Starting phenix.real_space_refine on Fri Aug 9 10:16:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dok_27596/08_2024/8dok_27596.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dok_27596/08_2024/8dok_27596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dok_27596/08_2024/8dok_27596.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dok_27596/08_2024/8dok_27596.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dok_27596/08_2024/8dok_27596.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dok_27596/08_2024/8dok_27596.cif" } resolution = 3.2 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= 0.001 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 16219 2.51 5 N 4324 2.21 5 O 5166 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 49": "OD1" <-> "OD2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 57": "OD1" <-> "OD2" Residue "A PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 321": "OD1" <-> "OD2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A ASP 410": "OD1" <-> "OD2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "B ASP 589": "OD1" <-> "OD2" Residue "B PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 634": "OE1" <-> "OE2" Residue "B GLU 657": "OE1" <-> "OE2" Residue "B ASP 659": "OD1" <-> "OD2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E GLU 164": "OE1" <-> "OE2" Residue "E PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 268": "OE1" <-> "OE2" Residue "E GLU 290": "OE1" <-> "OE2" Residue "E PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 492": "OE1" <-> "OE2" Residue "F ASP 589": "OD1" <-> "OD2" Residue "F PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 634": "OE1" <-> "OE2" Residue "G TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 73": "OD1" <-> "OD2" Residue "G TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 180": "OD1" <-> "OD2" Residue "I GLU 190": "OE1" <-> "OE2" Residue "I PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 503": "NH1" <-> "NH2" Residue "J ASP 589": "OD1" <-> "OD2" Residue "J PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 634": "OE1" <-> "OE2" Residue "M GLU 6": "OE1" <-> "OE2" Residue "M TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 100": "OE1" <-> "OE2" Residue "N TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25844 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3458 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 23, 'TRANS': 413} Chain breaks: 4 Chain: "B" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 970 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1003 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "E" Number of atoms: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3442 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 4 Chain: "F" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 939 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "G" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1003 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "H" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "I" Number of atoms: 3438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3438 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 23, 'TRANS': 410} Chain breaks: 4 Chain: "J" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 966 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "K" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1003 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "M" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "N" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "O" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "P" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "Q" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "R" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "S" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 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: 9 Unresolved non-hydrogen chiralities: 3 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: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "Z" 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: 18 Unresolved non-hydrogen chiralities: 6 Chain: "b" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" 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: 27 Unresolved non-hydrogen chiralities: 9 Chain: "j" 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: 15 Unresolved non-hydrogen chiralities: 5 Chain: "l" 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: "m" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 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: 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: "r" 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: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 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: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" 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: "I" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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 Time building chain proxies: 15.00, per 1000 atoms: 0.58 Number of scatterers: 25844 At special positions: 0 Unit cell: (162.68, 164.34, 149.