Starting phenix.real_space_refine on Fri Mar 22 03:32:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mph_9189/03_2024/6mph_9189.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mph_9189/03_2024/6mph_9189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mph_9189/03_2024/6mph_9189.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mph_9189/03_2024/6mph_9189.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mph_9189/03_2024/6mph_9189.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mph_9189/03_2024/6mph_9189.pdb" } resolution = 3.8 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= 0.014 sd= 0.126 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 165 5.16 5 C 20157 2.51 5 N 5316 2.21 5 O 6454 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ARG 30": "NH1" <-> "NH2" Residue "1 ARG 38": "NH1" <-> "NH2" Residue "1 ARG 66": "NH1" <-> "NH2" Residue "1 TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 94": "NH1" <-> "NH2" Residue "2 TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "2 ARG 61": "NH1" <-> "NH2" Residue "2 ARG 77": "NH1" <-> "NH2" Residue "2 ARG 96": "NH1" <-> "NH2" Residue "3 ARG 30": "NH1" <-> "NH2" Residue "3 ARG 38": "NH1" <-> "NH2" Residue "3 ARG 66": "NH1" <-> "NH2" Residue "3 TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 94": "NH1" <-> "NH2" Residue "4 TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 45": "NH1" <-> "NH2" Residue "4 ARG 61": "NH1" <-> "NH2" Residue "4 ARG 77": "NH1" <-> "NH2" Residue "4 ARG 96": "NH1" <-> "NH2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 30": "NH1" <-> "NH2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 94": "NH1" <-> "NH2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 45": "NH1" <-> "NH2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "L ARG 77": "NH1" <-> "NH2" Residue "L ARG 96": "NH1" <-> "NH2" Residue "N PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 62": "NH1" <-> "NH2" Residue "Q PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 53": "NH1" <-> "NH2" Residue "R TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 62": "NH1" <-> "NH2" Residue "f PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 62": "NH1" <-> "NH2" Residue "g PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 53": "NH1" <-> "NH2" Residue "h TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 53": "NH1" <-> "NH2" Residue "i TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32092 Number of models: 1 Model: "" Number of chains: 72 Chain: "1" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "2" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 858 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "3" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "4" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 858 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "6" 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: "A" 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: "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: 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: "D" 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: "E" 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: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "L" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 858 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} 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: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 787 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "Q" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain: "R" 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: "X" 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: "Y" 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: "Z" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 787 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "a" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 787 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "f" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain: "g" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain: "h" 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: "i" 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: 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: "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: "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: 12 Unresolved non-hydrogen chiralities: 4 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: "K" 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" 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: 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" 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: "c" 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: 12 Unresolved non-hydrogen chiralities: 4 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" 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: 12 Unresolved non-hydrogen chiralities: 4 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: "k" 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: "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: 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: "n" 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: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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: 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: "r" 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: "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: "t" 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: "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: 12 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: 15 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: 9 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "z" 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: "0" 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: "5" 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: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "8" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "9" 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: "AA" 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: "BA" 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: 12 Unresolved non-hydrogen chiralities: 4 Chain: "CA" 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: 12 Unresolved non-hydrogen chiralities: 4 Chain: "DA" 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: 12 Unresolved non-hydrogen chiralities: 4 Chain: "6" 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: 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: 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: 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: 16.53, per 1000 atoms: 0.52 Number of scatterers: 32092 At special positions: 0 Unit cell: (157.94, 156.88, 152.64, 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 165 16.00 O 6454 8.00 N 5316 7.00 C 20157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS 1 22 " - pdb=" SG CYS 1 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 23 " - pdb=" SG CYS 2 88 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 22 " - pdb=" SG CYS 3 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 