Starting phenix.real_space_refine (version: dev) on Sun Feb 26 04:59:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pc2_13316/02_2023/7pc2_13316.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pc2_13316/02_2023/7pc2_13316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pc2_13316/02_2023/7pc2_13316.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pc2_13316/02_2023/7pc2_13316.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pc2_13316/02_2023/7pc2_13316.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pc2_13316/02_2023/7pc2_13316.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.049 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 Process input model Symmetric amino acids flipped Residue "O ARG 26": "NH1" <-> "NH2" Residue "O PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 31": "NH1" <-> "NH2" Residue "O PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O ARG 58": "NH1" <-> "NH2" Residue "O TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 72": "NH1" <-> "NH2" Residue "O ASP 73": "OD1" <-> "OD2" Residue "O TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 120": "OD1" <-> "OD2" Residue "P ASP 9": "OD1" <-> "OD2" Residue "P GLU 17": "OE1" <-> "OE2" Residue "P TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 81": "OE1" <-> "OE2" Residue "P TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 106": "OE1" <-> "OE2" Residue "M ARG 26": "NH1" <-> "NH2" Residue "M PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 31": "NH1" <-> "NH2" Residue "M PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 57": "OD1" <-> "OD2" Residue "M ARG 58": "NH1" <-> "NH2" Residue "M TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 72": "NH1" <-> "NH2" Residue "M TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 17": "OE1" <-> "OE2" Residue "N TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 106": "OE1" <-> "OE2" Residue "Q ARG 26": "NH1" <-> "NH2" Residue "Q PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 31": "NH1" <-> "NH2" Residue "Q PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 46": "OE1" <-> "OE2" Residue "Q ARG 58": "NH1" <-> "NH2" Residue "Q TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 72": "NH1" <-> "NH2" Residue "Q TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 17": "OE1" <-> "OE2" Residue "R TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 81": "OE1" <-> "OE2" Residue "R TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 32": "OE1" <-> "OE2" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A ASP 113": "OD1" <-> "OD2" Residue "A ASP 141": "OD1" <-> "OD2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A ASP 325": "OD1" <-> "OD2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B ASP 47": "OD1" <-> "OD2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 107": "OD1" <-> "OD2" Residue "B ASP 140": "OD1" <-> "OD2" Residue "B GLU 153": "OE1" <-> "OE2" Residue "B ARG 166": "NH1" <-> "NH2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B GLU 268": "OE1" <-> "OE2" Residue "B ASP 321": "OD1" <-> "OD2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C ASP 141": "OD1" <-> "OD2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 211": "OE1" <-> "OE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 370": "OE1" <-> "OE2" Residue "C GLU 381": "OE1" <-> "OE2" Residue "C PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 589": "OD1" <-> "OD2" Residue "E GLU 648": "OE1" <-> "OE2" Residue "K GLU 23": "OE1" <-> "OE2" Residue "K PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 72": "OD1" <-> "OD2" Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 72": "OD1" <-> "OD2" Residue "G PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 31": "OD1" <-> "OD2" Residue "I PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 72": "OD1" <-> "OD2" Residue "I PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L ASP 82": "OD1" <-> "OD2" Residue "H TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 105": "OD1" <-> "OD2" Residue "J ASP 1": "OD1" <-> "OD2" Residue "J TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 96": "OE1" <-> "OE2" Residue "J ASP 105": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 27063 Number of models: 1 Model: "" Number of chains: 68 Chain: "O" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1031 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "P" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 821 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1031 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "N" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 821 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1031 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "R" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 821 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3499 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "B" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3499 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 4 Chain: "C" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3499 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "D" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "E" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "F" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "K" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "G" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "I" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "L" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "H" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "J" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 9 Chain: "X" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 8 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 11 Chain: "b" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 