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 5166 8.00 N 4324 7.00 C 16219 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.01 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.00 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.51 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " 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=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " " MAN S 8 " - " MAN S 9 " " MAN Y 4 " - " MAN Y 5 " " MAN Y 5 " - " MAN Y 6 " " MAN Y 8 " - " MAN Y 9 " " MAN Z 4 " - " MAN Z 5 " " MAN i 4 " - " MAN i 5 " " MAN i 5 " - " MAN i 6 " " MAN i 8 " - " MAN i 9 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 7 " - " MAN Y 10 " " BMA Z 3 " - " MAN Z 4 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 4 " ALPHA1-6 " BMA S 3 " - " MAN S 7 " " MAN S 7 " - " MAN S 8 " " BMA Y 3 " - " MAN Y 7 " " MAN Y 7 " - " MAN Y 8 " " BMA Z 3 " - " MAN Z 6 " " BMA i 3 " - " MAN i 7 " " MAN i 7 " - " MAN i 8 " " BMA j 3 " - " MAN j 5 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " NAG U 3 " " NAG U 3 " - " NAG U 4 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " NAG b 3 " " NAG b 3 " - " NAG b 4 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " NAG m 3 " " NAG m 3 " - " NAG m 4 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " NAG-ASN " NAG A1001 " - " ASN A 160 " " NAG A1002 " - " ASN A 241 " " NAG A1003 " - " ASN A 295 " " NAG A1004 " - " ASN A 301 " " NAG A1005 " - " ASN A 448 " " NAG A1006 " - " ASN A 156 " " NAG A1007 " - " ASN A 289 " " NAG A1008 " - " ASN A 392 " " NAG A1009 " - " ASN A 197 " " NAG A1010 " - " ASN A 130 " " NAG B 701 " - " ASN B 616 " " NAG B 702 " - " ASN B 625 " " NAG C 301 " - " ASN C 82B" " NAG E 601 " - " ASN E 160 " " NAG E 602 " - " ASN E 241 " " NAG E 603 " - " ASN E 295 " " NAG E 604 " - " ASN E 301 " " NAG E 605 " - " ASN E 355 " " NAG E 606 " - " ASN E 448 " " NAG E 607 " - " ASN E 156 " " NAG E 608 " - " ASN E 289 " " NAG E 609 " - " ASN E 386 " " NAG E 610 " - " ASN E 392 " " NAG E 611 " - " ASN E 197 " " NAG E 612 " - " ASN E 130 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 616 " " NAG F 703 " - " ASN F 625 " " NAG G 301 " - " ASN G 82B" " NAG I 601 " - " ASN I 160 " " NAG I 602 " - " ASN I 241 " " NAG I 603 " - " ASN I 295 " " NAG I 604 " - " ASN I 301 " " NAG I 605 " - " ASN I 355 " " NAG I 606 " - " ASN I 448 " " NAG I 607 " - " ASN I 156 " " NAG I 608 " - " ASN I 386 " " NAG I 609 " - " ASN I 392 " " NAG J 701 " - " ASN J 611 " " NAG J 702 " - " ASN J 616 " " NAG J 703 " - " ASN J 625 " " NAG K 301 " - " ASN K 82B" " NAG S 1 " - " ASN A 234 " " NAG T 1 " - " ASN A 276 " " NAG U 1 " - " ASN A 332 " " NAG V 1 " - " ASN A 386 " " NAG W 1 " - " ASN A 262 " " NAG X 1 " - " ASN B 637 " " NAG Y 1 " - " ASN E 234 " " NAG Z 1 " - " ASN E 276 " " NAG b 1 " - " ASN E 332 " " NAG g 1 " - " ASN E 262 " " NAG h 1 " - " ASN F 637 " " NAG i 1 " - " ASN I 234 " " NAG j 1 " - " ASN I 276 " " NAG l 1 " - " ASN I 289 " " NAG m 1 " - " ASN I 332 " " NAG p 1 " - " ASN I 197 " " NAG q 1 " - " ASN I 130 " " NAG r 1 " - " ASN I 262 " " NAG s 1 " - " ASN J 637 " Time building additional restraints: 12.02 Conformation dependent library (CDL) restraints added in 5.3 seconds 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5672 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 67 sheets defined 15.8% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.78 Creating SS restraints... Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.664A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.722A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'B' and resid 529 through 541 removed outlier: 4.127A pdb=" N ILE B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 539 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 4.070A pdb=" N ILE B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 60 through 65 Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 115 Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.534A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 474 through 480 removed outlier: 3.506A pdb=" N ASN E 478 " --> pdb=" O ILE E 475 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG E 480 