Starting phenix.real_space_refine on Sun Dec 10 16:28:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1s_15086/12_2023/8a1s_15086_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1s_15086/12_2023/8a1s_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_15086/12_2023/8a1s_15086.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1s_15086/12_2023/8a1s_15086.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1s_15086/12_2023/8a1s_15086_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1s_15086/12_2023/8a1s_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: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 67152 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "B" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "C" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "D" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "E" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "F" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "G" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "H" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "I" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "J" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "K" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "L" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "M" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "N" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "O" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "P" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 26.47, per 1000 atoms: 0.39 Number of scatterers: 67152 At special positions: 0 Unit cell: (212.541, 214.635, 157.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 432 16.00 O 12800 8.00 N 11008 7.00 C 42912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=128, symmetry=0 Simple disulfide: pdb=" SG CYS A 34 " - pdb=" SG CYS A 70 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 409 " - pdb=" SG CYS A 462 " distance=2.03 Simple disulfide: pdb=" SG CYS A 432 " - pdb=" SG CYS A 446 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 442 " distance=2.03 Simple disulfide: pdb=" SG CYS A 494 " - pdb=" SG CYS A 510 " distance=2.03 Simple disulfide: pdb=" SG CYS A 531 " - pdb=" SG CYS A 569 " distance=2.03 Simple disulfide: pdb=" SG CYS A 554 " - pdb=" SG CYS A 574 " distance=2.03 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 70 " distance=2.04 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 409 " - pdb=" SG CYS B 462 " distance=2.03 Simple disulfide: pdb=" SG CYS B 432 " - pdb=" SG CYS B 446 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 442 " distance=2.03 Simple disulfide: pdb=" SG CYS B 494 " - pdb=" SG CYS B 510 " distance=2.03 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 569 " distance=2.03 Simple disulfide: pdb=" SG CYS B 554 " - pdb=" SG CYS B 574 " distance=2.03 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 70 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 394 " distance=2.03 Simple disulfide: pdb=" SG CYS C 409 " - pdb=" SG CYS C 462 " distance=2.03 Simple disulfide: pdb=" SG CYS C 432 " - pdb=" SG CYS C 446 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 442 " distance=2.03 Simple disulfide: pdb=" SG CYS C 494 " - pdb=" SG CYS C 510 " distance=2.03 Simple disulfide: pdb=" SG CYS C 531 " - pdb=" SG CYS C 569 " distance=2.03 Simple disulfide: pdb=" SG CYS C 554 " - pdb=" SG CYS C 574 " distance=2.03 Simple disulfide: pdb=" SG CYS D 34 " - pdb=" SG CYS D 70 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 394 " distance=2.03 Simple disulfide: pdb=" SG CYS D 409 " - pdb=" SG CYS D 462 " distance=2.03 Simple disulfide: pdb=" SG CYS D 432 " - pdb=" SG CYS D 446 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 442 " distance=2.03 Simple disulfide: pdb=" SG CYS D 494 " - pdb=" SG CYS D 510 " distance=2.03 Simple disulfide: pdb=" SG CYS D 531 " - pdb=" SG CYS D 569 " distance=2.03 Simple disulfide: pdb=" SG CYS D 554 " - pdb=" SG CYS D 574 " distance=2.03 Simple disulfide: pdb=" SG CYS E 34 " - pdb=" SG CYS E 70 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 394 " distance=2.03 Simple disulfide: pdb=" SG CYS E 409 " - pdb=" SG CYS E 462 " distance=2.03 Simple disulfide: pdb=" SG CYS E 432 " - pdb=" SG CYS E 446 " distance=2.03 Simple disulfide: pdb=" SG CYS E 436 " - pdb=" SG CYS E 442 " distance=2.03 Simple disulfide: pdb=" SG CYS E 494 " - pdb=" SG CYS E 510 " distance=2.03 Simple disulfide: pdb=" SG CYS E 531 " - pdb=" SG CYS E 569 " distance=2.03 Simple disulfide: pdb=" SG CYS E 554 " - pdb=" SG CYS E 574 " distance=2.03 Simple disulfide: pdb=" SG CYS F 34 " - pdb=" SG CYS F 70 " distance=2.04 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 394 " distance=2.03 Simple disulfide: pdb=" SG CYS F 409 " - pdb=" SG CYS F 462 " distance=2.03 Simple disulfide: pdb=" SG CYS F 432 " - pdb=" SG CYS F 446 " distance=2.03 Simple disulfide: pdb=" SG CYS F 436 " - pdb=" SG CYS F 442 " distance=2.03 Simple disulfide: pdb=" SG CYS F 494 " - pdb=" SG CYS F 510 " distance=2.03 Simple disulfide: pdb=" SG CYS F 531 " - pdb=" SG CYS F 569 " distance=2.03 Simple disulfide: pdb=" SG CYS F 554 " - pdb=" SG CYS F 574 " distance=2.03 Simple disulfide: pdb=" SG CYS G 34 " - pdb=" SG CYS G 70 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 394 " distance=2.03 Simple disulfide: pdb=" SG CYS G 409 " - pdb=" SG CYS G 462 " distance=2.03 Simple disulfide: pdb=" SG CYS G 432 " - pdb=" SG CYS G 446 " distance=2.03 Simple disulfide: pdb=" SG CYS G 436 " - pdb=" SG CYS G 442 " distance=2.03 Simple disulfide: pdb=" SG CYS G 494 " - pdb=" SG CYS G 510 " distance=2.03 Simple disulfide: pdb=" SG CYS G 531 " - pdb=" SG CYS G 569 " distance=2.03 Simple disulfide: pdb=" SG CYS G 554 " - pdb=" SG CYS G 574 " distance=2.03 Simple disulfide: pdb=" SG CYS H 34 " - pdb=" SG CYS H 70 " distance=2.03 Simple disulfide: pdb=" SG CYS H 385 " - pdb=" SG CYS H 394 " distance=2.03 Simple disulfide: pdb=" SG CYS H 409 " - pdb=" SG CYS H 462 " distance=2.03 Simple disulfide: pdb=" SG CYS H 432 " - pdb=" SG CYS H 446 " distance=2.03 Simple disulfide: pdb=" SG CYS H 436 " - pdb=" SG CYS H 442 " distance=2.03 Simple disulfide: pdb=" SG CYS H 494 " - pdb=" SG CYS H 510 " distance=2.03 Simple disulfide: pdb=" SG CYS H 531 " - pdb=" SG CYS H 569 " distance=2.03 Simple disulfide: pdb=" SG CYS H 554 " - pdb=" SG CYS H 574 " distance=2.03 Simple disulfide: pdb=" SG CYS I 34 " - pdb=" SG CYS I 70 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 394 " distance=2.03 Simple disulfide: pdb=" SG CYS I 409 " - pdb=" SG CYS I 462 " distance=2.03 Simple disulfide: pdb=" SG CYS I 432 " - pdb=" SG CYS I 446 " distance=2.03 Simple disulfide: pdb=" SG CYS I 436 " - pdb=" SG CYS I 442 " distance=2.03 Simple disulfide: pdb=" SG CYS I 494 " - pdb=" SG CYS I 510 " distance=2.03 Simple disulfide: pdb=" SG CYS I 531 " - pdb=" SG CYS I 569 " distance=2.03 Simple disulfide: pdb=" SG CYS I 554 " - pdb=" SG CYS I 574 " distance=2.03 Simple disulfide: pdb=" SG CYS J 34 " - pdb=" SG CYS J 70 " distance=2.04 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 394 " distance=2.03 Simple disulfide: pdb=" SG CYS J 409 " - pdb=" SG CYS J 462 " distance=2.03 Simple disulfide: pdb=" SG CYS J 432 " - pdb=" SG CYS J 446 " distance=2.03 Simple disulfide: pdb=" SG CYS J 436 " - pdb=" SG CYS J 442 " distance=2.03 Simple disulfide: pdb=" SG CYS J 494 " - pdb=" SG CYS J 510 " distance=2.03 Simple disulfide: pdb=" SG CYS J 531 " - pdb=" SG CYS J 569 " distance=2.03 Simple disulfide: pdb=" SG CYS J 554 " - pdb=" SG CYS J 574 " distance=2.03 Simple disulfide: pdb=" SG CYS K 34 " - pdb=" SG CYS K 70 " distance=2.03 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 394 " distance=2.03 Simple disulfide: pdb=" SG CYS K 409 " - pdb=" SG CYS K 462 " distance=2.03 Simple disulfide: pdb=" SG CYS K 432 " - pdb=" SG CYS K 446 " distance=2.03 Simple disulfide: pdb=" SG CYS K 436 " - pdb=" SG CYS K 442 " distance=2.03 Simple disulfide: pdb=" SG CYS K 494 " - pdb=" SG CYS K 510 " distance=2.03 Simple disulfide: pdb=" SG CYS K 531 " - pdb=" SG CYS K 569 " distance=2.03 Simple disulfide: pdb=" SG CYS K 554 " - pdb=" SG CYS K 574 " distance=2.03 Simple disulfide: pdb=" SG CYS L 34 " - pdb=" SG CYS L 70 " distance=2.03 Simple disulfide: pdb=" SG CYS L 385 " - pdb=" SG CYS L 394 " distance=2.03 Simple disulfide: pdb=" SG CYS L 409 " - pdb=" SG CYS L 462 " distance=2.03 Simple disulfide: pdb=" SG CYS L 432 " - pdb=" SG CYS L 446 " distance=2.03 Simple disulfide: pdb=" SG CYS L 436 " - pdb=" SG CYS L 442 " distance=2.03 Simple disulfide: pdb=" SG CYS L 494 " - pdb=" SG CYS L 510 " distance=2.03 Simple disulfide: pdb=" SG CYS L 531 " - pdb=" SG CYS L 569 " distance=2.03 Simple disulfide: pdb=" SG CYS L 554 " - pdb=" SG CYS L 574 " distance=2.03 Simple disulfide: pdb=" SG CYS M 34 " - pdb=" SG CYS M 70 " distance=2.03 Simple disulfide: pdb=" SG CYS M 385 " - pdb=" SG CYS M 394 " distance=2.03 Simple disulfide: pdb=" SG CYS M 409 " - pdb=" SG CYS M 462 " distance=2.03 Simple disulfide: pdb=" SG CYS M 432 " - pdb=" SG CYS M 446 " distance=2.03 Simple disulfide: pdb=" SG CYS M 436 " - pdb=" SG CYS M 442 " distance=2.03 Simple disulfide: pdb=" SG CYS M 494 " - pdb=" SG CYS M 510 " distance=2.03 Simple disulfide: pdb=" SG CYS M 531 " - pdb=" SG CYS M 569 " distance=2.03 Simple disulfide: pdb=" SG CYS M 554 " - pdb=" SG CYS M 574 " distance=2.03 Simple disulfide: pdb=" SG CYS N 34 " - pdb=" SG CYS N 70 " distance=2.04 Simple disulfide: pdb=" SG CYS N 385 " - pdb=" SG CYS N 394 " distance=2.03 Simple disulfide: pdb=" SG CYS N 409 " - pdb=" SG CYS N 462 " distance=2.03 Simple disulfide: pdb=" SG CYS N 432 " - pdb=" SG CYS N 446 " distance=2.03 Simple disulfide: pdb=" SG CYS N 436 " - pdb=" SG CYS N 442 " distance=2.03 Simple disulfide: pdb=" SG CYS N 494 " - pdb=" SG CYS N 510 " distance=2.03 Simple disulfide: pdb=" SG CYS N 531 " - pdb=" SG CYS N 569 " distance=2.03 Simple disulfide: pdb=" SG CYS N 554 " - pdb=" SG CYS N 574 " distance=2.03 Simple disulfide: pdb=" SG CYS O 34 " - pdb=" SG CYS O 70 " distance=2.03 Simple disulfide: pdb=" SG CYS O 385 " - pdb=" SG CYS O 394 " distance=2.03 Simple disulfide: pdb=" SG CYS O 409 " - pdb=" SG CYS O 462 " distance=2.03 Simple disulfide: pdb=" SG CYS O 432 " - pdb=" SG CYS O 446 " distance=2.03 Simple disulfide: pdb=" SG CYS O 436 " - pdb=" SG CYS O 442 " distance=2.03 Simple disulfide: pdb=" SG CYS O 494 " - pdb=" SG CYS O 510 " distance=2.03 Simple disulfide: pdb=" SG CYS O 531 " - pdb=" SG CYS O 569 " distance=2.03 Simple disulfide: pdb=" SG CYS O 554 " - pdb=" SG CYS O 574 " distance=2.03 Simple disulfide: pdb=" SG CYS P 34 " - pdb=" SG CYS P 70 " distance=2.03 Simple disulfide: pdb=" SG CYS P 385 " - pdb=" SG CYS P 394 " distance=2.03 Simple disulfide: pdb=" SG CYS P 409 " - pdb=" SG CYS P 462 " distance=2.03 Simple disulfide: pdb=" SG CYS P 432 " - pdb=" SG CYS P 446 " distance=2.03 Simple disulfide: pdb=" SG CYS P 436 " - pdb=" SG CYS P 442 " distance=2.03 Simple disulfide: pdb=" SG CYS P 494 " - pdb=" SG CYS P 510 " distance=2.03 Simple disulfide: pdb=" SG CYS P 531 " - pdb=" SG CYS P 569 " distance=2.03 Simple disulfide: pdb=" SG CYS P 554 " - pdb=" SG CYS P 574 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 269 " " NAG B 701 " - " ASN B 269 " " NAG C 701 " - " ASN C 269 " " NAG D 701 " - " ASN D 269 " " NAG E 701 " - " ASN E 269 " " NAG F 701 " - " ASN F 269 " " NAG G 701 " - " ASN G 269 " " NAG H 701 " - " ASN H 269 " " NAG I 701 " - " ASN I 269 " " NAG J 701 " - " ASN J 269 " " NAG K 701 " - " ASN K 269 " " NAG L 701 " - " ASN L 269 " " NAG M 701 " - " ASN M 269 " " NAG N 701 " - " ASN N 269 " " NAG O 701 " - " ASN O 269 " " NAG P 701 " - " ASN P 269 " Time building additional restraints: 21.25 Conformation dependent library (CDL) restraints added in 9.1 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: 10.01 Creating SS restraints... Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 169 through 183 Processing helix chain 'A' and resid 187 through 201 Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 310 through 313 Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 324 through 344 Processing helix chain 'A' and resid 394 through 397 No H-bonds generated for 'chain 'A' and resid 394 through 397' Processing helix chain 'A' and resid 515 through 520 Processing helix chain 'B' and resid 32 through 38 Processing helix chain 'B' and resid 169 through 183 Processing helix chain 'B' and resid 187 through 201 Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 310 through 312 No H-bonds generated for 'chain 'B' and resid 310 through 312' Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'B' and resid 324 through 344 Processing helix chain 'B' and resid 394 through 397 No H-bonds generated for 'chain 'B' and resid 394 through 397' Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 515 through 520 Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 169 through 183 Processing helix chain 'C' and resid 187 through 201 removed outlier: 3.702A pdb=" N THR C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR C 192 " --> pdb=" O LYS C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 310 through 313 Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 324 through 344 Processing helix chain 'C' and resid 393 through 395 No H-bonds generated for 'chain 'C' and resid 393 through 395' Processing helix chain 'C' and resid 515 through 521 Processing helix chain 'D' and resid 32 through 38 Processing helix chain 'D' and resid 169 through 183 Processing helix chain 'D' and resid 187 through 201 removed outlier: 3.738A pdb=" N THR D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 310 through 313 Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 324 through 344 Processing helix chain 'D' and resid 393 through 395 No H-bonds generated for 'chain 'D' and resid 393 through 395' Processing helix chain 'D' and resid 515 through 521 Processing helix chain 'E' and resid 32 through 38 Processing helix chain 'E' and resid 169 through 183 Processing helix chain 'E' and resid 187 through 201 Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 310 through 313 No H-bonds generated for 'chain 'E' and resid 310 through 313' Processing helix chain 'E' and resid 324 through 344 Processing helix chain 'E' and resid 393 through 397 removed outlier: 3.992A pdb=" N ASN E 396 " --> pdb=" O LEU E 393 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU E 397 " --> pdb=" O CYS E 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 393 through 397' Processing helix chain 'E' and resid 515 through 521 Processing helix chain 'F' and resid 32 through 38 Processing helix chain 'F' and resid 169 through 183 Processing helix chain 'F' and resid 187 through 201 removed outlier: 3.541A pdb=" N THR F 191 " --> pdb=" O THR F 187 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR F 192 " --> pdb=" O LYS F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 295 Processing helix chain 'F' and resid 310 through 313 Processing helix chain 'F' and resid 316 through 318 No H-bonds generated for 'chain 'F' and resid 316 through 318' Processing helix chain 'F' and resid 324 through 344 Processing helix chain 'F' and resid 393 through 395 No H-bonds generated for 'chain 'F' and resid 393 through 395' Processing helix chain 'F' and resid 515 through 520 Processing helix chain 'G' and resid 32 through 38 Processing helix chain 'G' and resid 169 through 183 Processing helix chain 'G' and resid 187 through 201 removed outlier: 3.554A pdb=" N THR G 191 " --> pdb=" O THR G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 295 Processing helix chain 'G' and resid 310 through 313 Processing helix chain 'G' and resid 316 through 318 No H-bonds generated for 'chain 'G' and resid 316 through 318' Processing helix chain 'G' and resid 324 through 344 Processing helix chain 'G' and resid 394 through 397 No H-bonds generated for 'chain 'G' and resid 394 through 397' Processing helix chain 'G' and resid 437 through 439 No H-bonds generated for 'chain 'G' and resid 437 through 439' Processing helix chain 'G' and resid 515 through 521 Processing helix chain 'H' and resid 32 through 38 Processing helix chain 'H' and resid 169 through 183 Processing helix chain 'H' and resid 187 through 201 Processing helix chain 'H' and resid 289 through 295 Processing helix chain 'H' and resid 310 through 313 Processing helix chain 'H' and resid 316 through 318 No H-bonds generated for 'chain 'H' and resid 316 through 318' Processing helix chain 'H' and resid 324 through 344 Processing helix chain 'H' and resid 393 through 395 No H-bonds generated for 'chain 'H' and resid 393 through 395' Processing helix chain 'H' and resid 515 through 520 Processing helix chain 'I' and resid 32 through 38 Processing helix chain 'I' and resid 169 through 183 Processing helix chain 'I' and resid 187 through 201 removed outlier: 3.587A pdb=" N THR I 191 " --> pdb=" O THR I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 289 through 295 Processing helix chain 'I' and resid 310 through 313 Processing helix chain 'I' and resid 316 through 318 No H-bonds generated for 'chain 'I' and resid 316 through 318' Processing helix chain 'I' and resid 324 through 344 Processing helix chain 'I' and resid 394 through 397 No H-bonds generated for 'chain 'I' and resid 394 through 397' Processing helix chain 'I' and resid 515 through 519 Processing helix chain 'J' and resid 32 through 38 Processing helix chain 'J' and resid 169 through 183 Processing helix chain 'J' and resid 187 through 201 removed outlier: 3.624A pdb=" N THR J 191 " --> pdb=" O THR J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 295 Processing helix chain 'J' and resid 310 through 312 No H-bonds generated for 'chain 'J' and resid 310 through 312' Processing helix chain 'J' and resid 316 through 318 No H-bonds generated for 'chain 'J' and resid 316 through 318' Processing helix chain 'J' and resid 324 through 344 Processing helix chain 'J' and resid 394 through 397 No H-bonds generated for 'chain 'J' and resid 394 through 397' Processing helix chain 'J' and resid 437 through 439 No H-bonds generated for 'chain 'J' and resid 437 through 439' Processing helix chain 'J' and resid 515 through 520 Processing helix chain 'K' and resid 32 through 38 Processing helix chain 'K' and resid 169 through 183 Processing helix chain 'K' and resid 187 through 201 removed outlier: 3.761A pdb=" N THR K 191 " --> pdb=" O THR K 187 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR K 192 " --> pdb=" O LYS K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 289 through 295 Processing helix chain 'K' and resid 310 through 313 Processing helix chain 'K' and resid 316 through 318 No H-bonds generated for 'chain 'K' and resid 316 through 318' Processing helix chain 'K' and resid 324 through 344 Processing helix chain 'K' and resid 393 through 395 No H-bonds generated for 'chain 'K' and resid 393 through 395' Processing helix chain 'K' and resid 515 through 521 Processing helix chain 'L' and resid 32 through 38 Processing helix chain 'L' and resid 169 through 183 Processing helix chain 'L' and resid 187 through 201 removed outlier: 3.676A pdb=" N THR L 191 " --> pdb=" O THR L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 289 through 295 Processing helix chain 'L' and resid 310 through 313 Processing helix chain 'L' and resid 316 through 318 No H-bonds generated for 'chain 'L' and resid 316 through 318' Processing helix chain 'L' and resid 324 through 344 Processing helix chain 'L' and resid 393 through 395 No H-bonds generated for 'chain 'L' and resid 393 through 395' Processing helix chain 'L' and resid 515 through 521 Processing helix chain 'M' and resid 32 through 38 Processing helix chain 'M' and resid 169 through 183 Processing helix chain 'M' and resid 187 through 201 removed outlier: 3.588A pdb=" N TYR M 192 " --> pdb=" O LYS M 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 289 through 295 Processing helix chain 'M' and resid 310 through 313 Processing helix chain 'M' and resid 324 through 344 Processing helix chain 'M' and resid 393 through 397 removed outlier: 4.019A pdb=" N ASN M 396 " --> pdb=" O LEU M 393 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU M 397 " --> pdb=" O CYS M 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 393 through 397' Processing helix chain 'M' and resid 515 through 520 Processing helix chain 'N' and resid 32 through 38 Processing helix chain 'N' and resid 169 through 183 Processing helix chain 'N' and resid 187 through 201 removed outlier: 3.557A pdb=" N TYR N 192 " --> pdb=" O LYS N 188 " (cutoff:3.500A) Processing helix chain 'N' and resid 289 through 295 Processing helix chain 'N' and resid 310 through 313 Processing helix chain 'N' and