23 " - pdb=" SG CYS 4 88 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 598 " - pdb=" SG CYS 6 604 " distance=2.02 Simple disulfide: pdb=" SG CYS 6 605 " - pdb=" SG CYS A 501 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 433 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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 Q 22 " - pdb=" SG CYS Q 103 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 109 " - pdb=" SG CYS Q 112 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 88 " distance=2.03 Simple disulfide: pdb=" SG CYS a 23 " - pdb=" SG CYS a 88 " distance=2.03 Simple disulfide: pdb=" SG CYS f 22 " - pdb=" SG CYS f 103 " distance=2.03 Simple disulfide: pdb=" SG CYS f 109 " - pdb=" SG CYS f 112 " distance=2.03 Simple disulfide: pdb=" SG CYS g 22 " - pdb=" SG CYS g 103 " distance=2.03 Simple disulfide: pdb=" SG CYS g 109 " - pdb=" SG CYS g 112 " 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 0 4 " - " MAN 0 5 " " MAN S 4 " - " MAN S 5 " " MAN n 4 " - " MAN n 5 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " BMA 9 3 " - " MAN 9 4 " " BMA F 3 " - " MAN F 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " BMA S 3 " - " MAN S 4 " " BMA W 3 " - " MAN W 4 " " BMA c 3 " - " MAN c 4 " " BMA e 3 " - " MAN e 4 " " BMA j 3 " - " MAN j 4 " " BMA n 3 " - " MAN n 4 " " BMA r 3 " - " MAN r 4 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 4 " " BMA w 3 " - " MAN w 4 " " BMABA 3 " - " MANBA 4 " " BMACA 3 " - " MANCA 4 " " BMADA 3 " - " MANDA 4 " ALPHA1-6 " BMA 0 3 " - " MAN 0 6 " " BMA 9 3 " - " MAN 9 5 " " BMA F 3 " - " MAN F 5 " " BMA J 3 " - " MAN J 5 " " BMA S 3 " - " MAN S 6 " " BMA W 3 " - " MAN W 5 " " BMA j 3 " - " MAN j 5 " " BMA n 3 " - " MAN n 6 " " BMA r 3 " - " MAN r 5 " " BMA t 3 " - " MAN t 5 " " BMA w 3 " - " MAN w 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 5 1 " - " NAG 5 2 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 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 K 2 " - " BMA K 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " 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 p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG 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 z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGCA 2 " - " BMACA 3 " " NAGDA 1 " - " NAGDA 2 " " NAGDA 2 " - " BMADA 3 " NAG-ASN " NAG 5 1 " - " ASN C 295 " " NAG 6 701 " - " ASN 6 637 " " NAG 8 1 " - " ASN C 363 " " NAG 9 1 " - " ASN C 386 " " NAG A 635 " - " ASN A 339 " " NAG A 647 " - " ASN A 88 " " NAG B 634 " - " ASN B 339 " " NAG B 646 " - " ASN B 88 " " NAG C 635 " - " ASN C 339 " " NAG C 647 " - " ASN C 88 " " NAG D 701 " - " ASN D 637 " " NAG E 701 " - " ASN E 637 " " NAG F 1 " - " ASN A 332 " " NAG K 1 " - " ASN A 160 " " NAG T 1 " - " ASN A 295 " " NAG V 1 " - " ASN A 363 " " NAG W 1 " - " ASN A 386 " " NAG b 1 " - " ASN A 392 " " NAG c 1 " - " ASN B 332 " " NAG k 1 " - " ASN B 160 " " NAG o 1 " - " ASN B 295 " " NAG q 1 " - " ASN B 363 " " NAG r 1 " - " ASN B 386 " " NAG s 1 " - " ASN B 392 " " NAG t 1 " - " ASN C 332 " " NAG x 1 " - " ASN C 160 " " NAGAA 1 " - " ASN C 392 " Time building additional restraints: 14.44 Conformation dependent library (CDL) restraints added in 6.1 seconds 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7038 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 78 sheets defined 14.5% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.85 Creating SS restraints... Processing helix chain '1' and resid 60 through 64 Processing helix chain '1' and resid 83 through 87 removed outlier: 3.527A pdb=" N THR 1 87 " --> pdb=" O ALA 1 84 " (cutoff:3.500A) Processing helix chain '2' and resid 79 through 83 removed outlier: 3.513A pdb=" N ASP 2 82 " --> pdb=" O GLU 2 79 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL 2 83 " --> pdb=" O ALA 2 80 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 79 through 83' Processing helix chain '3' and resid 60 through 64 Processing helix chain '3' and resid 83 through 87 removed outlier: 3.535A pdb=" N THR 3 87 " --> pdb=" O ALA 3 84 " (cutoff:3.500A) Processing helix chain '4' and resid 79 through 83 removed outlier: 3.532A pdb=" N ASP 4 82 " --> pdb=" O GLU 4 79 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL 4 83 " --> pdb=" O ALA 4 80 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 79 through 83' Processing helix chain '6' and resid 529 through 534 Processing helix chain '6' and resid 537 through 543 Processing helix chain '6' and resid 570 through 595 removed outlier: 3.673A pdb=" N LYS 6 574 " --> pdb=" O VAL 6 570 " (cutoff:3.500A) Processing helix chain '6' and resid 611 through 616 removed outlier: 4.107A pdb=" N SER 6 615 " --> pdb=" O ASN 6 611 " (cutoff:3.500A) Processing helix chain '6' and resid 618 through 626 removed outlier: 3.537A pdb=" N ILE 6 622 " --> pdb=" O ASN 6 618 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TRP 6 623 " --> pdb=" O LEU 6 619 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP 6 624 " --> pdb=" O SER 6 620 " (cutoff:3.500A) Processing helix chain '6' and resid 627 through 635 Processing helix chain '6' and resid 641 through 664 Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.690A pdb=" N TYR A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 115 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.554A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.537A pdb=" N THR A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.807A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 62 removed outlier: 3.680A pdb=" N TYR B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 67 removed outlier: 4.184A pdb=" N HIS B 66 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASN B 67 " --> pdb=" O GLU B 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 63 through 67' Processing helix chain 'B' and resid 100 through 115 Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.520A pdb=" N CYS B 126 " --> pdb=" O THR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 475 through 480 removed outlier: 3.832A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 removed outlier: 3.667A pdb=" N TYR C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 67 removed outlier: 4.166A pdb=" N HIS C 66 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN C 67 " --> pdb=" O GLU C 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 63 through 67' Processing helix chain 'C' and resid 100 through 115 Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.605A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 480 removed outlier: 3.832A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 543 Processing helix chain 'D' and resid 570 through 595 removed outlier: 3.662A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 616 removed outlier: 4.110A pdb=" N SER D 615 " --> pdb=" O ASN D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.555A pdb=" N ILE D 622 " --> pdb=" O ASN D 618 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TRP D 623 " --> pdb=" O LEU D 619 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP D 624 " --> pdb=" O SER D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 641 through 664 Processing helix chain 'E' and resid 523 through 527 removed outlier: 3.578A pdb=" N ALA E 526 " --> pdb=" O LEU E 523 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 523 through 527' Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 537 through 543 Processing helix chain 'E' and resid 570 through 595 removed outlier: 3.654A pdb=" N LYS E 574 " --> pdb=" O VAL E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 616 removed outlier: 4.113A pdb=" N SER E 615 " --> pdb=" O ASN E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 626 removed outlier: 3.551A pdb=" N ILE E 622 " --> pdb=" O ASN E 618 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TRP E 623 " --> pdb=" O LEU E 619 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP E 624 " --> pdb=" O SER E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 641 through 664 Processing helix chain 'H' and resid 60 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.553A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.536A pdb=" N ASP L 82 " --> pdb=" O GLU L 79 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.903A pdb=" N SER M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'Q' and resid 62 through 65 removed outlier: 3.618A pdb=" N GLN Q 65 " --> pdb=" O ARG Q 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 62 through 65' Processing helix chain 'Q' and resid 94 through 98 removed outlier: 3.687A pdb=" N THR Q 98 " --> pdb=" O PRO Q 95 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 87 removed outlier: 3.910A pdb=" N SER X 87 " --> pdb=" O ALA X 84 " (cutoff:3.500A) Processing helix chain 'Y' and resid 83 through 87 removed outlier: 3.936A pdb=" N SER Y 87 " --> pdb=" O ALA Y 84 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 83 Processing helix chain 'a' and resid 79 through 83 Processing helix chain 'f' and resid 62 through 65 removed outlier: 3.624A pdb=" N GLN f 65 " --> pdb=" O ARG f 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 62 through 65' Processing helix chain 'f' and resid 94 through 98 removed outlier: 3.683A pdb=" N THR f 98 " --> pdb=" O PRO f 95 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 65 removed outlier: 3.662A pdb=" N GLN g 65 " --> pdb=" O ARG g 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 62 through 65' Processing helix chain 'g' and resid 94 through 98 removed outlier: 3.623A pdb=" N THR g 98 " --> pdb=" O PRO g 95 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain '1' and resid 11 through 12 removed outlier: 3.812A pdb=" N VAL 1 12 " --> pdb=" O THR 1 110 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP 1 34 " --> pdb=" O TYR 1 50 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TYR 1 50 " --> pdb=" O TRP 1 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP 1 36 " --> pdb=" O ILE 1 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 18 through 19 Processing sheet with id=AA4, first strand: chain '2' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain '2' and resid 45 through 49 removed outlier: 6.569A pdb=" N TRP 2 35 " --> pdb=" O LEU 2 47 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR 2 49 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU 2 33 " --> pdb=" O TYR 2 49 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY 2 84 " --> pdb=" O VAL 2 104 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL 2 104 " --> pdb=" O GLY 2 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '3' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain '3' and resid 11 through 12 removed outlier: 3.820A pdb=" N VAL 3 12 " --> pdb=" O THR 3 110 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TRP 3 34 " --> pdb=" O TYR 3 50 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N TYR 3 50 " --> pdb=" O TRP 3 34 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TRP 3 36 " --> pdb=" O ILE 3 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 18 through 19 Processing sheet with id=AA9, first strand: chain '4' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain '4' and resid 45 through 49 removed outlier: 6.558A pdb=" N TRP 4 35 " --> pdb=" O LEU 4 47 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR 4 49 " --> pdb=" O LEU 4 33 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU 4 33 " --> pdb=" O TYR 4 49 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY 4 84 " --> pdb=" O VAL 4 104 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL 4 104 " --> pdb=" O GLY 4 84 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '6' and resid 603 through 609 removed outlier: 3.542A pdb=" N VAL A 38 " --> pdb=" O CYS 6 604 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR 6 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N VAL A 36 " --> pdb=" O THR 6 606 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AB4, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.817A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.759A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AB7, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AB8, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.927A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 11.152A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 12.024A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.529A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.018A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 271 through 274 removed outlier: 11.018A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.529A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.024A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.152A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 302 through 312 removed outlier: 6.021A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 495 through 499 removed outlier: 5.149A pdb=" N VAL B 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR E 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 38 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS E 604 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 45 through 47 Processing sheet with id=AC4, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.799A pdb=" N VAL B 75 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.761A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) 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 201 through 203 Processing sheet with id=AC8, first strand: chain 'B' and resid 260 through 261 removed outlier: 6.950A pdb=" N LEU B 260 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 11.204A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 11.622A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.010A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.318A 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 274 removed outlier: 11.010A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 11.622A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 11.204A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER B 393 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 302 through 312 removed outlier: 6.042A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.133A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR D 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 38 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS D 604 