Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 19 09:59:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6udj_20739/08_2023/6udj_20739.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6udj_20739/08_2023/6udj_20739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6udj_20739/08_2023/6udj_20739.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6udj_20739/08_2023/6udj_20739.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6udj_20739/08_2023/6udj_20739.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6udj_20739/08_2023/6udj_20739.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 16575 2.51 5 N 4383 2.21 5 O 5499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 16": "OE1" <-> "OE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K ASP 53": "OD1" <-> "OD2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 96": "NH1" <-> "NH2" Residue "K PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 6": "OE1" <-> "OE2" Residue "Q GLU 16": "OE1" <-> "OE2" Residue "Q ASP 72": "OD1" <-> "OD2" Residue "Q TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 96": "NH1" <-> "NH2" Residue "Q PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E ARG 56": "NH1" <-> "NH2" Residue "E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 70": "OD1" <-> "OD2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E ARG 90": "NH1" <-> "NH2" Residue "E PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 1": "OE1" <-> "OE2" Residue "O ARG 18": "NH1" <-> "NH2" Residue "O PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 54": "NH1" <-> "NH2" Residue "O ARG 56": "NH1" <-> "NH2" Residue "O PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 90": "NH1" <-> "NH2" Residue "O PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 105": "OD1" <-> "OD2" Residue "I ASP 17": "OD1" <-> "OD2" Residue "I ARG 18": "NH1" <-> "NH2" Residue "I PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 54": "NH1" <-> "NH2" Residue "I ARG 56": "NH1" <-> "NH2" Residue "I PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 70": "OD1" <-> "OD2" Residue "I ARG 90": "NH1" <-> "NH2" Residue "I PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B ARG 70": "NH1" <-> "NH2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 92": "OD1" <-> "OD2" Residue "B ARG 94": "NH1" <-> "NH2" Residue "D PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 32": "OD1" <-> "OD2" Residue "D TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 56": "NH1" <-> "NH2" Residue "D TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "D ASP 95": "OD1" <-> "OD2" Residue "D TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 9": "NH1" <-> "NH2" Residue "L ARG 20": "NH1" <-> "NH2" Residue "L ASP 53": "OD1" <-> "OD2" Residue "L ARG 70": "NH1" <-> "NH2" Residue "L GLU 83": "OE1" <-> "OE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 92": "OD1" <-> "OD2" Residue "L ARG 94": "NH1" <-> "NH2" Residue "L PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 25": "OD1" <-> "OD2" Residue "N PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 56": "NH1" <-> "NH2" Residue "N TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 66": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N ASP 86": "OD1" <-> "OD2" Residue "N ASP 95": "OD1" <-> "OD2" Residue "N TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 9": "NH1" <-> "NH2" Residue "R ARG 20": "NH1" <-> "NH2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 92": "OD1" <-> "OD2" Residue "R ARG 94": "NH1" <-> "NH2" Residue "R PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 32": "OD1" <-> "OD2" Residue "H PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 56": "NH1" <-> "NH2" Residue "H TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 64": "NH1" <-> "NH2" Residue "H ASP 65": "OD1" <-> "OD2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H ASP 86": "OD1" <-> "OD2" Residue "H ASP 95": "OD1" <-> "OD2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 588": "NH1" <-> "NH2" Residue "C ASP 624": "OD1" <-> "OD2" Residue "C ASP 632": "OD1" <-> "OD2" Residue "C GLU 634": "OE1" <-> "OE2" Residue "C ASP 659": "OD1" <-> "OD2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 49": "OE1" <-> "OE2" Residue "G PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 107": "OD1" <-> "OD2" Residue "G GLU 153": "OE1" <-> "OE2" Residue "G TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 321": "OD1" <-> "OD2" Residue "G ARG 327": "NH1" <-> "NH2" Residue "G GLU 370": "OE1" <-> "OE2" Residue "G PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 456": "NH1" <-> "NH2" Residue "G ARG 469": "NH1" <-> "NH2" Residue "G ASP 474": "OD1" <-> "OD2" Residue "M ARG 588": "NH1" <-> "NH2" Residue "M GLU 621": "OE1" <-> "OE2" Residue "M ASP 632": "OD1" <-> "OD2" Residue "J TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 47": "OD1" <-> "OD2" Residue "J ASP 78": "OD1" <-> "OD2" Residue "J PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 107": "OD1" <-> "OD2" Residue "J GLU 153": "OE1" <-> "OE2" Residue "J TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 268": "OE1" <-> "OE2" Residue "J ARG 327": "NH1" <-> "NH2" Residue "J GLU 370": "OE1" <-> "OE2" Residue "J PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 456": "NH1" <-> "NH2" Residue "J PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 469": "NH1" <-> "NH2" Residue "J ASP 474": "OD1" <-> "OD2" Residue "F ARG 588": "NH1" <-> "NH2" Residue "F ASP 589": "OD1" <-> "OD2" Residue "F ASP 624": "OD1" <-> "OD2" Residue "F ASP 632": "OD1" <-> "OD2" Residue "F GLU 647": "OE1" <-> "OE2" Residue "P TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 47": "OD1" <-> "OD2" Residue "P GLU 49": "OE1" <-> "OE2" Residue "P GLU 92": "OE1" <-> "OE2" Residue "P PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 107": "OD1" <-> "OD2" Residue "P TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 327": "NH1" <-> "NH2" Residue "P GLU 340": "OE1" <-> "OE2" Residue "P GLU 370": "OE1" <-> "OE2" Residue "P PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 412": "OD1" <-> "OD2" Residue "P ARG 456": "NH1" <-> "NH2" Residue "P PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 469": "NH1" <-> "NH2" Residue "P ASP 474": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 26592 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "K" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "Q" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "E" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 820 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 820 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 820 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "D" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1050 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 9, 'TRANS': 120} Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "N" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1050 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 9, 'TRANS': 120} Chain: "R" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "H" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1050 