc_start: 0.2613 (OUTLIER) cc_final: 0.2177 (mm) REVERT: B 304 ASP cc_start: 0.5727 (t0) cc_final: 0.5337 (p0) REVERT: B 488 MET cc_start: -0.4143 (mmt) cc_final: -0.4375 (mmt) REVERT: C 99 GLU cc_start: -0.4076 (OUTLIER) cc_final: -0.5421 (mp0) REVERT: C 189 MET cc_start: 0.7242 (mmp) cc_final: 0.6641 (mtt) REVERT: C 488 MET cc_start: -0.3070 (mtt) cc_final: -0.4123 (mmt) REVERT: D 63 MET cc_start: -0.5738 (mmt) cc_final: -0.6429 (mmt) REVERT: E 105 MET cc_start: -0.3444 (ttm) cc_final: -0.3848 (mpp) REVERT: E 599 MET cc_start: 0.1691 (mmp) cc_final: 0.0457 (mmp) REVERT: F 59 MET cc_start: -0.1602 (mmm) cc_final: -0.2274 (mmm) REVERT: F 593 TYR cc_start: -0.0926 (OUTLIER) cc_final: -0.1134 (t80) REVERT: G 176 MET cc_start: 0.6666 (mtt) cc_final: 0.6387 (mtt) REVERT: G 533 MET cc_start: -0.5548 (ptp) cc_final: -0.6479 (mmm) REVERT: G 586 LEU cc_start: -0.0174 (mp) cc_final: -0.0575 (mp) REVERT: G 589 ARG cc_start: -0.4320 (OUTLIER) cc_final: -0.5552 (ppt170) REVERT: H 95 GLU cc_start: 0.1853 (OUTLIER) cc_final: 0.1215 (mt-10) REVERT: H 104 TRP cc_start: 0.3901 (t60) cc_final: 0.2046 (m-90) REVERT: H 176 MET cc_start: 0.7344 (mtt) cc_final: 0.6708 (mmp) REVERT: H 430 LEU cc_start: -0.0451 (OUTLIER) cc_final: -0.0925 (tp) REVERT: H 462 CYS cc_start: 0.4214 (m) cc_final: 0.3690 (m) REVERT: H 503 LEU cc_start: -0.2126 (OUTLIER) cc_final: -0.2337 (tp) REVERT: I 105 MET cc_start: -0.1226 (OUTLIER) cc_final: -0.1809 (mpp) REVERT: I 220 HIS cc_start: 0.0608 (OUTLIER) cc_final: -0.2212 (m-70) REVERT: I 329 LYS cc_start: 0.2094 (OUTLIER) cc_final: 0.1147 (tmtt) REVERT: I 340 HIS cc_start: 0.7263 (m-70) cc_final: 0.7021 (m-70) REVERT: I 485 ILE cc_start: 0.2897 (OUTLIER) cc_final: 0.2658 (mt) REVERT: I 488 MET cc_start: 0.2624 (mmp) cc_final: 0.1942 (mtp) REVERT: I 599 MET cc_start: 0.3971 (mmt) cc_final: 0.2095 (mmp) REVERT: J 189 MET cc_start: 0.5001 (mmm) cc_final: 0.4793 (mmm) REVERT: J 222 ARG cc_start: -0.1031 (OUTLIER) cc_final: -0.3259 (mmm-85) REVERT: J 523 VAL cc_start: 0.6780 (t) cc_final: 0.6556 (t) REVERT: J 599 MET cc_start: 0.0842 (mpt) cc_final: -0.2792 (mtm) REVERT: K 72 THR cc_start: 0.4419 (OUTLIER) cc_final: 0.4180 (m) REVERT: K 311 HIS cc_start: 0.7321 (OUTLIER) cc_final: 0.5852 (p90) REVERT: K 342 TYR cc_start: 0.2856 (OUTLIER) cc_final: 0.1168 (p90) REVERT: K 396 ASN cc_start: 0.2657 (OUTLIER) cc_final: 0.0674 (t0) REVERT: K 456 GLU cc_start: 0.1975 (pt0) cc_final: 0.0772 (tp30) REVERT: K 551 LEU cc_start: 0.1441 (mt) cc_final: 0.1235 (tp) REVERT: K 599 MET cc_start: 0.0823 (mmp) cc_final: -0.0429 (mtm) REVERT: L 63 MET cc_start: 0.1714 (mmt) cc_final: 0.0873 (tpp) REVERT: L 96 MET cc_start: 0.2601 (mtm) cc_final: 0.0991 (tpp) REVERT: L 97 ASN cc_start: 0.2921 (OUTLIER) cc_final: 0.0592 (t0) REVERT: L 143 ASP cc_start: 0.0705 (OUTLIER) cc_final: 0.0187 (m-30) REVERT: L 185 ASN cc_start: 0.4981 (m110) cc_final: 0.4731 (t0) REVERT: L 188 LYS cc_start: 0.5927 (mttt) cc_final: 0.5670 (mmmt) REVERT: L 272 ASN cc_start: -0.1386 (OUTLIER) cc_final: -0.2287 (m-40) REVERT: L 303 ILE cc_start: 0.5097 (OUTLIER) cc_final: 0.4726 (tp) REVERT: L 311 HIS cc_start: 0.3831 (OUTLIER) cc_final: 0.3298 (p90) REVERT: L 470 ASP cc_start: -0.1335 (OUTLIER) cc_final: -0.1583 (p0) REVERT: M 78 TYR cc_start: 0.2619 (m-80) cc_final: 0.2215 (m-80) REVERT: M 176 MET cc_start: -0.4492 (OUTLIER) cc_final: -0.4891 (mmp) REVERT: M 186 GLN cc_start: 0.5804 (tt0) cc_final: 0.5041 (mt0) REVERT: M 219 ASP cc_start: 0.3115 (OUTLIER) cc_final: 0.2877 (t0) REVERT: M 226 LEU cc_start: 0.4017 (OUTLIER) cc_final: 0.3331 (mp) REVERT: M 421 GLN cc_start: 0.6305 (mm-40) cc_final: 0.5999 (tt0) REVERT: M 589 ARG cc_start: 0.0446 (OUTLIER) cc_final: -0.2082 (ptm160) REVERT: M 598 LEU cc_start: 0.5782 (mt) cc_final: 0.5369 (pp) REVERT: N 35 LYS cc_start: 0.4787 (mttt) cc_final: 0.4427 (mmtm) REVERT: N 97 ASN cc_start: -0.3823 (OUTLIER) cc_final: -0.4051 (t0) REVERT: N 234 ASN cc_start: 0.6905 (m-40) cc_final: 0.5768 (t0) REVERT: N 250 PHE cc_start: 0.6163 (t80) cc_final: 0.5844 (t80) REVERT: N 311 HIS cc_start: 0.1306 (OUTLIER) cc_final: -0.0489 (p-80) REVERT: N 318 LYS cc_start: -0.2131 (OUTLIER) cc_final: -0.2893 (tttt) REVERT: N 599 MET cc_start: -0.0437 (ptp) cc_final: -0.0921 (ptm) REVERT: O 96 MET cc_start: 0.1713 (ptt) cc_final: -0.0514 (mtp) REVERT: O 136 MET cc_start: 0.8697 (mpp) cc_final: 0.7922 (mpp) REVERT: O 167 LEU cc_start: 0.1681 (OUTLIER) cc_final: 0.1421 (mt) REVERT: O 431 GLU cc_start: 0.1909 (mm-30) cc_final: 0.1507 (pt0) REVERT: O 488 MET cc_start: -0.2283 (tmt) cc_final: -0.2692 (ttt) REVERT: P 89 GLN cc_start: 0.1723 (OUTLIER) cc_final: 0.0067 (tp40) REVERT: P 96 MET cc_start: 0.2968 (mpp) cc_final: 0.1849 (ttt) REVERT: P 196 LEU cc_start: 0.0741 (OUTLIER) cc_final: 0.0444 (tp) REVERT: P 396 ASN cc_start: 0.6245 (OUTLIER) cc_final: 0.5356 (t0) outliers start: 275 outliers final: 149 residues processed: 750 average time/residue: 0.5877 time to fit residues: 767.4082 Evaluate side-chains 652 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 468 time to evaluate : 5.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 341 TYR Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 394 CYS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 593 TYR Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 417 HIS Chi-restraints excluded: chain G residue 589 ARG Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 396 ASN Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 512 SER Chi-restraints excluded: chain H residue 525 PHE Chi-restraints excluded: chain H residue 532 ILE Chi-restraints excluded: chain H residue 561 HIS Chi-restraints excluded: chain I residue 96 MET Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 220 HIS Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 329 LYS Chi-restraints excluded: chain I residue 452 VAL Chi-restraints excluded: chain I residue 485 ILE Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 220 HIS Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 276 GLN Chi-restraints excluded: chain J residue 305 ARG Chi-restraints excluded: chain J residue 402 LEU Chi-restraints excluded: chain J residue 430 LEU Chi-restraints excluded: chain J residue 448 ASP Chi-restraints excluded: chain J residue 533 MET Chi-restraints excluded: chain J residue 570 GLN Chi-restraints excluded: chain J residue 585 LEU Chi-restraints excluded: chain J residue 586 LEU Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain K residue 93 ASN Chi-restraints excluded: chain K residue 97 ASN Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 192 TYR Chi-restraints excluded: chain K residue 210 ASP Chi-restraints excluded: chain K residue 278 