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AD4, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.803A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.779A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AD7, first strand: chain 'C' and resid 201 through 203 Processing sheet with id=AD8, first strand: chain 'C' and resid 260 through 261 removed outlier: 6.945A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 11.161A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 12.011A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.516A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.970A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 271 through 273 removed outlier: 10.970A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.516A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.011A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.161A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 302 through 312 removed outlier: 6.014A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AE4, first strand: chain 'H' and resid 46 through 52 removed outlier: 6.755A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE6, first strand: chain 'L' and resid 45 through 49 removed outlier: 6.559A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL L 104 " --> pdb=" O GLY L 84 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 5 through 7 Processing sheet with id=AE8, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.749A pdb=" N THR M 95 " --> pdb=" O TYR M 33 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR M 33 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AF1, first strand: chain 'N' and resid 12 through 13 removed outlier: 3.589A pdb=" N VAL N 13 " --> pdb=" O ILE N 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'N' and resid 19 through 26 removed outlier: 4.135A pdb=" N ALA N 71 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 44 through 48 removed outlier: 6.589A pdb=" N TRP N 35 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Q' and resid 3 through 5 Processing sheet with id=AF5, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.610A pdb=" N ILE Q 34 " --> pdb=" O TRP Q 50 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TRP Q 50 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY Q 44 " --> pdb=" O ILE Q 40 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 10 through 12 Processing sheet with id=AF7, first strand: chain 'R' and resid 5 through 6 Processing sheet with id=AF8, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.057A pdb=" N LEU R 11 " --> pdb=" O GLU R 105 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TRP R 34 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.057A pdb=" N LEU R 11 " --> pdb=" O GLU R 105 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'X' and resid 5 through 7 Processing sheet with id=AG2, first strand: chain 'X' and resid 11 through 12 removed outlier: 3.738A pdb=" N THR X 95 " --> pdb=" O TYR X 33 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR X 33 " --> pdb=" O THR X 95 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP X 34 " --> pdb=" O TYR X 50 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR X 50 " --> pdb=" O TRP X 34 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N TRP X 36 " --> pdb=" O ILE X 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 11 through 12 Processing sheet with id=AG4, first strand: chain 'Y' and resid 5 through 7 Processing sheet with id=AG5, first strand: chain 'Y' and resid 11 through 12 removed outlier: 3.766A pdb=" N THR Y 95 " --> pdb=" O TYR Y 33 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR Y 33 " --> pdb=" O THR Y 95 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP Y 34 " --> pdb=" O TYR Y 50 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR Y 50 " --> pdb=" O TRP Y 34 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TRP Y 36 " --> pdb=" O ILE Y 48 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 11 through 12 Processing sheet with id=AG7, first strand: chain 'Z' and resid 12 through 13 removed outlier: 3.579A pdb=" N VAL Z 13 " --> pdb=" O ILE Z 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'Z' and resid 19 through 26 removed outlier: 4.067A pdb=" N ALA Z 71 " --> pdb=" O CYS Z 23 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 44 through 48 removed outlier: 6.610A pdb=" N TRP Z 35 " --> pdb=" O ILE Z 47 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'a' and resid 12 through 13 removed outlier: 3.584A pdb=" N VAL a 13 " --> pdb=" O ILE a 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'a' and resid 19 through 26 removed outlier: 4.087A pdb=" N ALA a 71 " --> pdb=" O CYS a 23 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'a' and resid 44 through 48 removed outlier: 6.601A pdb=" N TRP a 35 " --> pdb=" O ILE a 47 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'f' and resid 3 through 5 Processing sheet with id=AH5, first strand: chain 'f' and resid 10 through 12 removed outlier: 6.564A pdb=" N ILE f 34 " --> pdb=" O TRP f 50 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TRP f 50 " --> pdb=" O ILE f 34 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP f 36 " --> pdb=" O ILE f 48 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY f 44 " --> pdb=" O ILE f 40 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'f' and resid 10 through 12 Processing sheet with id=AH7, first strand: chain 'g' and resid 3 through 5 Processing sheet with id=AH8, first strand: chain 'g' and resid 10 through 12 removed outlier: 6.563A pdb=" N ILE g 34 " --> pdb=" O TRP g 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TRP g 50 " --> pdb=" O ILE g 34 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP g 36 " --> pdb=" O ILE g 48 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'g' and resid 10 through 12 Processing sheet with id=AI1, first strand: chain 'h' and resid 5 through 6 Processing sheet with id=AI2, first strand: chain 'h' and resid 10 through 13 removed outlier: 6.054A pdb=" N LEU h 11 " --> pdb=" O GLU h 105 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP h 34 " --> pdb=" O LEU h 47 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'h' and resid 10 through 13 removed outlier: 6.054A pdb=" N LEU h 11 " --> pdb=" O GLU h 105 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'i' and resid 5 through 6 Processing sheet with id=AI5, first strand: chain 'i' and resid 10 through 13 removed outlier: 6.043A pdb=" N LEU i 11 " --> pdb=" O GLU i 105 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TRP i 34 " --> pdb=" O LEU i 47 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'i' and resid 10 through 13 removed outlier: 6.043A pdb=" N LEU i 11 " --> pdb=" O GLU i 105 " (cutoff:3.500A) 1130 hydrogen bonds defined for protein. 2817 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: 12.68 Time building geometry restraints manager: 15.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9634 1.34 - 1.46: 7150 1.46 - 1.57: 15811 1.57 - 1.69: 1 1.69 - 1.81: 216 Bond restraints: 32812 Sorted by residual: bond pdb=" C1 NAG B 646 " pdb=" O5 NAG B 646 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C1 NAG C 647 " pdb=" O5 NAG C 647 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.03e+00 bond pdb=" C1 MAN t 4 " pdb=" C2 MAN t 4 " ideal model delta sigma weight residual 1.526 1.581 -0.055 2.00e-02 2.50e+03 7.60e+00 bond pdb=" C1 MAN v 4 " pdb=" O5 MAN v 4 " ideal model delta sigma weight residual 1.399 1.454 -0.055 2.00e-02 2.50e+03 7.56e+00 bond pdb=" C1 MAN e 4 " pdb=" O5 MAN e 4 " ideal model delta sigma weight residual 1.399 1.454 -0.055 2.00e-02 2.50e+03 7.50e+00 ... (remaining 32807 not shown) Histogram of bond angle deviations from ideal: 99.05 - 106.06: 804 106.06 - 113.07: 18846 113.07 - 120.08: 10485 120.08 - 127.10: 13958 127.10 - 134.11: 526 Bond angle restraints: 44619 Sorted by residual: angle pdb=" C ASN A 332 " pdb=" N VAL A 333 " pdb=" CA VAL A 333 " ideal model delta sigma weight residual 122.11 128.03 -5.92 1.12e+00 7.97e-01 2.79e+01 angle pdb=" CA LEU C 494 " pdb=" CB LEU C 494 " pdb=" CG LEU C 494 " ideal model delta sigma weight residual 116.30 131.49 -15.19 3.50e+00 8.16e-02 1.88e+01 angle pdb=" N PHE f 115 " pdb=" CA PHE f 115 " pdb=" C PHE f 115 " ideal model delta sigma weight residual 109.81 119.38 -9.57 2.21e+00 2.05e-01 1.87e+01 angle pdb=" N PHE Q 115 " pdb=" CA PHE Q 115 " pdb=" C PHE Q 115 " ideal model delta sigma weight residual 109.81 119.27 -9.46 2.21e+00 2.05e-01 1.83e+01 angle pdb=" CA LEU B 494 " pdb=" CB LEU B 494 " pdb=" CG LEU B 494 " ideal model delta sigma weight residual 116.30 131.27 -14.97 3.50e+00 8.16e-02 1.83e+01 ... (remaining 44614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.16: 19957 23.16 - 46.33: 942 46.33 - 69.49: 197 69.49 - 92.65: 209 92.65 - 115.81: 117 Dihedral angle restraints: 21422 sinusoidal: 10430 harmonic: 10992 Sorted by residual: dihedral pdb=" CA GLN L 50 " pdb=" C GLN L 50 " pdb=" N VAL L 51 " pdb=" CA VAL L 51 " ideal model delta harmonic sigma weight residual 180.00 -137.35 -42.65 0 5.00e+00 4.00e-02 7.28e+01 dihedral pdb=" CA GLN 4 50 " pdb=" C GLN 4 50 " pdb=" N VAL 4 51 " pdb=" CA VAL 4 51 " ideal model delta harmonic sigma weight residual -180.00 -137.41 -42.59 0 5.00e+00 4.00e-02 7.26e+01 dihedral pdb=" CA GLN 2 50 " pdb=" C GLN 2 50 " pdb=" N VAL 2 51 " pdb=" CA VAL 2 51 " ideal model delta harmonic sigma weight residual -180.00 -137.76 -42.24 0 5.00e+00 4.00e-02 7.14e+01 ... (remaining 21419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 5033 0.110 - 0.220: 295 0.220 - 0.330: 40 0.330 - 0.441: 0 0.441 - 0.551: 3 Chirality restraints: 5371 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.08e+01 chirality pdb=" C1 NAG s 1 " pdb=" ND2 ASN B 392 " pdb=" C2 NAG s 1 " pdb=" O5 NAG s 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.58e+00 chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN A 392 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.36e+00 ... (remaining 5368 not shown) Planarity restraints: 5490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE Q 115 " 0.050 5.00e-02 4.00e+02 7.56e-02 9.13e+00 pdb=" N PRO Q 116 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO Q 116 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO Q 116 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE g 115 " 0.050 5.00e-02 4.00e+02 7.48e-02 8.95e+00 pdb=" N PRO g 116 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO g 116 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO g 116 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE f 115 " -0.048 5.00e-02 4.00e+02 7.28e-02 8.48e+00 pdb=" N PRO f 116 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO f 116 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO f 116 " -0.041 5.00e-02 4.00e+02 ... (remaining 5487 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 9327 2.81 - 3.33: 26640 3.33 - 3.85: 54080 3.85 - 4.38: 59156 4.38 - 4.90: 102943 Nonbonded interactions: 252146 Sorted by model distance: nonbonded pdb=" OG1 THR B 373 " pdb=" N HIS B 374 " model vdw 2.286 2.520 nonbonded pdb=" OG1 THR C 373 " pdb=" N HIS C 374 " model vdw 2.290 2.520 nonbonded pdb=" OG1 THR A 373 " pdb=" N HIS A 374 " model vdw 2.294 2.520 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP g 79 " model vdw 2.298 2.440 nonbonded pdb=" OH TYR B 318 " pdb=" OD2 ASP Q 79 " model vdw 2.314 2.440 ... (remaining 252141 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 'S' selection = chain 'n' } ncs_group { reference = chain '1' selection = chain '3' selection = chain 'H' } ncs_group { reference = chain '2' selection = chain '4' selection = chain 'L' } ncs_group { reference = chain '5' selection = chain '7' selection = chain 'G' selection = chain 'O' selection = chain 'T' selection = chain 'U' selection = chain 'd' selection = chain 'l' selection = chain 'o' selection = chain 'p' selection = chain 'u' selection = chain 'y' } ncs_group { reference = chain '6' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain '8' selection = chain 'AA' selection = chain 'K' selection = chain 'P' selection = chain 'V' selection = chain 'b' selection = chain 'k' selection = chain 'm' selection = chain 'q' selection = chain 's' selection = chain 'x' selection = chain 'z' } ncs_group { reference = chain '9' selection = chain 'F' selection = chain 'J' selection = chain 'W' selection = chain 'j' selection = chain 'r' selection = chain 't' selection = chain 'w' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'BA' selection = chain 'CA' selection = chain 'DA' selection = chain 'I' selection = chain 'c' selection = chain 'e' selection = chain 'v' } ncs_group { reference = chain 'M' selection = chain 'X' selection = chain 'Y' } ncs_group { reference = chain 'N' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'Q' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'R' selection = chain 'h' selection = chain 'i' } 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: 4.510 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: 13.420 Check model and map are aligned: 0.490 Set scattering table: 0.290 Process input model: 85.580 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.820 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 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 : 0.007 0.067 32812 Z= 0.420 Angle : 0.926 15.191 44619 Z= 0.455 Chirality : 0.059 0.551 5371 Planarity : 0.006 0.076 5463 Dihedral : 18.405 115.815 14222 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.27 % Favored : 94.57 % Rotamer: Outliers : 6.01 % Allowed : 7.18 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -3.46 (0.11), residues: 3777 helix: -2.59 (0.18), residues: 429 sheet: -1.79 (0.13), residues: 1239 loop : -2.59 (0.11), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 96 HIS 0.008 0.001 HIS A 374 PHE 0.025 0.002 PHE C 288 TYR 0.016 0.002 TYR f 87 ARG 0.003 0.000 ARG A 503 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 615 time to evaluate : 3.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 70 LEU cc_start: 0.9177 (mt) cc_final: 0.8877 (mp) REVERT: 1 94 ARG cc_start: 0.8316 (tmm160) cc_final: 0.7868 (ttp80) REVERT: 2 3 VAL cc_start: 0.9238 (t) cc_final: 0.9021 (p) REVERT: 3 94 ARG cc_start: 0.8119 (tmm160) cc_final: 0.7496 (ttp80) REVERT: 4 3 VAL cc_start: 0.9281 (t) cc_final: 0.9040 (p) REVERT: 4 5 THR cc_start: 0.8265 (m) cc_final: 0.8022 (p) REVERT: 6 535 MET cc_start: 0.8557 (mmt) cc_final: 0.8334 (tpp) REVERT: 6 584 GLU cc_start: 0.8558 (tt0) cc_final: 0.8355 (tt0) REVERT: 6 601 LYS cc_start: 0.8698 (mttt) cc_final: 0.8393 (ttpp) REVERT: 6 657 GLU cc_start: 0.9312 (tt0) cc_final: 0.9027 (tm-30) REVERT: 6 659 ASP cc_start: 0.9201 (t0) cc_final: 0.8893 (m-30) REVERT: A 37 THR cc_start: 0.9248 (OUTLIER) cc_final: 0.8854 (p) REVERT: A 138 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8106 (tp) REVERT: A 475 MET cc_start: 0.8890 (mmm) cc_final: 0.8668 (mmm) REVERT: A 494 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8837 (pt) REVERT: B 138 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8081 (tp) REVERT: B 475 MET cc_start: 0.8937 (mmm) cc_final: 0.8706 (mmm) REVERT: C 138 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8236 (tp) REVERT: C 494 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8892 (pt) REVERT: D 543 ASN cc_start: 0.8952 (m-40) cc_final: 0.8721 (t0) REVERT: D 595 ILE cc_start: 0.9298 (pt) cc_final: 0.8796 (pt) REVERT: D 629 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9197 (mp) REVERT: D 633 LYS cc_start: 0.9579 (mttt) cc_final: 0.9372 (mtmm) REVERT: D 651 ASN cc_start: 0.9245 (t0) cc_final: 0.8917 (p0) REVERT: D 657 GLU cc_start: 0.9224 (tt0) cc_final: 0.9024 (tm-30) REVERT: D 659 ASP cc_start: 0.9182 (t0) cc_final: 0.8954 (m-30) REVERT: E 601 LYS cc_start: 0.8743 (mttt) cc_final: 0.8413 (ttpp) REVERT: E 629 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.8942 (mt) REVERT: E 633 LYS cc_start: 0.9554 (mttt) cc_final: 0.9354 (mtmm) REVERT: E 638 TYR cc_start: 0.8507 (m-80) cc_final: 0.7995 (m-10) REVERT: E 659 ASP cc_start: 0.9245 (t0) cc_final: 0.8935 (m-30) REVERT: H 94 ARG cc_start: 0.8402 (tmm160) cc_final: 0.7727 (ttp80) REVERT: L 3 VAL cc_start: 0.9215 (t) cc_final: 0.8976 (p) REVERT: N 54 ARG cc_start: 0.8622 (ptt-90) cc_final: 0.8349 (ptt90) REVERT: N 62 PHE cc_start: 0.8457 (m-80) cc_final: 0.8241 (m-10) REVERT: N 67 THR cc_start: 0.9475 (OUTLIER) cc_final: 0.9042 (p) REVERT: R 10 ILE cc_start: 0.9511 (mt) cc_final: 0.9291 (mm) REVERT: X 82 VAL cc_start: 0.8783 (t) cc_final: 0.8366 (t) REVERT: Y 100 LYS cc_start: 0.9500 (mptt) cc_final: 0.9274 (mmmm) REVERT: Z 54 ARG cc_start: 0.8554 (ptt-90) cc_final: 0.8353 (ptm160) REVERT: Z 67 THR cc_start: 0.9438 (OUTLIER) cc_final: 0.9030 (p) REVERT: a 28 LEU cc_start: 0.9182 (mp) cc_final: 0.8903 (mp) REVERT: a 54 ARG cc_start: 0.8574 (ptt-90) cc_final: 0.8253 (ptt90) REVERT: a 67 THR cc_start: 0.9416 (OUTLIER) cc_final: 0.8897 (p) REVERT: f 32 TYR cc_start: 0.9004 (m-80) cc_final: 0.8779 (m-10) REVERT: h 10 ILE cc_start: 0.9523 (mt) cc_final: 0.9299 (mm) REVERT: h 32 MET cc_start: 0.8551 (tpp) cc_final: 0.8053 (tpp) REVERT: h 50 ASP cc_start: 0.8858 (t0) cc_final: 0.8331 (t0) REVERT: h 51 THR cc_start: 0.9563 (OUTLIER) cc_final: 0.9344 (p) REVERT: h 70 ASP cc_start: 0.8929 (m-30) cc_final: 0.8418 (m-30) REVERT: h 104 LEU cc_start: 0.8666 (tp) cc_final: 0.8449 (mt) REVERT: i 32 MET cc_start: 0.8364 (tpp) cc_final: 0.7109 (tpp) REVERT: i 104 LEU cc_start: 0.8482 (tp) cc_final: 0.8149 (mt) outliers start: 200 outliers final: 45 residues processed: 797 average time/residue: 0.4947 time to fit residues: 592.8832 Evaluate side-chains 377 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 320 time to evaluate : 3.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain f residue 37 VAL Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain h residue 51 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 9.9990 chunk 284 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 191 optimal weight: 0.9990 chunk 151 optimal weight: 0.7980 chunk 293 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 218 optimal weight: 20.0000 chunk 340 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 58 ASN 1 60 ASN 1 65 ASN 2 38 GLN 3 58 ASN ** 3 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 38 GLN 6 577 GLN 6 611 ASN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN A 203 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN B 156 ASN B 203 GLN ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 156 ASN C 203 GLN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN D 577 GLN D 611 ASN E 575 GLN E 577 GLN E 611 ASN H 58 ASN H 60 ASN ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 GLN ** X 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 32 ASN ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 17 GLN a 17 GLN f 6 GLN f 118 GLN g 118 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 32812 Z= 0.320 Angle : 0.748 14.163 44619 Z= 0.365 Chirality : 0.048 0.402 5371 Planarity : 0.005 0.059 5463 Dihedral : 16.151 87.249 7364 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.18 % Allowed : 13.59 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.57 (0.12), residues: 3777 helix: -1.01 (0.23), residues: 435 sheet: -1.43 (0.14), residues: 1221 loop : -2.04 (0.12), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 1 54 HIS 0.008 0.001 HIS M 3 PHE 0.021 0.002 PHE f 115 TYR 0.018 0.002 TYR Z 49 ARG 0.008 0.001 ARG 1 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 372 time to evaluate : 3.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 1 GLN cc_start: 0.7850 (tp40) cc_final: 0.7409 (tp40) REVERT: 1 76 ASN cc_start: 0.9068 (t0) cc_final: 0.8832 (t0) REVERT: 1 94 ARG cc_start: 0.8017 (tmm160) cc_final: 0.7631 (ttp80) REVERT: 2 1 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7439 (m-30) REVERT: 2 45 ARG cc_start: 0.8944 (tpm170) cc_final: 0.8560 (tpm170) REVERT: 3 94 ARG cc_start: 0.7733 (tmm160) cc_final: 0.7519 (ttp80) REVERT: 6 659 ASP cc_start: 0.9169 (t0) cc_final: 0.8838 (m-30) REVERT: A 114 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8532 (tm-30) REVERT: B 125 LEU cc_start: 0.9645 (tp) cc_final: 0.9288 (tp) REVERT: B 138 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8018 (tt) REVERT: B 475 MET cc_start: 0.8943 (mmm) cc_final: 0.8741 (mmm) REVERT: C 114 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8632 (tm-30) REVERT: C 138 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8176 (tt) REVERT: D 601 LYS cc_start: 0.8863 (mttt) cc_final: 0.8606 (ttpp) REVERT: D 629 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9343 (mp) REVERT: D 651 ASN cc_start: 0.9376 (t0) cc_final: 0.8974 (p0) REVERT: D 659 ASP cc_start: 0.9132 (t0) cc_final: 0.8891 (m-30) REVERT: E 584 GLU cc_start: 0.8548 (tt0) cc_final: 0.8324 (tm-30) REVERT: E 601 LYS cc_start: 0.8866 (mttt) cc_final: 0.8526 (ttpp) REVERT: E 629 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9134 (mt) REVERT: E 638 TYR cc_start: 0.8606 (m-80) cc_final: 0.8101 (m-10) REVERT: E 659 ASP cc_start: 0.9121 (t0) cc_final: 0.8859 (m-30) REVERT: H 94 ARG cc_start: 0.8114 (tmm160) cc_final: 0.7488 (ttp80) REVERT: L 45 ARG cc_start: 0.8762 (tpm170) cc_final: 0.8387 (tpm170) REVERT: N 47 ILE cc_start: 0.9325 (OUTLIER) cc_final: 0.8943 (mt) REVERT: N 54 ARG cc_start: 0.8557 (ptt-90) cc_final: 0.8243 (ptt90) REVERT: N 67 THR cc_start: 0.9440 (OUTLIER) cc_final: 0.8968 (p) REVERT: Q 3 GLN cc_start: 0.8275 (mm110) cc_final: 0.8055 (mp10) REVERT: Q 118 GLN cc_start: 0.8899 (tm-30) cc_final: 0.8618 (tm-30) REVERT: R 103 GLU cc_start: 0.8237 (tm-30) cc_final: 0.8028 (tm-30) REVERT: X 23 ASN cc_start: 0.8808 (t0) cc_final: 0.8554 (t0) REVERT: X 64 LYS cc_start: 0.9136 (tppt) cc_final: 0.8525 (tppt) REVERT: Y 23 ASN cc_start: 0.9032 (t0) cc_final: 0.8768 (t0) REVERT: Y 100 LYS cc_start: 0.9491 (mptt) cc_final: 0.9290 (mmmm) REVERT: Z 67 THR cc_start: 0.9387 (OUTLIER) cc_final: 0.8934 (p) REVERT: a 28 LEU cc_start: 0.9159 (mp) cc_final: 0.8803 (mp) REVERT: a 67 THR cc_start: 0.9372 (OUTLIER) cc_final: 0.8931 (p) REVERT: f 3 GLN cc_start: 0.8349 (mm110) cc_final: 0.8099 (mp10) REVERT: f 70 MET cc_start: 0.8808 (mtp) cc_final: 0.8349 (mtm) REVERT: f 100 GLU cc_start: 0.8415 (tt0) cc_final: 0.8156 (tt0) REVERT: g 111 TYR cc_start: 0.8757 (m-80) cc_final: 0.8246 (m-80) REVERT: h 32 MET cc_start: 0.8453 (tpp) cc_final: 0.7937 (tpp) REVERT: i 32 MET cc_start: 0.8024 (tpp) cc_final: 0.7463 (tpp) outliers start: 139 outliers final: 82 residues processed: 492 average time/residue: 0.4904 time to fit residues: 373.9270 Evaluate side-chains 383 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 292 time to evaluate : 3.