resid 316 through 318 No H-bonds generated for 'chain 'N' and resid 316 through 318' Processing helix chain 'N' and resid 324 through 344 Processing helix chain 'N' and resid 393 through 395 No H-bonds generated for 'chain 'N' and resid 393 through 395' Processing helix chain 'N' and resid 437 through 439 No H-bonds generated for 'chain 'N' and resid 437 through 439' Processing helix chain 'N' and resid 515 through 520 Processing helix chain 'O' and resid 32 through 38 Processing helix chain 'O' and resid 169 through 183 Processing helix chain 'O' and resid 187 through 201 removed outlier: 3.527A pdb=" N THR O 191 " --> pdb=" O THR O 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 289 through 295 Processing helix chain 'O' and resid 310 through 313 Processing helix chain 'O' and resid 324 through 344 Processing helix chain 'O' and resid 394 through 397 No H-bonds generated for 'chain 'O' and resid 394 through 397' Processing helix chain 'O' and resid 437 through 439 No H-bonds generated for 'chain 'O' and resid 437 through 439' Processing helix chain 'O' and resid 515 through 521 Processing helix chain 'P' and resid 32 through 38 Processing helix chain 'P' and resid 169 through 183 Processing helix chain 'P' and resid 187 through 201 Processing helix chain 'P' and resid 289 through 295 Processing helix chain 'P' and resid 310 through 313 Processing helix chain 'P' and resid 316 through 318 No H-bonds generated for 'chain 'P' and resid 316 through 318' Processing helix chain 'P' and resid 324 through 344 Processing helix chain 'P' and resid 393 through 395 No H-bonds generated for 'chain 'P' and resid 393 through 395' Processing helix chain 'P' and resid 515 through 521 Processing sheet with id= A, first strand: chain 'A' and resid 84 through 88 removed outlier: 6.708A pdb=" N ALA A 211 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR A 158 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A 209 " --> pdb=" O THR A 158 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 91 through 121 Processing sheet with id= C, first strand: chain 'A' and resid 479 through 481 Processing sheet with id= D, first strand: chain 'A' and resid 528 through 530 removed outlier: 3.520A pdb=" N PHE A 529 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR A 573 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU A 562 " --> pdb=" O TYR A 573 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL A 575 " --> pdb=" O GLN A 560 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLN A 560 " --> pdb=" O VAL A 575 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 204 through 209 removed outlier: 6.768A pdb=" N ALA A 306 " --> pdb=" O THR A 207 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 378 through 387 removed outlier: 5.631A pdb=" N CYS A 462 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL A 381 " --> pdb=" O TYR A 460 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TYR A 460 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLN A 383 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ARG A 458 " --> pdb=" O GLN A 383 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N CYS A 385 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU A 456 " --> pdb=" O CYS A 385 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLU A 387 " --> pdb=" O LYS A 454 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LYS A 454 " --> pdb=" O GLU A 387 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TRP A 461 " --> pdb=" O HIS A 417 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N HIS A 417 " --> pdb=" O TRP A 461 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL A 463 " --> pdb=" O PRO A 415 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 84 through 88 removed outlier: 6.626A pdb=" N ALA B 211 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR B 158 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL B 209 " --> pdb=" O THR B 158 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 91 through 121 Processing sheet with id= I, first strand: chain 'B' and resid 479 through 481 Processing sheet with id= J, first strand: chain 'B' and resid 204 through 209 removed outlier: 6.764A pdb=" N ALA B 306 " --> pdb=" O THR B 207 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 378 through 387 removed outlier: 5.704A pdb=" N CYS B 462 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N VAL B 381 " --> pdb=" O TYR B 460 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR B 460 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLN B 383 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ARG B 458 " --> pdb=" O GLN B 383 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N CYS B 385 " --> pdb=" O GLU B 456 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU B 456 " --> pdb=" O CYS B 385 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLU B 387 " --> pdb=" O LYS B 454 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LYS B 454 " --> pdb=" O GLU B 387 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N TRP B 461 " --> pdb=" O HIS B 417 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N HIS B 417 " --> pdb=" O TRP B 461 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL B 463 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 525 through 529 removed outlier: 6.349A pdb=" N CYS B 574 " --> pdb=" O GLY B 526 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE B 528 " --> pdb=" O SER B 572 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER B 572 " --> pdb=" O PHE B 528 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N TYR B 573 " --> pdb=" O LEU B 562 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU B 562 " --> pdb=" O TYR B 573 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL B 575 " --> pdb=" O GLN B 560 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLN B 560 " --> pdb=" O VAL B 575 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 84 through 88 removed outlier: 6.615A pdb=" N ALA C 211 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR C 158 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL C 209 " --> pdb=" O THR C 158 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 91 through 121 Processing sheet with id= O, first strand: chain 'C' and resid 498 through 502 Processing sheet with id= P, first strand: chain 'C' and resid 49 through 52 removed outlier: 5.194A pdb=" N GLY C 60 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ASP C 52 " --> pdb=" O ASP C 58 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ASP C 58 " --> pdb=" O ASP C 52 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 204 through 210 removed outlier: 6.837A pdb=" N ALA C 306 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL C 209 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASP C 304 " --> pdb=" O VAL C 209 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 378 through 387 removed outlier: 5.954A pdb=" N CYS C 462 " --> pdb=" O GLY C 379 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N VAL C 381 " --> pdb=" O TYR C 460 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TYR C 460 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLN C 383 " --> pdb=" O ARG C 458 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ARG C 458 " --> pdb=" O GLN C 383 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N CYS C 385 " --> pdb=" O GLU C 456 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU C 456 " --> pdb=" O CYS C 385 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N GLU C 387 " --> pdb=" O LYS C 454 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LYS C 454 " --> pdb=" O GLU C 387 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TRP C 461 " --> pdb=" O HIS C 417 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N HIS C 417 " --> pdb=" O TRP C 461 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL C 463 " --> pdb=" O PRO C 415 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 525 through 529 removed outlier: 6.365A pdb=" N CYS C 574 " --> pdb=" O GLY C 526 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N PHE C 528 " --> pdb=" O SER C 572 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N SER C 572 " --> pdb=" O PHE C 528 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TYR C 573 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LEU C 562 " --> pdb=" O TYR C 573 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL C 575 " --> pdb=" O GLN C 560 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLN C 560 " --> pdb=" O VAL C 575 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 84 through 88 removed outlier: 6.642A pdb=" N ALA D 211 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR D 158 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL D 209 " --> pdb=" O THR D 158 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 91 through 121 Processing sheet with id= V, first strand: chain 'D' and resid 498 through 502 Processing sheet with id= W, first strand: chain 'D' and resid 204 through 210 removed outlier: 6.824A pdb=" N ALA D 306 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL D 209 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP D 304 " --> pdb=" O VAL D 209 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 378 through 387 removed outlier: 5.810A pdb=" N CYS D 462 " --> pdb=" O GLY D 379 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N VAL D 381 " --> pdb=" O TYR D 460 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N TYR D 460 " --> pdb=" O VAL D 381 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLN D 383 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ARG D 458 " --> pdb=" O GLN D 383 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N CYS D 385 " --> pdb=" O GLU D 456 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU D 456 " --> pdb=" O CYS D 385 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLU D 387 " --> pdb=" O LYS D 454 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LYS D 454 " --> pdb=" O GLU D 387 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TRP D 461 " --> pdb=" O HIS D 417 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N HIS D 417 " --> pdb=" O TRP D 461 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL D 463 " --> pdb=" O PRO D 415 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 558 through 566 removed outlier: 3.559A pdb=" N HIS D 561 " --> pdb=" O TYR D 573 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL D 571 " --> pdb=" O ALA D 563 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE D 565 " --> pdb=" O CYS D 569 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N CYS D 569 " --> pdb=" O ILE D 565 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 84 through 88 removed outlier: 6.690A pdb=" N ALA E 211 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR E 158 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL E 209 " --> pdb=" O THR E 158 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 91 through 121 Processing sheet with id= AB, first strand: chain 'E' and resid 498 through 502 Processing sheet with id= AC, first strand: chain 'E' and resid 204 through 209 removed outlier: 6.745A pdb=" N ALA E 306 " --> pdb=" O THR E 207 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 378 through 387 removed outlier: 6.020A pdb=" N CYS E 462 " --> pdb=" O GLY E 379 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL E 381 " --> pdb=" O TYR E 460 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TYR E 460 " --> pdb=" O VAL E 381 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLN E 383 " --> pdb=" O ARG E 458 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ARG E 458 " --> pdb=" O GLN E 383 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N CYS E 385 " --> pdb=" O GLU E 456 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLU E 456 " --> pdb=" O CYS E 385 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLU E 387 " --> pdb=" O LYS E 454 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LYS E 454 " --> pdb=" O GLU E 387 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TRP E 461 " --> pdb=" O HIS E 417 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N HIS E 417 " --> pdb=" O TRP E 461 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL E 463 " --> pdb=" O PRO E 415 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 558 through 566 removed outlier: 3.711A pdb=" N HIS E 561 " --> pdb=" O TYR E 573 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR E 573 " --> pdb=" O HIS E 561 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL E 571 " --> pdb=" O ALA E 563 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE E 565 " --> pdb=" O CYS E 569 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N CYS E 569 " --> pdb=" O ILE E 565 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 84 through 88 removed outlier: 6.720A pdb=" N ALA F 211 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR F 158 " --> pdb=" O VAL F 209 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL F 209 " --> pdb=" O THR F 158 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 91 through 121 Processing sheet with id= AH, first strand: chain 'F' and resid 383 through 387 removed outlier: 6.520A pdb=" N TRP F 461 " --> pdb=" O HIS F 417 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N HIS F 417 " --> pdb=" O TRP F 461 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL F 463 " --> pdb=" O PRO F 415 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 498 through 502 Processing sheet with id= AJ, first strand: chain 'F' and resid 204 through 209 removed outlier: 6.750A pdb=" N ALA F 306 " --> pdb=" O THR F 207 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'F' and resid 558 through 566 removed outlier: 3.644A pdb=" N HIS F 561 " --> pdb=" O TYR F 573 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR F 573 " --> pdb=" O HIS F 561 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL F 571 " --> pdb=" O ALA F 563 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE F 565 " --> pdb=" O CYS F 569 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N CYS F 569 " --> pdb=" O ILE F 565 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'G' and resid 84 through 88 removed outlier: 6.643A pdb=" N ALA G 211 " --> pdb=" O ILE G 156 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR G 158 " --> pdb=" O VAL G 209 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL G 209 " --> pdb=" O THR G 158 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'G' and resid 91 through 121 Processing sheet with id= AN, first strand: chain 'G' and resid 498 through 502 Processing sheet with id= AO, first strand: chain 'G' and resid 204 through 209 removed outlier: 6.829A pdb=" N ALA G 306 " --> pdb=" O THR G 207 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'G' and resid 378 through 387 removed outlier: 5.642A pdb=" N CYS G 462 " --> pdb=" O GLY G 379 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL G 381 " --> pdb=" O TYR G 460 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYR G 460 " --> pdb=" O VAL G 381 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN G 383 " --> pdb=" O ARG G 458 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ARG G 458 " --> pdb=" O GLN G 383 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N CYS G 385 " --> pdb=" O GLU G 456 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU G 456 " --> pdb=" O CYS G 385 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLU G 387 " --> pdb=" O LYS G 454 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LYS G 454 " --> pdb=" O GLU G 387 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TRP G 461 " --> pdb=" O HIS G 417 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N HIS G 417 " --> pdb=" O TRP G 461 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL G 463 " --> pdb=" O PRO G 415 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'G' and resid 525 through 529 removed outlier: 6.562A pdb=" N CYS G 574 " --> pdb=" O GLY G 526 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE G 528 " --> pdb=" O SER G 572 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER G 572 " --> pdb=" O PHE G 528 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N TYR G 573 " --> pdb=" O LEU G 562 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LEU G 562 " --> pdb=" O TYR G 573 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL G 575 " --> pdb=" O GLN G 560 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLN G 560 " --> pdb=" O VAL G 575 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'H' and resid 84 through 88 removed outlier: 6.704A pdb=" N ALA H 211 " --> pdb=" O ILE H 156 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR H 158 " --> pdb=" O VAL H 209 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL H 209 " --> pdb=" O THR H 158 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'H' and resid 91 through 121 Processing sheet with id= AT, first strand: chain 'H' and resid 479 through 481 Processing sheet with id= AU, first strand: chain 'H' and resid 204 through 209 removed outlier: 6.813A pdb=" N ALA H 306 " --> pdb=" O THR H 207 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'H' and resid 378 through 387 removed outlier: 5.762A pdb=" N CYS H 462 " --> pdb=" O GLY H 379 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL H 381 " --> pdb=" O TYR H 460 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N TYR H 460 " --> pdb=" O VAL H 381 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLN H 383 " --> pdb=" O ARG H 458 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG H 458 " --> pdb=" O GLN H 383 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N CYS H 385 " --> pdb=" O GLU H 456 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLU H 456 " --> pdb=" O CYS H 385 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLU H 387 " --> pdb=" O LYS H 454 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LYS H 454 " --> pdb=" O GLU H 387 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TRP H 461 " --> pdb=" O HIS H 417 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N HIS H 417 " --> pdb=" O TRP H 461 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL H 463 " --> pdb=" O PRO H 415 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'H' and resid 525 through 530 removed outlier: 6.381A pdb=" N CYS H 574 " --> pdb=" O GLY H 526 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE H 528 " --> pdb=" O SER H 572 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N SER H 572 " --> pdb=" O PHE H 528 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER H 530 " --> pdb=" O GLN H 570 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLN H 570 " --> pdb=" O SER H 530 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N TYR H 573 " --> pdb=" O LEU H 562 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU H 562 " --> pdb=" O TYR H 573 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL H 575 " --> pdb=" O GLN H 560 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLN H 560 " --> pdb=" O VAL H 575 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'I' and resid 84 through 88 removed outlier: 6.662A pdb=" N ALA I 211 " --> pdb=" O ILE I 156 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR I 158 " --> pdb=" O VAL I 209 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL I 209 " --> pdb=" O THR I 158 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'I' and resid 91 through 121 Processing sheet with id= AZ, first strand: chain 'I' and resid 479 through 481 Processing sheet with id= BA, first strand: chain 'I' and resid 204 through 209 removed outlier: 6.778A pdb=" N ALA I 306 " --> pdb=" O THR I 207 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'I' and resid 378 through 387 removed outlier: 5.602A pdb=" N CYS I 462 " --> pdb=" O GLY I 379 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL I 381 " --> pdb=" O TYR I 460 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N TYR I 460 " --> pdb=" O VAL I 381 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLN I 383 " --> pdb=" O ARG I 458 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ARG I 458 " --> pdb=" O GLN I 383 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N CYS I 385 " --> pdb=" O GLU I 456 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU I 456 " --> pdb=" O CYS I 385 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N GLU I 387 " --> pdb=" O LYS I 454 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LYS I 454 " --> pdb=" O GLU I 387 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N TRP I 461 " --> pdb=" O HIS I 417 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N HIS I 417 " --> pdb=" O TRP I 461 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL I 463 " --> pdb=" O PRO I 415 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'I' and resid 525 through 530 removed outlier: 6.279A pdb=" N CYS I 574 " --> pdb=" O GLY I 526 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE I 528 " --> pdb=" O SER I 572 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N SER I 572 " --> pdb=" O PHE I 528 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER I 530 " --> pdb=" O GLN I 570 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLN I 570 " --> pdb=" O SER I 530 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N TYR I 573 " --> pdb=" O LEU I 562 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU I 562 " --> pdb=" O TYR I 573 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL I 575 " --> pdb=" O GLN I 560 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLN I 560 " --> pdb=" O VAL I 575 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'J' and resid 84 through 88 removed outlier: 6.651A pdb=" N ALA J 211 " --> pdb=" O ILE J 156 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR J 158 " --> pdb=" O VAL J 209 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL J 209 " --> pdb=" O THR J 158 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'J' and resid 91 through 121 Processing sheet with id= BF, first strand: chain 'J' and resid 479 through 481 Processing sheet with id= BG, first strand: chain 'J' and resid 204 through 210 removed outlier: 6.743A pdb=" N ALA J 306 " --> pdb=" O THR J 207 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL J 209 " --> pdb=" O ASP J 304 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASP J 304 " --> pdb=" O VAL J 209 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'J' and resid 378 through 387 removed outlier: 5.716A pdb=" N CYS J 462 " --> pdb=" O GLY J 379 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL J 381 " --> pdb=" O TYR J 460 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N TYR J 460 " --> pdb=" O VAL J 381 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN J 383 " --> pdb=" O ARG J 458 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG J 458 " --> pdb=" O GLN J 383 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N CYS J 385 " --> pdb=" O GLU J 456 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU J 456 " --> pdb=" O CYS J 385 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLU J 387 " --> pdb=" O LYS J 454 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LYS J 454 " --> pdb=" O GLU J 387 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TRP J 461 " --> pdb=" O HIS J 417 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N HIS J 417 " --> pdb=" O TRP J 461 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL J 463 " --> pdb=" O PRO J 415 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'J' and resid 525 through 529 removed outlier: 6.349A pdb=" N CYS J 574 " --> pdb=" O GLY J 526 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE J 528 " --> pdb=" O SER J 572 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER J 572 " --> pdb=" O PHE J 528 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TYR J 573 " --> pdb=" O LEU J 562 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LEU J 562 " --> pdb=" O TYR J 573 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL J 575 " --> pdb=" O GLN J 560 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLN J 560 " --> pdb=" O VAL J 575 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'K' and resid 84 through 88 removed outlier: 6.623A pdb=" N ALA K 211 " --> pdb=" O ILE K 156 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR K 158 " --> pdb=" O VAL K 209 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL K 209 " --> pdb=" O THR K 158 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'K' and resid 91 through 121 Processing sheet with id= BL, first strand: chain 'K' and resid 498 through 502 Processing sheet with id= BM, first strand: chain 'K' and resid 204 through 210 removed outlier: 6.881A pdb=" N ALA K 306 " --> pdb=" O THR K 207 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL K 209 " --> pdb=" O ASP K 304 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP K 304 " --> pdb=" O VAL K 209 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'K' and resid 378 through 387 removed outlier: 5.914A pdb=" N CYS K 462 " --> pdb=" O GLY K 379 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL K 381 " --> pdb=" O TYR K 460 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TYR K 460 " --> pdb=" O VAL K 381 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLN K 383 " --> pdb=" O ARG K 458 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ARG K 458 " --> pdb=" O GLN K 383 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N CYS K 385 " --> pdb=" O GLU K 456 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU K 456 " --> pdb=" O CYS K 385 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLU K 387 " --> pdb=" O LYS K 454 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LYS K 454 " --> pdb=" O GLU K 387 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N TRP K 461 " --> pdb=" O HIS K 417 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N HIS K 417 " --> pdb=" O TRP K 461 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL K 463 " --> pdb=" O PRO K 415 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'K' and resid 525 through 529 removed outlier: 6.353A pdb=" N CYS K 574 " --> pdb=" O GLY K 526 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE K 528 " --> pdb=" O SER K 572 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER K 572 " --> pdb=" O PHE K 528 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N TYR K 573 " --> pdb=" O LEU K 562 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU K 562 " --> pdb=" O TYR K 573 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL K 575 " --> pdb=" O GLN K 560 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLN K 560 " --> pdb=" O VAL K 575 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'L' and resid 84 through 87 removed outlier: 6.676A pdb=" N ALA L 211 " --> pdb=" O ILE L 156 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR L 158 " --> pdb=" O VAL L 209 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL L 209 " --> pdb=" O THR L 158 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'L' and resid 91 through 121 Processing sheet with id= BR, first strand: chain 'L' and resid 498 through 502 Processing sheet with id= BS, first strand: chain 'L' and resid 204 through 210 removed outlier: 6.814A pdb=" N ALA L 306 " --> pdb=" O THR L 207 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL L 209 " --> pdb=" O ASP L 304 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP L 304 " --> pdb=" O VAL L 209 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'L' and resid 378 through 387 removed outlier: 5.795A pdb=" N CYS L 462 " --> pdb=" O GLY L 379 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N VAL L 381 " --> pdb=" O TYR L 460 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N TYR L 460 " --> pdb=" O VAL L 381 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN L 383 " --> pdb=" O ARG L 458 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ARG L 458 " --> pdb=" O GLN L 383 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N CYS L 385 " --> pdb=" O GLU L 456 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU L 456 " --> pdb=" O CYS L 385 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N GLU L 387 " --> pdb=" O LYS L 454 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LYS L 454 " --> pdb=" O GLU L 387 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TRP L 461 " --> pdb=" O HIS L 417 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N HIS L 417 " --> pdb=" O TRP L 461 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL L 463 " --> pdb=" O PRO L 415 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'L' and resid 558 through 566 removed outlier: 3.592A pdb=" N HIS L 561 " --> pdb=" O TYR L 573 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL L 571 " --> pdb=" O ALA L 563 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE L 565 " --> pdb=" O CYS L 569 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N CYS L 569 " --> pdb=" O ILE L 565 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'M' and resid 84 through 88 removed outlier: 6.720A pdb=" N ALA M 211 " --> pdb=" O ILE M 156 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR M 158 " --> pdb=" O VAL M 209 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL M 209 " --> pdb=" O THR M 158 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'M' and resid 91 through 121 Processing sheet with id= BX, first strand: chain 'M' and resid 498 through 502 Processing sheet with id= BY, first strand: chain 'M' and resid 204 through 210 removed outlier: 6.761A pdb=" N ALA M 306 " --> pdb=" O THR M 207 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL M 209 " --> pdb=" O ASP M 304 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASP M 304 " --> pdb=" O VAL M 209 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'M' and resid 378 through 387 removed outlier: 6.023A pdb=" N CYS M 462 " --> pdb=" O GLY M 379 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL M 381 " --> pdb=" O TYR M 460 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR M 460 " --> pdb=" O VAL M 381 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLN M 383 " --> pdb=" O ARG M 458 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ARG M 458 " --> pdb=" O GLN M 383 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N CYS M 385 " --> pdb=" O GLU M 456 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLU M 456 " --> pdb=" O CYS M 385 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLU M 387 " --> pdb=" O LYS M 454 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LYS M 454 " --> pdb=" O GLU M 387 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP M 461 " --> pdb=" O HIS M 417 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N HIS M 417 " --> pdb=" O TRP M 461 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL M 463 " --> pdb=" O PRO M 415 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'M' and resid 558 through 566 removed outlier: 3.747A pdb=" N HIS M 561 " --> pdb=" O TYR M 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR M 573 " --> pdb=" O HIS M 561 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL M 571 " --> pdb=" O ALA M 563 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE M 565 " --> pdb=" O CYS M 569 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N CYS M 569 " --> pdb=" O ILE M 565 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'N' and resid 84 through 88 removed outlier: 6.720A pdb=" N ALA N 211 " --> pdb=" O ILE N 156 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR N 158 " --> pdb=" O VAL N 209 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL N 209 " --> pdb=" O THR N 158 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'N' and resid 91 through 121 Processing sheet with id= CD, first strand: chain 'N' and resid 383 through 387 removed outlier: 6.500A pdb=" N TRP N 461 " --> pdb=" O HIS N 417 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N HIS N 417 " --> pdb=" O TRP N 461 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL N 463 " --> pdb=" O PRO N 415 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'N' and resid 498 through 502 Processing sheet with id= CF, first strand: chain 'N' and resid 204 through 209 removed outlier: 6.727A pdb=" N ALA N 306 " --> pdb=" O THR N 207 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'N' and resid 558 through 566 removed outlier: 3.945A pdb=" N HIS N 561 " --> pdb=" O TYR N 573 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR N 573 " --> pdb=" O HIS N 561 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL N 571 " --> pdb=" O ALA N 563 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE N 565 " --> pdb=" O CYS N 569 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N CYS N 569 " --> pdb=" O ILE N 565 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'O' and resid 84 through 88 removed outlier: 6.654A pdb=" N ALA O 211 " --> pdb=" O ILE O 156 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR O 158 " --> pdb=" O VAL O 209 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL O 209 " --> pdb=" O THR O 158 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'O' and resid 91 through 121 Processing sheet with id= CJ, first strand: chain 'O' and resid 499 through 502 Processing sheet with id= CK, first strand: chain 'O' and resid 204 through 210 removed outlier: 6.823A pdb=" N ALA O 306 " --> pdb=" O THR O 207 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL O 209 " --> pdb=" O ASP O 304 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASP O 304 " --> pdb=" O VAL O 209 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain 'O' and resid 378 through 387 removed outlier: 5.661A pdb=" N CYS O 462 " --> pdb=" O GLY O 379 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL O 381 " --> pdb=" O TYR O 460 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR O 460 " --> pdb=" O VAL O 381 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN O 383 " --> pdb=" O ARG O 458 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ARG O 458 " --> pdb=" O GLN O 383 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N CYS O 385 " --> pdb=" O GLU O 456 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU O 456 " --> pdb=" O CYS O 385 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLU O 387 " --> pdb=" O LYS O 454 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LYS O 454 " --> pdb=" O GLU O 387 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N TRP O 461 " --> pdb=" O HIS O 417 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N HIS O 417 " --> pdb=" O TRP O 461 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL O 463 " --> pdb=" O PRO O 415 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'O' and resid 525 through 529 removed outlier: 6.547A pdb=" N CYS O 574 " --> pdb=" O GLY O 526 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N PHE O 528 " --> pdb=" O SER O 572 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N SER O 572 " --> pdb=" O PHE O 528 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N TYR O 573 " --> pdb=" O LEU O 562 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU O 562 " --> pdb=" O TYR O 573 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL O 575 " --> pdb=" O GLN O 560 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLN O 560 " --> pdb=" O VAL O 575 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'P' and resid 84 through 88 removed outlier: 6.733A pdb=" N ALA P 211 " --> pdb=" O ILE P 156 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR P 158 " --> pdb=" O VAL P 209 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL P 209 " --> pdb=" O THR P 158 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'P' and resid 91 through 121 Processing sheet with id= CP, first strand: chain 'P' and resid 479 through 481 Processing sheet with id= CQ, first strand: chain 'P' and resid 204 through 210 removed outlier: 6.802A pdb=" N ALA P 306 " --> pdb=" O THR P 207 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL P 209 " --> pdb=" O ASP P 304 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASP P 304 " --> pdb=" O VAL P 209 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'P' and resid 378 through 387 removed outlier: 5.757A pdb=" N CYS P 462 " --> pdb=" O GLY P 379 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N VAL P 381 " --> pdb=" O TYR P 460 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TYR P 460 " --> pdb=" O VAL P 381 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLN P 383 " --> pdb=" O ARG P 458 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ARG P 458 " --> pdb=" O GLN P 383 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N CYS P 385 " --> pdb=" O GLU P 456 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLU P 456 " --> pdb=" O CYS P 385 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLU P 387 " --> pdb=" O LYS P 454 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LYS P 454 " --> pdb=" O GLU P 387 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TRP P 461 " --> pdb=" O HIS P 417 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N HIS P 417 " --> pdb=" O TRP P 461 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL P 463 " --> pdb=" O PRO P 415 " (cutoff:3.500A) Processing sheet with id= CS, first strand: chain 'P' and resid 525 through 530 removed outlier: 6.370A pdb=" N CYS P 574 " --> pdb=" O GLY P 526 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N PHE P 528 " --> pdb=" O SER P 572 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N SER P 572 " --> pdb=" O PHE P 528 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER P 530 " --> pdb=" O GLN P 570 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLN P 570 " --> pdb=" O SER P 530 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N TYR P 573 " --> pdb=" O LEU P 562 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU P 562 " --> pdb=" O TYR P 573 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL P 575 " --> pdb=" O GLN P 560 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLN P 560 " --> pdb=" O VAL P 575 " (cutoff:3.500A) 2847 hydrogen bonds defined for protein. 8325 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 23.90 Time building geometry restraints manager: 23.48 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 11.740 Check model and map are aligned: 0.750 Set scattering table: 0.490 Process input model: 141.010 Find NCS groups from input model: 3.940 Set up NCS constraints: 0.630 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:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.160 ------------------------------------------------------------------------------- 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 : 5.656 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 outliers start: 73 outliers final: 17 residues processed: 752 average time/residue: 0.6384 time to fit residues: 819.7905 Evaluate side-chains 446 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 429 time to evaluate : 5.529 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4729 time to fit residues: 23.3558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 716 optimal weight: 0.8980 chunk 642 optimal weight: 0.5980 chunk 356 optimal weight: 0.4980 chunk 219 optimal weight: 10.0000 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: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 186 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 570 GLN L 181 GLN L 186 GLN L 204 HIS L 276 GLN L 467 GLN L 570 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 276 GLN O 383 GLN O 467 GLN P 77 GLN P 181 GLN ** 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: 0.0154 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 68624 Z= 0.156 Angle : 0.622 16.231 93136 Z= 0.298 Chirality : 0.045 0.225 10816 Planarity : 0.004 0.061 11792 Dihedral : 10.668 95.202 10448 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.48 % Favored : 97.34 % Rotamer: Outliers : 1.80 % Allowed : 9.00 % Favored : 89.21 % 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: -0.15 (0.09), residues: 8432 helix: 1.09 (0.14), residues: 1376 sheet: 0.23 (0.09), residues: 3744 loop : -0.91 (0.11), residues: 3312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 51 HIS 0.007 0.001 HIS G 340 PHE 0.037 0.001 PHE P 225 TYR 0.022 0.001 TYR C 593 ARG 0.006 0.000 ARG N 458 *********************** 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 618 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 483 time to evaluate : 5.568 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 outliers start: 135 outliers final: 48 residues processed: 592 average time/residue: 0.6307 time to fit residues: 650.9276 Evaluate side-chains 446 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 398 time to evaluate : 5.467 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 48 outliers final: 1 residues processed: 48 average time/residue: 0.5039 time to fit residues: 53.8561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 427 optimal weight: 0.2980 chunk 238 optimal weight: 7.9990 chunk 640 optimal weight: 0.3980 chunk 524 optimal weight: 3.9990 chunk 212 optimal weight: 520.0000 chunk 771 optimal weight: 1.9990 chunk 833 optimal weight: 40.0000 chunk 687 optimal weight: 0.7980 chunk 765 optimal weight: 6.9990 chunk 263 optimal weight: 10.0000 chunk 618 optimal weight: 0.0010 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 233 GLN H 229 ASN ** H 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 144 GLN ** I 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 217 GLN J 234 ASN J 570 GLN K 560 GLN L 108 GLN L 154 ASN ** L 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 293 GLN L 401 ASN L 561 HIS M 249 ASN ** M 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 144 GLN ** N 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 217 GLN ** O 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 217 GLN O 561 HIS P 108 GLN P 181 GLN ** P 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 233 GLN P 399 GLN P 539 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0309 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 68624 Z= 0.144 Angle : 0.568 11.998 93136 Z= 0.275 Chirality : 0.044 0.575 10816 Planarity : 0.004 0.056 11792 Dihedral : 8.020 86.856 10448 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.66 % Favored : 97.18 % Rotamer: Outliers : 1.25 % Allowed : 9.79 % Favored : 88.95 % Cbeta Deviations : 0.01 % 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: 0.02 (0.09), residues: 8432 helix: 1.08 (0.14), residues: 1360 sheet: 0.40 (0.09), residues: 3632 loop : -0.77 (0.11), residues: 3440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 461 HIS 0.008 0.001 HIS L 220 PHE 0.021 0.001 PHE D 528 TYR 0.017 0.001 TYR N 460 ARG 0.007 0.000 ARG O 589 *********************** 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 523 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 429 time to evaluate : 5.570 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 outliers start: 94 outliers final: 41 residues processed: 502 average time/residue: 0.6324 time to fit residues: 554.0653 Evaluate side-chains 435 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 394 time to evaluate : 5.489 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.5165 time to fit residues: 47.5613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 762 optimal weight: 20.0000 chunk 580 optimal weight: 3.9990 chunk 400 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 368 optimal weight: 0.9990 chunk 518 optimal weight: 1.9990 chunk 774 optimal weight: 0.9980 chunk 819 optimal weight: 3.9990 chunk 404 optimal weight: 20.0000 chunk 733 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS A 383 GLN A 401 ASN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 ASN E 490 ASN E 561 HIS ** F 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN G 401 ASN ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 570 GLN H 144 GLN ** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 383 GLN ** J 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 ASN L 77 GLN L 97 ASN ** L 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 311 HIS L 383 GLN L 561 HIS ** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 220 HIS N 234 ASN N 299 HIS ** N 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 539 ASN P 144 GLN P 154 ASN ** P 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 293 GLN ** P 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0749 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 68624 Z= 0.246 Angle : 0.686 14.184 93136 Z= 0.345 Chirality : 0.047 0.384 10816 Planarity : 0.006 0.097 11792 Dihedral : 7.248 79.474 10448 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.19 % Favored : 96.64 % Rotamer: Outliers : 1.28 % Allowed : 10.30 % Favored : 88.42 % 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: -0.32 (0.09), residues: 8432 helix: 0.63 (0.14), residues: 1376 sheet: 0.24 (0.09), residues: 3616 loop : -0.98 (0.11), residues: 3440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP J 51 HIS 0.015 0.002 HIS M 220 PHE 0.035 0.002 PHE M 441 TYR 0.029 0.002 TYR J 573 ARG 0.024 0.001 ARG H 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 592 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 496 time to evaluate : 5.625 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 outliers start: 96 outliers final: 39 residues processed: 567 average time/residue: 0.6617 time to fit residues: 650.8392 Evaluate side-chains 463 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 424 time to evaluate : 5.547 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.5529 time to fit residues: 47.7043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 682 optimal weight: 0.7980 chunk 465 optimal weight: 9.9990 chunk 11 optimal weight: 30.0000 chunk 610 optimal weight: 0.5980 chunk 338 optimal weight: 20.0000 chunk 699 optimal weight: 0.8980 chunk 566 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 418 optimal weight: 3.9990 chunk 735 optimal weight: 6.9990 chunk 206 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 GLN F 401 ASN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 ASN ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 181 GLN J 570 GLN K 217 GLN ** K 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 401 ASN L 181 GLN ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 234 ASN ** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 217 GLN ** 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 69 ASN N 93 ASN ** N 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 259 GLN P 560 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0837 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.124 68624 Z= 0.193 Angle : 0.614 13.946 93136 Z= 0.307 Chirality : 0.045 0.381 10816 Planarity : 0.005 0.096 11792 Dihedral : 6.596 58.679 10448 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.08 % Favored : 96.74 % Rotamer: Outliers : 1.37 % Allowed : 10.91 % Favored : 87.71 % 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: -0.36 (0.09), residues: 8432 helix: 0.61 (0.14), residues: 1376 sheet: 0.20 (0.09), residues: 3616 loop : -0.99 (0.11), residues: 3440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 51 HIS 0.011 0.001 HIS K 220 PHE 0.034 0.002 PHE G 283 TYR 0.029 0.002 TYR N 67 ARG 0.011 0.001 ARG J 305 *********************** 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 566 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 463 time to evaluate : 5.740 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 outliers start: 103 outliers final: 47 residues processed: 531 average time/residue: 0.6580 time to fit residues: 602.6025 Evaluate side-chains 466 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 419 time to evaluate : 5.547 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.5149 time to fit residues: 53.4260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 275 optimal weight: 20.0000 chunk 738 optimal weight: 8.9990 chunk 162 optimal weight: 50.0000 chunk 481 optimal weight: 10.0000 chunk 202 optimal weight: 20.0000 chunk 820 optimal weight: 0.0270 chunk 681 optimal weight: 2.9990 chunk 379 optimal weight: 6.9990 chunk 68 optimal weight: 0.0870 chunk 271 optimal weight: 50.0000 chunk 430 optimal weight: 2.9990 overall best weight: 2.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN B 299 HIS C 97 ASN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN G 417 HIS ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN H 231 ASN ** H 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 272 ASN ** J 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 399 GLN ** L 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 471 ASN N 93 ASN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 144 GLN ** N 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 383 GLN N 401 ASN N 535 ASN O 53 ASN ** O 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 311 HIS O 570 GLN ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 233 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1133 moved from start: 0.6046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 68624 Z= 0.271 Angle : 0.750 13.837 93136 Z= 0.381 Chirality : 0.049 0.355 10816 Planarity : 0.006 0.137 11792 Dihedral : 7.067 59.595 10448 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.29 % Favored : 95.51 % Rotamer: Outliers : 1.36 % Allowed : 11.87 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.09), residues: 8432 helix: 0.29 (0.14), residues: 1372 sheet: 0.16 (0.09), residues: 3260 loop : -1.35 (0.10), residues: 3800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 104 HIS 0.015 0.002 HIS M 220 PHE 0.051 0.002 PHE K 278 TYR 0.033 0.002 TYR G 460 ARG 0.014 0.001 ARG K 149 *********************** 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 575 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 473 time to evaluate : 5.557 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 outliers start: 102 outliers final: 55 residues processed: 553 average time/residue: 0.6567 time to fit residues: 622.9950 Evaluate side-chains 474 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 419 time to evaluate : 5.462 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 55 outliers final: 1 residues processed: 55 average time/residue: 0.5310 time to fit residues: 61.9965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 791 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 467 optimal weight: 3.9990 chunk 599 optimal weight: 5.9990 chunk 464 optimal weight: 8.9990 chunk 690 optimal weight: 0.8980 chunk 458 optimal weight: 5.9990 chunk 817 optimal weight: 50.0000 chunk 511 optimal weight: 3.9990 chunk 498 optimal weight: 20.0000 chunk 377 optimal weight: 0.6980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN A 230 GLN ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 HIS ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN F 220 HIS ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 233 GLN ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 ASN H 154 ASN H 293 GLN I 77 GLN I 144 GLN ** I 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 HIS ** I 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 560 GLN ** I 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 570 GLN ** K 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 490 ASN ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 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 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 217 GLN M 234 ASN M 259 GLN ** M 293 GLN ** 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 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 