PHE Chi-restraints excluded: chain K residue 299 HIS Chi-restraints excluded: chain K residue 305 ARG Chi-restraints excluded: chain K residue 311 HIS Chi-restraints excluded: chain K residue 342 TYR Chi-restraints excluded: chain K residue 378 PHE Chi-restraints excluded: chain K residue 396 ASN Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain K residue 461 TRP Chi-restraints excluded: chain K residue 512 SER Chi-restraints excluded: chain L residue 31 PHE Chi-restraints excluded: chain L residue 85 TYR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain L residue 97 ASN Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain L residue 143 ASP Chi-restraints excluded: chain L residue 155 ARG Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 220 HIS Chi-restraints excluded: chain L residue 234 ASN Chi-restraints excluded: chain L residue 272 ASN Chi-restraints excluded: chain L residue 296 ILE Chi-restraints excluded: chain L residue 299 HIS Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 311 HIS Chi-restraints excluded: chain L residue 377 THR Chi-restraints excluded: chain L residue 403 LEU Chi-restraints excluded: chain L residue 437 THR Chi-restraints excluded: chain L residue 440 ILE Chi-restraints excluded: chain L residue 463 VAL Chi-restraints excluded: chain L residue 470 ASP Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 589 ARG Chi-restraints excluded: chain L residue 590 LEU Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 93 ASN Chi-restraints excluded: chain M residue 97 ASN Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 176 MET Chi-restraints excluded: chain M residue 219 ASP Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 266 TYR Chi-restraints excluded: chain M residue 301 VAL Chi-restraints excluded: chain M residue 416 VAL Chi-restraints excluded: chain M residue 436 CYS Chi-restraints excluded: chain M residue 523 VAL Chi-restraints excluded: chain M residue 539 ASN Chi-restraints excluded: chain M residue 573 TYR Chi-restraints excluded: chain M residue 574 CYS Chi-restraints excluded: chain M residue 581 THR Chi-restraints excluded: chain M residue 589 ARG Chi-restraints excluded: chain N residue 68 THR Chi-restraints excluded: chain N residue 87 ILE Chi-restraints excluded: chain N residue 97 ASN Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 206 ILE Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 226 LEU Chi-restraints excluded: chain N residue 242 ILE Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 265 ASP Chi-restraints excluded: chain N residue 303 ILE Chi-restraints excluded: chain N residue 311 HIS Chi-restraints excluded: chain N residue 318 LYS Chi-restraints excluded: chain N residue 386 THR Chi-restraints excluded: chain N residue 391 ASP Chi-restraints excluded: chain N residue 437 THR Chi-restraints excluded: chain N residue 445 VAL Chi-restraints excluded: chain N residue 525 PHE Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 93 ASN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 137 LYS Chi-restraints excluded: chain O residue 167 LEU Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 206 ILE Chi-restraints excluded: chain O residue 265 ASP Chi-restraints excluded: chain O residue 312 PHE Chi-restraints excluded: chain O residue 393 LEU Chi-restraints excluded: chain O residue 407 PHE Chi-restraints excluded: chain O residue 514 ASP Chi-restraints excluded: chain O residue 575 VAL Chi-restraints excluded: chain O residue 588 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain P residue 89 GLN Chi-restraints excluded: chain P residue 158 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 255 ASP Chi-restraints excluded: chain P residue 264 LYS Chi-restraints excluded: chain P residue 272 ASN Chi-restraints excluded: chain P residue 299 HIS Chi-restraints excluded: chain P residue 385 CYS Chi-restraints excluded: chain P residue 396 ASN Chi-restraints excluded: chain P residue 463 VAL Chi-restraints excluded: chain P residue 484 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 791 optimal weight: 0.9990 chunk 92 optimal weight: 50.0000 chunk 467 optimal weight: 1.9990 chunk 599 optimal weight: 1.9990 chunk 464 optimal weight: 6.9990 chunk 690 optimal weight: 1.9990 chunk 458 optimal weight: 0.0050 chunk 817 optimal weight: 20.0000 chunk 511 optimal weight: 7.9990 chunk 498 optimal weight: 0.5980 chunk 377 optimal weight: 0.9980 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN B 186 GLN B 204 HIS ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 ASN F 53 ASN F 561 HIS ** G 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN ** H 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 ASN H 345 ASN ** I 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 231 ASN J 32 GLN ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 217 GLN J 401 ASN ** J 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 561 HIS ** J 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 217 GLN K 259 GLN K 490 ASN ** K 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 GLN ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 151 GLN ** M 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 471 ASN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 299 HIS N 383 GLN N 490 ASN ** O 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 200 ASN P 217 GLN ** P 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 345 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1363 moved from start: 0.8024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 68624 Z= 0.184 Angle : 0.664 12.879 93136 Z= 0.338 Chirality : 0.047 0.398 10816 Planarity : 0.006 0.099 11792 Dihedral : 7.332 59.915 10461 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.07 % Favored : 95.75 % Rotamer: Outliers : 2.31 % Allowed : 14.70 % Favored : 83.00 % 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: -1.36 (0.09), residues: 8432 helix: 0.01 (0.14), residues: 1279 sheet: -0.26 (0.09), residues: 3353 loop : -1.80 (0.10), residues: 3800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP P 51 HIS 0.020 0.001 HIS I 220 PHE 0.054 0.002 PHE D 344 TYR 0.025 0.002 TYR L 341 ARG 0.010 0.001 ARG K 339 *********************** 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 643 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 470 time to evaluate : 5.