Starting phenix.real_space_refine on Fri Dec 15 19:10:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osy_20189/12_2023/6osy_20189.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osy_20189/12_2023/6osy_20189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osy_20189/12_2023/6osy_20189.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osy_20189/12_2023/6osy_20189.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osy_20189/12_2023/6osy_20189.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osy_20189/12_2023/6osy_20189.pdb" } resolution = 4.3 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= 0.006 sd= 0.138 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 174 5.16 5 C 20328 2.51 5 N 5316 2.21 5 O 6645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 GLU 32": "OE1" <-> "OE2" Residue "2 GLU 91": "OE1" <-> "OE2" Residue "2 PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 167": "OD1" <-> "OD2" Residue "2 TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 321": "OD1" <-> "OD2" Residue "2 ASP 325": "OD1" <-> "OD2" Residue "2 PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 370": "OE1" <-> "OE2" Residue "2 PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 60": "OD1" <-> "OD2" Residue "6 ASP 82": "OD1" <-> "OD2" Residue "6 ASP 85": "OD1" <-> "OD2" Residue "6 GLU 100": "OE1" <-> "OE2" Residue "7 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 52": "NH1" <-> "NH2" Residue "7 ASP 69": "OD1" <-> "OD2" Residue "7 TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 42": "OD1" <-> "OD2" Residue "8 ARG 61": "NH1" <-> "NH2" Residue "8 ASP 76": "OD1" <-> "OD2" Residue "8 TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 589": "OD1" <-> "OD2" Residue "A ASP 659": "OD1" <-> "OD2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 167": "OD1" <-> "OD2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 321": "OD1" <-> "OD2" Residue "B ASP 325": "OD1" <-> "OD2" Residue "B PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 82": "OD1" <-> "OD2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "E TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 49": "OD1" <-> "OD2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ASP 69": "OD1" <-> "OD2" Residue "E TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 42": "OD1" <-> "OD2" Residue "F ARG 61": "NH1" <-> "NH2" Residue "F ASP 76": "OD1" <-> "OD2" Residue "F TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 589": "OD1" <-> "OD2" Residue "G ASP 659": "OD1" <-> "OD2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H ARG 41": "NH1" <-> "NH2" Residue "H TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H ASP 86": "OD1" <-> "OD2" Residue "H ARG 94": "NH1" <-> "NH2" Residue "H ARG 96": "NH1" <-> "NH2" Residue "I PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 38": "NH1" <-> "NH2" Residue "I ARG 41": "NH1" <-> "NH2" Residue "I TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 66": "NH1" <-> "NH2" Residue "I ARG 71": "NH1" <-> "NH2" Residue "I ASP 72": "OD1" <-> "OD2" Residue "I ARG 94": "NH1" <-> "NH2" Residue "I ARG 96": "NH1" <-> "NH2" Residue "J ARG 24": "NH1" <-> "NH2" Residue "J ASP 28": "OD1" <-> "OD2" Residue "J ARG 46": "NH1" <-> "NH2" Residue "J GLU 55": "OE1" <-> "OE2" Residue "J ARG 61": "NH1" <-> "NH2" Residue "J GLU 70": "OE1" <-> "OE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 32": "OE1" <-> "OE2" Residue "K GLU 91": "OE1" <-> "OE2" Residue "K PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 167": "OD1" <-> "OD2" Residue "K TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 321": "OD1" <-> "OD2" Residue "K ASP 325": "OD1" <-> "OD2" Residue "K PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 474": "OD1" <-> "OD2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L ASP 28": "OD1" <-> "OD2" Residue "L ARG 46": "NH1" <-> "NH2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 60": "OD1" <-> "OD2" Residue "O TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 52": "NH1" <-> "NH2" Residue "O ASP 69": "OD1" <-> "OD2" Residue "O TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ASP 76": "OD1" <-> "OD2" Residue "P TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 81": "OE1" <-> "OE2" Residue "P PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 659": "OD1" <-> "OD2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 38": "NH1" <-> "NH2" Residue "R ARG 41": "NH1" <-> "NH2" Residue "R TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 66": "NH1" <-> "NH2" Residue "R ARG 71": "NH1" <-> "NH2" Residue "R ASP 72": "OD1" <-> "OD2" Residue "R ARG 94": "NH1" <-> "NH2" Residue "R ARG 96": "NH1" <-> "NH2" Residue "S ARG 24": "NH1" <-> "NH2" Residue "S ASP 28": "OD1" <-> "OD2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S GLU 55": "OE1" <-> "OE2" Residue "S ARG 61": "NH1" <-> "NH2" Residue "S GLU 70": "OE1" <-> "OE2" Residue "S GLU 81": "OE1" <-> "OE2" Residue "S ASP 82": "OD1" <-> "OD2" Residue "S PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 32463 Number of models: 1 Model: "" Number of chains: 78 Chain: "2" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "5" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "6" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "7" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "8" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "B" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "C" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "D" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "F" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "G" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "H" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "I" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "J" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 802 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 98} Chain: "K" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 802 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 98} Chain: "M" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "O" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "P" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "Q" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "R" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "S" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 802 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 98} Chain: "T" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 4 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Y" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 6 Chain: "b" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 5 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 9 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "j" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 4 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "m" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 5 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "o" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 4 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 6 Chain: "r" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 5 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 4 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 4 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "3" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 5 Chain: "4" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "9" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "AA" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "BA" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 6 Chain: "CA" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "DA" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "EA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "FA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 5 Chain: "GA" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "HA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 9 Chain: "IA" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "JA" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "2" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 16.98, per 1000 atoms: 0.52 Number of scatterers: 32463 At special positions: 0 Unit cell: (157.768, 157.768, 154.548, 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 174 16.00 O 6645 8.00 N 5316 7.00 C 20328 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS 2 54 " - pdb=" SG CYS 2 74 " distance=2.04 Simple disulfide: pdb=" SG CYS 2 119 " - pdb=" SG CYS 2 205 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 126 " - pdb=" SG CYS 2 196 " distance=2.01 Simple disulfide: pdb=" SG CYS 2 131 " - pdb=" SG CYS 2 157 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 201 " - pdb=" SG CYS 2 433 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 218 " - pdb=" SG CYS 2 247 " distance=2.04 Simple disulfide: pdb=" SG CYS 2 228 " - pdb=" SG CYS 2 239 " distance=2.05 Simple disulfide: pdb=" SG CYS 2 296 " - pdb=" SG CYS 2 331 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 378 " - pdb=" SG CYS 2 445 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 385 " - pdb=" SG CYS 2 418 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 22 " - pdb=" SG CYS 5 92 " distance=2.02 Simple disulfide: pdb=" SG CYS 6 23 " - pdb=" SG CYS 6 88 " distance=2.03 Simple disulfide: pdb=" SG CYS 8 22 " - pdb=" SG CYS 8 92 " distance=2.02 Simple disulfide: pdb=" SG CYS 8 98 " - pdb=" SG CYS 8 100A" distance=2.02 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.01 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.04 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.02 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.01 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 433 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.04 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.05 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.02 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 98 " - pdb=" SG CYS F 100A" distance=2.02 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.04 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.02 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.01 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.03 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.05 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.02 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.02 Simple disulfide: pdb=" SG CYS P 98 " - pdb=" SG CYS P 100A" distance=2.02 Simple disulfide: pdb=" SG CYS Q 598 " - pdb=" SG CYS Q 604 " distance=2.01 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 92 " distance=2.04 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN a 4 " - " MAN a 5 " " MAN g 4 " - " MAN g 5 " " MAN g 5 " - " MAN g 6 " " MAN q 4 " - " MAN q 5 " " MAN w 4 " - " MAN w 5 " " MAN w 5 " - " MAN w 6 " " MANBA 4 " - " MANBA 5 " " MANHA 4 " - " MANHA 5 " " MANHA 5 " - " MANHA 6 " ALPHA1-3 " BMA 1 3 " - " MAN 1 4 " " BMA 3 3 " - " MAN 3 4 " " BMA T 3 " - " MAN T 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA a 3 " - " MAN a 4 " " BMA e 3 " - " MAN e 4 " " BMA g 3 " - " MAN g 4 " " MAN g 7 " - " MAN g 8 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 4 " " BMA l 3 " - " MAN l 4 " " BMA m 3 " - " MAN m 4 " " BMA q 3 " - " MAN q 4 " " BMA u 3 " - " MAN u 4 " " BMA w 3 " - " MAN w 4 " " MAN w 7 " - " MAN w 8 " " BMA y 3 " - " MAN y 4 " " BMA z 3 " - " MAN z 4 " " BMABA 3 " - " MANBA 4 " " BMAFA 3 " - " MANFA 4 " " BMAHA 3 " - " MANHA 4 " " MANHA 7 " - " MANHA 8 " " BMAJA 3 " - " MANJA 4 " ALPHA1-6 " BMA 3 3 " - " MAN 3 5 " " BMA 9 3 " - " MAN 9 4 " " BMA W 3 " - " MAN W 5 " " BMA Y 3 " - " MAN Y 4 " " BMA a 3 " - " MAN a 6 " " BMA e 3 " - " MAN e 5 " " BMA g 3 " - " MAN g 7 " " MAN g 7 " - " MAN g 9 " " BMA m 3 " - " MAN m 5 " " BMA o 3 " - " MAN o 4 " " BMA q 3 " - " MAN q 6 " " BMA u 3 " - " MAN u 5 " " BMA w 3 " - " MAN w 7 " " MAN w 7 " - " MAN w 9 " " BMABA 3 " - " MANBA 6 " " BMAFA 3 " - " MANFA 5 " " BMAHA 3 " - " MANHA 7 " " MANHA 7 " - " MANHA 9 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " 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 X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG 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 i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " 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 w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGDA 1 " - " NAGDA 2 " " NAGEA 1 " - " NAGEA 2 " " NAGEA 2 " - " BMAEA 3 " " NAGFA 1 " - " NAGFA 2 " " NAGFA 2 " - " BMAFA 3 " " NAGGA 1 " - " NAGGA 2 " " NAGHA 1 " - " NAGHA 2 " " NAGHA 2 " - " BMAHA 3 " " NAGIA 1 " - " NAGIA 2 " " NAGJA 1 " - " NAGJA 2 " " NAGJA 2 " - " BMAJA 3 " NAG-ASN " NAG 0 1 " - " ASN K 133 " " NAG 1 1 " - " ASN K 137 " " NAG 2 635 " - " ASN 2 355 " " NAG 3 1 " - " ASN K 156 " " NAG 4 1 " - " ASN K 160 " " NAG 9 1 " - " ASN K 197 " " NAG A 701 " - " ASN A 637 " " NAG A 702 " - " ASN A 611 " " NAG B 635 " - " ASN B 355 " " NAG G 701 " - " ASN G 637 " " NAG G 702 " - " ASN G 611 " " NAG K 635 " - " ASN K 355 " " NAG Q 701 " - " ASN Q 637 " " NAG Q 702 " - " ASN Q 611 " " NAG T 1 " - " ASN 2 88 " " NAG U 1 " - " ASN 2 133 " " NAG V 1 " - " ASN 2 137 " " NAG W 1 " - " ASN 2 156 " " NAG X 1 " - " ASN 2 160 " " NAG Y 1 " - " ASN 2 197 " " NAG Z 1 " - " ASN 2 234 " " NAG a 1 " - " ASN 2 262 " " NAG b 1 " - " ASN 2 295 " " NAG c 1 " - " ASN 2 301 " " NAG d 1 " - " ASN 2 363 " " NAG e 1 " - " ASN 2 386 " " NAG f 1 " - " ASN 2 392 " " NAG g 1 " - " ASN 2 332 " " NAG h 1 " - " ASN 2 448 " " NAG i 1 " - " ASN 2 276 " " NAG j 1 " - " ASN B 88 " " NAG k 1 " - " ASN B 133 " " NAG l 1 " - " ASN B 137 " " NAG m 1 " - " ASN B 156 " " NAG n 1 " - " ASN B 160 " " NAG o 1 " - " ASN B 197 " " NAG p 1 " - " ASN B 234 " " NAG q 1 " - " ASN B 262 " " NAG r 1 " - " ASN B 295 " " NAG s 1 " - " ASN B 301 " " NAG t 1 " - " ASN B 363 " " NAG u 1 " - " ASN B 386 " " NAG v 1 " - " ASN B 392 " " NAG w 1 " - " ASN B 332 " " NAG x 1 " - " ASN B 448 " " NAG y 1 " - " ASN B 276 " " NAG z 1 " - " ASN K 88 " " NAGAA 1 " - " ASN K 234 " " NAGBA 1 " - " ASN K 262 " " NAGCA 1 " - " ASN K 295 " " NAGDA 1 " - " ASN K 301 " " NAGEA 1 " - " ASN K 363 " " NAGFA 1 " - " ASN K 386 " " NAGGA 1 " - " ASN K 392 " " NAGHA 1 " - " ASN K 332 " " NAGIA 1 " - " ASN K 448 " " NAGJA 1 " - " ASN K 276 " Time building additional restraints: 15.91 Conformation dependent library (CDL) restraints added in 5.8 seconds 