7 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 8 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 8 Chain: "r" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 11 Chain: "s" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 9 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 9 Chain: "z" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 8 Chain: "0" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "1" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "2" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "3" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 8 Chain: "6" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 11 Chain: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "8" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "9" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 15.11, per 1000 atoms: 0.56 Number of scatterers: 27063 At special positions: 0 Unit cell: (182.75, 173.4, 123.25, 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 156 16.00 O 5670 8.00 N 4398 7.00 C 16839 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 105 " - pdb=" SG CYS O 110 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 105 " - pdb=" SG CYS Q 110 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=1.74 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.36 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.42 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.72 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=1.94 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.94 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.56 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 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 ALPHA1-2 " MAN 5 5 " - " MAN 5 6 " " MAN 5 7 " - " MAN 5 8 " " MAN 6 4 " - " MAN 6 5 " " MAN 6 5 " - " MAN 6 6 " " MAN 6 8 " - " MAN 6 9 " " MAN 6 10 " - " MAN 6 11 " " MAN W 5 " - " MAN W 6 " " MAN W 8 " - " MAN W 9 " " MAN X 4 " - " MAN X 5 " " MAN a 4 " - " MAN a 5 " " MAN a 5 " - " MAN a 6 " " MAN a 8 " - " MAN a 9 " " MAN a 10 " - " MAN a 11 " " MAN b 5 " - " MAN b 6 " " MAN l 4 " - " MAN l 5 " " MAN q 5 " - " MAN q 6 " " MAN q 7 " - " MAN q 8 " " MAN r 4 " - " MAN r 5 " " MAN r 5 " - " MAN r 6 " " MAN r 8 " - " MAN r 9 " " MAN r 10 " - " MAN r 11 " " MAN s 5 " - " MAN s 6 " " MAN s 8 " - " MAN s 9 " " MAN y 5 " - " MAN y 6 " " MAN y 8 " - " MAN y 9 " " MAN z 4 " - " MAN z 5 " ALPHA1-3 " BMA 1 3 " - " MAN 1 4 " " BMA 5 3 " - " MAN 5 7 " " MAN 5 4 " - " MAN 5 5 " " BMA 6 3 " - " MAN 6 4 " " MAN 6 7 " - " MAN 6 8 " " BMA W 3 " - " MAN W 8 " " MAN W 4 " - " MAN W 7 " " BMA X 3 " - " MAN X 4 " " MAN X 6 " - " MAN X 7 " " BMA a 3 " - " MAN a 4 " " MAN a 7 " - " MAN a 8 " " BMA b 3 " - " MAN b 7 " " MAN b 4 " - " MAN b 5 " " BMA e 3 " - " MAN e 4 " " BMA l 3 " - " MAN l 4 " " MAN l 6 " - " MAN l 7 " " BMA n 3 " - " MAN n 4 " " BMA q 3 " - " MAN q 7 " " MAN q 4 " - " MAN q 5 " " BMA r 3 " - " MAN r 4 " " MAN r 7 " - " MAN r 8 " " BMA s 3 " - " MAN s 8 " " MAN s 4 " - " MAN s 7 " " BMA y 3 " - " MAN y 8 " " MAN y 4 " - " MAN y 7 " " BMA z 3 " - " MAN z 4 " " MAN z 6 " - " MAN z 7 " ALPHA1-6 " BMA 1 3 " - " MAN 1 5 " " BMA 5 3 " - " MAN 5 4 " " BMA 6 3 " - " MAN 6 7 " " MAN 6 7 " - " MAN 6 10 " " BMA W 3 " - " MAN W 4 " " MAN W 4 " - " MAN W 5 " " BMA X 3 " - " MAN X 6 " " MAN X 6 " - " MAN X 8 " " BMA a 3 " - " MAN a 7 " " MAN a 7 " - " MAN a 10 " " BMA b 3 " - " MAN b 4 " " BMA e 3 " - " MAN e 5 " " BMA l 3 " - " MAN l 6 " " MAN l 6 " - " MAN l 8 " " BMA n 3 " - " MAN n 5 " " BMA q 3 " - " MAN q 4 " " BMA r 3 " - " MAN r 7 " " MAN r 7 " - " MAN r 10 " " BMA s 3 " - " MAN s 4 " " MAN s 4 " - " MAN s 5 " " BMA y 3 " - " MAN y 4 " " MAN y 4 " - " MAN y 5 " " BMA z 3 " - " MAN z 6 " " MAN z 6 " - " MAN z 8 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 5 2 " - " BMA 5 3 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG 9 1 " - " NAG 9 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " NAG-ASN " NAG 0 1 " - " ASN C 301 " " NAG 1 1 " - " ASN C 363 " " NAG 2 1 " - " ASN C 386 " " NAG 3 1 " - " ASN C 392 " " NAG 4 1 " - " ASN C 448 " " NAG 5 1 " - " ASN C 295 " " NAG 6 1 " - " ASN C 332 " " NAG 7 1 " - " ASN L 72 " " NAG 8 1 " - " ASN H 72 " " NAG 9 1 " - " ASN J 72 " " NAG A 601 " - " ASN A 339 " " NAG A 602 " - " ASN A 355 " " NAG A 603 " - " ASN A 411 " " NAG A 604 " - " ASN A 137 " " NAG A 605 " - " ASN A 234 " " NAG B 601 " - " ASN B 234 " " NAG B 602 " - " ASN B 355 " " NAG B 603 " - " ASN B 339 " " NAG B 604 " - " ASN B 411 " " NAG B 605 " - " ASN B 137 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 339 " " NAG C 604 " - " ASN C 411 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 637 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG S 1 " - " ASN A 88 " " NAG T 1 " - " ASN A 133 " " NAG U 1 " - " ASN A 156 " " NAG V 1 " - " ASN A 160 " " NAG W 1 " - " ASN A 262 " " NAG X 1 " - " ASN A 276 " " NAG Y 1 " - " ASN A 301 " " NAG Z 1 " - " ASN A 448 " " NAG a 1 " - " ASN A 332 " " NAG b 1 " - " ASN A 295 " " NAG c 1 " - " ASN A 392 " " NAG d 1 " - " ASN A 197 " " NAG e 1 " - " ASN A 363 " " NAG f 1 " - " ASN A 386 " " NAG g 1 " - " ASN B 88 " " NAG h 1 " - " ASN B 133 " " NAG i 1 " - " ASN B 156 " " NAG j 1 " - " ASN B 160 " " NAG k 1 " - " ASN B 197 " " NAG l 1 " - " ASN B 276 " " NAG m 1 " - " ASN B 301 " " NAG n 1 " - " ASN B 363 " " NAG o 1 " - " ASN B 386 " " NAG p 1 " - " ASN B 448 " " NAG q 1 " - " ASN B 295 " " NAG r 1 " - " ASN B 332 " " NAG s 1 " - " ASN B 262 " " NAG t 1 " - " ASN B 392 " " NAG u 1 " - " ASN C 88 " " NAG v 1 " - " ASN C 156 " " NAG w 1 " - " ASN C 160 " " NAG x 1 " - " ASN C 197 " " NAG y 1 " - " ASN C 262 " " NAG z 1 " - " ASN C 276 " Time building additional restraints: 14.12 Conformation dependent library (CDL) restraints