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 536 removed outlier: 3.889A pdb=" N ILE F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR F 536 " --> pdb=" O ALA F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.550A pdb=" N ILE F 573 " --> pdb=" O THR F 569 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 removed outlier: 3.965A pdb=" N ASN F 625 " --> pdb=" O GLU F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 661 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.658A pdb=" N THR G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 98 No H-bonds generated for 'chain 'I' and resid 96 through 98' Processing helix chain 'I' and resid 99 through 116 Processing helix chain 'I' and resid 122 through 126 removed outlier: 3.549A pdb=" N CYS I 126 " --> pdb=" O THR I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 197 No H-bonds generated for 'chain 'I' and resid 195 through 197' Processing helix chain 'I' and resid 334 through 353 Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 475 through 479 Processing helix chain 'J' and resid 529 through 537 removed outlier: 3.895A pdb=" N ILE J 535 " --> pdb=" O GLY J 531 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR J 536 " --> pdb=" O ALA J 532 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 596 removed outlier: 3.827A pdb=" N ILE J 573 " --> pdb=" O THR J 569 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS J 574 " --> pdb=" O VAL J 570 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN J 575 " --> pdb=" O TRP J 571 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP J 596 " --> pdb=" O PHE J 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 618 through 624 Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 638 through 662 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 99 through 100C removed outlier: 3.636A pdb=" N SER K 100B" --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY K 100C" --> pdb=" O ARG K 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 99 through 100C' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 60 through 64 Processing helix chain 'N' and resid 79 through 84 removed outlier: 3.910A pdb=" N ALA N 84 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 100D through 100H Processing helix chain 'P' and resid 79 through 84 removed outlier: 3.547A pdb=" N ALA P 84 " --> pdb=" O ALA P 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 64 Processing helix chain 'R' and resid 79 through 84 removed outlier: 4.195A pdb=" N ALA R 84 " --> pdb=" O ALA R 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.497A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.352A pdb=" N LYS A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.473A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.157A pdb=" N LYS A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.612A pdb=" N ILE A 294 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N LEU A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.119A pdb=" N VAL A 292 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 9.689A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.215A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 357 through 361 Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 7.130A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.215A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.689A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 11.119A pdb=" N VAL A 292 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N LEU A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.612A pdb=" N ILE A 294 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 10.157A pdb=" N LYS A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 457 current: chain 'A' and resid 413 through 418 Processing sheet with id=AA9, first strand: chain 'A' and resid 302 through 312 removed outlier: 6.790A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS A 319 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 377 Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.549A pdb=" N VAL C 5 " --> pdb=" O LYS C 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.769A pdb=" N GLU C 10 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG C 38 " --> pdb=" O TYR C 47 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N TYR C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.769A pdb=" N GLU C 10 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 100E through 100F Processing sheet with id=AB6, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.724A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.658A pdb=" N VAL D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR D 49 