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 1 ASP Chi-restraints excluded: chain 4 residue 38 GLN Chi-restraints excluded: chain 4 residue 42 GLN Chi-restraints excluded: chain 4 residue 92 VAL Chi-restraints excluded: chain 6 residue 513 VAL Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain 6 residue 538 THR Chi-restraints excluded: chain 6 residue 604 CYS Chi-restraints excluded: chain 6 residue 639 THR Chi-restraints excluded: chain 6 residue 641 ILE Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain B residue 53 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 604 CYS Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 80 ASP Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 94 THR Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain h residue 60 ASP Chi-restraints excluded: chain h residue 63 VAL Chi-restraints excluded: chain i residue 60 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 283 optimal weight: 8.9990 chunk 231 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 341 optimal weight: 2.9990 chunk 368 optimal weight: 4.9990 chunk 303 optimal weight: 9.9990 chunk 338 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 273 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 30AHIS 3 39 GLN ** 3 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 65 ASN 4 30AHIS ** 6 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30AHIS ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN ** X 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 6 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 32812 Z= 0.420 Angle : 0.758 11.957 44619 Z= 0.367 Chirality : 0.048 0.416 5371 Planarity : 0.004 0.050 5463 Dihedral : 14.136 85.652 7336 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 5.29 % Allowed : 13.32 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.16 (0.13), residues: 3777 helix: -0.25 (0.24), residues: 435 sheet: -1.21 (0.14), residues: 1218 loop : -1.85 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 96 HIS 0.006 0.001 HIS A 72 PHE 0.027 0.002 PHE f 115 TYR 0.028 0.002 TYR 6 638 ARG 0.009 0.001 ARG g 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 309 time to evaluate : 3.630 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: 1 94 ARG cc_start: 0.7938 (tmm160) cc_final: 0.7616 (ttp80) REVERT: 2 1 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7303 (m-30) REVERT: 2 45 ARG cc_start: 0.9045 (tpm170) cc_final: 0.8663 (tpm170) REVERT: 4 1 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7251 (m-30) REVERT: 6 595 ILE cc_start: 0.9212 (pt) cc_final: 0.8917 (tt) REVERT: A 138 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8319 (tp) REVERT: B 475 MET cc_start: 0.8985 (mmm) cc_final: 0.8616 (mmm) REVERT: B 480 ARG cc_start: 0.9412 (OUTLIER) cc_final: 0.8169 (mtm110) REVERT: C 104 MET cc_start: 0.9542 (OUTLIER) cc_final: 0.8863 (ttm) REVERT: C 114 GLN cc_start: 0.8983 (mm-40) cc_final: 0.8637 (tm-30) REVERT: C 138 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8056 (tp) REVERT: C 150 MET cc_start: 0.8570 (tmm) cc_final: 0.7615 (tmm) REVERT: D 584 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7798 (tm-30) REVERT: D 601 LYS cc_start: 0.8897 (mttt) cc_final: 0.8629 (ttmm) REVERT: D 659 ASP cc_start: 0.9095 (t0) cc_final: 0.8856 (m-30) REVERT: E 584 GLU cc_start: 0.8615 (tt0) cc_final: 0.8323 (tm-30) REVERT: E 601 LYS cc_start: 0.8936 (mttt) cc_final: 0.8693 (ttmm) REVERT: E 659 ASP cc_start: 0.9132 (t0) cc_final: 0.8786 (m-30) REVERT: H 94 ARG cc_start: 0.8050 (tmm160) cc_final: 0.7457 (ttp80) REVERT: N 54 ARG cc_start: 0.8573 (ptt-90) cc_final: 0.8214 (ptt90) REVERT: N 67 THR cc_start: 0.9430 (OUTLIER) cc_final: 0.8925 (p) REVERT: Q 3 GLN cc_start: 0.8420 (mm110) cc_final: 0.8122 (mp10) REVERT: Q 118 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8706 (tm-30) REVERT: X 30 ARG cc_start: 0.8764 (tpp80) cc_final: 0.8140 (tpp80) REVERT: X 44 GLN cc_start: 0.8295 (pp30) cc_final: 0.7977 (pp30) REVERT: X 53 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7314 (p0) REVERT: X 100 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8268 (mt-10) REVERT: X 100 MET cc_start: 0.9212 (mpp) cc_final: 0.8841 (mmm) REVERT: Y 30 ARG cc_start: 0.8740 (tpp80) cc_final: 0.8479 (tpp80) REVERT: Y 53 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7365 (p0) REVERT: Y 100 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8006 (mt-10) REVERT: Z 67 THR cc_start: 0.9376 (OUTLIER) cc_final: 0.8860 (p) REVERT: a 67 THR cc_start: 0.9378 (OUTLIER) cc_final: 0.8940 (p) REVERT: a 83 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7866 (pp20) REVERT: f 3 GLN cc_start: 0.8497 (mm110) cc_final: 0.8186 (mp10) REVERT: f 100 GLU cc_start: 0.8412 (tt0) cc_final: 0.8174 (tt0) REVERT: g 3 GLN cc_start: 0.8282 (mp10) cc_final: 0.7824 (mp10) REVERT: g 111 TYR cc_start: 0.8762 (m-80) cc_final: 0.8341 (m-80) REVERT: h 32 MET cc_start: 0.8608 (tpp) cc_final: 0.8100 (tpp) REVERT: i 32 MET cc_start: 0.8195 (tpp) cc_final: 0.7863 (tpp) outliers start: 176 outliers final: 114 residues processed: 457 average time/residue: 0.4566 time to fit residues: 327.9128 Evaluate side-chains 389 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 264 time to evaluate : 4.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 1 ASP Chi-restraints excluded: chain 2 residue 73 LEU Chi-restraints excluded: chain 3 residue 12 VAL Chi-restraints excluded: chain 4 residue 1 ASP Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 4 residue 4 MET Chi-restraints excluded: chain 4 residue 38 GLN Chi-restraints excluded: chain 4 residue 73 LEU Chi-restraints excluded: chain 4 residue 92 VAL Chi-restraints excluded: chain 6 residue 513 VAL Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain 6 residue 538 THR Chi-restraints excluded: chain 6 residue 583 VAL Chi-restraints excluded: chain 6 residue 598 CYS Chi-restraints excluded: chain 6 residue 604 CYS Chi-restraints excluded: chain 6 residue 635 ILE Chi-restraints excluded: chain 6 residue 639 THR Chi-restraints excluded: chain 6 residue 641 ILE Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 53 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 480 ARG Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 80 ASP Chi-restraints excluded: chain Q residue 82 ASP Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 48 ILE Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 