added in 4.1 seconds 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5700 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 57 sheets defined 15.4% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'O' and resid 111 through 116 removed outlier: 3.568A pdb=" N TYR O 116 " --> pdb=" O TRP O 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.813A pdb=" N PHE P 83 " --> pdb=" O SER P 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 116 removed outlier: 3.548A pdb=" N TYR M 116 " --> pdb=" O TRP M 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.895A pdb=" N PHE N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 116 removed outlier: 3.533A pdb=" N TYR Q 116 " --> pdb=" O TRP Q 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.848A pdb=" N PHE R 83 " --> pdb=" O SER R 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.235A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP A 113 " --> pdb=" O ILE A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.587A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.567A pdb=" N VAL A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.695A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.596A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 115 removed outlier: 4.214A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TRP B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.523A pdb=" N CYS B 126 " --> pdb=" O THR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 352 removed outlier: 3.584A pdb=" N VAL B 346 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.634A pdb=" N THR B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 481 removed outlier: 3.615A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 115 removed outlier: 4.195A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP C 113 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.721A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 351 removed outlier: 3.576A pdb=" N VAL C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.578A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.904A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 596 removed outlier: 3.660A pdb=" N VAL D 580 " --> pdb=" O LEU D 576 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN D 590 " --> pdb=" O TYR D 586 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 592 " --> pdb=" O ARG D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 627 through 634 removed outlier: 3.819A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 648 removed outlier: 3.546A pdb=" N GLY D 644 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 645 " --> pdb=" O ILE D 641 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 662 removed outlier: 3.601A pdb=" N ASN D 656 " --> pdb=" O GLN D 652 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU D 657 " --> pdb=" O GLN D 653 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN D 658 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP D 659 " --> pdb=" O LYS D 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 527 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 543 removed outlier: 4.011A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 596 removed outlier: 3.933A pdb=" N LEU E 576 " --> pdb=" O GLY E 572 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL E 580 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU E 581 " --> pdb=" O GLN E 577 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL E 583 " --> pdb=" O ARG E 579 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP E 589 " --> pdb=" O ARG E 585 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU E 592 " --> pdb=" O ARG E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 624 Processing helix chain 'E' and resid 627 through 634 removed outlier: 3.823A pdb=" N LYS E 633 " --> pdb=" O LEU E 629 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 649 removed outlier: 3.508A pdb=" N GLY E 644 " --> pdb=" O GLN E 640 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU E 645 " --> pdb=" O ILE E 641 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU E 648 " --> pdb=" O GLY E 644 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 662 removed outlier: 3.836A pdb=" N ASN E 656 " --> pdb=" O GLN E 652 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU E 657 " --> pdb=" O GLN E 653 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP E 659 " --> pdb=" O LYS E 655 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 527 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.906A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 removed outlier: 3.970A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU F 581 " --> pdb=" O GLN F 577 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 627 through 634 removed outlier: 3.677A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 648 removed outlier: 3.612A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU F 645 " --> pdb=" O ILE F 641 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 663 removed outlier: 3.612A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU F 657 " --> pdb=" O GLN F 653 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN F 658 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP F 659 " --> pdb=" O LYS F 655 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.687A pdb=" N TYR K 32 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 64 removed outlier: 3.674A pdb=" N GLN K 64 " --> pdb=" O ARG K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.549A pdb=" N ASP G 31 " --> pdb=" O ASN G 28 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR G 32 " --> pdb=" O ILE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'G' and resid 60 through 64 removed outlier: 3.709A pdb=" N GLN G 64 " --> pdb=" O ARG