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AB9, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.193A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC2, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC4, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC5, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.292A pdb=" N LYS E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.254A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.935A pdb=" N LEU E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 12.200A pdb=" N PHE E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 10.928A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.538A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER E 334 " --> pdb=" O LYS E 293 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 271 through 273 removed outlier: 11.538A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.928A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.200A pdb=" N PHE E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.935A pdb=" N LEU E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.574A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD1, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.651A pdb=" N GLU G 10 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG G 38 " --> pdb=" O TYR G 47 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N TYR G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.651A pdb=" N GLU G 10 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER G 102 " --> pdb=" O THR G 94 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 100E through 100F Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.658A pdb=" N VAL H 19 " --> pdb=" O ILE H 75 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.543A pdb=" N VAL H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR H 49 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AD7, first strand: chain 'I' and resid 494 through 499 removed outlier: 5.137A pdb=" N VAL J 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL I 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N THR J 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N TYR I 40 " --> pdb=" O CYS J 604 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N CYS J 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 45 through 47 Processing sheet with id=AD9, first strand: chain 'I' and resid 53 through 55 removed outlier: 3.535A pdb=" N PHE I 53 " --> pdb=" O CYS I 218 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 66 through 67 removed outlier: 6.328A pdb=" N HIS I 66 " --> pdb=" O SER I 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AE3, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=AE4, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.648A pdb=" N LYS I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.239A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY I 451 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 10.510A pdb=" N GLU I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 11.873A pdb=" N LEU I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 12.450A pdb=" N PHE I 288 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 10.746A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 11.465A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 11.995A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 284 through 298 current: chain 'I' and resid 357 through 360 Processing sheet with id=AE6, first strand: chain 'I' and resid 271 through 274 removed outlier: 11.995A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 11.465A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.746A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 12.450A pdb=" N PHE I 288 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 11.873A pdb=" N LEU I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.510A pdb=" N GLU I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY I 451 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 443 through 457 current: chain 'I' and resid 414 through 418 Processing sheet with id=AE7, first strand: chain 'I' and resid 302 through 312 removed outlier: 4.926A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 374 through 377 Processing sheet with id=AE9, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AF1, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.472A pdb=" N GLU K 10 " --> pdb=" O SER K 110 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N TYR K 33 " --> pdb=" O TRP K 52 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N TRP K 52 " --> pdb=" O TYR K 33 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL K 35 " --> pdb=" O GLN K 50 