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 9, 'TRANS': 120} Chain: "C" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 982 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "G" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3378 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain breaks: 5 Chain: "M" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 982 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "J" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3378 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain breaks: 5 Chain: "F" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 982 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "P" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3378 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain breaks: 5 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 chiralities: 9 Chain: "T" 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 chiralities: 9 Chain: "U" 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 chiralities: 9 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: 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 chiralities: 5 Chain: "Y" 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: "Z" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "a" 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: "b" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "c" 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: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "e" 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 chiralities: 3 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 Chain: "g" 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 chiralities: 3 Chain: "h" 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 chiralities: 3 Chain: "i" 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 chiralities: 5 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: 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 chiralities: 5 Chain: "m" 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: "n" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "o" 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: "p" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "q" 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: "r" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "s" 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 chiralities: 3 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: 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 chiralities: 3 Chain: "v" 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 chiralities: 3 Chain: "w" 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 chiralities: 5 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: 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: "z" 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 chiralities: 5 Chain: "0" 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: "1" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "2" 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: "3" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "6" 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 chiralities: 3 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: 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 chiralities: 3 Chain: "9" 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 chiralities: 3 Chain: "AA" 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 chiralities: 5 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 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: "M" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 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: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "J" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "P" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Time building chain proxies: 13.04, per 1000 atoms: 0.49 Number of scatterers: 26592 At special positions: 0 Unit cell: (153.265, 150.094, 154.322, 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 135 16.00 O 5499 8.00 N 4383 7.00 C 16575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.05 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.05 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.04 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS G 501 " distance=2.04 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.05 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.05 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.04 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.02 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS M 598 " - pdb=" SG CYS M 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 605 " - pdb=" SG CYS J 501 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.03 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.05 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.04 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 157 " distance=2.03 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.06 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.04 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.03 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS P 501 " distance=2.04 Simple disulfide: pdb=" SG CYS P 54 " - pdb=" SG CYS P 74 " distance=2.03 Simple disulfide: pdb=" SG CYS P 119 " - pdb=" SG CYS P 205 " distance=2.05 Simple disulfide: pdb=" SG CYS P 126 " - pdb=" SG CYS P 196 " distance=2.04 Simple disulfide: pdb=" SG CYS P 131 " - pdb=" SG CYS P 157 " distance=2.03 Simple disulfide: pdb=" SG CYS P 218 " - pdb=" SG CYS P 247 " distance=2.06 Simple disulfide: pdb=" SG CYS P 228 " - pdb=" SG CYS P 239 " distance=2.04 Simple disulfide: pdb=" SG CYS P 296 " - pdb=" SG CYS P 331 " distance=2.03 Simple disulfide: pdb=" SG CYS P 378 " - pdb=" SG CYS P 445 " distance=2.04 Simple disulfide: pdb=" SG CYS P 385 " - pdb=" SG CYS P 418 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " " MAN T 4 " - " MAN T 5 " " MAN T 5 " - " MAN T 6 " " MAN U 4 " - " MAN U 5 " " MAN U 5 " - " MAN U 6 " ALPHA1-3 " BMA 3 3 " - " MAN 3 6 " " MAN 3 4 " - " MAN 3 5 " " BMA S 3 " - " MAN S 4 " " MAN S 7 " - " MAN S 8 " " BMA T 3 " - " MAN T 4 " " MAN T 7 " - " MAN T 8 " " BMA U 3 " - " MAN U 4 " " MAN U 7 " - " MAN U 8 " " BMA X 3 " - " MAN X 4 " " BMA b 3 " - " MAN b 6 " " MAN b 4 " - " MAN b 5 " " BMA i 3 " - " MAN i 4 " " BMA l 3 " - " MAN l 4 " " BMA p 3 " - " MAN p 6 " " MAN p 4 " - " MAN p 5 " " BMA w 3 " - " MAN w 4 " " BMA z 3 " - " MAN z 4 " " BMAAA 3 " - " MANAA 4 " ALPHA1-6 " BMA 1 3 " - " MAN 1 4 " " BMA 3 3 " - " MAN 3 4 " " BMA 5 3 " - " MAN 5 4 " " BMA S 3 " - " MAN S 7 " " MAN S 7 " - " MAN S 9 " " BMA T 3 " - " MAN T 7 " " MAN T 7 " - " MAN T 9 " " BMA U 3 " - " MAN U 7 " " MAN U 7 " - " MAN U 9 " " BMA X 3 " - " MAN X 5 " " BMA Z 3 " - " MAN Z 4 " " BMA b 3 " - " MAN b 4 " " BMA d 3 " - " MAN d 4 " " BMA i 3 " - " MAN i 5 " " BMA l 3 " - " MAN l 5 " " BMA n 3 " - " MAN n 4 " " BMA p 3 " - " MAN p 4 " " BMA r 3 " - " MAN r 4 " " BMA w 3 " - " MAN w 5 " " BMA z 3 " - " MAN z 5 " " BMAAA 3 " - " MANAA 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " 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 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 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 X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " 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 n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " 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 u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " NAG-ASN " NAG 0 1 " - " ASN P 160 " " NAG 1 1 " - " ASN P 197 " " NAG 2 1 " - " ASN P 234 " " NAG 3 1 " - " ASN P 276 " " NAG 4 1 " - " ASN P 295 " " NAG 5 1 " - " ASN P 301 " " NAG 6 1 " - " ASN P 386 " " NAG 7 1 " - " ASN P 392 " " NAG 8 1 " - " ASN P 363 " " NAG 9 1 " - " ASN P 448 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 637 " " NAG C 703 " - " ASN C 618 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 618 " " NAG G 630 " - " ASN G 339 " " NAG G 631 " - " ASN G 355 " " NAG J 630 " - " ASN J 339 " " NAG J 631 " - " ASN J 355 " " NAG M 701 " - " ASN M 611 " " NAG M 702 " - " ASN M 637 " " NAG M 703 " - " ASN M 618 " " NAG P 630 " - " ASN P 339 " " NAG P 631 " - " ASN P 355 " " NAG S 1 " - " ASN G 332 " " NAG T 1 " - " ASN J 332 " " NAG U 1 " - " ASN P 332 " " NAG V 1 " - " ASN G 88 " " NAG W 1 " - " ASN G 133 " " NAG X 1 " - " ASN G 156 " " NAG Y 1 " - " ASN G 160 " " NAG Z 1 " - " ASN G 197 " " NAG a 1 " - " ASN G 234 " " NAG b 1 " - " ASN G 276 " " NAG c 1 " - " ASN G 295 " " NAG d 1 " - " ASN G 301 " " NAG e 1 " - " ASN G 386 " " NAG f 1 " - " ASN G 392 " " NAG g 1 " - " ASN G 363 " " NAG h 1 " - " ASN G 448 " " NAG i 1 " - " ASN G 262 " " NAG j 1 " - " ASN J 88 " " NAG k 1 " - " ASN J 133 " " NAG l 1 " - " ASN J 156 " " NAG m 1 " - " ASN J 160 " " NAG n 1 " - " ASN J 197 " " NAG o 1 " - " ASN J 234 " " NAG p 1 " - " ASN J 276 " " NAG q 1 " - " ASN J 295 " " NAG r 1 " - " ASN J 301 " " NAG s 1 " - " ASN J 386 " " NAG t 1 " - " ASN J 392 " " NAG u 1 " - " ASN J 363 " " NAG v 1 " - " ASN J 448 " " NAG w 1 " - " ASN J 262 " " NAG x 1 " - " ASN P 88 " " NAG y 1 " - " ASN P 133 " " NAG z 1 " - " ASN P 156 " " NAGAA 1 " - " ASN P 262 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.88 Conformation dependent library (CDL) restraints added in 3.6 seconds 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5676 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 63 sheets defined 15.9% alpha, 50.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 61 through 64 removed outlier: 4.098A pdb=" N ASN A 64 " --> pdb=" O PRO A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.951A pdb=" N THR A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 100D through 100H Processing helix chain 'K' and resid 61 through 64 removed outlier: 3.907A pdb=" N ASN K 64 " --> pdb=" O PRO K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 61 through 64' Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.878A pdb=" N THR K 87 " --> pdb=" O PRO K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 100D through 100H Processing helix chain 'Q' and resid 83 through 87 removed outlier: 3.808A pdb=" N THR Q 87 " --> pdb=" O PRO Q 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100D through 100H Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.812A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.953A pdb=" N PHE O 83 " --> pdb=" O PRO O 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.967A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 35C Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.602A pdb=" N SER D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 87 removed outlier: 3.604A pdb=" N SER N 87 " --> pdb=" O PRO N 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 542 removed outlier: 3.651A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 596 removed outlier: 3.915A pdb=" N LYS C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA C 578 " --> pdb=" O LYS C 574 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG C 579 " --> pdb=" O GLN C 575 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL C 580 " --> pdb=" O LEU C 576 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP C 589 " --> pdb=" O ARG C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 624 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 661 removed outlier: 3.532A pdb=" N ILE C 642 " --> pdb=" O TYR C 638 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN C 651 " --> pdb=" O GLU C 647 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 74 Processing helix chain 'G' and resid 98 through 115 removed outlier: 3.693A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 475 through 481 Processing helix chain 'M' and resid 529 through 534 Processing helix chain 'M' and resid 536 through 542 removed outlier: 3.689A pdb=" N GLN M 540 " --> pdb=" O THR M 536 " (cutoff:3.500A) Processing helix chain 'M' and resid 570 through 596 removed outlier: 4.015A pdb=" N LYS M 574 " --> pdb=" O VAL M 570 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA M 578 " --> pdb=" O LYS M 574 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG M 579 " --> pdb=" O GLN M 575 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL M 580 " --> pdb=" O LEU M 576 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP M 589 " --> pdb=" O ARG M 585 " (cutoff:3.500A) Processing helix chain 'M' and resid 618 through 625 Processing helix chain 'M' and resid 627 through 636 Processing helix chain 'M' and resid 638 through 661 Processing helix chain 'J' and resid 70 through 74 Processing helix chain 'J' and resid 98 through 115 removed outlier: 3.675A pdb=" N GLU J 102 " --> pdb=" O ASN J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 354 removed outlier: 3.908A pdb=" N LYS J 351 " --> pdb=" O LYS J 347 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N HIS J 352 " --> pdb=" O GLN J 348 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE J 353 " --> pdb=" O LEU J 349 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 373 Processing helix chain 'J' and resid 475 through 484 removed outlier: 4.130A pdb=" N GLU J 482 " --> pdb=" O ASN J 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 527 removed outlier: 4.438A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.689A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 595 removed outlier: 3.989A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 661 removed outlier: 3.582A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 74 Processing helix chain 'P' and resid 98 through 115 removed outlier: 3.639A pdb=" N GLU P 102 " --> pdb=" O ASN P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 335 through 354 removed outlier: 4.018A pdb=" N LYS P 351 " --> pdb=" O LYS P 347 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N HIS P 352 " --> pdb=" O GLN P 348 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE P 353 " --> pdb=" O LEU P 349 " (cutoff:3.500A) Processing helix chain 'P' and resid 368 through 373 Processing helix chain 'P' and resid 475 through 484 removed outlier: 4.227A pdb=" N GLU P 482 " --> pdb=" O ASN P 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.584A pdb=" N GLN A 77 " --> pdb=" O ASP A 72 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP A 72 " --> pdb=" O GLN A 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.780A pdb=" N GLY A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 12 removed outlier: 7.035A pdb=" N THR A 94 " --> pdb=" O ASP A 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.546A pdb=" N VAL K 12 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.546A pdb=" N VAL K 12 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR K 94 " --> pdb=" O ASP K 101 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Q' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'Q' and resid 11 through 12 removed outlier: 3.728A pdb=" N GLY Q 49 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Q' and resid 11 through 12 removed outlier: 6.966A pdb=" N THR Q 94 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.859A pdb=" N LEU E 33 " --> pdb=" O PHE E 49 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N PHE E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.942A pdb=" N THR E 97 " --> pdb=" O ARG E 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'O' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.826A pdb=" N LEU O 33 " --> pdb=" O PHE O 49 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N PHE O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP O 35 " --> pdb=" O VAL O 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 10 through 13 removed outlier: 4.024A pdb=" N THR O 97 " --> pdb=" O ARG O 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 4 through 5 Processing sheet with id=AB8, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.874A pdb=" N LEU I 33 " --> pdb=" O PHE I 49 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP I 35 " --> pdb=" O VAL I 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.874A pdb=" N THR I 97 " --> pdb=" O ARG I 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 9 through 14 removed outlier: 6.541A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 18 through 22 Processing sheet with id=AC3, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.920A pdb=" N VAL D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N CYS D 92 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY D 106 " --> pdb=" O TYR D 90 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N TYR D 90 " --> pdb=" O GLY D 106 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA D 108 " --> pdb=" O GLY D 88 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY D 88 " --> pdb=" O ALA D 108 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR D 35E" --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL D 50 " --> pdb=" O THR D 35E" (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 9 through 14 removed outlier: 6.555A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 18 through 22 Processing sheet with id=AC7, first strand: chain 'N' and resid 5 through 6 Processing sheet with id=AC8, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.967A pdb=" N TRP N 103 " --> pdb=" O ARG N 94 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ARG N 94 " --> pdb=" O TRP N 103 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLY N 105 " --> pdb=" O CYS N 92 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N CYS N 92 " --> pdb=" O GLY N 105 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR N 35E" --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL N 50 " --> pdb=" O THR N 35E" (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'R' and resid 9 through 14 removed outlier: 6.356A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'R' and resid 18 through 22 Processing sheet with id=AD2, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.963A pdb=" N TRP H 103 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG H 94 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N GLY H 105 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N CYS H 92 " --> pdb=" O GLY H 105 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR H 35E" --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL H 50 " --> pdb=" O THR H 35E" (cutoff:3.500A) removed outlier: 6.702A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 603 through 609 removed outlier: 8.323A pdb=" N CYS C 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N TYR G 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR C 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N VAL G 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N VAL C 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.726A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AD9, first strand: chain 'G' and resid 200 through 203 removed outlier: 6.072A pdb=" N ALA G 200 " --> pdb=" O ALA G 433 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N TYR G 435 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.378A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 393 through 395 removed outlier: 6.388A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLY G 441 " --> pdb=" O ASN G 300 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASN G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.911A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 11.734A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 11.011A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.005A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 271 through 274 removed outlier: 6.768A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 315 through 323 removed outlier: 6.611A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 374 through 378 removed outlier: 3.796A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 11.005A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 11.011A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.734A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 11.911A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASN G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLY G 441 " --> pdb=" O ASN G 300 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 603 through 609 removed outlier: 8.318A pdb=" N CYS M 604 " --> pdb=" O TYR J 40 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N TYR J 40 " --> pdb=" O CYS M 604 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR M 606 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N VAL J 38 " --> pdb=" O THR M 606 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL M 608 " --> pdb=" O VAL J 36 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 45 through 47 removed outlier: 3.639A pdb=" N ILE J 225 " --> pdb=" O VAL J 245 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL J 242 " --> pdb=" O LEU J 86 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 75 through 76 Processing sheet with id=AE9, first strand: chain 'J' and resid 91 through 94 Processing sheet with id=AF1, first strand: chain 'J' and resid 169 through 177 Processing sheet with id=AF2, first strand: chain 'J' and resid 200 through 203 removed outlier: 6.123A pdb=" N ALA J 200 " --> pdb=" O ALA J 433 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TYR J 435 " --> pdb=" O ALA J 200 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR J 202 " --> pdb=" O TYR J 435 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 259 through 261 removed outlier: 3.558A pdb=" N GLY J 451 " --> pdb=" O LEU J 260 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE J 358 " --> pdb=" O GLU J 466 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE J 468 " --> pdb=" O ILE J 358 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ARG J 360 " --> pdb=" O PHE J 468 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 393 through 395 removed outlier: 6.474A pdb=" N ILE J 358 " --> pdb=" O GLU J 466 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE J 468 " --> pdb=" O ILE J 358 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ARG J 360 " --> pdb=" O PHE J 468 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N GLY J 441 " --> pdb=" O ASN J 300 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ASN J 300 " --> pdb=" O GLY J 441 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY J 451 " --> pdb=" O THR J 290 " (cutoff:3.500A) removed outlier: 10.755A pdb=" N THR J 290 " --> pdb=" O GLY J 451 " (cutoff:3.500A) removed outlier: 11.925A pdb=" N ILE J 453 " --> pdb=" O PHE J 288 " (cutoff:3.500A) removed outlier: 11.867A pdb=" N PHE J 288 " --> pdb=" O ILE J 453 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N THR J 455 " --> pdb=" O VAL J 286 " (cutoff:3.500A) removed outlier: 11.041A pdb=" N VAL J 286 " --> pdb=" O THR J 455 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 271 through 274 removed outlier: 6.804A pdb=" N ASN J 301 " --> pdb=" O ILE J 322 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE J 322 " --> pdb=" O ASN J 301 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR J 303 " --> pdb=" O GLY J 321 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN J 315 " --> pdb=" O ILE J 309 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 315 through 323 removed outlier: 6.601A pdb=" N GLN J 315 " --> pdb=" O ILE J 309 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR J 303 " --> pdb=" O GLY J 321 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE J 322 " --> pdb=" O ASN J 301 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN J 301 " --> pdb=" O ILE J 322 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLN J 293 " --> pdb=" O SER J 334 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER J 334 " --> pdb=" O GLN J 293 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE J 382 " --> pdb=" O LYS J 421 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 374 through 378 removed outlier: 4.039A pdb=" N PHE J 382 " --> pdb=" O LYS J 421 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER J 334 " --> pdb=" O GLN J 293 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLN J 293 " --> pdb=" O SER J 334 " (cutoff:3.500A) removed outlier: 11.041A pdb=" N VAL J 286 " --> pdb=" O THR J 455 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N THR J 455 " --> pdb=" O VAL J 286 " (cutoff:3.500A) removed outlier: 11.867A pdb=" N PHE J 288 " --> pdb=" O ILE J 453 " (cutoff:3.500A) removed outlier: 11.925A pdb=" N ILE J 453 " --> pdb=" O PHE J 288 " (cutoff:3.500A) removed outlier: 10.755A pdb=" N THR J 290 " --> pdb=" O GLY J 451 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY J 451 " --> pdb=" O THR J 290 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ASN J 300 " --> pdb=" O GLY J 441 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N GLY J 441 " --> pdb=" O ASN J 300 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY J 451 " --> pdb=" O LEU J 260 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 603 through 609 removed outlier: 5.631A pdb=" N VAL P 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 45 through 47 removed outlier: 4.482A pdb=" N VAL P 242 " --> pdb=" O LEU P 86 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 53 through 55 Processing sheet with id=AG2, first strand: chain 'P' and resid 91 through 94 Processing sheet with id=AG3, first strand: chain 'P' and resid 169 through 177 Processing sheet with id=AG4, first strand: chain 'P' and resid 200 through 203 removed outlier: 6.133A pdb=" N ALA P 200 " --> pdb=" O ALA P 433 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N TYR P 435 " --> pdb=" O ALA P 200 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR P 202 " --> pdb=" O TYR P 435 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'P' and resid 259 through 261 removed outlier: 6.254A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 393 through 395 removed outlier: 5.499A pdb=" N GLY P 441 " --> pdb=" O ASN P 300 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ASN P 300 " --> pdb=" O GLY P 441 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY P 451 " --> pdb=" O THR P 290 " (cutoff:3.500A) removed outlier: 10.723A pdb=" N THR P 290 " --> pdb=" O GLY P 451 " (cutoff:3.500A) removed outlier: 11.896A pdb=" N ILE P 453 " --> pdb=" O PHE P 288 " (cutoff:3.500A) removed outlier: 11.929A pdb=" N PHE P 288 " --> pdb=" O ILE P 453 " (cutoff:3.500A) removed outlier: 10.987A pdb=" N THR P 455 " --> pdb=" O VAL P 286 " (cutoff:3.500A) removed outlier: 11.107A pdb=" N VAL P 286 " --> pdb=" O THR P 455 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 271 through 274 removed outlier: 6.770A pdb=" N ASN P 301 " --> pdb=" O ILE P 322 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE P 322 " --> pdb=" O ASN P 301 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N THR P 303 " --> pdb=" O GLY P 321 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN P 315 " --> pdb=" O ILE P 309 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'P' and resid 315 through 323 removed outlier: 6.601A pdb=" N GLN P 315 " --> pdb=" O ILE P 309 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N THR P 303 " --> pdb=" O GLY P 321 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE P 322 " --> pdb=" O ASN P 301 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN P 301 " --> pdb=" O ILE P 322 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN P 293 " --> pdb=" O SER P 334 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER P 334 " --> pdb=" O GLN P 293 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA P 329 " --> pdb=" O CYS P 418 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE P 382 " --> pdb=" O LYS P 421 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'P' and resid 374 through 378 removed outlier: 4.067A pdb=" N PHE P 382 " --> pdb=" O LYS P 421 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA P 329 " --> pdb=" O CYS P 418 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER P 334 " --> pdb=" O GLN P 293 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN P 293 " --> pdb=" O SER P 334 " (cutoff:3.500A) removed outlier: 11.107A pdb=" N VAL P 286 " --> pdb=" O THR P 455 " (cutoff:3.500A) removed outlier: 10.987A pdb=" N THR P 455 " --> pdb=" O VAL P 286 " (cutoff:3.500A) removed outlier: 11.929A pdb=" N PHE P 288 " --> pdb=" O ILE P 453 " (cutoff:3.500A) removed outlier: 11.896A pdb=" N ILE P 453 " --> pdb=" O PHE P 288 " (cutoff:3.500A) removed outlier: 10.723A pdb=" N THR P 290 " --> pdb=" O GLY P 451 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY P 451 " --> pdb=" O THR P 290 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ASN P 300 " --> pdb=" O GLY P 441 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLY P 441 " --> pdb=" O ASN P 300 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) 1090 hydrogen bonds defined for protein. 2844 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: 10.62 Time building geometry restraints manager: 13.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 6727 1.33 - 1.46: 8608 1.46 - 1.60: 11584 1.60 - 1.73: 1 1.73 - 1.86: 179 Bond restraints: 27099 Sorted by residual: bond pdb=" C ALA G 204 " pdb=" N CYS G 205 " ideal model delta sigma weight residual 1.331 1.210 0.121 1.63e-02 3.76e+03 5.51e+01 bond pdb=" C ALA J 204 " pdb=" N CYS J 205 " ideal model delta sigma weight residual 1.328 1.232 0.095 1.67e-02 3.59e+03 3.27e+01 bond pdb=" CG1 ILE P 443 " pdb=" CD1 ILE P 443 " ideal model delta sigma weight residual 1.513 1.387 0.126 3.90e-02 6.57e+02 1.04e+01 bond pdb=" C TRP P 427 " pdb=" O TRP P 427 " ideal model delta sigma weight residual 1.235 1.195 0.040 1.34e-02 5.57e+03 9.03e+00 bond pdb=" C TRP J 427 " pdb=" O TRP J 427 " ideal model delta sigma weight residual 1.235 1.195 0.040 1.34e-02 5.57e+03 8.83e+00 ... (remaining 27094 not shown) Histogram of bond angle deviations from ideal: 98.24 - 105.48: 490 105.48 - 112.71: 14982 112.71 - 119.95: 9304 119.95 - 127.18: 11608 127.18 - 134.42: 402 Bond angle restraints: 36786 Sorted by residual: angle pdb=" C ARG N 100 " pdb=" N ALA N 100A" pdb=" CA ALA N 100A" ideal model delta sigma weight residual 120.06 128.21 -8.15 1.19e+00 7.06e-01 4.69e+01 angle pdb=" C GLY I 50 " pdb=" N THR I 51 " pdb=" CA THR I 51 " ideal model delta sigma weight residual 121.54 133.93 -12.39 1.91e+00 2.74e-01 4.21e+01 angle pdb=" C TRP J 427 " pdb=" N GLN J 428 " pdb=" CA GLN J 428 " ideal model delta sigma weight residual 122.07 131.11 -9.04 1.43e+00 4.89e-01 3.99e+01 angle pdb=" C ARG H 100 " pdb=" N ALA H 100A" pdb=" CA ALA H 100A" ideal model delta sigma weight residual 120.09 127.89 -7.80 1.25e+00 6.40e-01 3.90e+01 angle pdb=" C ARG D 100 " pdb=" N ALA D 100A" pdb=" CA ALA D 100A" ideal model delta sigma weight residual 120.09 127.41 -7.32 1.25e+00 6.40e-01 3.43e+01 ... (remaining 36781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 13350 17.42 - 34.84: 1148 34.84 - 52.26: 216 52.26 - 69.68: 58 69.68 - 87.10: 27 Dihedral angle restraints: 14799 sinusoidal: 5949 harmonic: 8850 Sorted by residual: dihedral pdb=" CB CYS G 378 " pdb=" SG CYS G 378 " pdb=" SG CYS G 445 " pdb=" CB CYS G 445 " ideal model delta sinusoidal sigma weight residual -86.00 -165.14 79.14 1 1.00e+01 1.00e-02 7.79e+01 dihedral pdb=" CA GLN E 27 " pdb=" C GLN E 27 " pdb=" N GLY E 27A" pdb=" CA GLY E 27A" ideal model delta harmonic sigma weight residual 180.00 137.33 42.67 0 5.00e+00 4.00e-02 7.28e+01 dihedral pdb=" CA GLN I 27 " pdb=" C GLN I 27 " pdb=" N GLY I 27A" pdb=" CA GLY I 27A" ideal model delta harmonic sigma weight residual 180.00 137.45 42.55 0 5.00e+00 4.00e-02 7.24e+01 ... (remaining 14796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3291 0.068 - 0.136: 1074 0.136 - 0.205: 171 0.205 - 0.273: 32 0.273 - 0.341: 22 Chirality restraints: 4590 Sorted by residual: chirality pdb=" CB THR J 123 " pdb=" CA THR J 123 " pdb=" OG1 THR J 123 " pdb=" CG2 THR J 123 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" C5 BMA w 3 " pdb=" C4 BMA w 3 " pdb=" C6 BMA w 3 " pdb=" O5 BMA w 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" C5 BMA i 3 " pdb=" C4 BMA i 3 " pdb=" C6 BMA i 3 " pdb=" O5 BMA i 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 4587 not shown) Planarity restraints: 4494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR O 51 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C THR O 51 " -0.056 2.00e-02 2.50e+03 pdb=" O THR O 51 " 0.021 2.00e-02 2.50e+03 pdb=" N SER O 52 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 51 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C THR E 51 " -0.056 2.00e-02 2.50e+03 pdb=" O THR E 51 " 0.021 2.00e-02 2.50e+03 pdb=" N SER E 52 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY G 312 " 0.051 5.00e-02 4.00e+02 7.74e-02 9.59e+00 pdb=" N PRO G 313 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO G 313 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO G 313 " 0.043 5.00e-02 4.00e+02 ... (remaining 4491 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5354 2.78 - 3.31: 21843 3.31 - 3.84: 45892 3.84 - 4.37: 54480 4.37 - 4.90: 90530 Nonbonded interactions: 218099 Sorted by model distance: nonbonded pdb=" O ASN J 355 " pdb=" OG SER J 397 " model vdw 2.252 2.440 nonbonded pdb=" O LYS J 421 " pdb=" O HOH J 701 " model vdw 2.262 2.440 nonbonded pdb=" O LYS G 421 " pdb=" O HOH G 701 " model vdw 2.274 2.440 nonbonded pdb=" O ASN G 355 " pdb=" OG SER G 397 " model vdw 2.286 2.440 nonbonded pdb=" NE2 GLN H 6 " pdb=" O GLY H 104 " model vdw 2.297 2.520 ... (remaining 218094 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 '4' selection = chain '7' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'c' selection = chain 'f' selection = chain 'j' selection = chain 'k' selection = chain 'm' selection = chain 'o' selection = chain 'q' selection = chain 't' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain '1' selection = chain '5' selection = chain 'Z' selection = chain 'd' selection = chain 'n' selection = chain 'r' } ncs_group { reference = chain '3' selection = chain 'b' selection = chain 'p' } ncs_group { reference = chain '6' selection = chain '8' selection = chain '9' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 's' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain 'A' selection = chain 'K' selection = chain 'Q' } ncs_group { reference = chain 'AA' selection = chain 'X' selection = chain 'i' selection = chain 'l' selection = chain 'w' selection = chain 'z' } ncs_group { reference = chain 'B' selection = chain 'L' selection = chain 'R' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'O' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'P' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 7.820 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 69.240 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.580 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 : 0.010 0.126 27099 Z= 0.654 Angle : 1.156 12.480 36786 Z= 0.588 Chirality : 0.069 0.341 4590 Planarity : 0.007 0.077 4434 Dihedral : 13.984 87.104 8988 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.11 % Favored : 95.83 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.93 (0.13), residues: 3018 helix: -2.30 (0.18), residues: 429 sheet: -0.64 (0.15), residues: 975 loop : -1.35 (0.14), residues: 1614 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 491 time to evaluate : 2.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 500 average time/residue: 1.5280 time to fit residues: 876.1695 Evaluate side-chains 401 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 397 time to evaluate : 2.624 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 3.5545 ------------------------------------------------------------------------------- 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: 10.0000 chunk 227 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 235 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 272 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 82AASN K 82AASN K 99 GLN B 37 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 66CASN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66CASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN C 591 GLN C 652 GLN G 114 GLN G 183 GLN G 185 ASN G 280 ASN G 356 ASN G 377 ASN G 411 ASN G 422 GLN M 575 GLN M 607 ASN J 85 HIS J 103 GLN J 183 GLN J 185 ASN J 280 ASN J 356 ASN J 377 ASN J 411 ASN J 422 GLN F 577 GLN F 630 GLN P 411 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 27099 Z= 0.180 Angle : 0.631 8.909 36786 Z= 0.322 Chirality : 0.044 0.187 4590 Planarity : 0.005 0.058 4434 Dihedral : 5.758 34.836 3363 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.14), residues: 3018 helix: -0.28 (0.25), residues: 429 sheet: -0.30 (0.16), residues: 975 loop : -0.90 (0.15), residues: 1614 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 438 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 29 residues processed: 477 average time/residue: 1.4708 time to fit residues: 812.4832 Evaluate side-chains 430 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 401 time to evaluate : 3.035 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 16 residues processed: 13 average time/residue: 0.4821 time to fit residues: 12.7630 ------------------------------------------------------------------------------- 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: 7.9990 chunk 84 optimal weight: 0.0570 chunk 226 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 272 optimal weight: 6.9990 chunk 294 optimal weight: 5.9990 chunk 243 optimal weight: 7.9990 chunk 270 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 218 optimal weight: 1.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 99 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN C 652 GLN G 293 GLN M 543 ASN M 607 ASN M 630 GLN J 356 ASN J 377 ASN J 411 ASN F 575 GLN F 577 GLN F 630 GLN P 183 GLN P 280 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 27099 Z= 0.345 Angle : 0.732 9.930 36786 Z= 0.366 Chirality : 0.048 0.232 4590 Planarity : 0.005 0.062 4434 Dihedral : 5.863 34.157 3363 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 3.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.15), residues: 3018 helix: 0.16 (0.26), residues: 429 sheet: -0.19 (0.16), residues: 975 loop : -0.75 (0.15), residues: 1614 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 391 time to evaluate : 3.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 65 residues processed: 461 average time/residue: 1.4511 time to fit residues: 774.3720 Evaluate side-chains 468 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 403 time to evaluate : 3.114 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 39 residues processed: 26 average time/residue: 0.5590 time to fit residues: 24.4838 ------------------------------------------------------------------------------- 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: 5.9990 chunk 205 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 183 optimal weight: 0.4980 chunk 273 optimal weight: 2.9990 chunk 289 optimal weight: 0.7980 chunk 143 optimal weight: 0.9980 chunk 259 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 99 GLN Q 99 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN C 575 GLN C 577 GLN G 183 GLN G 293 GLN G 411 ASN M 607 ASN M 630 GLN J 356 ASN F 630 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 27099 Z= 0.167 Angle : 0.600 9.519 36786 Z= 0.303 Chirality : 0.043 0.172 4590 Planarity : 0.004 0.053 4434 Dihedral : 5.299 31.419 3363 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.39 (0.15), residues: 3018 helix: 0.52 (0.26), residues: 429 sheet: -0.00 (0.16), residues: 969 loop : -0.57 (0.15), residues: 1620 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 421 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 51 residues processed: 483 average time/residue: 1.3857 time to fit residues: 780.1186 Evaluate side-chains 442 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 391 time to evaluate : 3.138 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 42 residues processed: 10 average time/residue: 0.4640 time to fit residues: 10.9905 ------------------------------------------------------------------------------- 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: 2.9990 chunk 164 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 247 optimal weight: 10.0000 chunk 200 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 148 optimal weight: 0.7980 chunk 260 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN K 99 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 ASN G 183 GLN G 377 ASN M 607 ASN M 630 GLN ** M 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 GLN J 356 ASN P 293 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 27099 Z= 0.208 Angle : 0.628 10.158 36786 Z= 0.314 Chirality : 0.044 0.189 4590 Planarity : 0.004 0.050 4434 Dihedral : 5.242 31.359 3363 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 3.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.22 (0.15), residues: 3018 helix: 0.74 (0.27), residues: 420 sheet: 0.10 (0.16), residues: 969 loop : -0.47 (0.15), residues: 1629 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 400 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 60 residues processed: 469 average time/residue: 1.4055 time to fit residues: 770.9071 Evaluate side-chains 461 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 401 time to evaluate : 2.935 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 45 residues processed: 15 average time/residue: 0.3750 time to fit residues: 12.9522 ------------------------------------------------------------------------------- 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: 10.0000 chunk 261 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 170 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 290 optimal weight: 3.9990 chunk 240 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66CASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 ASN C 652 GLN G 85 HIS M 575 GLN M 607 ASN M 630 GLN M 653 GLN ** J 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 356 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.104 27099 Z= 0.360 Angle : 0.733 13.252 36786 Z= 0.363 Chirality : 0.048 0.252 4590 Planarity : 0.005 0.053 4434 Dihedral : 5.604 33.484 3363 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 3.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.35 (0.15), residues: 3018 helix: 0.45 (0.26), residues: 429 sheet: 0.10 (0.16), residues: 975 loop : -0.56 (0.15), residues: 1614 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 401 time to evaluate : 2.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 66 residues processed: 468 average time/residue: 1.4333 time to fit residues: 778.7107 Evaluate side-chains 467 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 401 time to evaluate : 2.819 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 46 residues processed: 20 average time/residue: 0.2734 time to fit residues: 13.6306 ------------------------------------------------------------------------------- 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: 4.9990 chunk 32 optimal weight: 20.0000 chunk 165 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 289 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN C 577 GLN C 652 GLN G 377 ASN M 575 GLN M 607 ASN M 630 GLN J 356 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 27099 Z= 0.305 Angle : 0.699 10.334 36786 Z= 0.347 Chirality : 0.047 0.228 4590 Planarity : 0.005 0.052 4434 Dihedral : 5.530 33.950 3363 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 3.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.25 (0.15), residues: 3018 helix: 0.61 (0.26), residues: 420 sheet: 0.19 (0.16), residues: 969 loop : -0.54 (0.15), residues: 1629 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 403 time to evaluate : 2.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 63 residues processed: 471 average time/residue: 1.4340 time to fit residues: 784.2626 Evaluate side-chains 468 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 405 time to evaluate : 2.871 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 49 residues processed: 14 average time/residue: 0.4080 time to fit residues: 12.5512 ------------------------------------------------------------------------------- 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: 0.9990 chunk 115 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 196 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 26 optimal weight: 30.0000 chunk 227 optimal weight: 5.9990 chunk 263 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN C 575 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 GLN G 377 ASN M 575 GLN M 607 ASN M 630 GLN J 356 ASN F 630 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 27099 Z= 0.217 Angle : 0.638 11.763 36786 Z= 0.319 Chirality : 0.044 0.199 4590 Planarity : 0.004 0.051 4434 Dihedral : 5.294 33.449 3363 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 3.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.12 (0.15), residues: 3018 helix: 0.76 (0.27), residues: 420 sheet: 0.25 (0.16), residues: 963 loop : -0.45 (0.15), residues: 1635 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 403 time to evaluate : 2.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 60 residues processed: 463 average time/residue: 1.4236 time to fit residues: 767.6830 Evaluate side-chains 457 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 397 time to evaluate : 2.810 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 47 residues processed: 13 average time/residue: 0.6097 time to fit residues: 14.5603 ------------------------------------------------------------------------------- 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: 3.9990 chunk 269 optimal weight: 0.9990 chunk 276 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 211 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 243 optimal weight: 4.9990 chunk 254 optimal weight: 6.9990 chunk 268 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 ASN G 377 ASN M 575 GLN M 607 ASN M 630 GLN J 356 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 27099 Z= 0.179 Angle : 0.608 12.250 36786 Z= 0.305 Chirality : 0.043 0.188 4590 Planarity : 0.004 0.065 4434 Dihedral : 5.085 31.864 3363 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.03 (0.15), residues: 3018 helix: 0.69 (0.27), residues: 429 sheet: 0.35 (0.16), residues: 969 loop : -0.38 (0.15), residues: 1620 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 402 time to evaluate : 3.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 54 residues processed: 457 average time/residue: 1.4166 time to fit residues: 755.6675 Evaluate side-chains 445 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 391 time to evaluate : 2.683 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 48 residues processed: 6 average time/residue: 0.2962 time to fit residues: 6.6560 ------------------------------------------------------------------------------- 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: 7.9990 chunk 284 optimal weight: 7.9990 chunk 173 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 198 optimal weight: 0.5980 chunk 298 optimal weight: 2.9990 chunk 275 optimal weight: 7.9990 chunk 237 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN D 83 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 ASN G 356 ASN M 575 GLN M 607 ASN M 630 GLN J 356 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.075 27099 Z= 0.376 Angle : 0.746 10.366 36786 Z= 0.370 Chirality : 0.049 0.254 4590 Planarity : 0.005 0.059 4434 Dihedral : 5.532 33.276 3363 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.17 (0.15), residues: 3018 helix: 0.59 (0.27), residues: 420 sheet: 0.27 (0.16), residues: 969 loop : -0.48 (0.15), residues: 1629 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 398 time to evaluate : 2.817 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 59 residues processed: 452 average time/residue: 1.4532 time to fit residues: 760.4731 Evaluate side-chains 446 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 387 time to evaluate : 2.924 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 48 residues processed: 11 average time/residue: 0.4488 time to fit residues: 11.5178 ------------------------------------------------------------------------------- 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: 4.9990 chunk 253 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 238 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 244 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 ASN G 356 ASN G 377 ASN M 607 ASN M 630 GLN J 356 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.156179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.105721 restraints weight = 27333.408| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.10 r_work: 0.2987 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 27099 Z= 0.232 Angle : 0.655 11.564 36786 Z= 0.328 Chirality : 0.045 0.203 4590 Planarity : 0.004 0.062 4434 Dihedral : 5.315 33.887 3363 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.07 (0.15), residues: 3018 helix: 0.71 (0.27), residues: 417 sheet: 0.34 (0.16), residues: 969 loop : -0.43 (0.15), residues: 1632 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11491.34 seconds wall clock time: 204 minutes 28.52 seconds (12268.52 seconds total)