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.0898 (mtm) cc_final: -0.0386 (ptt) REVERT: A 227 LEU cc_start: 0.5352 (tt) cc_final: 0.5121 (tt) REVERT: A 503 LEU cc_start: 0.2662 (OUTLIER) cc_final: 0.2065 (mm) REVERT: B 59 MET cc_start: 0.2605 (tpt) cc_final: 0.2275 (ttt) REVERT: B 105 MET cc_start: 0.3676 (mmt) cc_final: 0.3218 (mmp) REVERT: B 106 ASN cc_start: 0.7123 (t0) cc_final: 0.5980 (t0) REVERT: B 209 VAL cc_start: -0.0281 (m) cc_final: -0.0873 (p) REVERT: C 99 GLU cc_start: -0.4016 (OUTLIER) cc_final: -0.5317 (mp0) REVERT: C 488 MET cc_start: -0.2887 (mtt) cc_final: -0.3995 (mmt) REVERT: D 63 MET cc_start: -0.5642 (mmt) cc_final: -0.6344 (mmt) REVERT: E 105 MET cc_start: -0.3459 (ttm) cc_final: -0.3863 (mpp) REVERT: E 599 MET cc_start: 0.1854 (mmp) cc_final: 0.0700 (mmp) REVERT: F 593 TYR cc_start: -0.1023 (OUTLIER) cc_final: -0.1639 (t80) REVERT: G 176 MET cc_start: 0.6672 (mtt) cc_final: 0.6394 (mtt) REVERT: G 533 MET cc_start: -0.5520 (ptp) cc_final: -0.6404 (mmm) REVERT: G 589 ARG cc_start: -0.3614 (OUTLIER) cc_final: -0.4868 (ppt170) REVERT: H 89 GLN cc_start: 0.5702 (OUTLIER) cc_final: 0.5308 (mp10) REVERT: H 104 TRP cc_start: 0.3981 (t60) cc_final: 0.2378 (m-90) REVERT: H 176 MET cc_start: 0.7385 (mtt) cc_final: 0.6721 (mmp) REVERT: H 305 ARG cc_start: 0.1599 (OUTLIER) cc_final: 0.0697 (ptp90) REVERT: H 430 LEU cc_start: -0.0614 (OUTLIER) cc_final: -0.1175 (tp) REVERT: H 462 CYS cc_start: 0.3833 (m) cc_final: 0.3220 (m) REVERT: I 96 MET cc_start: -0.0830 (tpt) cc_final: -0.1495 (tpt) REVERT: I 329 LYS cc_start: 0.2628 (OUTLIER) cc_final: 0.1954 (tmtt) REVERT: I 340 HIS cc_start: 0.7508 (m-70) cc_final: 0.7294 (m-70) REVERT: I 488 MET cc_start: 0.2192 (mmp) cc_final: 0.1788 (mmm) REVERT: I 599 MET cc_start: 0.3908 (mmt) cc_final: 0.0864 (mtm) REVERT: J 53 ASN cc_start: 0.7004 (OUTLIER) cc_final: 0.6403 (t0) REVERT: J 206 ILE cc_start: -0.2130 (OUTLIER) cc_final: -0.2679 (pt) REVERT: J 222 ARG cc_start: -0.0378 (OUTLIER) cc_final: -0.4086 (ptt180) REVERT: J 488 MET cc_start: 0.2944 (mmm) cc_final: 0.2408 (mmm) REVERT: J 599 MET cc_start: 0.0886 (mpt) cc_final: -0.2854 (mtm) REVERT: K 303 ILE cc_start: -0.1499 (OUTLIER) cc_final: -0.1879 (tp) REVERT: K 311 HIS cc_start: 0.7530 (OUTLIER) cc_final: 0.5444 (p90) REVERT: K 342 TYR cc_start: 0.1644 (OUTLIER) cc_final: 0.0038 (t80) REVERT: K 456 GLU cc_start: 0.0584 (pt0) cc_final: -0.0272 (tp30) REVERT: K 599 MET cc_start: 0.0496 (mmp) cc_final: -0.1136 (mtt) REVERT: L 63 MET cc_start: 0.1586 (mmt) cc_final: 0.0677 (tpp) REVERT: L 96 MET cc_start: 0.2645 (mtm) cc_final: 0.1206 (tpt) REVERT: L 97 ASN cc_start: 0.3316 (OUTLIER) cc_final: 0.1146 (t0) REVERT: L 188 LYS cc_start: 0.5923 (mttt) cc_final: 0.5626 (mmmt) REVERT: L 219 ASP cc_start: 0.2723 (OUTLIER) cc_final: 0.1962 (p0) REVERT: L 251 LYS cc_start: 0.7041 (tttt) cc_final: 0.6676 (tppt) REVERT: L 272 ASN cc_start: -0.1168 (OUTLIER) cc_final: -0.1535 (m-40) REVERT: M 31 PHE cc_start: 0.2492 (OUTLIER) cc_final: 0.1267 (p90) REVERT: M 73 THR cc_start: -0.3502 (OUTLIER) cc_final: -0.3796 (p) REVERT: M 78 TYR cc_start: 0.1724 (m-80) cc_final: 0.1314 (m-80) REVERT: M 128 LYS cc_start: 0.5693 (tmmt) cc_final: 0.5230 (tmmt) REVERT: M 130 SER cc_start: 0.7859 (m) cc_final: 0.7013 (p) REVERT: M 176 MET cc_start: -0.4762 (OUTLIER) cc_final: -0.5191 (mmp) REVERT: M 421 GLN cc_start: 0.6166 (mm-40) cc_final: 0.5905 (tt0) REVERT: M 598 LEU cc_start: 0.5444 (mt) cc_final: 0.5200 (pp) REVERT: N 97 ASN cc_start: -0.3132 (OUTLIER) cc_final: -0.3398 (t0) REVERT: N 234 ASN cc_start: 0.6746 (m-40) cc_final: 0.5747 (t0) REVERT: N 311 HIS cc_start: 0.1774 (OUTLIER) cc_final: 0.0781 (p-80) REVERT: N 391 ASP cc_start: 0.5565 (p0) cc_final: 0.4668 (t0) REVERT: N 585 LEU cc_start: 0.3504 (OUTLIER) cc_final: 0.2538 (tt) REVERT: O 96 MET cc_start: 0.1463 (ptt) cc_final: -0.0555 (mtp) REVERT: O 136 MET cc_start: 0.8564 (mpp) cc_final: 0.7977 (mpp) REVERT: O 204 HIS cc_start: 0.2368 (OUTLIER) cc_final: -0.0680 (m-70) REVERT: O 431 GLU cc_start: 0.1724 (mm-30) cc_final: 0.1221 (mp0) REVERT: O 488 MET cc_start: -0.2707 (tmt) cc_final: -0.3580 (ttm) REVERT: O 498 TYR cc_start: 0.3975 (m-80) cc_final: 0.1302 (m-80) REVERT: P 96 MET cc_start: 0.2689 (mpp) cc_final: 0.1474 (ttt) REVERT: P 135 ARG cc_start: 0.7228 (ttp80) cc_final: 0.6654 (tmt-80) REVERT: P 189 MET cc_start: -0.1723 (mmm) cc_final: -0.2052 (mmm) REVERT: P 196 LEU cc_start: 0.0738 (OUTLIER) cc_final: 0.0393 (tp) REVERT: P 385 CYS cc_start: 0.3509 (OUTLIER) cc_final: 0.2160 (p) REVERT: P 394 CYS cc_start: 0.5136 (p) cc_final: 0.4698 (p) REVERT: P 396 ASN cc_start: 0.6028 (OUTLIER) cc_final: 0.4992 (t0) REVERT: P 417 HIS cc_start: 0.6264 (OUTLIER) cc_final: 0.5295 (t70) REVERT: P 418 LEU cc_start: 0.2724 (mm) cc_final: 0.1943 (mt) REVERT: P 447 GLU cc_start: -0.4696 (tt0) cc_final: -0.6338 (mp0) outliers start: 173 outliers final: 105 residues processed: 608 average time/residue: 0.6031 time to fit residues: 634.9301 Evaluate side-chains 573 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 440 time to evaluate : 5.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 471 ASN Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 394 CYS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 189 MET Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 593 TYR Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 417 HIS Chi-restraints excluded: chain G residue 589 ARG Chi-restraints excluded: chain G residue 590 LEU Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 305 ARG Chi-restraints excluded: chain H residue 378 PHE Chi-restraints excluded: chain H residue 396 ASN Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 512 SER Chi-restraints excluded: chain H residue 561 HIS Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 329 LYS Chi-restraints excluded: chain I residue 452 VAL Chi-restraints excluded: chain I residue 523 VAL Chi-restraints excluded: chain J residue 53 ASN Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 206 ILE Chi-restraints excluded: chain J residue 210 ASP Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 305 ARG Chi-restraints excluded: chain J residue 402 LEU Chi-restraints excluded: chain J residue 533 MET Chi-restraints excluded: chain J residue 570 GLN Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 93 ASN Chi-restraints excluded: chain K residue 164 THR Chi-restraints excluded: chain K residue 192 TYR Chi-restraints excluded: chain K residue 303 ILE Chi-restraints excluded: chain K residue 305 ARG Chi-restraints excluded: chain K residue 311 HIS Chi-restraints excluded: chain K residue 342 TYR Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain K residue 441 PHE Chi-restraints excluded: chain K residue 461 TRP Chi-restraints excluded: chain K residue 512 SER Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain L residue 97 ASN Chi-restraints excluded: chain L residue 155 ARG Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 219 ASP