383 GLN O 144 GLN O 204 HIS O 417 HIS O 570 GLN ** P 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 345 ASN P 417 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1319 moved from start: 0.7207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.129 68624 Z= 0.300 Angle : 0.790 18.089 93136 Z= 0.403 Chirality : 0.050 0.406 10816 Planarity : 0.007 0.139 11792 Dihedral : 7.228 59.303 10448 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.87 % Favored : 94.94 % Rotamer: Outliers : 1.28 % Allowed : 12.46 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.09), residues: 8432 helix: 0.10 (0.14), residues: 1311 sheet: -0.09 (0.09), residues: 3485 loop : -1.62 (0.10), residues: 3636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP G 461 HIS 0.015 0.002 HIS O 204 PHE 0.046 0.002 PHE K 278 TYR 0.052 0.002 TYR G 460 ARG 0.019 0.001 ARG N 149 *********************** 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 591 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 495 time to evaluate : 5.734 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 outliers start: 96 outliers final: 43 residues processed: 558 average time/residue: 0.6512 time to fit residues: 634.7769 Evaluate side-chains 480 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 437 time to evaluate : 5.665 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.5324 time to fit residues: 50.5745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 488 optimal weight: 10.0000 chunk 246 optimal weight: 50.0000 chunk 160 optimal weight: 20.0000 chunk 158 optimal weight: 50.0000 chunk 519 optimal weight: 0.4980 chunk 556 optimal weight: 2.9990 chunk 404 optimal weight: 1.9990 chunk 76 optimal weight: 50.0000 chunk 642 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- 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 186 GLN ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 HIS ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 ASN F 53 ASN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 272 ASN J 32 GLN J 53 ASN ** J 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 276 GLN J 401 ASN J 486 ASN ** J 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 259 GLN K 299 HIS L 106 ASN L 108 GLN L 154 ASN ** L 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 293 GLN ** L 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 217 GLN ** M 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 ASN O 144 GLN ** O 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 231 ASN ** P 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 234 ASN ** P 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1253 moved from start: 0.7392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 68624 Z= 0.192 Angle : 0.645 15.460 93136 Z= 0.326 Chirality : 0.046 0.369 10816 Planarity : 0.005 0.087 11792 Dihedral : 6.805 59.801 10448 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.77 % Favored : 96.06 % Rotamer: Outliers : 0.68 % Allowed : 13.58 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.09), residues: 8432 helix: 0.45 (0.14), residues: 1302 sheet: -0.10 (0.09), residues: 3441 loop : -1.48 (0.10), residues: 3689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP L 51 HIS 0.009 0.001 HIS H 220 PHE 0.031 0.001 PHE K 312 TYR 0.025 0.002 TYR L 341 ARG 0.007 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 518 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 467 time to evaluate : 5.720 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: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 21 residues processed: 498 average time/residue: 0.6681 time to fit residues: 580.4951 Evaluate side-chains 465 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 444 time to evaluate : 5.563 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.5496 time to fit residues: 29.5777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 743 optimal weight: 0.0270 chunk 783 optimal weight: 0.7980 chunk 714 optimal weight: 1.9990 chunk 761 optimal weight: 6.9990 chunk 782 optimal weight: 0.0980 chunk 458 optimal weight: 10.0000 chunk 331 optimal weight: 2.9990 chunk 598 optimal weight: 1.9990 chunk 233 optimal weight: 50.0000 chunk 688 optimal weight: 0.8980 chunk 720 optimal weight: 10.0000 overall best weight: 0.7640 ------------------------------------------------------------------------------- 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 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 ASN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 GLN ** G 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 345 ASN H 561 HIS I 134 GLN I 217 GLN ** J 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 217 GLN J 570 GLN K 154 ASN ** K 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 311 HIS ** L 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 383 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 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1190 moved from start: 0.7443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 68624 Z= 0.154 Angle : 0.592 14.978 93136 Z= 0.295 Chirality : 0.044 0.345 10816 Planarity : 0.005 0.068 11792 Dihedral : 6.357 59.408 10448 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.42 % Favored : 96.41 % Rotamer: Outliers : 0.29 % Allowed : 13.93 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.09), residues: 8432 helix: 0.65 (0.14), residues: 1299 sheet: -0.02 (0.09), residues: 3579 loop : -1.31 (0.10), residues: 3554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP L 51 HIS 0.012 0.001 HIS O 417 PHE 0.031 0.001 PHE G 278 TYR 0.042 0.001 TYR L 78 ARG 0.009 0.000 ARG H 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 473 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 451 time to evaluate : 5.618 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 outliers start: 22 outliers final: 9 residues processed: 469 average time/residue: 0.6667 time to fit residues: 546.5959 Evaluate side-chains 431 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 422 time to evaluate : 5.745 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.5374 time to fit residues: 17.5497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 758 optimal weight: 0.8980 chunk 500 optimal weight: 5.9990 chunk 805 optimal weight: 9.9990 chunk 491 optimal weight: 3.9990 chunk 382 optimal weight: 8.9990 chunk 559 optimal weight: 3.9990 chunk 844 optimal weight: 20.0000 chunk 777 optimal weight: 0.2980 chunk 672 optimal weight: 9.9990 chunk 69 optimal weight: 30.0000 chunk 519 optimal weight: 0.0000 overall best weight: 1.8388 ------------------------------------------------------------------------------- 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 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN D 234 ASN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 217 GLN I 561 HIS ** J 181 GLN ** 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 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 ASN ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 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 186 GLN ** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1338 moved from start: 0.7929 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= 0.207 Angle : 0.666 14.261 93136 Z= 0.334 Chirality : 0.046 0.364 10816 Planarity : 0.006 0.071 11792 Dihedral : 6.623 59.316 10448 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.52 % Favored : 95.30 % Rotamer: Outliers : 0.40 % Allowed : 14.18 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.09), residues: 8432 helix: 0.63 (0.14), residues: 1274 sheet: -0.05 (0.09), residues: 3553 loop : -1.40 (0.10), residues: 3605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP L 51 HIS 0.011 0.001 HIS H 220 PHE 0.031 0.002 PHE N 278 TYR 0.042 0.002 TYR L 78 ARG 0.008 0.001 ARG K 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 488 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 458 time to evaluate : 5.585 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 outliers start: 30 outliers final: 24 residues processed: 472 average time/residue: 0.6580 time to fit residues: 539.3088 Evaluate side-chains 469 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 445 time to evaluate : 5.594 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.5126 time to fit residues: 31.2145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 412 optimal weight: 5.9990 chunk 534 optimal weight: 0.8980 chunk 716 optimal weight: 0.4980 chunk 206 optimal weight: 9.9990 chunk 620 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 673 optimal weight: 0.6980 chunk 281 optimal weight: 40.0000 chunk 691 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 561 HIS I 134 GLN I 217 GLN ** J 181 GLN ** 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 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 186 GLN ** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 421 GLN ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5624 r_free = 0.5624 target = 0.370874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5596 r_free = 0.5596 target = 0.363328 restraints weight = 112784.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.5593 r_free = 0.5593 target = 0.363017 restraints weight = 115422.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5592 r_free = 0.5592 target = 0.362232 restraints weight = 92501.671| |-----------------------------------------------------------------------------| r_work (final): 0.5592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1660 moved from start: 0.7918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 68624 Z= 0.149 Angle : 0.587 14.223 93136 Z= 0.292 Chirality : 0.044 0.335 10816 Planarity : 0.005 0.064 11792 Dihedral : 6.218 59.676 10448 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.13 % Favored : 96.69 % Rotamer: Outliers : 0.24 % Allowed : 14.26 % Favored : 85.50 % 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: -0.72 (0.09), residues: 8432 helix: 0.73 (0.14), residues: 1283 sheet: 0.01 (0.09), residues: 3355 loop : -1.32 (0.10), residues: 3794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP L 51 HIS 0.005 0.001 HIS K 561 PHE 0.027 0.001 PHE J 525 TYR 0.055 0.001 TYR L 78 ARG 0.007 0.000 ARG D 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11290.27 seconds wall clock time: 203 minutes 1.57 seconds (12181.57 seconds total)