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7044 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 72 sheets defined 14.1% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.06 Creating SS restraints... Processing helix chain '2' and resid 58 through 62 removed outlier: 3.565A pdb=" N GLU 2 62 " --> pdb=" O LYS 2 59 " (cutoff:3.500A) Processing helix chain '2' and resid 100 through 115 removed outlier: 3.505A pdb=" N MET 2 104 " --> pdb=" O MET 2 100 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS 2 105 " --> pdb=" O VAL 2 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE 2 109 " --> pdb=" O HIS 2 105 " (cutoff:3.500A) Processing helix chain '2' and resid 122 through 126 removed outlier: 4.012A pdb=" N CYS 2 126 " --> pdb=" O THR 2 123 " (cutoff:3.500A) Processing helix chain '2' and resid 195 through 198 Processing helix chain '2' and resid 335 through 350 Processing helix chain '2' and resid 351 through 353 No H-bonds generated for 'chain '2' and resid 351 through 353' Processing helix chain '2' and resid 368 through 373 removed outlier: 3.836A pdb=" N THR 2 372 " --> pdb=" O ASP 2 368 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR 2 373 " --> pdb=" O LEU 2 369 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 368 through 373' Processing helix chain '2' and resid 387 through 390 removed outlier: 3.795A pdb=" N LEU 2 390 " --> pdb=" O THR 2 387 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 387 through 390' Processing helix chain '2' and resid 474 through 479 removed outlier: 3.882A pdb=" N ASP 2 477 " --> pdb=" O ASP 2 474 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN 2 478 " --> pdb=" O MET 2 475 " (cutoff:3.500A) Processing helix chain '5' and resid 83 through 86 Processing helix chain '5' and resid 100D through 100H removed outlier: 3.921A pdb=" N PHE 5 100G" --> pdb=" O VAL 5 100D" (cutoff:3.500A) Processing helix chain '6' and resid 79 through 83 Processing helix chain '7' and resid 78 through 82 removed outlier: 3.762A pdb=" N ASP 7 81 " --> pdb=" O ASP 7 78 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE 7 82 " --> pdb=" O ARG 7 79 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 78 through 82' Processing helix chain '8' and resid 83 through 87 removed outlier: 3.669A pdb=" N THR 8 87 " --> pdb=" O PRO 8 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 517 removed outlier: 3.521A pdb=" N GLY A 516 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 517 " --> pdb=" O GLY A 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 517' Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 570 through 595 removed outlier: 3.702A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 616 removed outlier: 4.490A pdb=" N SER A 615 " --> pdb=" O ASN A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.537A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 661 Processing helix chain 'B' and resid 58 through 62 removed outlier: 3.573A pdb=" N GLU B 62 " --> pdb=" O LYS B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 115 removed outlier: 3.633A pdb=" N HIS B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE B 109 " --> pdb=" O HIS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.653A pdb=" N LEU B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N CYS B 126 " --> pdb=" O THR B 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 122 through 126' Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.845A pdb=" N THR B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 373' Processing helix chain 'B' and resid 387 through 390 removed outlier: 3.807A pdb=" N LEU B 390 " --> pdb=" O THR B 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 387 through 390' Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'C' and resid 83 through 86 Processing helix chain 'C' and resid 100D through 100H removed outlier: 3.916A pdb=" N PHE C 100G" --> pdb=" O VAL C 100D" (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'F' and resid 61 through 64 removed outlier: 4.073A pdb=" N GLN F 64 " --> pdb=" O ARG F 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 64' Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.713A pdb=" N THR F 87 " --> pdb=" O PRO F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 513 through 517 removed outlier: 3.521A pdb=" N GLY G 516 " --> pdb=" O VAL G 513 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA G 517 " --> pdb=" O GLY G 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 513 through 517' Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 570 through 595 removed outlier: 3.729A pdb=" N LYS G 574 " --> pdb=" O VAL G 570 " (cutoff:3.500A) Processing helix chain 'G' and resid 611 through 615 removed outlier: 3.710A pdb=" N TRP G 614 " --> pdb=" O ASN G 611 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER G 615 " --> pdb=" O SER G 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 611 through 615' Processing helix chain 'G' and resid 619 through 624 Processing helix chain 'G' and resid 627 through 635 Processing helix chain 'G' and resid 641 through 661 Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.692A pdb=" N GLN H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.084A pdb=" N ASP H 86 " --> pdb=" O THR H 83 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR H 87 " --> pdb=" O ASP H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.646A pdb=" N GLN I 64 " --> pdb=" O PRO I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'I' and resid 83 through 87 removed outlier: 4.024A pdb=" N ASP I 86 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR I 87 " --> pdb=" O ASP I 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 83 through 87' Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.145A pdb=" N ILE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 62 removed outlier: 3.587A pdb=" N GLU K 62 " --> pdb=" O LYS K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 115 removed outlier: 3.541A pdb=" N MET K 104 " --> pdb=" O MET K 100 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS K 105 " --> pdb=" O VAL K 101 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE K 109 " --> pdb=" O HIS K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 126 removed outlier: 4.006A pdb=" N CYS K 126 " --> pdb=" O THR K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 198 Processing helix chain 'K' and resid 335 through 350 Processing helix chain 'K' and resid 351 through 353 No H-bonds generated for 'chain 'K' and resid 351 through 353' Processing helix chain 'K' and resid 368 through 373 removed outlier: 3.657A pdb=" N THR K 372 " --> pdb=" O ASP K 368 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR K 373 " --> pdb=" O LEU K 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 368 through 373' Processing helix chain 'K' and resid 387 through 390 removed outlier: 3.821A pdb=" N LEU K 390 " --> pdb=" O THR K 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 387 through 390' Processing helix chain 'K' and resid 475 through 479 removed outlier: 3.534A pdb=" N ASN K 478 " --> pdb=" O MET K 475 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.213A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 100D through 100H removed outlier: 