G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.750A pdb=" N TYR I 32 " --> pdb=" O ILE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'O' and resid 58 through 60 removed outlier: 5.065A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 4 through 7 removed outlier: 3.834A pdb=" N SER P 7 " --> pdb=" O SER P 22 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER P 22 " --> pdb=" O SER P 7 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU P 70 " --> pdb=" O SER P 67 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER P 67 " --> pdb=" O GLU P 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 45 through 48 removed outlier: 6.584A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'M' and resid 58 through 60 removed outlier: 5.093A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.849A pdb=" N SER N 7 " --> pdb=" O SER N 22 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER N 22 " --> pdb=" O SER N 7 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER N 67 " --> pdb=" O GLU N 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.523A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASN N 92 " --> pdb=" O ARG N 96 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ARG N 96 " --> pdb=" O ASN N 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.523A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'Q' and resid 58 through 60 removed outlier: 5.157A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 4 through 7 removed outlier: 3.657A pdb=" N SER R 7 " --> pdb=" O SER R 22 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER R 22 " --> pdb=" O SER R 7 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU R 70 " --> pdb=" O SER R 67 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER R 67 " --> pdb=" O GLU R 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.558A pdb=" N LEU R 11 " --> pdb=" O GLU R 106 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.292A pdb=" N VAL D 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N VAL A 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR D 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N TYR A 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N CYS D 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.872A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.668A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AB9, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AC1, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AC2, first strand: chain 'A' and resid 200 through 202 removed outlier: 6.447A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.004A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 376 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.633A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 307 through 308 Processing sheet with id=AC6, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.245A pdb=" N VAL F 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N VAL B 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR F 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N TYR B 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N CYS F 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.881A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.728A pdb=" N VAL B 75 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 91 through 93 Processing sheet with id=AD1, first strand: chain 'B' and resid 130 through 133 Processing sheet with id=AD2, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AD3, first strand: chain 'B' and resid 259 through 261 removed outlier: 5.965A pdb=" N LEU B 260 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLY B 441 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ASN B 300 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS B 330 " --> pdb=" O THR B 297 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 421 " --> pdb=" O PHE B 382 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 376 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 271 through 273 removed outlier: 3.730A pdb=" N SER B 393 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 307 through 308 Processing sheet with id=AD6, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.233A pdb=" N VAL E 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N VAL C 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N THR E 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N TYR C 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N CYS E 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.863A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.730A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AE1, first strand: chain 'C' and resid 154 through 162 Processing sheet with id=AE2, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AE3, first strand: chain 'C' and resid 259 through 261 removed outlier: 5.994A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.609A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 307 through 308 Processing sheet with id=AE6, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AE7, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.518A pdb=" N THR K 110 " --> pdb=" O ALA K 10 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TRP K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.518A pdb=" N THR K 110 " --> pdb=" O ALA K 10 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.567A pdb=" N THR G 110 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.567A pdb=" N THR G 110 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 18 through 24 Processing sheet with id=AF3, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AF4, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.571A pdb=" N THR I 110 " --> pdb=" O ALA I 10 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.571A pdb=" N THR I 110 " --> pdb=" O ALA I 10 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.542A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.771A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.728A pdb=" N VAL H 19 " --> pdb=" O ILE H 75 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 45 through 48 removed outlier: 6.787A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AG2, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.636A pdb=" N ILE J 48 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 10 through 11 799 hydrogen bonds defined for protein. 