Chi-restraints excluded: chain L residue 272 ASN Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 376 PHE Chi-restraints excluded: chain L residue 377 THR Chi-restraints excluded: chain L residue 403 LEU Chi-restraints excluded: chain L residue 590 LEU Chi-restraints excluded: chain M residue 31 PHE Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 167 LEU Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 176 MET Chi-restraints excluded: chain M residue 234 ASN Chi-restraints excluded: chain M residue 301 VAL Chi-restraints excluded: chain M residue 436 CYS Chi-restraints excluded: chain M residue 523 VAL Chi-restraints excluded: chain M residue 529 PHE Chi-restraints excluded: chain M residue 539 ASN Chi-restraints excluded: chain M residue 574 CYS Chi-restraints excluded: chain M residue 581 THR Chi-restraints excluded: chain N residue 87 ILE Chi-restraints excluded: chain N residue 97 ASN Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 242 ILE Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 303 ILE Chi-restraints excluded: chain N residue 311 HIS Chi-restraints excluded: chain N residue 437 THR Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain O residue 63 MET Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 93 ASN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 206 ILE Chi-restraints excluded: chain O residue 247 ILE Chi-restraints excluded: chain O residue 511 VAL Chi-restraints excluded: chain O residue 575 VAL Chi-restraints excluded: chain O residue 588 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 158 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 264 LYS Chi-restraints excluded: chain P residue 385 CYS Chi-restraints excluded: chain P residue 396 ASN Chi-restraints excluded: chain P residue 417 HIS Chi-restraints excluded: chain P residue 484 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 505 optimal weight: 0.9990 chunk 326 optimal weight: 8.9990 chunk 488 optimal weight: 9.9990 chunk 246 optimal weight: 50.0000 chunk 160 optimal weight: 10.0000 chunk 158 optimal weight: 40.0000 chunk 519 optimal weight: 0.9980 chunk 556 optimal weight: 2.9990 chunk 404 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 642 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN ** G 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN H 144 GLN ** H 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 GLN I 220 HIS I 561 HIS J 77 GLN ** J 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 144 GLN ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 217 GLN M 220 HIS ** M 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 144 GLN ** O 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 276 GLN O 570 GLN ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 217 GLN ** P 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1404 moved from start: 0.8205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 68624 Z= 0.185 Angle : 0.648 14.583 93136 Z= 0.326 Chirality : 0.046 0.381 10816 Planarity : 0.005 0.070 11792 Dihedral : 7.024 58.829 10461 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.90 % Favored : 94.94 % Rotamer: Outliers : 2.19 % Allowed : 14.78 % Favored : 83.04 % 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: -1.15 (0.09), residues: 8432 helix: 0.29 (0.14), residues: 1277 sheet: -0.14 (0.09), residues: 3341 loop : -1.69 (0.10), residues: 3814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 104 HIS 0.008 0.001 HIS K 220 PHE 0.038 0.001 PHE P 225 TYR 0.022 0.002 TYR L 341 ARG 0.009 0.001 ARG M 451 *********************** 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 639 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 475 time to evaluate : 5.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.0898 (mtm) cc_final: 0.0163 (ptp) REVERT: A 503 LEU cc_start: 0.2345 (OUTLIER) cc_final: 0.1840 (mm) REVERT: B 59 MET cc_start: 0.2580 (tpt) cc_final: 0.2351 (ttt) REVERT: B 209 VAL cc_start: -0.0230 (m) cc_final: -0.0816 (p) REVERT: C 99 GLU cc_start: -0.3785 (OUTLIER) cc_final: -0.5136 (mp0) REVERT: C 488 MET cc_start: -0.2739 (mtt) cc_final: -0.3898 (mmt) REVERT: D 63 MET cc_start: -0.5711 (mmt) cc_final: -0.6332 (mmt) REVERT: E 105 MET cc_start: -0.3479 (ttm) cc_final: -0.3851 (mpp) REVERT: E 599 MET cc_start: 0.1902 (mmt) cc_final: 0.0781 (mmp) REVERT: F 593 TYR cc_start: -0.0612 (OUTLIER) cc_final: -0.0942 (t80) REVERT: G 96 MET cc_start: 0.1677 (ttp) cc_final: 0.1298 (tmm) REVERT: G 176 MET cc_start: 0.6671 (mtt) cc_final: 0.6396 (mtt) REVERT: G 533 MET cc_start: -0.5467 (ptp) cc_final: -0.6422 (mmm) REVERT: G 589 ARG cc_start: -0.3161 (OUTLIER) cc_final: -0.4318 (ppt170) REVERT: H 89 GLN cc_start: 0.5753 (OUTLIER) cc_final: 0.5395 (mp10) REVERT: H 95 GLU cc_start: 0.1500 (OUTLIER) cc_final: 0.1023 (mt-10) REVERT: H 104 TRP cc_start: 0.3915 (t60) cc_final: 0.2379 (m-90) REVERT: H 176 MET cc_start: 0.7518 (mtt) cc_final: 0.6891 (mmp) REVERT: H 305 ARG cc_start: 0.1422 (OUTLIER) cc_final: 0.0701 (ptp90) REVERT: H 430 LEU cc_start: -0.1128 (OUTLIER) cc_final: -0.1813 (tp) REVERT: H 462 CYS cc_start: 0.3695 (m) cc_final: 0.3017 (m) REVERT: I 96 MET cc_start: -0.0858 (tpt) cc_final: -0.1480 (tpt) REVERT: I 263 THR cc_start: 0.5036 (OUTLIER) cc_final: 0.4763 (t) REVERT: I 329 LYS cc_start: 0.2715 (OUTLIER) cc_final: 0.2041 (tmtt) REVERT: I 340 HIS cc_start: 0.7624 (m-70) cc_final: 0.7404 (m-70) REVERT: I 391 ASP cc_start: 0.0426 (p0) cc_final: -0.1635 (t70) REVERT: I 488 MET cc_start: 0.2179 (mmp) cc_final: 0.1770 (mmm) REVERT: I 599 MET cc_start: 0.3718 (mmt) cc_final: 0.1129 (mtm) REVERT: J 222 ARG cc_start: -0.0493 (OUTLIER) cc_final: -0.4242 (ptt180) REVERT: J 476 PHE cc_start: 0.1714 (OUTLIER) cc_final: 0.0994 (m-80) REVERT: J 525 PHE cc_start: 0.2833 (t80) cc_final: 0.1969 (p90) REVERT: J 599 MET cc_start: 0.1350 (mpt) cc_final: -0.2616 (mtm) REVERT: K 201 TYR cc_start: 0.3864 (m-80) cc_final: 0.3545 (m-80) REVERT: K 303 ILE cc_start: -0.1208 (OUTLIER) cc_final: -0.1642 (tp) REVERT: K 311 HIS cc_start: 0.7705 (OUTLIER) cc_final: 0.5578 (p90) REVERT: K 339 ARG cc_start: 0.3463 (mtm180) cc_final: 0.3015 (tpm170) REVERT: K 342 TYR cc_start: 0.1890 (OUTLIER) cc_final: 0.0271 (t80) REVERT: K 387 GLU cc_start: 0.5548 (tp30) cc_final: 0.5325 (tp30) REVERT: K 413 TYR cc_start: 0.3929 (m-80) cc_final: 0.3140 (m-10) REVERT: K 599 MET cc_start: 0.0419 (mmp) cc_final: -0.1190 (mtt) REVERT: L 63 MET cc_start: 0.1664 (mmt) cc_final: 0.0549 (tpp) REVERT: L 96 MET cc_start: 0.2721 (mtm) cc_final: 0.1422 (tpt) REVERT: L 97 ASN cc_start: 0.3507 (OUTLIER) cc_final: 0.1181 (t0) REVERT: L 188 LYS cc_start: 0.5973 (mttt) cc_final: 0.5692 (mmmt) REVERT: L 219 ASP cc_start: 