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLN K 50 " --> pdb=" O VAL K 35 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.472A pdb=" N GLU K 10 " --> pdb=" O SER K 110 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 100E through 100F Processing sheet with id=AF4, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.531A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.625A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AF7, first strand: chain 'M' and resid 5 through 7 removed outlier: 3.565A pdb=" N THR M 21 " --> pdb=" O SER M 7 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS M 22 " --> pdb=" O LEU M 78 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN M 77 " --> pdb=" O ASP M 72 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER M 79 " --> pdb=" O SER M 70 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AF9, first strand: chain 'M' and resid 47 through 51 removed outlier: 4.823A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TRP M 36 " --> pdb=" O GLY M 49 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL M 89 " --> pdb=" O GLN M 39 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 20 through 22 Processing sheet with id=AG2, first strand: chain 'N' and resid 45 through 49 removed outlier: 6.695A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 11 through 12 Processing sheet with id=AG4, first strand: chain 'O' and resid 18 through 23 removed outlier: 3.882A pdb=" N LYS O 81 " --> pdb=" O VAL O 68 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 57 through 59 removed outlier: 4.815A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL O 89 " --> pdb=" O GLN O 39 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'O' and resid 57 through 59 removed outlier: 4.815A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR O 94 " --> pdb=" O ASP O 101 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 45 through 48 removed outlier: 3.754A pdb=" N ILE P 45 " --> pdb=" O GLN P 37 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN P 37 " --> pdb=" O ILE P 45 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 4 through 6 removed outlier: 3.577A pdb=" N SER Q 79 " --> pdb=" O SER Q 70 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER Q 70 " --> pdb=" O SER Q 79 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS Q 81 " --> pdb=" O VAL Q 68 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 11 through 12 Processing sheet with id=AH1, first strand: chain 'Q' and resid 57 through 58 removed outlier: 4.873A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY Q 49 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL Q 89 " --> pdb=" O GLN Q 39 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N THR Q 94 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP Q 101 " --> pdb=" O THR Q 94 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.937A pdb=" N LEU R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'R' and resid 19 through 22 Processing sheet with id=AH4, first strand: chain 'R' and resid 45 through 48 removed outlier: 4.885A pdb=" N LEU R 46 " --> pdb=" O GLN R 37 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLN R 37 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE R 48 " --> pdb=" O TRP R 35 " (cutoff:3.500A) 841 hydrogen bonds defined for protein. 2175 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: 9.86 Time building geometry restraints manager: 13.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4013 1.30 - 1.43: 7222 1.43 - 1.56: 14985 1.56 - 1.69: 5 1.69 - 1.82: 180 Bond restraints: 26405 Sorted by residual: bond pdb=" C CYS I 331 " pdb=" N ASN I 332 " ideal model delta sigma weight residual 1.330 1.201 0.128 1.39e-02 5.18e+03 8.50e+01 bond pdb=" CA ALA E 70 " pdb=" C ALA E 70 " ideal model delta sigma weight residual 1.526 1.435 0.091 1.29e-02 6.01e+03 4.96e+01 bond pdb=" C ASN I 156 " pdb=" N CYS I 157 " ideal model delta sigma weight residual 1.329 1.231 0.098 1.44e-02 4.82e+03 4.62e+01 bond pdb=" C ASN I 130 " pdb=" N CYS I 131 " ideal model delta sigma weight residual 1.329 1.414 -0.084 1.36e-02 5.41e+03 3.85e+01 bond pdb=" C LEU I 129 " pdb=" O LEU I 129 " ideal model delta sigma weight residual 1.236 1.174 0.062 1.21e-02 6.83e+03 2.63e+01 ... (remaining 26400 not shown) Histogram of bond angle deviations from ideal: 98.15 - 105.33: 498 105.33 - 112.51: 14476 112.51 - 119.69: 8214 119.69 - 126.87: 12217 126.87 - 134.05: 454 Bond angle restraints: 35859 Sorted by residual: angle pdb=" N HIS A 72 " pdb=" CA HIS A 72 " pdb=" C HIS A 72 " ideal model delta sigma weight residual 113.97 100.01 13.96 1.28e+00 6.10e-01 1.19e+02 angle pdb=" N SER H 7 " pdb=" CA SER H 7 " pdb=" C SER H 7 " ideal