3.984A pdb=" N PHE M 100G" --> pdb=" O VAL M 100D" (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'P' and resid 61 through 64 removed outlier: 4.123A pdb=" N GLN P 64 " --> pdb=" O ARG P 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 61 through 64' Processing helix chain 'P' and resid 83 through 87 removed outlier: 3.731A pdb=" N THR P 87 " --> pdb=" O PRO P 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 513 through 517 removed outlier: 3.545A pdb=" N GLY Q 516 " --> pdb=" O VAL Q 513 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA Q 517 " --> pdb=" O GLY Q 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 513 through 517' Processing helix chain 'Q' and resid 529 through 534 Processing helix chain 'Q' and resid 570 through 595 removed outlier: 3.728A pdb=" N LYS Q 574 " --> pdb=" O VAL Q 570 " (cutoff:3.500A) Processing helix chain 'Q' and resid 611 through 616 removed outlier: 4.362A pdb=" N SER Q 615 " --> pdb=" O ASN Q 611 " (cutoff:3.500A) Processing helix chain 'Q' and resid 619 through 624 Processing helix chain 'Q' and resid 627 through 635 Processing helix chain 'Q' and resid 641 through 661 Processing helix chain 'R' and resid 61 through 64 removed outlier: 3.720A pdb=" N GLN R 64 " --> pdb=" O PRO R 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 61 through 64' Processing helix chain 'R' and resid 83 through 87 removed outlier: 3.971A pdb=" N ASP R 86 " --> pdb=" O THR R 83 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR R 87 " --> pdb=" O ASP R 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 83 through 87' Processing helix chain 'S' and resid 79 through 83 removed outlier: 4.184A pdb=" N ILE S 83 " --> pdb=" O PRO S 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '2' and resid 495 through 499 removed outlier: 6.045A pdb=" N VAL 2 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR A 606 " --> pdb=" O VAL 2 36 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS A 604 " --> pdb=" O VAL 2 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 45 through 47 removed outlier: 4.022A pdb=" N ILE 2 225 " --> pdb=" O VAL 2 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain '2' and resid 91 through 93 Processing sheet with id=AA5, first strand: chain '2' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain '2' and resid 202 through 203 removed outlier: 7.002A pdb=" N THR 2 202 " --> pdb=" O TYR 2 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 260 through 261 removed outlier: 7.883A pdb=" N GLY 2 451 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 11.652A pdb=" N THR 2 290 " --> pdb=" O GLY 2 451 " (cutoff:3.500A) removed outlier: 11.755A pdb=" N ILE 2 453 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) removed outlier: 12.160A pdb=" N PHE 2 288 " --> pdb=" O ILE 2 453 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N THR 2 455 " --> pdb=" O VAL 2 286 " (cutoff:3.500A) removed outlier: 10.998A pdb=" N VAL 2 286 " --> pdb=" O THR 2 455 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLN 2 293 " --> pdb=" O SER 2 334 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER 2 334 " --> pdb=" O GLN 2 293 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '2' and resid 271 through 273 removed outlier: 10.998A pdb=" N VAL 2 286 " --> pdb=" O THR 2 455 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N THR 2 455 " --> pdb=" O VAL 2 286 " (cutoff:3.500A) removed outlier: 12.160A pdb=" N PHE 2 288 " --> pdb=" O ILE 2 453 " (cutoff:3.500A) removed outlier: 11.755A pdb=" N ILE 2 453 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) removed outlier: 11.652A pdb=" N THR 2 290 " --> pdb=" O GLY 2 451 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N GLY 2 451 " --> pdb=" O THR 2 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '2' and resid 304 through 308 Processing sheet with id=AB1, first strand: chain '2' and resid 359 through 361 removed outlier: 3.647A pdb=" N ILE 2 359 " --> pdb=" O TRP 2 395 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER 2 393 " --> pdb=" O PHE 2 361 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '5' and resid 11 through 12 removed outlier: 3.834A pdb=" N VAL 5 12 " --> pdb=" O THR 5 108 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR 5 33 " --> pdb=" O THR 5 95 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TRP 5 34 " --> pdb=" O TYR 5 50 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR 5 50 " --> pdb=" O TRP 5 34 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TRP 5 36 " --> pdb=" O ILE 5 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '5' and resid 17 through 22 Processing sheet with id=AB4, first strand: chain '5' and resid 99 through 100A Processing sheet with id=AB5, first strand: chain '6' and resid 9 through 13 removed outlier: 3.689A pdb=" N THR 6 102 " --> pdb=" O TYR 6 86 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLN 6 37 " --> pdb=" O LEU 6 46 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU 6 46 " --> pdb=" O GLN 6 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '6' and resid 18 through 23 removed outlier: 3.643A pdb=" N CYS 6 23 " --> pdb=" O ALA 6 71 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA 6 71 " --> pdb=" O CYS 6 23 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '7' and resid 10 through 13 removed outlier: 6.407A pdb=" N TRP 7 34 " --> pdb=" O LEU 7 46 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG 7 44 " --> pdb=" O GLN 7 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '7' and resid 19 through 24 Processing sheet with id=AB9, first strand: chain '8' and resid 3 through 6 Processing sheet with id=AC1, first strand: chain '8' and resid 10 through 11 removed outlier: 6.648A pdb=" N VAL 8 10 " --> pdb=" O VAL 8 110 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG 8 38 " --> pdb=" O TRP 8 47 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N TRP 8 47 " --> pdb=" O ARG 8 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '8' and resid 10 through 11 removed outlier: 6.648A pdb=" N VAL 8 10 " --> pdb=" O VAL 8 110 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR 8 102 " --> pdb=" O ARG 8 94 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 495 through 499 removed outlier: 6.009A pdb=" N VAL B 36 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR G 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS G 604 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.067A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 91 through 93 Processing sheet with id=AC6, first strand: chain 'B' and resid 169 through 177 Processing sheet with id=AC7, first strand: chain 'B' and resid 202 through 203 removed outlier: 7.019A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 424 " --> pdb=" O MET B 434 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 260 through 261 removed outlier: 7.650A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 11.869A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 11.895A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 12.171A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.041A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 271 through 273 removed outlier: 11.041A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 12.171A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 11.895A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 11.869A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE B 358 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N PHE B 468 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 359 " --> pdb=" O TRP B 395 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER B 393 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 304 through 308 Processing sheet with id=AD2, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.825A pdb=" N VAL C 12 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR C 33 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR C 50 " --> pdb=" O TRP C 34 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 17 through 22 Processing sheet with id=AD4, first strand: chain 'C' and resid 100 through 100A Processing sheet with id=AD5, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.739A pdb=" N THR D 102 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA D 84 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 18 through 23 removed outlier: 3.557A pdb=" N CYS D 23 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 10 through 13 removed outlier: 5.678A pdb=" N GLN E 36 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU E 45 " --> pdb=" O GLN E 36 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 19 through 24 Processing sheet with id=AD9, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AE1, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.667A pdb=" N VAL F 10 " --> pdb=" O VAL F 110 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.667A pdb=" N VAL F 10 " --> pdb=" O VAL F 110 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE4, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.773A pdb=" N TYR H 58 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY H 50 " --> pdb=" O TYR H 58 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.773A pdb=" N TYR H 58 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY H 50 " --> pdb=" O TYR H 58 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'I' and resid 58 through 59 removed outlier: 3.891A pdb=" N TYR I 58 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY I 50 " --> pdb=" O TYR I 58 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY I 50 " --> pdb=" O TRP I 34 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 58 through 59 removed outlier: 3.891A pdb=" N TYR I 58 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY I 50 " --> pdb=" O TYR I 58 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY I 50 " --> pdb=" O TRP I 34 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.935A pdb=" N THR J 53 " --> pdb=" O HIS J 49 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS J 49 " --> pdb=" O THR J 53 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N HIS J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU J 33 " --> pdb=" O HIS J 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 495 through 499 removed outlier: 6.061A pdb=" N VAL K 36 " --> pdb=" O THR Q 606 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR Q 606 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS Q 604 " --> pdb=" O VAL K 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 45 through 47 removed outlier: 4.112A pdb=" N ILE K 225 " --> pdb=" O VAL K 245 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 91 through 93 Processing sheet with id=AF5, first strand: chain 'K' and resid 169 through 177 Processing sheet with id=AF6, first strand: chain 'K' and resid 202 through 203 removed outlier: 7.045A pdb=" N THR K 202 " --> pdb=" O TYR K 435 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 260 through 261 removed outlier: 7.471A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 11.640A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 11.641A pdb=" N ILE K 453 " --> pdb=" O PHE K 288 " (cutoff:3.500A) removed outlier: 12.065A pdb=" N PHE K 288 " --> pdb=" O ILE K 453 " (cutoff:3.500A) removed outlier: 10.710A pdb=" N THR K 455 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 11.011A pdb=" N VAL K 286 " --> pdb=" O THR K 455 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLN K 293 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER K 334 " --> pdb=" O GLN K 293 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 271 through 273 removed outlier: 11.011A pdb=" N VAL K 286 " --> pdb=" O THR K 455 " (cutoff:3.500A) removed outlier: 10.710A pdb=" N THR K 455 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 12.065A pdb=" N PHE K 288 " --> pdb=" O ILE K 453 " (cutoff:3.500A) removed outlier: 11.641A pdb=" N ILE K 453 " --> pdb=" O PHE K 288 " (cutoff:3.500A) removed outlier: 11.640A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 304 through 308 Processing sheet with id=AG1, first strand: chain 'K' and resid 359 through 361 removed outlier: 3.646A pdb=" N ILE K 359 " --> pdb=" O TRP K 395 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER K 393 " --> pdb=" O PHE K 361 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG3, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.961A pdb=" N THR L 53 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS L 49 " --> pdb=" O THR L 53 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N HIS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU L 33 " --> pdb=" O HIS L 49 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.743A pdb=" N VAL M 12 " --> pdb=" O THR M 108 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR M 33 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.743A pdb=" N VAL M 12 " --> pdb=" O THR M 108 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS M 96 " --> pdb=" O TYR M 100O" (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY M 98 " --> pdb=" O TYR M 100M" (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR M 100M" --> pdb=" O GLY M 98 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 17 through 22 Processing sheet with id=AG7, first strand: chain 'N' and resid 9 through 13 removed outlier: 3.706A pdb=" N THR N 102 " --> pdb=" O TYR N 86 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 18 through 23 removed outlier: 3.673A pdb=" N CYS N 23 " --> pdb=" O ALA N 71 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA N 71 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'O' and resid 10 through 13 removed outlier: 5.852A pdb=" N GLN O 36 " --> pdb=" O LEU O 45 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU O 45 " --> pdb=" O GLN O 36 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'O' and resid 19 through 24 Processing sheet with id=AH2, first strand: chain 'P' and resid 3 through 5 Processing sheet with id=AH3, first strand: chain 'P' and resid 10 through 11 removed outlier: 6.702A pdb=" N VAL P 10 " --> pdb=" O VAL P 110 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'P' and resid 10 through 11 removed outlier: 6.702A pdb=" N VAL P 10 " --> pdb=" O VAL P 110 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'R' and resid 3 through 7 Processing sheet with id=AH6, first strand: chain 'R' and resid 58 through 59 removed outlier: 3.833A pdb=" N TYR R 58 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY R 50 " --> pdb=" O TYR R 58 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N TRP R 47 " --> pdb=" O ARG R 38 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ARG R 38 " --> pdb=" O TRP R 47 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'R' and resid 58 through 59 removed outlier: 3.833A pdb=" N TYR R 58 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY R 50 " --> pdb=" O TYR R 58 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N TRP R 47 " --> pdb=" O ARG R 38 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ARG R 38 " --> pdb=" O TRP R 47 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AH9, first strand: chain 'S' and resid 53 through 54 removed outlier: 4.017A pdb=" N THR S 53 " --> pdb=" O HIS S 49 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N HIS S 49 " --> pdb=" O THR S 53 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP S 35 " --> pdb=" O LEU S 47 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N HIS S 49 " --> pdb=" O LEU S 33 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU S 33 " --> pdb=" O HIS S 49 " (cutoff:3.500A) 1050 hydrogen bonds defined for protein. 2652 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: 13.20 Time building geometry restraints manager: 16.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9656 1.34 - 1.46: 9036 1.46 - 1.59: 14218 1.59 - 1.71: 29 1.71 - 1.83: 229 Bond restraints: 33168 Sorted by residual: bond pdb=" C1 NAG i 1 " pdb=" O5 NAG i 1 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C1 NAG y 1 " pdb=" O5 NAG y 1 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" C1 MAN y 4 " pdb=" C2 MAN y 4 " ideal model delta sigma weight residual 1.526 1.646 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" C1 MAN i 4 " pdb=" C2 MAN i 4 " ideal model delta sigma weight residual 1.526 1.634 -0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" C1 MANJA 4 " pdb=" C2 MANJA 4 " ideal model delta sigma weight residual 1.526 1.632 -0.106 2.00e-02 2.50e+03 2.79e+01 ... (remaining 33163 not shown) Histogram of bond angle deviations from ideal: 96.36 - 104.74: 582 104.74 - 113.13: 18731 113.13 - 121.52: 17448 121.52 - 129.90: 7990 129.90 - 138.29: 330 Bond angle restraints: 45081 Sorted by residual: angle pdb=" C ILE 8 48 " pdb=" N GLY 8 49 " pdb=" CA GLY 8 49 " ideal model delta sigma weight residual 121.35 113.60 7.75 1.03e+00 9.43e-01 5.66e+01 angle pdb=" C ASP 7 49 " pdb=" N THR 7 50 " pdb=" CA THR 7 50 " ideal model delta sigma weight residual 121.54 135.61 -14.07 1.91e+00 2.74e-01 5.42e+01 angle pdb=" C ASP E 49 " pdb=" N THR E 50 " pdb=" CA THR E 50 " ideal model delta sigma weight residual 121.54 135.45 -13.91 1.91e+00 2.74e-01 5.31e+01 angle pdb=" C ASP O 49 " pdb=" N THR O 50 " pdb=" CA THR O 50 " ideal model delta sigma weight residual 121.54 135.44 -13.90 1.91e+00 2.74e-01 5.30e+01 angle pdb=" N VAL A 570 " pdb=" CA VAL A 570 " pdb=" C VAL A 570 " ideal model delta sigma weight residual 113.47 106.69 6.78 1.01e+00 9.80e-01 4.50e+01 ... (remaining 45076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.65: 18188 20.65 - 41.30: 1878 41.30 - 61.95: 349 61.95 - 82.61: 48 82.61 - 103.26: 12 Dihedral angle restraints: 20475 sinusoidal: 9474 harmonic: 11001 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 -178.63 -88.37 1 1.00e+01 1.00e-02 9.33e+01 dihedral pdb=" CA CYS B 201 " pdb=" C CYS B 201 " pdb=" N THR B 202 " pdb=" CA THR B 202 " ideal model delta harmonic sigma weight residual -180.00 -140.39 -39.61 0 5.00e+00 4.00e-02 6.28e+01 dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 88 " pdb=" CB CYS J 88 " ideal model delta sinusoidal sigma weight residual 93.00 162.40 -69.40 1 1.00e+01 1.00e-02 6.22e+01 ... (remaining 20472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 5168 0.157 - 0.314: 344 0.314 - 0.470: 29 0.470 - 0.627: 3 0.627 - 0.784: 3 Chirality restraints: 5547 Sorted by residual: chirality pdb=" C1 NAGJA 1 " pdb=" ND2 ASN K 276 " pdb=" C2 NAGJA 1 " pdb=" O5 NAGJA 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" C1 NAG y 1 " pdb=" ND2 ASN B 276 " pdb=" C2 NAG y 1 " pdb=" O5 NAG y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" C1 NAG i 1 " pdb=" ND2 ASN 2 276 " pdb=" C2 NAG i 1 " pdb=" O5 NAG i 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.22e+01 ... (remaining 5544 not shown) Planarity restraints: 5526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE 8 100D" 0.081 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO 8 100E" -0.210 5.00e-02 4.00e+02 pdb=" CA PRO 8 100E" 0.063 5.00e-02 4.00e+02 pdb=" CD PRO 8 100E" 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE P 100D" 0.080 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO P 100E" -0.207 5.00e-02 4.00e+02 pdb=" CA PRO P 100E" 0.062 5.00e-02 4.00e+02 pdb=" CD PRO P 100E" 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE F 100D" -0.071 5.00e-02 4.00e+02 1.06e-01 1.78e+01 pdb=" N PRO F 100E" 0.182 5.00e-02 4.00e+02 pdb=" CA PRO F 100E" -0.053 5.00e-02 4.00e+02 pdb=" CD PRO F 100E" -0.058 5.00e-02 4.00e+02 ... (remaining 5523 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 9960 2.81 - 3.33: 26013 3.33 - 3.86: 54732 3.86 - 4.38: 55599 4.38 - 4.90: 96473 Nonbonded interactions: 242777 Sorted by model distance: nonbonded pdb=" O ASP A 632 " pdb=" OG SER A 636 " model vdw 2.290 2.440 nonbonded pdb=" OD1 ASP 5 56 " pdb=" O2 BMA V 3 " model vdw 2.301 2.440 nonbonded pdb=" OD1 ASP C 56 " pdb=" O2 BMA l 3 " model vdw 2.302 2.440 nonbonded pdb=" OD1 ASP M 56 " pdb=" O2 BMA 1 3 " model vdw 2.306 2.440 nonbonded pdb=" OG SER K 334 " pdb=" OG1 THR K 337 " model vdw 2.307 2.440 ... (remaining 242772 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 'AA' selection = chain 'CA' selection = chain 'DA' selection = chain 'GA' selection = chain 'IA' selection = chain 'U' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'f' selection = chain 'h' selection = chain 'k' selection = chain 'p' selection = chain 'r' selection = chain 's' selection = chain 'v' selection = chain 'x' } ncs_group { reference = chain '1' selection = chain '9' selection = chain 'JA' selection = chain 'T' selection = chain 'V' selection = chain 'Y' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'o' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain '2' selection = chain 'B' selection = chain 'K' } ncs_group { reference = chain '3' selection = chain 'FA' selection = chain 'W' selection = chain 'e' selection = chain 'm' selection = chain 'u' } ncs_group { reference = chain '4' selection = chain 'EA' selection = chain 'X' selection = chain 'd' selection = chain 'n' selection = chain 't' } ncs_group { reference = chain '5' selection = chain 'C' selection = chain 'M' } ncs_group { reference = chain '6' selection = chain 'D' selection = chain 'N' } ncs_group { reference = chain '7' selection = chain 'E' selection = chain 'O' } ncs_group { reference = chain '8' selection = chain 'F' selection = chain 'P' } ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'Q' } ncs_group { reference = chain 'BA' selection = chain 'a' selection = chain 'q' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'R' } ncs_group { reference = chain 'HA' selection = chain 'g' selection = chain 'w' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.130 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: 0.040 Extract box with map and model: 11.410 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 87.990 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.840 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 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 : 0.014 0.140 33168 Z= 0.917 Angle : 1.524 19.169 45081 Z= 0.790 Chirality : 0.087 0.784 5547 Planarity : 0.010 0.121 5469 Dihedral : 16.115 103.256 13278 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 2.64 % Allowed : 17.57 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.11), residues: 3768 helix: -4.26 (0.12), residues: 396 sheet: -1.27 (0.14), residues: 1188 loop : -2.75 (0.11), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP 8 50 HIS 0.015 0.003 HIS H 100 PHE 0.047 0.006 PHE 2 288 TYR 0.035 0.004 TYR F 59 ARG 0.016 0.001 ARG 8 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 605 time to evaluate : 3.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 46 residues processed: 684 average time/residue: 0.4888 time to fit residues: 514.4419 Evaluate side-chains 435 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 389 time to evaluate : 3.599 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 1 residues processed: 46 average time/residue: 0.2874 time to fit residues: 30.1638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 6.9990 chunk 284 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 293 optimal weight: 20.0000 chunk 113 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 218 optimal weight: 6.9990 chunk 340 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 66 HIS 2 67 ASN 2 94 ASN ** 2 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 302 ASN 2 348 GLN 2 352 HIS 2 374 HIS 2 478 ASN 8 6 GLN ** 8 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 GLN B 66 HIS B 67 ASN B 94 ASN B 287 GLN B 348 GLN B 374 HIS F 6 GLN ** G 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 HIS I 3 GLN J 6 GLN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 HIS K 67 ASN K 94 ASN K 99 ASN ** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 348 GLN K 374 HIS L 49 HIS O 6 GLN P 6 GLN P 64 GLN Q 577 GLN R 3 GLN S 49 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 33168 Z= 0.262 Angle : 0.826 14.055 45081 Z= 0.403 Chirality : 0.048 0.260 5547 Planarity : 0.006 0.097 5469 Dihedral : 9.860 59.655 6357 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.54 % Allowed : 6.25 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.12), residues: 3768 helix: -2.35 (0.21), residues: 417 sheet: -0.89 (0.15), residues: 1110 loop : -2.31 (0.12), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 100F HIS 0.010 0.001 HIS I 77 PHE 0.032 0.002 PHE P 100D TYR 0.022 0.002 TYR K 484 ARG 0.013 0.001 ARG F 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 544 time to evaluate : 3.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 562 average time/residue: 0.4655 time to fit residues: 414.5256 Evaluate side-chains 387 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 378 time to evaluate : 3.880 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2977 time to fit residues: 10.6609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 9.9990 chunk 105 optimal weight: 0.5980 chunk 283 optimal weight: 10.0000 chunk 231 optimal weight: 0.1980 chunk 93 optimal weight: 7.9990 chunk 341 optimal weight: 6.9990 chunk 368 optimal weight: 30.0000 chunk 303 optimal weight: 6.9990 chunk 338 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 273 optimal weight: 9.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 66 HIS 2 67 ASN ** 2 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 258 GLN ** 2 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 478 ASN 6 52 ASN 8 64 GLN 8 101 GLN A 616 ASN B 66 HIS ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 616 ASN ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 38 GLN ** K 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 203 GLN ** K 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 ASN O 6 GLN P 6 GLN ** Q 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 HIS R 100 HIS ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 33168 Z= 0.351 Angle : 0.838 14.770 45081 Z= 0.405 Chirality : 0.048 0.240 5547 Planarity : 0.006 0.090 5469 Dihedral : 9.535 59.360 6357 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.36 % Allowed : 6.40 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.13), residues: 3768 helix: -1.41 (0.24), residues: 414 sheet: -0.90 (0.15), residues: 1116 loop : -2.20 (0.12), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 100F HIS 0.008 0.001 HIS 2 85 PHE 0.024 0.003 PHE P 100D TYR 0.034 0.002 TYR Q 638 ARG 0.006 0.001 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 482 time to evaluate : 3.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 493 average time/residue: 0.4508 time to fit residues: 358.8629 Evaluate side-chains 369 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 361 time to evaluate : 3.826 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2940 time to fit residues: 9.1257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 9.9990 chunk 256 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 229 optimal weight: 20.0000 chunk 342 optimal weight: 4.9990 chunk 362 optimal weight: 30.0000 chunk 178 optimal weight: 5.9990 chunk 324 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 348 GLN 6 52 ASN 7 6 GLN B 66 HIS ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** Q 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 33168 Z= 0.394 Angle : 0.850 14.359 45081 Z= 0.412 Chirality : 0.049 0.248 5547 Planarity : 0.006 0.089 5469 Dihedral : 9.409 59.923 6357 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 0.24 % Allowed : 5.02 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.13), residues: 3768 helix: -1.06 (0.25), residues: 414 sheet: -0.72 (0.16), residues: 1095 loop : -2.14 (0.12), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 100F HIS 0.007 0.001 HIS 2 85 PHE 0.025 0.003 PHE E 70 TYR 0.021 0.002 TYR B 484 ARG 0.007 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 471 time to evaluate : 3.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 479 average time/residue: 0.4460 time to fit residues: 343.7454 Evaluate side-chains 363 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 359 time to evaluate : 3.803 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2910 time to fit residues: 7.3662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 7.9990 chunk 205 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 269 optimal weight: 0.9980 chunk 149 optimal weight: 20.0000 chunk 309 optimal weight: 20.0000 chunk 250 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 185 optimal weight: 0.6980 chunk 325 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 203 GLN 2 287 GLN 2 478 ASN ** 6 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 6 GLN B 66 HIS ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN F 6 GLN H 77 HIS ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 HIS ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 33168 Z= 0.267 Angle : 0.773 14.285 45081 Z= 0.372 Chirality : 0.047 0.243 5547 Planarity : 0.005 0.086 5469 Dihedral : 8.876 59.414 6357 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 0.06 % Allowed : 3.66 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.13), residues: 3768 helix: -0.69 (0.26), residues: 414 sheet: -0.59 (0.16), residues: 1134 loop : -2.09 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP 8 100F HIS 0.013 0.001 HIS P 35 PHE 0.024 0.002 PHE E 70 TYR 0.025 0.001 TYR Q 638 ARG 0.004 0.000 ARG S 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 489 time to evaluate : 3.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 491 average time/residue: 0.4453 time to fit residues: 352.3054 Evaluate side-chains 364 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 3.579 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 0.9980 chunk 326 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 212 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 362 optimal weight: 6.9990 chunk 301 optimal weight: 20.0000 chunk 167 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 52 ASN B 66 HIS ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN D 52 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 616 ASN Q 656 ASN R 77 HIS S 6 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 33168 Z= 0.209 Angle : 0.750 31.863 45081 Z= 0.356 Chirality : 0.047 0.248 5547 Planarity : 0.005 0.083 5469 Dihedral : 8.242 59.303 6357 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.09 % Allowed : 2.55 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.14), residues: 3768 helix: -0.07 (0.28), residues: 384 sheet: -0.40 (0.16), residues: 1101 loop : -1.93 (0.13), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP F 100F HIS 0.008 0.001 HIS P 35 PHE 0.016 0.002 PHE I 78 TYR 0.022 0.001 TYR B 484 ARG 0.004 0.000 ARG S 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 496 time to evaluate : 3.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 499 average time/residue: 0.4584 time to fit residues: 366.7404 Evaluate side-chains 371 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 369 time to evaluate : 3.678 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2747 time to fit residues: 5.9312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 206 optimal weight: 30.0000 chunk 264 optimal weight: 10.0000 chunk 205 optimal weight: 20.0000 chunk 305 optimal weight: 9.9990 chunk 202 optimal weight: 2.9990 chunk 361 optimal weight: 30.0000 chunk 226 optimal weight: 8.9990 chunk 220 optimal weight: 30.0000 chunk 166 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 478 ASN 5 32 ASN ** 5 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 51 ASN 7 6 GLN B 66 HIS ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN C 32 ASN E 36 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 315 GLN ** K 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 656 ASN ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 33168 Z= 0.467 Angle : 0.907 36.606 45081 Z= 0.434 Chirality : 0.050 0.319 5547 Planarity : 0.006 0.159 5469 Dihedral : 8.866 59.827 6357 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 0.06 % Allowed : 3.27 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.13), residues: 3768 helix: -0.21 (0.27), residues: 381 sheet: -0.49 (0.16), residues: 1107 loop : -2.13 (0.12), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP P 36 HIS 0.013 0.002 HIS P 35 PHE 0.022 0.003 PHE 7 70 TYR 0.028 0.002 TYR G 638 ARG 0.023 0.001 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 449 time to evaluate : 3.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 450 average time/residue: 0.4547 time to fit residues: 329.8325 Evaluate side-chains 352 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 3.515 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 20.0000 chunk 144 optimal weight: 0.9980 chunk 215 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 229 optimal weight: 0.8980 chunk 246 optimal weight: 7.9990 chunk 178 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 284 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 51 ASN 6 89 HIS 7 6 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 HIS ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN M 32 ASN N 52 ASN N 89 HIS S 6 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 33168 Z= 0.230 Angle : 0.782 32.195 45081 Z= 0.373 Chirality : 0.047 0.283 5547 Planarity : 0.005 0.129 5469 Dihedral : 8.270 59.412 6357 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.03 % Allowed : 1.14 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.13), residues: 3768 helix: -0.14 (0.27), residues: 399 sheet: -0.40 (0.16), residues: 1092 loop : -1.99 (0.13), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP F 100F HIS 0.006 0.001 HIS K 85 PHE 0.026 0.002 PHE 7 70 TYR 0.034 0.002 TYR G 638 ARG 0.009 0.000 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 487 time to evaluate : 4.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 488 average time/residue: 0.4652 time to fit residues: 364.9335 Evaluate side-chains 368 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 3.839 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.2661 > 50: distance: 30 - 52: 5.584 distance: 34 - 60: 13.031 distance: 39 - 68: 10.855 distance: 46 - 72: 11.586 distance: 52 - 53: 5.449 distance: 53 - 54: 13.683 distance: 54 - 55: 12.132 distance: 54 - 60: 6.299 distance: 56 - 57: 5.924 distance: 57 - 58: 6.044 distance: 57 - 59: 13.937 distance: 60 - 61: 4.163 distance: 61 - 62: 8.511 distance: 61 - 64: 6.554 distance: 62 - 63: 10.727 distance: 62 - 68: 7.875 distance: 64 - 65: 10.952 distance: 65 - 66: 7.594 distance: 65 - 67: 13.027 distance: 68 - 69: 8.109 distance: 69 - 70: 5.760 distance: 70 - 72: 16.200 distance: 72 - 73: 6.854 distance: 73 - 76: 7.244 distance: 74 - 75: 4.491 distance: 74 - 80: 8.560 distance: 76 - 77: 11.066 distance: 76 - 78: 6.865 distance: 77 - 79: 17.093 distance: 80 - 81: 4.410 distance: 81 - 82: 11.004 distance: 81 - 84: 8.025 distance: 82 - 94: 3.074 distance: 84 - 85: 4.385 distance: 85 - 86: 6.249 distance: 85 - 87: 6.442 distance: 86 - 88: 8.320 distance: 87 - 89: 14.923 distance: 87 - 90: 4.315 distance: 88 - 89: 10.314 distance: 89 - 91: 11.255 distance: 90 - 92: 5.470 distance: 91 - 93: 3.282 distance: 92 - 93: 3.324 distance: 94 - 95: 18.683 distance: 95 - 96: 8.903 distance: 96 - 97: 10.100 distance: 96 - 98: 12.462 distance: 98 - 99: 3.109 distance: 99 - 100: 5.605 distance: 99 - 102: 3.941 distance: 100 - 101: 40.146 distance: 100 - 104: 19.123 distance: 102 - 103: 4.781 distance: 103 - 138: 11.932 distance: 104 - 105: 29.071 distance: 105 - 106: 20.578 distance: 105 - 108: 19.523 distance: 106 - 107: 11.417 distance: 106 - 110: 18.599 distance: 108 - 109: 34.892 distance: 110 - 111: 5.623 distance: 111 - 112: 8.963 distance: 112 - 113: 8.726 distance: 112 - 114: 5.319 distance: 114 - 115: 10.890 distance: 115 - 116: 8.106 distance: 115 - 118: 5.078 distance: 116 - 117: 15.191 distance: 116 - 123: 6.727 distance: 118 - 119: 13.384 distance: 119 - 120: 4.936 distance: 120 - 121: 5.240 distance: 121 - 122: 17.155