0.2754 (OUTLIER) cc_final: 0.2140 (p0) REVERT: L 272 ASN cc_start: -0.1028 (OUTLIER) cc_final: -0.2651 (t0) REVERT: M 31 PHE cc_start: 0.2496 (OUTLIER) cc_final: 0.1402 (p90) REVERT: M 78 TYR cc_start: 0.1791 (m-80) cc_final: 0.1461 (m-80) REVERT: M 128 LYS cc_start: 0.5777 (tmmt) cc_final: 0.5248 (tmmt) REVERT: M 313 PHE cc_start: 0.1596 (OUTLIER) cc_final: 0.1271 (m-80) REVERT: M 399 GLN cc_start: 0.5900 (mp-120) cc_final: 0.5625 (mp-120) REVERT: M 525 PHE cc_start: 0.4715 (t80) cc_final: 0.4441 (t80) REVERT: N 97 ASN cc_start: -0.3627 (OUTLIER) cc_final: -0.4280 (t0) REVERT: N 234 ASN cc_start: 0.6651 (m-40) cc_final: 0.5765 (t0) REVERT: N 311 HIS cc_start: 0.1537 (OUTLIER) cc_final: 0.0599 (p-80) REVERT: N 399 GLN cc_start: 0.2709 (tp40) cc_final: 0.1957 (tp40) REVERT: O 96 MET cc_start: 0.2042 (ptt) cc_final: 0.0016 (mtp) REVERT: O 204 HIS cc_start: 0.2505 (OUTLIER) cc_final: 0.0458 (m170) REVERT: O 431 GLU cc_start: 0.1976 (mm-30) cc_final: 0.1484 (mp0) REVERT: O 498 TYR cc_start: 0.3871 (m-80) cc_final: 0.1158 (m-80) REVERT: P 96 MET cc_start: 0.2641 (mpp) cc_final: 0.1403 (ttt) REVERT: P 135 ARG cc_start: 0.7250 (ttp80) cc_final: 0.6822 (tmt-80) REVERT: P 196 LEU cc_start: 0.0844 (OUTLIER) cc_final: 0.0518 (tp) REVERT: P 385 CYS cc_start: 0.3278 (OUTLIER) cc_final: 0.2010 (p) REVERT: P 394 CYS cc_start: 0.5294 (p) cc_final: 0.4773 (p) REVERT: P 396 ASN cc_start: 0.6119 (OUTLIER) cc_final: 0.5058 (t0) REVERT: P 418 LEU cc_start: 0.2647 (mm) cc_final: 0.1668 (mt) REVERT: P 447 GLU cc_start: -0.4763 (tt0) cc_final: -0.6441 (mp0) outliers start: 164 outliers final: 110 residues processed: 603 average time/residue: 0.6271 time to fit residues: 659.5270 Evaluate side-chains 586 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 450 time to evaluate : 5.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 189 MET Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 593 TYR Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 417 HIS Chi-restraints excluded: chain G residue 585 LEU Chi-restraints excluded: chain G residue 589 ARG Chi-restraints excluded: chain G residue 590 LEU Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 305 ARG Chi-restraints excluded: chain H residue 378 PHE Chi-restraints excluded: chain H residue 396 ASN Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 512 SER Chi-restraints excluded: chain H residue 561 HIS Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 329 LYS Chi-restraints excluded: chain I residue 452 VAL Chi-restraints excluded: chain I residue 523 VAL Chi-restraints excluded: chain I residue 565 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain J residue 210 ASP Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 271 THR Chi-restraints excluded: chain J residue 476 PHE Chi-restraints excluded: chain J residue 533 MET Chi-restraints excluded: chain J residue 570 GLN Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 93 ASN Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 164 THR Chi-restraints excluded: chain K residue 192 TYR Chi-restraints excluded: chain K residue 303 ILE Chi-restraints excluded: chain K residue 305 ARG Chi-restraints excluded: chain K residue 311 HIS Chi-restraints excluded: chain K residue 342 TYR Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain K residue 441 PHE Chi-restraints excluded: chain K residue 512 SER Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain L residue 97 ASN Chi-restraints excluded: chain L residue 155 ARG Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 193 LEU Chi-restraints excluded: chain L residue 219 ASP Chi-restraints excluded: chain L residue 272 ASN Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 333 THR Chi-restraints excluded: chain L residue 376 PHE Chi-restraints excluded: chain L residue 403 LEU Chi-restraints excluded: chain L residue 463 VAL Chi-restraints excluded: chain L residue 589 ARG Chi-restraints excluded: chain L residue 590 LEU Chi-restraints excluded: chain M residue 31 PHE Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 176 MET Chi-restraints excluded: chain M residue 301 VAL Chi-restraints excluded: chain M residue 313 PHE Chi-restraints excluded: chain M residue 416 VAL Chi-restraints excluded: chain M residue 436 CYS Chi-restraints excluded: chain M residue 440 ILE Chi-restraints excluded: chain M residue 523 VAL Chi-restraints excluded: chain M residue 529 PHE Chi-restraints excluded: chain M residue 581 THR Chi-restraints excluded: chain M residue 589 ARG Chi-restraints excluded: chain N residue 87 ILE Chi-restraints excluded: chain N residue 97 ASN Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 242 ILE Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 303 ILE Chi-restraints excluded: chain N residue 311 HIS Chi-restraints excluded: chain N residue 539 ASN Chi-restraints excluded: chain O residue 63 MET Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 137 LYS Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 303 ILE Chi-restraints excluded: chain O residue 511 VAL Chi-restraints excluded: chain O residue 575 VAL Chi-restraints excluded: chain O residue 588 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 158 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 255 ASP Chi-restraints excluded: chain P residue 264 LYS Chi-restraints excluded: chain P residue 385 CYS Chi-restraints excluded: chain P residue 396 ASN Chi-restraints excluded: chain P residue 484 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 743 optimal weight: 0.7980 chunk 783 optimal weight: 10.0000 chunk 714 optimal weight: 6.9990 chunk 761 optimal weight: 3.9990 chunk 782 optimal weight: 2.9990 chunk 458 optimal weight: 0.2980 chunk 331 optimal weight: 0.0040 chunk 598 optimal weight: 6.9990 chunk 233 optimal weight: 0.5980 chunk 688 optimal weight: 0.5980 chunk 720 optimal weight: 0.5980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 233 GLN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 ASN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 ASN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 217 GLN I 259 GLN J 53 ASN J 134 GLN ** J 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 570 GLN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 217 GLN ** K 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 401 ASN ** L 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 217 GLN M 259 GLN ** M 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 560 GLN ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 217 GLN ** P 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 259 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1298 moved from start: 0.8148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 68624 Z= 0.149 Angle : 0.592 14.492 93136 Z= 0.296 Chirality : 0.044 0.346 10816 Planarity : 0.005 0.066 11792 Dihedral : 6.568 59.846 10459 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.57 % Favored : 96.25 % Rotamer: Outliers : 1.76 % Allowed : 15.18 % Favored : 83.06 % 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: -0.96 (0.09), residues: 8432 helix: 0.52 (0.14), residues: 1274 sheet: -0.09 (0.09), residues: 3352 loop : -1.52 (0.10), residues: 3806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP P 461 HIS 0.004 0.001 HIS K 220 PHE 0.049 0.001 PHE D 344 TYR 0.022 0.001 TYR M 78 ARG 0.010 0.000 ARG J 305 *********************** 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 582 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 450 time to evaluate : 5.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 LEU cc_start: 0.2186 (OUTLIER) cc_final: 0.1653 (mm) REVERT: B 209 VAL cc_start: -0.0535 (m) cc_final: -0.1115 (p) REVERT: D 63 MET cc_start: -0.5742 (mmt) cc_final: -0.6589 (mmt) REVERT: E 105 MET cc_start: -0.3497 (ttm) cc_final: -0.3854 (mpp) REVERT: E 599 MET cc_start: 0.1953 (mmt) cc_final: 0.0855 (mmp) REVERT: F 593 TYR cc_start: -0.0622 (OUTLIER) cc_final: -0.0954 (t80) REVERT: G 176 MET cc_start: 0.6665 (mtt) cc_final: 0.6393 (mtt) REVERT: G 533 MET cc_start: -0.5483 (ptp) cc_final: -0.6439 (mmm) REVERT: G 586 LEU cc_start: 0.0718 (OUTLIER) cc_final: 0.0157 (mp) REVERT: G 589 ARG cc_start: -0.3170 (OUTLIER) cc_final: -0.4254 (ppt170) REVERT: H 95 GLU cc_start: 0.1307 (OUTLIER) cc_final: 0.0966 (mt-10) REVERT: H 104 TRP cc_start: 0.3849 (t60) cc_final: 0.2442 (m-90) REVERT: H 176 MET cc_start: 0.7556 (mtt) cc_final: 0.6986 (mmp) REVERT: H 430 LEU cc_start: -0.1271 (OUTLIER) cc_final: -0.1974 (tp) REVERT: H 462 CYS cc_start: 0.2994 (m) cc_final: 0.2341 (m) REVERT: I 96 MET cc_start: -0.0846 (tpt) cc_final: -0.1498 (tpt) REVERT: I 263 THR cc_start: 0.5137 (OUTLIER) cc_final: 0.4870 (t) REVERT: I 329 LYS cc_start: 0.2713 (OUTLIER) cc_final: 0.2057 (tmtt) REVERT: I 391 ASP cc_start: 0.0503 (p0) cc_final: -0.1592 (t70) REVERT: I 488 MET cc_start: 0.2003 (mmp) cc_final: 0.1606 (mmm) REVERT: I 558 PHE cc_start: 0.2883 (m-80) cc_final: 0.1968 (m-10) REVERT: I 599 MET cc_start: 0.3850 (mmt) cc_final: 0.0668 (mtm) REVERT: J 136 MET cc_start: 0.6031 (mmp) cc_final: 0.5578 (tpt) REVERT: J 476 PHE cc_start: 0.1831 (OUTLIER) cc_final: 0.0988 (m-80) REVERT: J 525 PHE cc_start: 0.2917 (t80) cc_final: 0.1977 (p90) REVERT: J 599 MET cc_start: 0.1007 (mpt) cc_final: -0.2825 (mtm) REVERT: K 59 MET cc_start: 0.0105 (mtt) cc_final: -0.1437 (tpp) REVERT: K 311 HIS cc_start: 0.7827 (OUTLIER) cc_final: 0.5470 (p90) REVERT: K 339 ARG cc_start: 0.3673 (mtm180) cc_final: 0.3078 (tpm170) REVERT: K 342 TYR cc_start: 0.1465 (OUTLIER) cc_final: 0.0101 (t80) REVERT: K 413 TYR cc_start: 0.4187 (m-80) cc_final: 0.3619 (m-10) REVERT: K 456 GLU cc_start: -0.0307 (pt0) cc_final: -0.0800 (tp30) REVERT: K 599 MET cc_start: 0.0396 (mmp) cc_final: -0.1194 (mtt) REVERT: L 63 MET cc_start: 0.1782 (mmt) cc_final: 0.0531 (tpp) REVERT: L 96 MET cc_start: 0.2783 (mtm) cc_final: 0.1794 (tpt) REVERT: L 188 LYS cc_start: 0.6161 (mttt) cc_final: 0.5840 (mmmt) REVERT: M 31 PHE cc_start: 0.2248 (OUTLIER) cc_final: 0.1202 (p90) REVERT: M 73 THR cc_start: -0.3626 (OUTLIER) cc_final: -0.3988 (p) REVERT: M 96 MET cc_start: 0.3916 (mmt) cc_final: 0.3289 (ptm) REVERT: M 128 LYS cc_start: 0.5709 (tmmt) cc_final: 0.5220 (tmmt) REVERT: M 313 PHE cc_start: 0.1523 (OUTLIER) cc_final: 0.1244 (m-80) REVERT: M 525 PHE cc_start: 0.4989 (t80) cc_final: 0.4456 (t80) REVERT: M 528 PHE cc_start: 0.4781 (m-80) cc_final: 0.4575 (t80) REVERT: N 234 ASN cc_start: 0.6542 (m-40) cc_final: 0.5739 (t0) REVERT: O 96 MET cc_start: 0.1586 (ptt) cc_final: -0.0265 (mtp) REVERT: O 431 GLU cc_start: 0.2422 (mm-30) cc_final: 0.1845 (pm20) REVERT: O 488 MET cc_start: -0.1926 (tmt) cc_final: -0.2659 (ttm) REVERT: O 498 TYR cc_start: 0.3480 (m-80) cc_final: 0.0693 (m-80) REVERT: P 96 MET cc_start: 0.2461 (mpp) cc_final: 0.1277 (ttt) REVERT: P 196 LEU cc_start: 0.0774 (OUTLIER) cc_final: 0.0483 (tp) REVERT: P 385 CYS cc_start: 0.3424 (OUTLIER) cc_final: 0.1887 (p) REVERT: P 394 CYS cc_start: 0.5373 (OUTLIER) cc_final: 0.4644 (p) REVERT: P 431 GLU cc_start: 0.1825 (mm-30) cc_final: 0.0280 (mp0) REVERT: P 447 GLU cc_start: -0.4986 (tt0) cc_final: -0.6507 (mp0) outliers start: 132 outliers final: 93 residues processed: 550 average time/residue: 0.6112 time to fit residues: 581.9567 Evaluate side-chains 537 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 427 time to evaluate : 5.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 394 CYS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 189 MET Chi-restraints excluded: chain F residue 225 PHE Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 593 TYR Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 589 ARG Chi-restraints excluded: chain G residue 590 LEU Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 272 ASN Chi-restraints excluded: chain H residue 378 PHE Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 561 HIS Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 329 LYS Chi-restraints excluded: chain I residue 452 VAL Chi-restraints excluded: chain I residue 565 ILE Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain J residue 210 ASP Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 476 PHE Chi-restraints excluded: chain J residue 533 MET Chi-restraints excluded: chain J residue 565 ILE Chi-restraints excluded: chain J residue 570 GLN Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain K residue 192 TYR Chi-restraints excluded: chain K residue 311 HIS Chi-restraints excluded: chain K residue 342 TYR Chi-restraints excluded: chain K residue 441 PHE Chi-restraints excluded: chain K residue 512 SER Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 155 ARG Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 193 LEU Chi-restraints excluded: chain L residue 333 THR Chi-restraints excluded: chain L residue 376 PHE Chi-restraints excluded: chain L residue 463 VAL Chi-restraints excluded: chain L residue 590 LEU Chi-restraints excluded: chain M residue 31 PHE Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 176 MET Chi-restraints excluded: chain M residue 313 PHE Chi-restraints excluded: chain M residue 436 CYS Chi-restraints excluded: chain M residue 523 VAL Chi-restraints excluded: chain M residue 581 THR Chi-restraints excluded: chain N residue 87 ILE Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 242 ILE Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 