2007 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: 10.79 Time building geometry restraints manager: 14.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.52: 23853 1.52 - 1.89: 3753 1.89 - 2.25: 0 2.25 - 2.62: 0 2.62 - 2.98: 11 Bond restraints: 27617 Sorted by residual: bond pdb=" C GLY H 27 " pdb=" N TYR H 32 " ideal model delta sigma weight residual 1.330 2.981 -1.651 1.30e-02 5.92e+03 1.61e+04 bond pdb=" C GLY L 27 " pdb=" N TYR L 32 " ideal model delta sigma weight residual 1.330 2.915 -1.585 1.30e-02 5.92e+03 1.49e+04 bond pdb=" C TYR L 91 " pdb=" N GLU L 96 " ideal model delta sigma weight residual 1.332 2.895 -1.563 1.29e-02 6.01e+03 1.47e+04 bond pdb=" C ASP C 141 " pdb=" N MET C 150 " ideal model delta sigma weight residual 1.333 2.930 -1.597 1.36e-02 5.41e+03 1.38e+04 bond pdb=" C GLY J 27 " pdb=" N TYR J 32 " ideal model delta sigma weight residual 1.330 2.925 -1.596 1.38e-02 5.25e+03 1.34e+04 ... (remaining 27612 not shown) Histogram of bond angle deviations from ideal: 39.24 - 60.97: 9 60.97 - 82.69: 2 82.69 - 104.42: 390 104.42 - 126.15: 36540 126.15 - 147.88: 562 Bond angle restraints: 37503 Sorted by residual: angle pdb=" O GLY J 27 " pdb=" C GLY J 27 " pdb=" N TYR J 32 " ideal model delta sigma weight residual 122.60 46.07 76.53 1.07e+00 8.73e-01 5.12e+03 angle pdb=" O GLY H 27 " pdb=" C GLY H 27 " pdb=" N TYR H 32 " ideal model delta sigma weight residual 122.96 41.61 81.35 1.22e+00 6.72e-01 4.45e+03 angle pdb=" O GLY L 27 " pdb=" C GLY L 27 " pdb=" N TYR L 32 " ideal model delta sigma weight residual 122.95 48.05 74.90 1.15e+00 7.56e-01 4.24e+03 angle pdb=" O TYR J 91 " pdb=" C TYR J 91 " pdb=" N GLU J 96 " ideal model delta sigma weight residual 122.59 39.24 83.35 1.33e+00 5.65e-01 3.93e+03 angle pdb=" O TYR H 91 " pdb=" C TYR H 91 " pdb=" N GLU H 96 " ideal model delta sigma weight residual 122.59 45.81 76.78 1.33e+00 5.65e-01 3.33e+03 ... (remaining 37498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.59: 15115 21.59 - 43.19: 1114 43.19 - 64.78: 237 64.78 - 86.38: 48 86.38 - 107.97: 12 Dihedral angle restraints: 16526 sinusoidal: 7638 harmonic: 8888 Sorted by residual: dihedral pdb=" CB CYS B 218 " pdb=" SG CYS B 218 " pdb=" SG CYS B 247 " pdb=" CB CYS B 247 " ideal model delta sinusoidal sigma weight residual 93.00 168.04 -75.04 1 1.00e+01 1.00e-02 7.12e+01 dihedral pdb=" CB CYS Q 105 " pdb=" SG CYS Q 105 " pdb=" SG CYS Q 110 " pdb=" CB CYS Q 110 " ideal model delta sinusoidal sigma weight residual -86.00 -15.12 -70.88 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CB CYS B 54 " pdb=" SG CYS B 54 " pdb=" SG CYS B 74 " pdb=" CB CYS B 74 " ideal model delta sinusoidal sigma weight residual 93.00 22.99 70.01 1 1.00e+01 1.00e-02 6.32e+01 ... (remaining 16523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.172: 4715 0.172 - 0.345: 28 0.345 - 0.517: 5 0.517 - 0.690: 0 0.690 - 0.862: 1 Chirality restraints: 4749 Sorted by residual: chirality pdb=" CA SER H 7 " pdb=" N SER H 7 " pdb=" C SER H 7 " pdb=" CB SER H 7 " both_signs ideal model delta sigma weight residual False 2.51 1.65 0.86 2.00e-01 2.50e+01 1.86e+01 chirality pdb=" C1 NAG A 603 " pdb=" ND2 ASN A 411 " pdb=" C2 NAG A 603 " pdb=" O5 NAG A 603 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" CA SER M 108 " pdb=" N SER M 108 " pdb=" C SER M 108 " pdb=" CB SER M 108 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.85e+00 ... (remaining 4746 not shown) Planarity restraints: 4545 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY H 27 " -0.202 2.00e-02 2.50e+03 2.71e-01 7.35e+02 pdb=" C GLY H 27 " 0.448 2.00e-02 2.50e+03 pdb=" O GLY H 27 " -0.229 2.00e-02 2.50e+03 pdb=" N TYR H 32 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 141 " 0.175 2.00e-02 2.50e+03 2.63e-01 6.89e+02 pdb=" C ASP C 141 " -0.414 2.00e-02 2.50e+03 pdb=" O ASP C 141 " 0.269 2.00e-02 2.50e+03 pdb=" N MET C 150 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR L 91 " 0.169 2.00e-02 2.50e+03 2.50e-01 6.24e+02 pdb=" C TYR L 91 " -0.417 2.00e-02 2.50e+03 pdb=" O TYR L 91 " 0.214 2.00e-02 2.50e+03 pdb=" N GLU L 96 " 0.034 2.00e-02 2.50e+03 ... (remaining 4542 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 120 2.43 - 3.05: 17279 3.05 - 3.66: 35564 3.66 - 4.28: 56675 4.28 - 4.90: 95883 Nonbonded interactions: 205521 Sorted by model distance: nonbonded pdb=" OD1 ASP M 104 " pdb=" N CYS M 105 " model vdw 1.809 2.520 nonbonded pdb=" CA CYS B 218 " pdb=" SG CYS B 247 " model vdw 1.853 3.064 nonbonded pdb=" O SER H 7 " pdb=" OG SER H 7 " model vdw 2.010 2.440 nonbonded pdb=" OD1 ASP M 120 " pdb=" N VAL M 121 " model vdw 2.043 2.520 nonbonded pdb=" O SER Q 108 " pdb=" O6 NAG b 1 " model vdw 2.098 2.440 ... (remaining 205516 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 '0' selection = chain '2' selection = chain '3' selection = chain 'Y' selection = chain 'c' selection = chain 'f' selection = chain 'm' selection = chain 'o' selection = chain 't' selection = chain 'u' } ncs_group { reference = chain '1' selection = chain 'e' selection = chain 'n' } ncs_group { reference = chain '4' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'Z' selection = chain 'd' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'p' selection = chain 'v' selection = chain 'w' selection = chain 'x' } ncs_group { reference = (chain '5' and resid 5 through 8) selection = (chain 'W' and resid 6 through 9) selection = (chain 'X' and resid 5 through 8) selection = (chain 'b' and resid 4 through 7) selection = (chain 'l' and resid 5 through 8) selection = (chain 'q' and resid 5 through 8) selection = (chain 's' and resid 6 through 9) selection = (chain 'y' and resid 6 through 9) selection = (chain 'z' and resid 5 through 8) } ncs_group { reference = chain '6' selection = chain 'a' selection = chain 'r' } ncs_group { reference = (chain 'A' and (resid 32 through 506 or resid 601 through 604)) selection = (chain 'B' and (resid 32 through 506 or resid 601 through 604)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 16839 2.51 5 N 4398 2.21 5 O 5670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.830 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: 0.020 Extract box with map and model: 17.190 Check model and map are aligned: 0.400 Process input model: 73.130 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Set scattering table: 0.220 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0524 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 : 0.033 1.651 27617 Z= 1.889 Angle : 1.531 83.352 37503 Z= 1.124 Chirality : 0.052 0.862 4749 Planarity : 0.013 0.271 4481 Dihedral : 15.165 107.970 10685 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.13), residues: 3009 helix: -4.00 (0.14), residues: 381 sheet: -1.46 (0.15), residues: 1014 loop : -2.94 (0.13), residues: 1614 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 496 time to evaluate : 2.926 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: 40 outliers final: 4 residues processed: 527 average time/residue: 1.3190 time to fit residues: 813.1832 Evaluate side-chains 243 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 239 time to evaluate : 2.874 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 1 average time/residue: 0.4116 time to fit residues: 4.9518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 77 optimal weight: 0.0670 chunk 153 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 235 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 272 optimal weight: 0.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 1 GLN ** O 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN O 74 ASN ** O 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 82 GLN ** O 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 80 HIS ** M 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN N 79 GLN ** N 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN ** Q 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 32 ASN R 92 ASN A 33 ASN A 67 ASN A 99 ASN A 183 GLN A 185 ASN A 249 HIS A 280 ASN A 287 GLN A 289 ASN A 293 GLN A 462 ASN B 33 ASN B 183 GLN B 185 ASN B 293 GLN B 377 ASN B 398 ASN B 432 GLN C 33 ASN C 72 HIS C 185 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 HIS C 280 ASN C 293 GLN ** C 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 ASN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN E 650 GLN ** E 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN F 652 GLN K 3 GLN K 43 GLN G 43 GLN I 6 GLN I 43 GLN L 37 GLN L 79 GLN H 3 GLN H 6 GLN H 34 ASN J 79 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0976 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 27617 Z= 0.258 Angle : 0.767 11.859 37503 Z= 0.407 Chirality : 0.053 1.241 4749 Planarity : 0.005 0.056 4481 Dihedral : 8.108 107.797 5024 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.30 % Favored : 93.67 % Rotamer Outliers : 5.55 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.14), residues: 3031 helix: -2.34 (0.22), residues: 390 sheet: -0.87 (0.16), residues: 1047 loop : -2.47 (0.14), residues: 1594 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 289 time to evaluate : 2.988 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: 149 outliers final: 38 residues processed: 400 average time/residue: 1.0387 time to fit residues: 507.3173 Evaluate side-chains 255 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 217 time to evaluate : 2.684 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 24 residues processed: 14 average time/residue: 0.6710 time to fit residues: 16.2126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 226 optimal weight: 0.9990 chunk 185 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 272 optimal weight: 5.9990 chunk 294 optimal weight: 4.9990 chunk 243 optimal weight: 0.9980 chunk 270 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 218 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 117 GLN M 82 GLN ** M 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 109 HIS A 374 HIS B 99 ASN B 356 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 GLN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 ASN G 62 GLN L 79 GLN J 79 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1321 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.100 27617 Z= 0.246 Angle : 0.713 12.378 37503 Z= 0.374 Chirality : 0.048 0.743 4749 Planarity : 0.005 0.054 4481 Dihedral : 7.893 107.201 5024 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer Outliers : 5.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.81 % 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: -2.03 (0.14), residues: 3031 helix: -1.53 (0.24), residues: 408 sheet: -0.28 (0.16), residues: 963 loop : -2.01 (0.14), residues: 1660 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 259 time to evaluate : 2.922 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: 155 outliers final: 54 residues processed: 373 average time/residue: 1.0626 time to fit residues: 482.4889 Evaluate side-chains 279 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 225 time to evaluate : 2.660 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 38 residues processed: 16 average time/residue: 0.6471 time to fit residues: 17.3349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 2.9990 chunk 205 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 273 optimal weight: 4.9990 chunk 289 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 259 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 1 GLN O 109 HIS M 13 GLN ** M 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS A 422 GLN B 114 GLN B 130 GLN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN C 352 HIS E 575 GLN E 591 GLN E 651 ASN F 543 ASN G 3 GLN I 59 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2030 moved from start: 0.5991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.113 27617 Z= 0.319 Angle : 0.815 18.990 37503 Z= 0.428 Chirality : 0.052 0.676 4749 Planarity : 0.005 0.063 4481 Dihedral : 7.950 107.926 5024 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer Outliers : 6.48 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.82 (0.14), residues: 3031 helix: -1.24 (0.25), residues: 387 sheet: -0.01 (0.16), residues: 957 loop : -1.99 (0.14), residues: 1687 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 301 time to evaluate : 3.062 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 outliers start: 174 outliers final: 78 residues processed: 427 average time/residue: 1.1081 time to fit residues: 577.8277 Evaluate side-chains 315 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 237 time to evaluate : 2.912 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 61 residues processed: 17 average time/residue: 0.4238 time to fit residues: 15.1957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 215 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 247 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 260 optimal weight: 3.9990 chunk 73 optimal weight: 0.0270 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 1 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 117 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN F 543 ASN L 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2323 moved from start: 0.6848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.111 27617 Z= 0.258 Angle : 0.746 16.172 37503 Z= 0.389 Chirality : 0.062 2.663 4749 Planarity : 0.005 0.078 4481 Dihedral : 7.806 104.017 5024 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer Outliers : 5.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.54 (0.14), residues: 3031 helix: -0.93 (0.25), residues: 399 sheet: 0.30 (0.17), residues: 903 loop : -1.85 (0.14), residues: 1729 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 266 time to evaluate : 3.022 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 outliers start: 160 outliers final: 92 residues processed: 386 average time/residue: 0.9921 time to fit residues: 472.4499 Evaluate side-chains 325 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 233 time to evaluate : 2.795 Switching outliers to nearest non-outliers outliers start: 92 outliers final: 69 residues processed: 23 average time/residue: 0.4624 time to fit residues: 19.5585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 170 optimal weight: 0.6980 chunk 71 optimal weight: 0.0070 chunk 290 optimal weight: 0.9980 chunk 240 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 96 optimal weight: 0.0050 chunk 152 optimal weight: 2.9990 overall best weight: 0.5012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 74 ASN ** M 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 74 ASN A 170 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2404 moved from start: 0.7275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 27617 Z= 0.212 Angle : 0.699 15.455 37503 Z= 0.359 Chirality : 0.049 1.304 4749 Planarity : 0.004 0.065 4481 Dihedral : 7.583 103.244 5024 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer Outliers : 5.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.15), residues: 3031 helix: -0.62 (0.26), residues: 399 sheet: 0.41 (0.17), residues: 903 loop : -1.75 (0.14), residues: 1729 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 249 time to evaluate : 2.633 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 outliers start: 143 outliers final: 93 residues processed: 362 average time/residue: 0.9958 time to fit residues: 449.2599 Evaluate side-chains 331 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 238 time to evaluate : 2.955 Switching outliers to nearest non-outliers outliers start: 93 outliers final: 77 residues processed: 16 average time/residue: 0.6480 time to fit residues: 18.2699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 165 optimal weight: 0.0970 chunk 211 optimal weight: 0.2980 chunk 164 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 289 optimal weight: 9.9990 chunk 180 optimal weight: 0.5980 chunk 176 optimal weight: 0.8980 chunk 133 optimal weight: 0.0980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 74 ASN A 170 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2499 moved from start: 0.7622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 27617 Z= 0.202 Angle : 0.680 11.537 37503 Z= 0.349 Chirality : 0.048 1.179 4749 Planarity : 0.005 0.104 4481 Dihedral : 7.421 107.559 5024 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer Outliers : 4.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.15), residues: 3031 helix: -0.22 (0.27), residues: 384 sheet: 0.45 (0.17), residues: 888 loop : -1.57 (0.14), residues: 1759 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 263 time to evaluate : 3.022 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 outliers start: 127 outliers final: 89 residues processed: 358 average time/residue: 0.8859 time to fit residues: 400.8919 Evaluate side-chains 325 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 236 time to evaluate : 2.786 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 75 residues processed: 14 average time/residue: 0.5958 time to fit residues: 15.5333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 56 optimal weight: 0.0870 chunk 183 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 chunk 263 optimal weight: 2.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 1 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 590 GLN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2780 moved from start: 0.8262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 27617 Z= 0.239 Angle : 0.718 13.611 37503 Z= 0.373 Chirality : 0.049 1.092 4749 Planarity : 0.005 0.071 4481 Dihedral : 7.527 108.145 5024 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer Outliers : 4.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.15), residues: 3031 helix: -0.20 (0.27), residues: 390 sheet: 0.50 (0.17), residues: 873 loop : -1.64 (0.14), residues: 1768 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 258 time to evaluate : 3.104 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: 122 outliers final: 86 residues processed: 359 average time/residue: 1.0082 time to fit residues: 450.7936 Evaluate side-chains 318 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 232 time to evaluate : 3.135 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 72 residues processed: 14 average time/residue: 0.6940 time to fit residues: 17.3230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 0.9990 chunk 252 optimal weight: 0.9980 chunk 269 optimal weight: 0.7980 chunk 276 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 211 optimal weight: 0.1980 chunk 82 optimal weight: 0.0980 chunk 243 optimal weight: 0.9980 chunk 254 optimal weight: 0.9980 chunk 268 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2938 moved from start: 0.8775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.171 27617 Z= 0.234 Angle : 0.718 16.265 37503 Z= 0.368 Chirality : 0.049 1.077 4749 Planarity : 0.005 0.065 4481 Dihedral : 7.414 105.843 5024 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 3.91 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.12 (0.15), residues: 3031 helix: -0.16 (0.28), residues: 372 sheet: 0.40 (0.17), residues: 903 loop : -1.56 (0.14), residues: 1756 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 253 time to evaluate : 3.021 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 outliers start: 105 outliers final: 73 residues processed: 340 average time/residue: 0.9849 time to fit residues: 414.9258 Evaluate side-chains 304 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 231 time to evaluate : 3.130 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 65 residues processed: 8 average time/residue: 0.3481 time to fit residues: 8.9579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 0.7980 chunk 284 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 chunk 135 optimal weight: 0.6980 chunk 198 optimal weight: 1.9990 chunk 298 optimal weight: 0.7980 chunk 275 optimal weight: 10.0000 chunk 237 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 145 optimal weight: 0.0010 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN ** G 71AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN H 37 GLN J 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3157 moved from start: 0.9358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 27617 Z= 0.228 Angle : 0.750 15.127 37503 Z= 0.387 Chirality : 0.050 1.048 4749 Planarity : 0.005 0.077 4481 Dihedral : 7.402 106.691 5024 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer Outliers : 3.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.10 (0.15), residues: 3031 helix: -0.32 (0.27), residues: 390 sheet: 0.47 (0.17), residues: 870 loop : -1.51 (0.14), residues: 1771 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 254 time to evaluate : 3.337 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 outliers start: 87 outliers final: 69 residues processed: 326 average time/residue: 0.9789 time to fit residues: 401.3489 Evaluate side-chains 305 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 236 time to evaluate : 2.844 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 60 residues processed: 10 average time/residue: 0.2949 time to fit residues: 9.2153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 0.9990 chunk 253 optimal weight: 6.9990 chunk 72 optimal weight: 0.5980 chunk 219 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 238 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 32 ASN R 79 GLN A 72 HIS A 105 HIS ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 GLN C 374 HIS C 422 GLN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 GLN ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.162528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.142763 restraints weight = 68937.791| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 3.78 r_work: 0.4132 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4347 moved from start: 1.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.219 27617 Z= 0.370 Angle : 0.923 15.481 37503 Z= 0.485 Chirality : 0.059 1.073 4749 Planarity : 0.007 0.204 4481 Dihedral : 7.904 109.277 5024 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.29 % Favored : 92.64 % Rotamer Outliers : 3.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.15), residues: 3031 helix: -0.79 (0.27), residues: 341 sheet: -0.03 (0.17), residues: 909 loop : -1.75 (0.14), residues: 1781 =============================================================================== Job complete usr+sys time: 8768.82 seconds wall clock time: 158 minutes 53.55 seconds (9533.55 seconds total)