model delta sigma weight residual 112.55 124.13 -11.58 1.35e+00 5.49e-01 7.36e+01 angle pdb=" N GLN E 432 " pdb=" CA GLN E 432 " pdb=" C GLN E 432 " ideal model delta sigma weight residual 109.96 122.68 -12.72 1.49e+00 4.50e-01 7.28e+01 angle pdb=" CA GLY I 263 " pdb=" C GLY I 263 " pdb=" O GLY I 263 " ideal model delta sigma weight residual 122.28 114.28 8.00 1.00e+00 1.00e+00 6.41e+01 angle pdb=" CA GLY A 263 " pdb=" C GLY A 263 " pdb=" O GLY A 263 " ideal model delta sigma weight residual 122.47 114.96 7.51 1.08e+00 8.57e-01 4.83e+01 ... (remaining 35854 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.75: 15998 23.75 - 47.50: 840 47.50 - 71.26: 184 71.26 - 95.01: 101 95.01 - 118.76: 83 Dihedral angle restraints: 17206 sinusoidal: 8356 harmonic: 8850 Sorted by residual: dihedral pdb=" CB CYS M 22 " pdb=" SG CYS M 22 " pdb=" SG CYS M 92 " pdb=" CB CYS M 92 " ideal model delta sinusoidal sigma weight residual 93.00 30.57 62.43 1 1.00e+01 1.00e-02 5.16e+01 dihedral pdb=" CB CYS I 126 " pdb=" SG CYS I 126 " pdb=" SG CYS I 196 " pdb=" CB CYS I 196 " ideal model delta sinusoidal sigma weight residual -86.00 -143.88 57.88 1 1.00e+01 1.00e-02 4.50e+01 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 35.40 57.60 1 1.00e+01 1.00e-02 4.46e+01 ... (remaining 17203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 4230 0.164 - 0.328: 80 0.328 - 0.492: 13 0.492 - 0.657: 7 0.657 - 0.821: 2 Chirality restraints: 4332 Sorted by residual: chirality pdb=" C1 NAG A1007 " pdb=" ND2 ASN A 289 " pdb=" C2 NAG A1007 " pdb=" O5 NAG A1007 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-01 2.50e+01 1.68e+01 chirality pdb=" C1 NAG E 602 " pdb=" ND2 ASN E 241 " pdb=" C2 NAG E 602 " pdb=" O5 NAG E 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" CA TRP E 69 " pdb=" N TRP E 69 " pdb=" C TRP E 69 " pdb=" CB TRP E 69 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.01e+01 ... (remaining 4329 not shown) Planarity restraints: 4444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1007 " -0.352 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG A1007 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG A1007 " -0.159 2.00e-02 2.50e+03 pdb=" N2 NAG A1007 " 0.532 2.00e-02 2.50e+03 pdb=" O7 NAG A1007 " -0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG V 1 " 0.238 2.00e-02 2.50e+03 2.02e-01 5.12e+02 pdb=" C7 NAG V 1 " -0.061 2.00e-02 2.50e+03 pdb=" C8 NAG V 1 " 0.160 2.00e-02 2.50e+03 pdb=" N2 NAG V 1 " -0.345 2.00e-02 2.50e+03 pdb=" O7 NAG V 1 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 1 " -0.238 2.00e-02 2.50e+03 1.97e-01 4.87e+02 pdb=" C7 NAG T 1 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG T 1 " -0.168 2.00e-02 2.50e+03 pdb=" N2 NAG T 1 " 0.324 2.00e-02 2.50e+03 pdb=" O7 NAG T 1 " 0.017 2.00e-02 2.50e+03 ... (remaining 4441 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 735 2.69 - 3.24: 24020 3.24 - 3.79: 39448 3.79 - 4.35: 54433 4.35 - 4.90: 91257 Nonbonded interactions: 209893 Sorted by model distance: nonbonded pdb=" OD1 ASP A 57 " pdb=" N ALA A 58 " model vdw 2.136 3.120 nonbonded pdb=" O SER A 264 " pdb=" NE2 HIS A 287 " model vdw 2.201 3.120 nonbonded pdb=" NZ LYS I 444 " pdb=" O7 NAG m 1 " model vdw 2.206 3.120 nonbonded pdb=" O CYS A 74 " pdb=" O PRO A 76 " model vdw 2.214 3.040 nonbonded pdb=" OD2 ASP C 73 " pdb=" O3 NAG S 1 " model vdw 2.215 3.040 ... (remaining 209888 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 132 or resid 152 through 396 or resid 408 throu \ gh 504 or resid 1001 through 1009)) selection = (chain 'E' and (resid 33 through 458 or resid 464 through 504 or resid 601 throu \ gh 609)) selection = chain 'I' } ncs_group { reference = (chain 'B' and (resid 522 through 542 or resid 568 through 662 or resid 701 thro \ ugh 702)) selection = (chain 'F' and (resid 522 through 662 or resid 701 through 702)) selection = (chain 'J' and (resid 522 through 542 or resid 568 through 662 or resid 701 thro \ ugh 702)) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 1 through 106) selection = (chain 'L' and resid 1 through 106) } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } ncs_group { reference = (chain 'S' and (resid 1 or resid 4 through 9)) selection = (chain 'Y' and (resid 2 or resid 5 through 10)) selection = (chain 'i' and (resid 1 or resid 4 through 9)) } ncs_group { reference = chain 'T' selection = chain 'W' selection = chain 'X' selection = chain 'g' selection = chain 'h' selection = chain 'r' selection = chain 's' } ncs_group { reference = chain 'U' selection = chain 'b' selection = chain 'm' } ncs_group { reference = chain 'V' selection = chain 'l' selection = chain 'p' selection = chain 'q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 