82 VAL Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain Z residue 47 ILE Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 47 ILE Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 94 THR Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain g residue 82 ASP Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain h residue 60 ASP Chi-restraints excluded: chain h residue 63 VAL Chi-restraints excluded: chain i residue 60 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 2.9990 chunk 256 optimal weight: 4.9990 chunk 177 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 229 optimal weight: 9.9990 chunk 342 optimal weight: 0.9990 chunk 362 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 chunk 324 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 60 ASN ** 4 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 HIS ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 GLN ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 76 ASN ** g 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32812 Z= 0.193 Angle : 0.661 11.695 44619 Z= 0.319 Chirality : 0.046 0.428 5371 Planarity : 0.004 0.065 5463 Dihedral : 12.240 79.337 7329 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.55 % Allowed : 15.87 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.77 (0.13), residues: 3777 helix: 0.54 (0.26), residues: 399 sheet: -1.13 (0.14), residues: 1269 loop : -1.53 (0.13), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 112 HIS 0.004 0.001 HIS X 3 PHE 0.021 0.002 PHE f 115 TYR 0.017 0.001 TYR 6 638 ARG 0.008 0.001 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 325 time to evaluate : 3.606 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: 1 94 ARG cc_start: 0.7809 (tmm160) cc_final: 0.7581 (ttp80) REVERT: 2 4 MET cc_start: 0.3910 (OUTLIER) cc_final: 0.3457 (mtt) REVERT: 2 45 ARG cc_start: 0.9037 (tpm170) cc_final: 0.8630 (tpm170) REVERT: 4 1 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7207 (m-30) REVERT: 4 4 MET cc_start: 0.3633 (OUTLIER) cc_final: 0.2773 (ptp) REVERT: 4 24 ARG cc_start: 0.8702 (mmt90) cc_final: 0.8177 (mmt-90) REVERT: 6 601 LYS cc_start: 0.8977 (mttt) cc_final: 0.8555 (ttpt) REVERT: 6 647 GLU cc_start: 0.8513 (tp30) cc_final: 0.7837 (tp30) REVERT: A 104 MET cc_start: 0.9473 (OUTLIER) cc_final: 0.9092 (ttm) REVERT: A 114 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8703 (tm-30) REVERT: C 104 MET cc_start: 0.9505 (OUTLIER) cc_final: 0.8712 (ttm) REVERT: C 138 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8083 (tp) REVERT: D 584 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7916 (tm-30) REVERT: D 601 LYS cc_start: 0.8854 (mttt) cc_final: 0.8576 (ttmm) REVERT: E 584 GLU cc_start: 0.8570 (tt0) cc_final: 0.8287 (tm-30) REVERT: E 601 LYS cc_start: 0.8824 (mttt) cc_final: 0.8587 (ttmm) REVERT: H 94 ARG cc_start: 0.7845 (tmm160) cc_final: 0.7356 (ttp80) REVERT: L 36 TYR cc_start: 0.4993 (m-80) cc_final: 0.4790 (m-10) REVERT: M 100 MET cc_start: 0.9136 (mpp) cc_final: 0.8593 (mmm) REVERT: N 54 ARG cc_start: 0.8559 (ptt-90) cc_final: 0.8246 (ptt90) REVERT: N 96 TRP cc_start: 0.8077 (m100) cc_final: 0.7282 (m100) REVERT: Q 3 GLN cc_start: 0.8464 (mm110) cc_final: 0.8182 (mp10) REVERT: Q 118 GLN cc_start: 0.8943 (tm-30) cc_final: 0.8632 (tm-30) REVERT: X 64 LYS cc_start: 0.9090 (tppt) cc_final: 0.8558 (tppt) REVERT: X 100 MET cc_start: 0.9158 (mpp) cc_final: 0.8674 (mpp) REVERT: Y 30 ARG cc_start: 0.8797 (tpp80) cc_final: 0.8262 (tpp80) REVERT: Y 53 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.6923 (p0) REVERT: Y 64 LYS cc_start: 0.9112 (tppt) cc_final: 0.8590 (tppt) REVERT: Y 100 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7994 (mt-10) REVERT: Z 67 THR cc_start: 0.9402 (OUTLIER) cc_final: 0.8922 (p) REVERT: Z 96 TRP cc_start: 0.7882 (m100) cc_final: 0.7271 (m100) REVERT: f 3 GLN cc_start: 0.8523 (mm110) cc_final: 0.8295 (mp10) REVERT: g 3 GLN cc_start: 0.8265 (mp10) cc_final: 0.7874 (mp10) REVERT: h 32 MET cc_start: 0.8451 (tpp) cc_final: 0.8071 (tpp) REVERT: i 32 MET cc_start: 0.7997 (tpp) cc_final: 0.7718 (tpp) outliers start: 118 outliers final: 77 residues processed: 416 average time/residue: 0.4564 time to fit residues: 297.7603 Evaluate side-chains 369 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 284 time to evaluate : 3.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 4 MET Chi-restraints excluded: chain 4 residue 1 ASP Chi-restraints excluded: chain 4 residue 4 MET Chi-restraints excluded: chain 4 residue 73 LEU Chi-restraints excluded: chain 4 residue 92 VAL Chi-restraints excluded: chain 6 residue 513 VAL Chi-restraints excluded: chain 6 residue 522 PHE Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain 6 residue 604 CYS Chi-restraints excluded: chain 6 residue 639 THR Chi-restraints excluded: chain 6 residue 641 ILE Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 53 PHE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 100 LYS Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain Z residue 47 ILE Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 94 THR Chi-restraints excluded: chain g residue 31 ASP Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain i residue 60 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/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: 68.042 > 50: distance: 46 - 56: 33.631 distance: 56 - 57: 25.472 distance: 57 - 58: 49.687 distance: 57 - 60: 46.173 distance: 58 - 59: 43.867 distance: 58 - 64: 53.500 distance: 60 - 61: 7.534 distance: 61 - 62: 14.054 distance: 61 - 63: 15.569 distance: 65 - 66: 23.258 distance: 65 - 68: 5.072 distance: 66 - 67: 36.182 distance: 66 - 72: 32.410 distance: 68 - 69: 31.821 distance: 69 - 70: 14.492 distance: 69 - 71: 20.132 distance: 73 - 74: 43.674 distance: 73 - 76: 9.271 distance: 74 - 75: 54.613 distance: 74 - 80: 41.883 distance: 76 - 77: 23.112 distance: 77 - 78: 36.286 distance: 77 - 79: 29.522 distance: 80 - 81: 38.977 distance: 81 - 82: 41.440 distance: 81 - 84: 52.655 distance: 82 - 83: 59.944 distance: 82 - 88: 10.999 distance: 84 - 85: 33.101 distance: 85 - 86: 46.086 distance: 88 - 89: 8.601 distance: 89 - 90: 47.575 distance: 89 - 92: 42.973 distance: 90 - 91: 20.888 distance: 90 - 99: 68.042 distance: 92 - 93: 46.060 distance: 93 - 94: 27.705 distance: 94 - 95: 18.993 distance: 95 - 96: 9.328 distance: 96 - 97: 10.130 distance: 96 - 98: 6.226 distance: 99 - 100: 33.279 distance: 99 - 105: 53.031 distance: 100 - 101: 7.747 distance: 100 - 103: 32.622 distance: 103 - 104: 32.362 distance: 104 - 105: 35.061 distance: 106 - 107: 56.425 distance: 107 - 108: 44.591 distance: 107 - 110: 5.441 distance: 108 - 109: 20.552 distance: 108 - 112: 44.983 distance: 110 - 111: 37.681 distance: 112 - 113: 33.815 distance: 113 - 114: 7.365 distance: 114 - 115: 47.867 distance: 114 - 116: 12.533 distance: 116 - 117: 43.178 distance: 117 - 118: 21.996 distance: 117 - 120: 33.093 distance: 118 - 119: 60.857 distance: 118 - 124: 26.482 distance: 120 - 121: 37.285 distance: 120 - 122: 44.809 distance: 121 - 123: 56.092 distance: 124 - 125: 10.995 distance: 124 - 130: 11.776 distance: 125 - 126: 51.037 distance: 125 - 128: 15.830 distance: 126 - 127: 60.787 distance: 126 - 131: 28.046 distance: 128 - 129: 36.421 distance: 129 - 130: 28.353