386 THR Chi-restraints excluded: chain N residue 391 ASP Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 93 ASN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 137 LYS Chi-restraints excluded: chain O residue 156 ILE Chi-restraints excluded: chain O residue 247 ILE Chi-restraints excluded: chain O residue 461 TRP Chi-restraints excluded: chain O residue 511 VAL Chi-restraints excluded: chain O residue 575 VAL Chi-restraints excluded: chain O residue 588 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 95 GLU 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 385 CYS Chi-restraints excluded: chain P residue 394 CYS Chi-restraints excluded: chain P residue 423 HIS Chi-restraints excluded: chain P residue 484 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 758 optimal weight: 3.9990 chunk 500 optimal weight: 3.9990 chunk 805 optimal weight: 40.0000 chunk 491 optimal weight: 1.9990 chunk 382 optimal weight: 10.0000 chunk 559 optimal weight: 0.0980 chunk 844 optimal weight: 20.0000 chunk 777 optimal weight: 30.0000 chunk 672 optimal weight: 10.0000 chunk 69 optimal weight: 40.0000 chunk 519 optimal weight: 0.4980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 ASN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 HIS ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 399 GLN I 217 GLN J 134 GLN ** J 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 383 GLN ** J 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** K 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 217 GLN ** K 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 217 GLN ** M 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 204 HIS ** O 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 217 GLN P 230 GLN P 311 HIS ** P 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1491 moved from start: 0.8663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 68624 Z= 0.227 Angle : 0.699 12.286 93136 Z= 0.352 Chirality : 0.047 0.388 10816 Planarity : 0.006 0.082 11792 Dihedral : 6.919 59.084 10459 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.29 % Favored : 94.54 % Rotamer: Outliers : 1.80 % Allowed : 15.31 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % Twisted Proline : 0.45 % 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: -1.07 (0.09), residues: 8432 helix: 0.48 (0.14), residues: 1262 sheet: -0.13 (0.09), residues: 3159 loop : -1.59 (0.10), residues: 4011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP P 461 HIS 0.012 0.001 HIS K 220 PHE 0.049 0.002 PHE O 558 TYR 0.025 0.002 TYR L 341 ARG 0.012 0.001 ARG M 149 ********************** 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 597 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 462 time to evaluate : 5.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 LEU cc_start: 0.2306 (OUTLIER) cc_final: 0.1791 (mm) REVERT: A 599 MET cc_start: -0.2519 (pmm) cc_final: -0.4887 (ptt) REVERT: C 488 MET cc_start: -0.3000 (mtt) cc_final: -0.4293 (mmt) REVERT: D 63 MET cc_start: -0.5731 (mmt) cc_final: -0.6566 (mmt) REVERT: E 105 MET cc_start: -0.3396 (ttm) cc_final: -0.3758 (mpp) REVERT: E 599 MET cc_start: 0.1931 (mmt) cc_final: 0.0874 (mmp) REVERT: F 593 TYR cc_start: 0.0241 (OUTLIER) cc_final: -0.0160 (t80) REVERT: G 96 MET cc_start: 0.1443 (ttp) cc_final: 0.0517 (ttp) REVERT: G 176 MET cc_start: 0.6667 (mtt) cc_final: 0.6393 (mtt) REVERT: G 533 MET cc_start: -0.5411 (ptp) cc_final: -0.6469 (mmm) REVERT: G 589 ARG cc_start: -0.2947 (OUTLIER) cc_final: -0.4306 (ppt170) REVERT: H 56 ASN cc_start: 0.4273 (m-40) cc_final: 0.2952 (t0) REVERT: H 95 GLU cc_start: 0.1729 (OUTLIER) cc_final: 0.1142 (mt-10) REVERT: H 104 TRP cc_start: 0.3882 (t60) cc_final: 0.2478 (m-90) REVERT: H 176 MET cc_start: 0.7528 (mtt) cc_final: 0.6969 (mmp) REVERT: H 430 LEU cc_start: -0.1169 (OUTLIER) cc_final: -0.1849 (tp) REVERT: H 462 CYS cc_start: 0.3105 (m) cc_final: 0.2450 (m) REVERT: H 589 ARG cc_start: 0.4116 (tpm170) cc_final: 0.3397 (ptt180) REVERT: H 599 MET cc_start: 0.2228 (tmm) cc_final: 0.1253 (tpp) REVERT: I 96 MET cc_start: -0.2068 (tpt) cc_final: -0.2798 (tpt) REVERT: I 263 THR cc_start: 0.5415 (OUTLIER) cc_final: 0.5204 (t) REVERT: I 329 LYS cc_start: 0.2725 (OUTLIER) cc_final: 0.2075 (tmtt) REVERT: I 340 HIS cc_start: 0.7607 (m-70) cc_final: 0.7381 (m-70) REVERT: I 391 ASP cc_start: 0.0603 (p0) cc_final: -0.1678 (t70) REVERT: I 488 MET cc_start: 0.1935 (mmp) cc_final: 0.1526 (mmm) REVERT: I 599 MET cc_start: 0.3861 (mmt) cc_final: 0.0693 (mtm) REVERT: J 222 ARG cc_start: -0.0618 (OUTLIER) cc_final: -0.4392 (ptt180) REVERT: J 333 THR cc_start: 0.8843 (m) cc_final: 0.8545 (p) REVERT: J 488 MET cc_start: 0.3234 (mmm) cc_final: 0.2866 (mmm) REVERT: J 525 PHE cc_start: 0.2921 (t80) cc_final: 0.2357 (p90) REVERT: J 599 MET cc_start: 0.1372 (mpt) cc_final: -0.2864 (mtm) REVERT: K 59 MET cc_start: 0.0490 (mtt) cc_final: -0.0875 (tpt) REVERT: K 311 HIS cc_start: 0.7994 (OUTLIER) cc_final: 0.6368 (p-80) REVERT: K 342 TYR cc_start: 0.2283 (OUTLIER) cc_final: 0.0673 (t80) REVERT: K 456 GLU cc_start: -0.0508 (pt0) cc_final: -0.1055 (tp30) REVERT: K 599 MET cc_start: 0.0666 (mmp) cc_final: -0.0860 (mtt) REVERT: L 63 MET cc_start: 0.1903 (mmt) cc_final: 0.0817 (tpp) REVERT: L 85 TYR cc_start: 0.4021 (OUTLIER) cc_final: 0.3459 (p90) REVERT: L 96 MET cc_start: 0.2664 (mtm) cc_final: 0.1850 (tpt) REVERT: L 188 LYS cc_start: 0.6143 (mttt) cc_final: 0.5834 (mmmt) REVERT: M 31 PHE cc_start: 0.2647 (OUTLIER) cc_final: 0.1482 (p90) REVERT: M 73 THR cc_start: -0.3015 (OUTLIER) cc_final: -0.3329 (p) REVERT: M 96 MET cc_start: 0.3902 (mmt) cc_final: 0.3291 (mmt) REVERT: M 128 LYS cc_start: 0.5876 (tmmt) cc_final: 0.5432 (tmmt) REVERT: M 313 PHE cc_start: 0.0988 (OUTLIER) cc_final: 0.0781 (m-10) REVERT: M 399 GLN cc_start: 0.5774 (mp-120) cc_final: 0.5531 (mp-120) REVERT: M 525 PHE cc_start: 0.4944 (t80) cc_final: 0.4646 (t80) REVERT: N 97 ASN cc_start: -0.3197 (OUTLIER) cc_final: -0.3976 (t0) REVERT: N 234 ASN cc_start: 0.6636 (m-40) cc_final: 0.5798 (t0) REVERT: N 311 HIS cc_start: 0.1589 (OUTLIER) cc_final: 0.0724 (p-80) REVERT: O 58 ASP cc_start: 0.0410 (OUTLIER) cc_final: 0.0005 (m-30) REVERT: O 79 ILE cc_start: 0.5868 (mt) cc_final: 0.5622 (pt) REVERT: O 96 MET cc_start: 0.2783 (ptt) cc_final: 0.1541 (mtp) REVERT: O 107 TYR cc_start: 0.7636 (t80) cc_final: 0.7253 (t80) REVERT: O 204 HIS cc_start: 0.2912 (OUTLIER) cc_final: 0.0831 (m170) REVERT: O 233 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8031 (tm-30) REVERT: O 431 GLU cc_start: 0.2656 (mm-30) cc_final: 0.2311 (pm20) REVERT: O 488 MET cc_start: -0.2642 (tmt) cc_final: -0.3312 (ttm) REVERT: O 498 TYR cc_start: 0.3893 (m-80) cc_final: 0.1322 (m-80) REVERT: P 96 MET cc_start: 0.2576 (mpp) cc_final: 0.1517 (ttt) REVERT: P 196 LEU cc_start: 0.0948 (OUTLIER) cc_final: 0.0622 (tp) REVERT: P 385 CYS cc_start: 0.3483 (OUTLIER) cc_final: 0.2453 (p) REVERT: P 394 CYS cc_start: 0.5451 (OUTLIER) cc_final: 0.4833 (p) REVERT: P 431 GLU cc_start: 0.1540 (mm-30) cc_final: -0.0027 (mp0) REVERT: P 447 GLU cc_start: -0.4795 (tt0) cc_final: -0.6482 (mp0) outliers start: 135 outliers final: 102 residues processed: 566 average time/residue: 0.6218 time to fit residues: 607.1628 Evaluate side-chains 572 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 449 time to evaluate : 5.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 593 TYR Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 589 ARG Chi-restraints excluded: chain G residue 590 LEU Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 272 ASN Chi-restraints excluded: chain H residue 305 ARG Chi-restraints excluded: chain H residue 378 PHE Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 512 SER Chi-restraints excluded: chain H residue 561 HIS Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 329 LYS Chi-restraints excluded: chain I residue 452 VAL Chi-restraints excluded: chain I residue 523 VAL Chi-restraints excluded: chain I residue 565 ILE Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain J residue 210 ASP Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 271 THR Chi-restraints excluded: chain J residue 402 LEU Chi-restraints excluded: chain J residue 476 PHE Chi-restraints excluded: chain J residue 533 MET Chi-restraints excluded: chain J residue 565 ILE Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 93 ASN Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain K residue 192 TYR Chi-restraints excluded: chain K residue 311 HIS Chi-restraints excluded: chain K residue 342 TYR Chi-restraints excluded: chain K residue 441 PHE Chi-restraints excluded: chain K residue 461 TRP Chi-restraints excluded: chain K residue 512 SER Chi-restraints excluded: chain L residue 85 TYR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain L residue 97 ASN Chi-restraints excluded: chain L residue 155 ARG Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 193 LEU Chi-restraints excluded: chain L residue 333 THR Chi-restraints excluded: chain L residue 376 PHE Chi-restraints excluded: chain L residue 463 VAL Chi-restraints excluded: chain L residue 589 ARG Chi-restraints excluded: chain L residue 590 LEU Chi-restraints excluded: chain M residue 31 PHE Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 176 MET Chi-restraints excluded: chain M residue 234 ASN Chi-restraints excluded: chain M residue 313 PHE Chi-restraints excluded: chain M residue 385 CYS Chi-restraints excluded: chain M residue 416 VAL Chi-restraints excluded: chain M residue 436 CYS Chi-restraints excluded: chain M residue 523 VAL Chi-restraints excluded: chain M residue 529 PHE Chi-restraints excluded: chain M residue 539 ASN Chi-restraints excluded: chain M residue 574 CYS Chi-restraints excluded: chain M residue 581 THR Chi-restraints excluded: chain N residue 87 ILE Chi-restraints excluded: chain N residue 97 ASN Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 242 ILE Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 303 ILE Chi-restraints excluded: chain N residue 311 HIS Chi-restraints excluded: chain N residue 386 THR Chi-restraints excluded: chain N residue 391 ASP Chi-restraints excluded: chain N residue 445 VAL Chi-restraints excluded: chain N residue 539 ASN Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 93 ASN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 137 LYS Chi-restraints excluded: chain O residue 156 ILE Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 247 ILE Chi-restraints excluded: chain O residue 378 PHE Chi-restraints excluded: chain O residue 461 TRP Chi-restraints excluded: chain O residue 588 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 95 GLU 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 342 TYR Chi-restraints excluded: chain P residue 385 CYS Chi-restraints excluded: chain P residue 394 CYS Chi-restraints excluded: chain P residue 484 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 412 optimal weight: 4.9990 chunk 534 optimal weight: 5.9990 chunk 716 optimal weight: 2.9990 chunk 206 optimal weight: 7.9990 chunk 620 optimal weight: 0.7980 chunk 99 optimal weight: 30.0000 chunk 186 optimal weight: 50.0000 chunk 673 optimal weight: 1.9990 chunk 281 optimal weight: 50.0000 chunk 691 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 GLN ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 HIS B 32 GLN B 154 ASN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN D 97 ASN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 259 GLN I 539 ASN ** J 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 144 GLN ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 220 HIS ** N 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 276 GLN ** P 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 423 HIS ** 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 = 0.5562 r_free = 0.5562 target = 0.360772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5531 r_free = 0.5531 target = 0.352453 restraints weight = 107860.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.5528 r_free = 0.5528 target = 0.351757 restraints weight = 107543.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5526 r_free = 0.5526 target = 0.351137 restraints weight = 84655.196| |-----------------------------------------------------------------------------| r_work (final): 0.5526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2244 moved from start: 0.9686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 68624 Z= 0.320 Angle : 0.855 18.140 93136 Z= 0.435 Chirality : 0.052 0.441 10816 Planarity : 0.007 0.114 11792 Dihedral : 7.648 59.760 10459 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.58 % Favored : 93.23 % Rotamer: Outliers : 1.95 % Allowed : 15.37 % Favored : 82.69 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % Twisted Proline : 0.67 % Twisted General : 0.11 % 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: -1.51 (0.09), residues: 8432 helix: -0.00 (0.14), residues: 1297 sheet: -0.34 (0.09), residues: 3225 loop : -1.93 (0.09), residues: 3910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP O 461 HIS 0.033 0.002 HIS O 204 PHE 0.051 0.003 PHE M 278 TYR 0.053 0.003 TYR D 498 ARG 0.016 0.001 ARG M 149 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11472.34 seconds wall clock time: 205 minutes 53.59 seconds (12353.59 seconds total)