4.080 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 74.930 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 0.006 0.128 26405 Z= 0.397 Angle : 0.916 13.956 35859 Z= 0.517 Chirality : 0.067 0.821 4332 Planarity : 0.009 0.300 4383 Dihedral : 17.804 118.760 11402 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.77 % Favored : 96.07 % Rotamer: Outliers : 0.71 % Allowed : 1.05 % Favored : 98.24 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 3025 helix: 0.78 (0.28), residues: 384 sheet: -0.25 (0.17), residues: 923 loop : -0.69 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP I 112 HIS 0.011 0.001 HIS E 61 PHE 0.024 0.002 PHE I 233 TYR 0.016 0.001 TYR Q 100B ARG 0.005 0.000 ARG I 504 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 300 time to evaluate : 2.696 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: A 56 SER cc_start: 0.7932 (t) cc_final: 0.7723 (m) REVERT: A 439 ILE cc_start: 0.8903 (mm) cc_final: 0.8513 (mm) REVERT: D 31 ASN cc_start: 0.8201 (m-40) cc_final: 0.7986 (m-40) REVERT: E 155 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7753 (mmt90) REVERT: E 439 ILE cc_start: 0.8944 (mm) cc_final: 0.8607 (mm) REVERT: F 626 MET cc_start: 0.7765 (ttm) cc_final: 0.7517 (ttm) REVERT: I 190 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7654 (mt-10) REVERT: I 502 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8342 (tttp) REVERT: M 29 MET cc_start: 0.2029 (mtp) cc_final: 0.1790 (ttm) REVERT: M 100 MET cc_start: 0.3357 (mmt) cc_final: 0.3119 (mmt) REVERT: N 90 MET cc_start: 0.4396 (tpp) cc_final: 0.4077 (ttp) REVERT: O 100 PHE cc_start: 0.6912 (p90) cc_final: 0.6700 (p90) REVERT: R 31 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6372 (pmt-80) outliers start: 19 outliers final: 9 residues processed: 319 average time/residue: 0.3382 time to fit residues: 177.5834 Evaluate side-chains 271 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 259 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 155 ARG Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 502 LYS Chi-restraints excluded: chain I residue 503 ARG Chi-restraints excluded: chain R residue 31 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 255 optimal weight: 30.0000 chunk 228 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 236 optimal weight: 30.0000 chunk 91 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 176 optimal weight: 0.9980 chunk 274 optimal weight: 20.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN I 67 ASN J 590 GLN M 77 GLN P 37 GLN ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 ASN ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26405 Z= 0.242 Angle : 0.648 10.417 35859 Z= 0.322 Chirality : 0.050 0.619 4332 Planarity : 0.005 0.058 4383 Dihedral : 15.097 99.731 5847 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.46 % Rotamer: Outliers : 1.65 % Allowed : 6.37 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 3025 helix: 0.74 (0.28), residues: 399 sheet: -0.22 (0.17), residues: 907 loop : -0.53 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 427 HIS 0.013 0.001 HIS E 61 PHE 0.029 0.002 PHE M 100K TYR 0.015 0.001 TYR L 91 ARG 0.007 0.000 ARG I 504 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 274 time to evaluate : 2.801 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: A 57 ASP cc_start: 0.7391 (t0) cc_final: 0.6977 (t0) REVERT: A 439 ILE cc_start: 0.8941 (mm) cc_final: 0.8541 (mm) REVERT: E 64 GLU cc_start: 0.2276 (OUTLIER) cc_final: 0.1261 (tt0) REVERT: E 166 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7686 (ttp80) REVERT: E 439 ILE cc_start: 0.8981 (mm) cc_final: 0.8632 (mm) REVERT: I 33 ASN cc_start: 0.6368 (p0) cc_final: 0.6116 (p0) REVERT: J 523 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8572 (pp) REVERT: M 29 MET cc_start: 0.2015 (mtp) cc_final: 0.1746 (ttm) REVERT: M 100 MET cc_start: 0.3290 (mmt) cc_final: 0.3020 (mmt) REVERT: N 90 MET cc_start: 0.4455 (tpp) cc_final: 0.4093 (ttp) outliers start: 44 outliers final: 26 residues processed: 292 average time/residue: 0.2970 time to fit residues: 141.4177 Evaluate side-chains 277 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 249 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 410 ASP Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain P residue 37 GLN Chi-restraints excluded: chain P residue 93 SER Chi-restraints excluded: chain R residue 31 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 152 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 274 optimal weight: 50.0000 chunk 296 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 272 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: