Starting phenix.real_space_refine on Wed Feb 21 23:54:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot1_20191/02_2024/6ot1_20191.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot1_20191/02_2024/6ot1_20191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot1_20191/02_2024/6ot1_20191.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot1_20191/02_2024/6ot1_20191.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot1_20191/02_2024/6ot1_20191.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot1_20191/02_2024/6ot1_20191.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.106 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 20226 2.51 5 N 5331 2.21 5 O 6525 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 632": "OD1" <-> "OD2" Residue "B ASP 659": "OD1" <-> "OD2" Residue "B ASP 664": "OD1" <-> "OD2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 78": "OD1" <-> "OD2" Residue "G GLU 87": "OE1" <-> "OE2" Residue "G PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 140": "OD1" <-> "OD2" Residue "G GLU 153": "OE1" <-> "OE2" Residue "G PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 164": "OE1" <-> "OE2" Residue "G TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 56": "NH1" <-> "NH2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H ARG 94": "NH1" <-> "NH2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "H ARG 105": "NH1" <-> "NH2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L GLU 50": "OE1" <-> "OE2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ASP 60": "OD1" <-> "OD2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 77": "NH1" <-> "NH2" Residue "L ASP 82": "OD1" <-> "OD2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "m PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 100": "OE1" <-> "OE2" Residue "q ARG 61": "NH1" <-> "NH2" Residue "q TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 100": "OD1" <-> "OD2" Residue "r TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 52": "NH1" <-> "NH2" Residue "r PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 632": "OD1" <-> "OD2" Residue "O ASP 659": "OD1" <-> "OD2" Residue "O ASP 664": "OD1" <-> "OD2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 78": "OD1" <-> "OD2" Residue "E GLU 87": "OE1" <-> "OE2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 140": "OD1" <-> "OD2" Residue "E GLU 153": "OE1" <-> "OE2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 164": "OE1" <-> "OE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "A ARG 66": "NH1" <-> "NH2" Residue "A ARG 94": "NH1" <-> "NH2" Residue "A ASP 101": "OD1" <-> "OD2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C ARG 24": "NH1" <-> "NH2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C ASP 60": "OD1" <-> "OD2" Residue "C ARG 61": "NH1" <-> "NH2" Residue "C PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ASP 82": "OD1" <-> "OD2" Residue "C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 100": "OE1" <-> "OE2" Residue "J ARG 61": "NH1" <-> "NH2" Residue "J TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 100": "OD1" <-> "OD2" Residue "K TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 52": "NH1" <-> "NH2" Residue "K PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 632": "OD1" <-> "OD2" Residue "D ASP 659": "OD1" <-> "OD2" Residue "D ASP 664": "OD1" <-> "OD2" Residue "P TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 78": "OD1" <-> "OD2" Residue "P GLU 87": "OE1" <-> "OE2" Residue "P PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 140": "OD1" <-> "OD2" Residue "P GLU 153": "OE1" <-> "OE2" Residue "P PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 164": "OE1" <-> "OE2" Residue "P TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 38": "NH1" <-> "NH2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "M TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 56": "NH1" <-> "NH2" Residue "M ARG 66": "NH1" <-> "NH2" Residue "M ARG 94": "NH1" <-> "NH2" Residue "M ASP 101": "OD1" <-> "OD2" Residue "M ARG 105": "NH1" <-> "NH2" Residue "N GLU 17": "OE1" <-> "OE2" Residue "N ARG 24": "NH1" <-> "NH2" Residue "N GLU 50": "OE1" <-> "OE2" Residue "N ARG 54": "NH1" <-> "NH2" Residue "N ASP 60": "OD1" <-> "OD2" Residue "N ARG 61": "NH1" <-> "NH2" Residue "N PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 77": "NH1" <-> "NH2" Residue "N ASP 82": "OD1" <-> "OD2" Residue "N PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 105": "OE1" <-> "OE2" Residue "Q PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 100": "OE1" <-> "OE2" Residue "S ARG 61": "NH1" <-> "NH2" Residue "S TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 100": "OD1" <-> "OD2" Residue "T TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 52": "NH1" <-> "NH2" Residue "T PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32247 Number of models: 1 Model: "" Number of chains: 75 Chain: "B" 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: "G" 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: "H" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 945 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "L" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 105} Chain: "m" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "n" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "q" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "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: "O" 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: 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: "A" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 945 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "C" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 105} Chain: "F" 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: "I" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "J" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "K" 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: "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: "P" 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: "M" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 945 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "N" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 105} Chain: "Q" 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: "R" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "S" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "T" 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: "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: 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: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: "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: 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: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 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: 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: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "l" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 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: "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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 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: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "4" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "6" 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: 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: "9" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "AA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "BA" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "CA" 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: "DA" 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: "EA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "FA" 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: "GA" 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "P" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 16.85, per 1000 atoms: 0.52 Number of scatterers: 32247 At special positions: 0 Unit cell: (160.988, 153.475, 155.621, 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 6525 8.00 N 5331 7.00 C 20226 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.04 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.02 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 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 92 " distance=2.03 Simple disulfide: pdb=" SG CYS q 98 " - pdb=" SG CYS q 100A" distance=2.03 Simple disulfide: pdb=" SG CYS r 23 " - pdb=" SG CYS r 87 " distance=2.04 Simple disulfide: pdb=" SG CYS O 598 " - pdb=" SG CYS O 604 " distance=2.02 Simple disulfide: pdb=" SG CYS O 605 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 98 " - pdb=" SG CYS J 100A" distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 87 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS P 501 " distance=2.03 Simple disulfide: pdb=" SG CYS P 54 " - pdb=" SG CYS P 74 " distance=2.04 Simple disulfide: pdb=" SG CYS P 119 " - pdb=" SG CYS P 205 " distance=2.03 Simple disulfide: pdb=" SG CYS P 126 " - pdb=" SG CYS P 196 " distance=2.03 Simple disulfide: pdb=" SG CYS P 131 " - pdb=" SG CYS P 157 " distance=2.03 Simple disulfide: pdb=" SG CYS P 201 " - pdb=" SG CYS P 433 " distance=2.02 Simple disulfide: pdb=" SG CYS P 218 " - pdb=" SG CYS P 247 " distance=2.03 Simple disulfide: pdb=" SG CYS P 228 " - pdb=" SG CYS P 239 " distance=2.03 Simple disulfide: pdb=" SG CYS P 296 " - pdb=" SG CYS P 331 " distance=2.02 Simple disulfide: pdb=" SG CYS P 378 " - pdb=" SG CYS P 445 " distance=2.03 Simple disulfide: pdb=" SG CYS P 385 " - pdb=" SG CYS P 418 " 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 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS S 98 " - pdb=" SG CYS S 100A" distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 87 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN d 4 " - " MAN d 5 " " MAN w 4 " - " MAN w 5 " " MANBA 4 " - " MANBA 5 " ALPHA1-3 " BMA 1 3 " - " MAN 1 4 " " BMA 3 3 " - " MAN 3 4 " " BMA 8 3 " - " MAN 8 4 " " BMA V 3 " - " MAN V 4 " " BMA a 3 " - " MAN a 4 " " BMA d 3 " - " MAN d 4 " " BMA f 3 " - " MAN f 4 " " BMA i 3 " - " MAN i 4 " " BMA k 3 " - " MAN k 4 " " BMA t 3 " - " MAN t 4 " " BMA w 3 " - " MAN w 4 " " BMA y 3 " - " MAN y 4 " " BMABA 3 " - " MANBA 4 " " BMADA 3 " - " MANDA 4 " " BMAGA 3 " - " MANGA 4 " ALPHA1-6 " BMA 1 3 " - " MAN 1 5 " " BMA 3 3 " - " MAN 3 5 " " BMA V 3 " - " MAN V 5 " " BMA d 3 " - " MAN d 6 " " BMA f 3 " - " MAN f 5 " " BMA i 3 " - " MAN i 5 " " BMA k 3 " - " MAN k 5 " " BMA w 3 " - " MAN w 6 " " BMA y 3 " - " MAN y 5 " " BMABA 3 " - " MANBA 6 " " BMADA 3 " - " MANDA 5 " " BMAGA 3 " - " MANGA 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 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 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 Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGCA 2 " - " BMACA 3 " " NAGDA 1 " - " NAGDA 2 " " NAGDA 2 " - " BMADA 3 " " NAGEA 1 " - " NAGEA 2 " " NAGEA 2 " - " BMAEA 3 " " NAGFA 1 " - " NAGFA 2 " " NAGGA 1 " - " NAGGA 2 " " NAGGA 2 " - " BMAGA 3 " NAG-ASN " NAG 0 1 " - " ASN E 448 " " NAG 1 1 " - " ASN E 276 " " NAG 2 1 " - " ASN P 88 " " NAG 3 1 " - " ASN P 137 " " NAG 4 1 " - " ASN P 156 " " NAG 5 1 " - " ASN P 160 " " NAG 6 1 " - " ASN P 197 " " NAG 7 1 " - " ASN P 234 " " NAG 8 1 " - " ASN P 262 " " NAG 9 1 " - " ASN P 295 " " NAG B 701 " - " ASN B 637 " " NAG D 701 " - " ASN D 637 " " NAG E 625 " - " ASN E 133 " " NAG E 632 " - " ASN E 339 " " NAG E 633 " - " ASN E 355 " " NAG G 625 " - " ASN G 133 " " NAG G 632 " - " ASN G 339 " " NAG G 633 " - " ASN G 355 " " NAG O 701 " - " ASN O 637 " " NAG P 625 " - " ASN P 133 " " NAG P 632 " - " ASN P 339 " " NAG P 633 " - " ASN P 355 " " NAG U 1 " - " ASN G 88 " " NAG V 1 " - " ASN G 137 " " NAG W 1 " - " ASN G 156 " " NAG X 1 " - " ASN G 160 " " NAG Y 1 " - " ASN G 197 " " NAG Z 1 " - " ASN G 234 " " NAG a 1 " - " ASN G 262 " " NAG b 1 " - " ASN G 295 " " NAG c 1 " - " ASN G 301 " " NAG d 1 " - " ASN G 332 " " NAG e 1 " - " ASN G 363 " " NAG f 1 " - " ASN G 386 " " NAG g 1 " - " ASN G 392 " " NAG h 1 " - " ASN G 448 " " NAG i 1 " - " ASN G 276 " " NAG j 1 " - " ASN E 88 " " NAG k 1 " - " ASN E 137 " " NAG l 1 " - " ASN E 156 " " NAG o 1 " - " ASN E 160 " " NAG p 1 " - " ASN E 197 " " NAG s 1 " - " ASN E 234 " " NAG t 1 " - " ASN E 262 " " NAG u 1 " - " ASN E 295 " " NAG v 1 " - " ASN E 301 " " NAG w 1 " - " ASN E 332 " " NAG x 1 " - " ASN E 363 " " NAG y 1 " - " ASN E 386 " " NAG z 1 " - " ASN E 392 " " NAGAA 1 " - " ASN P 301 " " NAGBA 1 " - " ASN P 332 " " NAGCA 1 " - " ASN P 363 " " NAGDA 1 " - " ASN P 386 " " NAGEA 1 " - " ASN P 392 " " NAGFA 1 " - " ASN P 448 " " NAGGA 1 " - " ASN P 276 " Time building additional restraints: 14.47 Conformation dependent library (CDL) restraints added in 5.8 seconds 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7086 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 93 sheets defined 11.9% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.76 Creating SS restraints... Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 removed outlier: 3.894A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 595 removed outlier: 3.617A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.606A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 664 removed outlier: 3.740A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 removed outlier: 3.826A pdb=" N GLU G 62 " --> pdb=" O LYS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 115 removed outlier: 3.588A pdb=" N HIS G 105 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.880A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 349 removed outlier: 3.691A pdb=" N GLU G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 354 Processing helix chain 'G' and resid 425 through 429 removed outlier: 4.406A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 480 removed outlier: 4.089A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.593A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.018A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 28 through 32 removed outlier: 3.671A pdb=" N ASP m 31 " --> pdb=" O LEU m 28 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN m 32 " --> pdb=" O VAL m 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 28 through 32' Processing helix chain 'n' and resid 79 through 83 removed outlier: 3.517A pdb=" N GLU n 83 " --> pdb=" O ALA n 80 " (cutoff:3.500A) Processing helix chain 'q' and resid 83 through 87 removed outlier: 3.990A pdb=" N THR q 87 " --> pdb=" O PRO q 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 529 through 534 Processing helix chain 'O' and resid 537 through 543 removed outlier: 3.892A pdb=" N ASN O 543 " --> pdb=" O VAL O 539 " (cutoff:3.500A) Processing helix chain 'O' and resid 572 through 595 removed outlier: 3.617A pdb=" N ALA O 578 " --> pdb=" O LYS O 574 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU O 581 " --> pdb=" O GLN O 577 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU O 584 " --> pdb=" O VAL O 580 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP O 589 " --> pdb=" O ARG O 585 " (cutoff:3.500A) Processing helix chain 'O' and resid 627 through 636 removed outlier: 3.607A pdb=" N LYS O 633 " --> pdb=" O LEU O 629 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU O 634 " --> pdb=" O GLN O 630 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER O 636 " --> pdb=" O ASP O 632 " (cutoff:3.500A) Processing helix chain 'O' and resid 641 through 664 removed outlier: 3.740A pdb=" N GLU O 647 " --> pdb=" O TYR O 643 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU O 648 " --> pdb=" O GLY O 644 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN O 653 " --> pdb=" O SER O 649 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU O 663 " --> pdb=" O ASP O 659 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP O 664 " --> pdb=" O LEU O 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 62 removed outlier: 3.827A pdb=" N GLU E 62 " --> pdb=" O LYS E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 115 removed outlier: 3.587A pdb=" N HIS E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE E 109 " --> pdb=" O HIS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.880A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 349 removed outlier: 3.691A pdb=" N GLU E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 354 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.408A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 480 removed outlier: 4.088A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.593A pdb=" N THR A 87 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 4.018A pdb=" N VAL C 83 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.672A pdb=" N ASP F 31 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN F 32 " --> pdb=" O VAL F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.517A pdb=" N GLU I 83 " --> pdb=" O ALA I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.990A pdb=" N THR J 87 " --> pdb=" O PRO J 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.893A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 595 removed outlier: 3.617A pdb=" N ALA D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.606A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER D 636 " --> pdb=" O ASP D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 664 removed outlier: 3.741A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP D 664 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 62 removed outlier: 3.826A pdb=" N GLU P 62 " --> pdb=" O LYS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 115 removed outlier: 3.587A pdb=" N HIS P 105 " --> pdb=" O VAL P 101 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE P 109 " --> pdb=" O HIS P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 126 removed outlier: 3.881A pdb=" N LEU P 125 " --> pdb=" O LEU P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 335 through 349 removed outlier: 3.690A pdb=" N GLU P 340 " --> pdb=" O ALA P 336 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS P 347 " --> pdb=" O GLY P 343 " (cutoff:3.500A) Processing helix chain 'P' and resid 349 through 354 Processing helix chain 'P' and resid 425 through 429 removed outlier: 4.407A pdb=" N ARG P 429 " --> pdb=" O MET P 426 " (cutoff:3.500A) Processing helix chain 'P' and resid 475 through 480 removed outlier: 4.088A pdb=" N TRP P 479 " --> pdb=" O MET P 475 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.593A pdb=" N THR M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.019A pdb=" N VAL N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 32 removed outlier: 3.672A pdb=" N ASP Q 31 " --> pdb=" O LEU Q 28 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN Q 32 " --> pdb=" O VAL Q 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 28 through 32' Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.518A pdb=" N GLU R 83 " --> pdb=" O ALA R 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 87 removed outlier: 3.991A pdb=" N THR S 87 " --> pdb=" O PRO S 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 609 removed outlier: 7.991A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.509A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 91 through 92 removed outlier: 3.563A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 154 through 155 Processing sheet with id=AA5, first strand: chain 'G' and resid 158 through 162 Processing sheet with id=AA6, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'G' and resid 260 through 261 removed outlier: 6.791A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 11.206A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.368A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 11.896A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 260 through 261 removed outlier: 6.791A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 297 through 298 Processing sheet with id=AB1, first strand: chain 'G' and resid 304 through 308 Processing sheet with id=AB2, first strand: chain 'G' and resid 330 through 334 Processing sheet with id=AB3, first strand: chain 'G' and resid 375 through 378 Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.561A pdb=" N SER H 70 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.694A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE H 32 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N TYR H 52 " --> pdb=" O PHE H 32 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.694A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG H 94 " --> pdb=" O VAL H 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.584A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU L 89 " --> pdb=" O HIS L 34 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'm' and resid 11 through 12 removed outlier: 3.503A pdb=" N THR m 105 " --> pdb=" O TYR m 90 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR m 33 " --> pdb=" O THR m 95 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP m 34 " --> pdb=" O TYR m 50 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR m 50 " --> pdb=" O TRP m 34 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP m 36 " --> pdb=" O ILE m 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'm' and resid 11 through 12 removed outlier: 3.503A pdb=" N THR m 105 " --> pdb=" O TYR m 90 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N CYS m 92 " --> pdb=" O TRP m 101 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N TRP m 101 " --> pdb=" O CYS m 92 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR m 94 " --> pdb=" O ASP m 100Q" (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY m 98 " --> pdb=" O TYR m 100M" (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'm' and resid 18 through 22 Processing sheet with id=AC3, first strand: chain 'n' and resid 9 through 13 removed outlier: 3.761A pdb=" N ALA n 84 " --> pdb=" O LEU n 104 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR n 87 " --> pdb=" O TYR n 36 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP n 35 " --> pdb=" O ILE n 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'n' and resid 19 through 20 Processing sheet with id=AC5, first strand: chain 'n' and resid 23 through 26 removed outlier: 3.663A pdb=" N ALA n 71 " --> pdb=" O CYS n 23 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'q' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'q' and resid 10 through 11 removed outlier: 6.365A pdb=" N VAL q 10 " --> pdb=" O VAL q 110 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS q 35 " --> pdb=" O VAL q 93 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'q' and resid 10 through 11 removed outlier: 6.365A pdb=" N VAL q 10 " --> pdb=" O VAL q 110 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS q 92 " --> pdb=" O TRP q 103 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TRP q 103 " --> pdb=" O CYS q 92 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG q 94 " --> pdb=" O GLN q 101 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'q' and resid 17 through 19 Processing sheet with id=AD1, first strand: chain 'q' and resid 49 through 52 removed outlier: 3.500A pdb=" N SER q 58 " --> pdb=" O TRP q 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'r' and resid 5 through 6 Processing sheet with id=AD3, first strand: chain 'r' and resid 10 through 13 removed outlier: 6.452A pdb=" N TRP r 34 " --> pdb=" O LEU r 46 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR r 48 " --> pdb=" O ARG r 52 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'r' and resid 10 through 13 Processing sheet with id=AD5, first strand: chain 'O' and resid 603 through 609 removed outlier: 7.992A pdb=" N THR O 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N VAL E 38 " --> pdb=" O THR O 606 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL O 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.507A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 91 through 92 removed outlier: 3.562A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 154 through 155 Processing sheet with id=AD9, first strand: chain 'E' and resid 158 through 162 Processing sheet with id=AE1, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AE2, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.790A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.206A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.367A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.896A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.023A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.790A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 297 through 298 Processing sheet with id=AE5, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AE6, first strand: chain 'E' and resid 330 through 334 Processing sheet with id=AE7, first strand: chain 'E' and resid 375 through 378 Processing sheet with id=AE8, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.559A pdb=" N SER A 70 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.692A pdb=" N VAL A 12 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N PHE A 32 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N TYR A 52 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY A 50 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.692A pdb=" N VAL A 12 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A 94 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 5 through 7 Processing sheet with id=AF3, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.584A pdb=" N GLU C 105 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU C 89 " --> pdb=" O HIS C 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.503A pdb=" N THR F 105 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR F 33 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR F 50 " --> pdb=" O TRP F 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.503A pdb=" N THR F 105 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N CYS F 92 " --> pdb=" O TRP F 101 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N TRP F 101 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR F 94 " --> pdb=" O ASP F 100Q" (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY F 98 " --> pdb=" O TYR F 100M" (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 18 through 22 Processing sheet with id=AF7, first strand: chain 'I' and resid 9 through 13 removed outlier: 3.760A pdb=" N ALA I 84 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR I 87 " --> pdb=" O TYR I 36 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP I 35 " --> pdb=" O ILE I 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 19 through 20 Processing sheet with id=AF9, first strand: chain 'I' and resid 23 through 26 removed outlier: 3.664A pdb=" N ALA I 71 " --> pdb=" O CYS I 23 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AG2, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.364A pdb=" N VAL J 10 " --> pdb=" O VAL J 110 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS J 35 " --> pdb=" O VAL J 93 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.364A pdb=" N VAL J 10 " --> pdb=" O VAL J 110 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS J 92 " --> pdb=" O TRP J 103 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TRP J 103 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ARG J 94 " --> pdb=" O GLN J 101 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 17 through 19 Processing sheet with id=AG5, first strand: chain 'J' and resid 49 through 52 removed outlier: 3.502A pdb=" N SER J 58 " --> pdb=" O TRP J 50 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 5 through 6 Processing sheet with id=AG7, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.452A pdb=" N TRP K 34 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR K 48 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 10 through 13 Processing sheet with id=AG9, first strand: chain 'D' and resid 603 through 609 removed outlier: 7.991A pdb=" N THR D 606 " --> pdb=" O VAL P 38 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N VAL P 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL D 608 " --> pdb=" O VAL P 36 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'P' and resid 45 through 47 removed outlier: 3.510A pdb=" N ILE P 225 " --> pdb=" O VAL P 245 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'P' and resid 91 through 92 removed outlier: 3.562A pdb=" N GLU P 91 " --> pdb=" O CYS P 239 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'P' and resid 154 through 155 Processing sheet with id=AH4, first strand: chain 'P' and resid 158 through 162 Processing sheet with id=AH5, first strand: chain 'P' and resid 181 through 183 Processing sheet with id=AH6, first strand: chain 'P' and resid 260 through 261 removed outlier: 6.791A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLY P 451 " --> pdb=" O THR P 290 " (cutoff:3.500A) removed outlier: 11.206A pdb=" N THR P 290 " --> pdb=" O GLY P 451 " (cutoff:3.500A) removed outlier: 11.368A pdb=" N ILE P 453 " --> pdb=" O PHE P 288 " (cutoff:3.500A) removed outlier: 11.896A pdb=" N PHE P 288 " --> pdb=" O ILE P 453 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N THR P 455 " --> pdb=" O VAL P 286 " (cutoff:3.500A) removed outlier: 10.547A pdb=" N VAL P 286 " --> pdb=" O THR P 455 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'P' and resid 260 through 261 removed outlier: 6.791A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG P 360 " --> pdb=" O PHE P 468 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'P' and resid 297 through 298 Processing sheet with id=AH9, first strand: chain 'P' and resid 304 through 308 Processing sheet with id=AI1, first strand: chain 'P' and resid 330 through 334 Processing sheet with id=AI2, first strand: chain 'P' and resid 375 through 378 Processing sheet with id=AI3, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.561A pdb=" N SER M 70 " --> pdb=" O ALA M 79 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.691A pdb=" N VAL M 12 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE M 32 " --> pdb=" O TYR M 52 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N TYR M 52 " --> pdb=" O PHE M 32 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP M 34 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.691A pdb=" N VAL M 12 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG M 94 " --> pdb=" O VAL M 102 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AI7, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.585A pdb=" N GLU N 105 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU N 89 " --> pdb=" O HIS N 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'Q' and resid 11 through 12 removed outlier: 3.502A pdb=" N THR Q 105 " --> pdb=" O TYR Q 90 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR Q 33 " --> pdb=" O THR Q 95 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR Q 50 " --> pdb=" O TRP Q 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'Q' and resid 11 through 12 removed outlier: 3.502A pdb=" N THR Q 105 " --> pdb=" O TYR Q 90 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N CYS Q 92 " --> pdb=" O TRP Q 101 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N TRP Q 101 " --> pdb=" O CYS Q 92 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR Q 94 " --> pdb=" O ASP Q 100Q" (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY Q 98 " --> pdb=" O TYR Q 100M" (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'Q' and resid 18 through 22 Processing sheet with id=AJ2, first strand: chain 'R' and resid 9 through 13 removed outlier: 3.760A pdb=" N ALA R 84 " --> pdb=" O LEU R 104 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR R 87 " --> pdb=" O TYR R 36 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP R 35 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'R' and resid 19 through 20 Processing sheet with id=AJ4, first strand: chain 'R' and resid 23 through 26 removed outlier: 3.663A pdb=" N ALA R 71 " --> pdb=" O CYS R 23 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AJ6, first strand: chain 'S' and resid 10 through 11 removed outlier: 6.362A pdb=" N VAL S 10 " --> pdb=" O VAL S 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS S 35 " --> pdb=" O VAL S 93 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'S' and resid 10 through 11 removed outlier: 6.362A pdb=" N VAL S 10 " --> pdb=" O VAL S 110 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N CYS S 92 " --> pdb=" O TRP S 103 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TRP S 103 " --> pdb=" O CYS S 92 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ARG S 94 " --> pdb=" O GLN S 101 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'S' and resid 17 through 19 Processing sheet with id=AJ9, first strand: chain 'S' and resid 49 through 52 removed outlier: 3.500A pdb=" N SER S 58 " --> pdb=" O TRP S 50 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'T' and resid 5 through 6 Processing sheet with id=AK2, first strand: chain 'T' and resid 10 through 13 removed outlier: 6.452A pdb=" N TRP T 34 " --> pdb=" O LEU T 46 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR T 48 " --> pdb=" O ARG T 52 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'T' and resid 10 through 13 924 hydrogen bonds defined for protein. 2214 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: 12.46 Time building geometry restraints manager: 15.45 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: 9970 1.34 - 1.46: 8484 1.46 - 1.58: 14276 1.58 - 1.70: 0 1.70 - 1.82: 216 Bond restraints: 32946 Sorted by residual: bond pdb=" C THR G 123 " pdb=" N PRO G 124 " ideal model delta sigma weight residual 1.334 1.379 -0.045 8.40e-03 1.42e+04 2.89e+01 bond pdb=" C THR P 123 " pdb=" N PRO P 124 " ideal model delta sigma weight residual 1.334 1.378 -0.044 8.40e-03 1.42e+04 2.73e+01 bond pdb=" C THR E 123 " pdb=" N PRO E 124 " ideal model delta sigma weight residual 1.334 1.377 -0.043 8.40e-03 1.42e+04 2.63e+01 bond pdb=" C1 NAG 2 1 " pdb=" O5 NAG 2 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.15e+00 bond pdb=" C1 BMA z 3 " pdb=" C2 BMA z 3 " ideal model delta sigma weight residual 1.519 1.568 -0.049 2.00e-02 2.50e+03 6.12e+00 ... (remaining 32941 not shown) Histogram of bond angle deviations from ideal: 98.73 - 105.83: 715 105.83 - 112.94: 18611 112.94 - 120.04: 10843 120.04 - 127.15: 14120 127.15 - 134.26: 501 Bond angle restraints: 44790 Sorted by residual: angle pdb=" C GLY L 68 " pdb=" N THR L 69 " pdb=" CA THR L 69 " ideal model delta sigma weight residual 121.54 131.18 -9.64 1.91e+00 2.74e-01 2.55e+01 angle pdb=" C GLY C 68 " pdb=" N THR C 69 " pdb=" CA THR C 69 " ideal model delta sigma weight residual 121.54 131.08 -9.54 1.91e+00 2.74e-01 2.50e+01 angle pdb=" C GLY N 68 " pdb=" N THR N 69 " pdb=" CA THR N 69 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.49e+01 angle pdb=" C CYS J 98 " pdb=" N ASP J 99 " pdb=" CA ASP J 99 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C CYS q 98 " pdb=" N ASP q 99 " pdb=" CA ASP q 99 " ideal model delta sigma weight residual 121.54 130.43 -8.89 1.91e+00 2.74e-01 2.17e+01 ... (remaining 44785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.69: 19477 21.69 - 43.39: 1540 43.39 - 65.08: 238 65.08 - 86.78: 177 86.78 - 108.47: 99 Dihedral angle restraints: 21531 sinusoidal: 10467 harmonic: 11064 Sorted by residual: dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -151.91 65.91 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -151.90 65.90 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CB CYS P 119 " pdb=" SG CYS P 119 " pdb=" SG CYS P 205 " pdb=" CB CYS P 205 " ideal model delta sinusoidal sigma weight residual -86.00 -151.87 65.87 1 1.00e+01 1.00e-02 5.68e+01 ... (remaining 21528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 4669 0.087 - 0.175: 688 0.175 - 0.262: 52 0.262 - 0.350: 30 0.350 - 0.437: 6 Chirality restraints: 5445 Sorted by residual: chirality pdb=" C2 NAG V 1 " pdb=" C1 NAG V 1 " pdb=" C3 NAG V 1 " pdb=" N2 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.05 -0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" C2 NAG 3 1 " pdb=" C1 NAG 3 1 " pdb=" C3 NAG 3 1 " pdb=" N2 NAG 3 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.06 -0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" C2 NAG k 1 " pdb=" C1 NAG k 1 " pdb=" C3 NAG k 1 " pdb=" N2 NAG k 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.06 -0.43 2.00e-01 2.50e+01 4.63e+00 ... (remaining 5442 not shown) Planarity restraints: 5547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU G 275 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.74e+00 pdb=" C GLU G 275 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU G 275 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN G 276 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU P 275 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C GLU P 275 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU P 275 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN P 276 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 275 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.64e+00 pdb=" C GLU E 275 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU E 275 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN E 276 " -0.016 2.00e-02 2.50e+03 ... (remaining 5544 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 393 2.59 - 3.17: 25306 3.17 - 3.75: 47473 3.75 - 4.32: 64453 4.32 - 4.90: 107153 Nonbonded interactions: 244778 Sorted by model distance: nonbonded pdb=" OE1 GLU O 647 " pdb=" NH2 ARG D 542 " model vdw 2.015 2.520 nonbonded pdb=" NH2 ARG B 542 " pdb=" OE1 GLU D 647 " model vdw 2.021 2.520 nonbonded pdb=" CB ASP q 76B" pdb=" OH TYR E 318 " model vdw 2.032 3.440 nonbonded pdb=" OH TYR G 318 " pdb=" CB ASP S 76B" model vdw 2.048 3.440 nonbonded pdb=" OE1 GLU B 647 " pdb=" NH2 ARG O 542 " model vdw 2.048 2.520 ... (remaining 244773 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '2' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '9' selection = chain 'AA' selection = chain 'FA' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'h' selection = chain 'j' selection = chain 'o' selection = chain 'p' selection = chain 's' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain '1' selection = chain '3' selection = chain 'DA' selection = chain 'GA' selection = chain 'V' selection = chain 'f' selection = chain 'i' selection = chain 'k' selection = chain 'y' } ncs_group { reference = chain '4' selection = chain 'CA' selection = chain 'EA' selection = chain 'W' selection = chain 'e' selection = chain 'g' selection = chain 'l' selection = chain 'x' selection = chain 'z' } ncs_group { reference = chain '8' selection = chain 'a' selection = chain 't' } ncs_group { reference = chain 'A' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'BA' selection = chain 'd' selection = chain 'w' } ncs_group { reference = chain 'C' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'P' } ncs_group { reference = chain 'F' selection = chain 'Q' selection = chain 'm' } ncs_group { reference = chain 'I' selection = chain 'R' selection = chain 'n' } ncs_group { reference = chain 'J' selection = chain 'S' selection = chain 'q' } ncs_group { reference = chain 'K' selection = chain 'T' selection = chain 'r' } 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.230 Check model and map are aligned: 0.470 Set scattering table: 0.270 Process input model: 84.590 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.860 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 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 0.059 32946 Z= 0.474 Angle : 1.010 9.796 44790 Z= 0.513 Chirality : 0.063 0.437 5445 Planarity : 0.007 0.064 5490 Dihedral : 18.251 108.471 14274 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 0.72 % Allowed : 9.69 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -4.15 (0.11), residues: 3801 helix: -4.64 (0.10), residues: 387 sheet: -2.13 (0.14), residues: 1230 loop : -2.84 (0.10), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 112 HIS 0.006 0.001 HIS F 3 PHE 0.031 0.002 PHE S 100D TYR 0.013 0.002 TYR Q 100M ARG 0.021 0.001 ARG E 327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 434 time to evaluate : 3.793 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: B 519 PHE cc_start: 0.8400 (m-80) cc_final: 0.8016 (m-10) REVERT: B 654 GLU cc_start: 0.8443 (tp30) cc_final: 0.8176 (tp30) REVERT: B 657 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8302 (tm-30) REVERT: G 272 ILE cc_start: 0.8932 (pt) cc_final: 0.8458 (mt) REVERT: G 426 MET cc_start: 0.7357 (mmm) cc_final: 0.7137 (mmt) REVERT: H 36 TRP cc_start: 0.2994 (m100) cc_final: 0.2702 (m100) REVERT: L 50 GLU cc_start: 0.4860 (mt-10) cc_final: 0.4481 (mm-30) REVERT: m 103 LYS cc_start: 0.8402 (mmmm) cc_final: 0.8096 (mppt) REVERT: r 17 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7926 (mt-10) REVERT: A 32 PHE cc_start: 0.7258 (m-80) cc_final: 0.6722 (m-10) REVERT: C 50 GLU cc_start: 0.5097 (mt-10) cc_final: 0.4727 (mm-30) REVERT: F 13 LYS cc_start: 0.8038 (mmtm) cc_final: 0.7757 (mmmt) REVERT: F 103 LYS cc_start: 0.8489 (mmmm) cc_final: 0.8165 (mppt) REVERT: I 49 TYR cc_start: 0.8377 (p90) cc_final: 0.8108 (p90) REVERT: D 519 PHE cc_start: 0.8575 (m-80) cc_final: 0.8237 (m-10) REVERT: P 439 ILE cc_start: 0.8856 (pt) cc_final: 0.8563 (pt) REVERT: N 50 GLU cc_start: 0.4691 (mt-10) cc_final: 0.4323 (mm-30) REVERT: Q 103 LYS cc_start: 0.8159 (mmmm) cc_final: 0.7945 (mppt) REVERT: T 11 LEU cc_start: 0.9046 (tp) cc_final: 0.8792 (tt) REVERT: T 78 ASP cc_start: 0.8748 (t70) cc_final: 0.8489 (t70) outliers start: 24 outliers final: 8 residues processed: 458 average time/residue: 0.4833 time to fit residues: 346.2820 Evaluate side-chains 303 residues out of total 3345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 295 time to evaluate : 4.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain T residue 42 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 50.0000 chunk 286 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 193 optimal weight: 9.9990 chunk 153 optimal weight: 0.6980 chunk 296 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 220 optimal weight: 20.0000 chunk 343 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN B 656 ASN G 67 ASN G 82 GLN G 103 GLN G 183 GLN G 203 GLN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN L 93 GLN ** m 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 60 ASN n 37 GLN n 38 GLN n 51 ASN O 575 GLN O 656 ASN E 67 ASN E 82 GLN E 103 GLN E 183 GLN E 203 GLN E 258 GLN A 77 GLN C 93 GLN ** F 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 ASN I 37 GLN I 38 GLN I 51 ASN D 575 GLN D 656 ASN P 67 ASN P 82 GLN P 103 GLN P 183 GLN P 203 GLN P 258 GLN M 3 GLN M 77 GLN N 93 GLN ** Q 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 60 ASN R 37 GLN R 38 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 32946 Z= 0.301 Angle : 0.724 10.926 44790 Z= 0.362 Chirality : 0.047 0.280 5445 Planarity : 0.005 0.053 5490 Dihedral : 14.725 85.050 7343 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.45 % Allowed : 15.13 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.12), residues: 3801 helix: -3.34 (0.17), residues: 396 sheet: -1.75 (0.14), residues: 1200 loop : -2.44 (0.11), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 571 HIS 0.004 0.001 HIS E 330 PHE 0.025 0.002 PHE J 100D TYR 0.017 0.001 TYR H 59 ARG 0.008 0.000 ARG P 151 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 327 time to evaluate : 3.547 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: B 519 PHE cc_start: 0.8298 (m-80) cc_final: 0.8035 (m-10) REVERT: B 654 GLU cc_start: 0.8543 (tp30) cc_final: 0.8226 (tp30) REVERT: B 657 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8318 (tm-30) REVERT: G 203 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8672 (tt0) REVERT: G 272 ILE cc_start: 0.8930 (pt) cc_final: 0.8529 (mt) REVERT: L 50 GLU cc_start: 0.4847 (mt-10) cc_final: 0.4573 (mm-30) REVERT: m 32 ASN cc_start: 0.8737 (m-40) cc_final: 0.8475 (m110) REVERT: m 43 LYS cc_start: 0.9411 (mmmm) cc_final: 0.9045 (mmmm) REVERT: m 103 LYS cc_start: 0.8413 (mmmm) cc_final: 0.8104 (mppt) REVERT: q 76 ASP cc_start: 0.8075 (t0) cc_final: 0.7807 (t0) REVERT: q 100 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7731 (t80) REVERT: r 17 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7973 (mt-10) REVERT: C 50 GLU cc_start: 0.5111 (mt-10) cc_final: 0.4851 (mm-30) REVERT: F 43 LYS cc_start: 0.9381 (mmmm) cc_final: 0.9170 (mmmm) REVERT: F 103 LYS cc_start: 0.8503 (mmmm) cc_final: 0.8176 (mppt) REVERT: K 1 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7624 (pt0) REVERT: P 255 VAL cc_start: 0.9062 (OUTLIER) cc_final: 0.8841 (m) REVERT: N 50 GLU cc_start: 0.4883 (mt-10) cc_final: 0.4568 (mm-30) REVERT: Q 32 ASN cc_start: 0.8686 (m-40) cc_final: 0.8423 (m110) REVERT: Q 103 LYS cc_start: 0.8137 (mmmm) cc_final: 0.7931 (mppt) REVERT: S 100 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.7712 (t80) REVERT: T 78 ASP cc_start: 0.8682 (t70) cc_final: 0.8435 (t70) outliers start: 82 outliers final: 42 residues processed: 389 average time/residue: 0.4895 time to fit residues: 302.1122 Evaluate side-chains 342 residues out of total 3345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 295 time to evaluate : 3.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain n residue 53 ASP Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 100 TYR Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 457 ASP Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain P residue 496 VAL Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 74 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 0.0040 chunk 106 optimal weight: 4.9990 chunk 285 optimal weight: 6.9990 chunk 233 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 343 optimal weight: 5.9990 chunk 371 optimal weight: 2.9990 chunk 306 optimal weight: 0.9990 chunk 341 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 275 optimal weight: 4.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 203 GLN N 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 32946 Z= 0.247 Angle : 0.682 9.993 44790 Z= 0.334 Chirality : 0.047 0.270 5445 Planarity : 0.004 0.053 5490 Dihedral : 12.481 76.171 7342 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.44 % Allowed : 16.92 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -3.04 (0.12), residues: 3801 helix: -2.57 (0.21), residues: 396 sheet: -1.53 (0.14), residues: 1221 loop : -2.25 (0.12), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 571 HIS 0.005 0.001 HIS F 3 PHE 0.031 0.002 PHE L 98 TYR 0.015 0.001 TYR A 59 ARG 0.011 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 314 time to evaluate : 4.208 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: B 519 PHE cc_start: 0.8262 (m-80) cc_final: 0.8009 (m-10) REVERT: B 654 GLU cc_start: 0.8507 (tp30) cc_final: 0.8202 (tp30) REVERT: B 657 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8351 (tm-30) REVERT: G 272 ILE cc_start: 0.8921 (pt) cc_final: 0.8581 (mt) REVERT: L 50 GLU cc_start: 0.5030 (mt-10) cc_final: 0.4790 (mm-30) REVERT: m 32 ASN cc_start: 0.8604 (m-40) cc_final: 0.8350 (m110) REVERT: m 103 LYS cc_start: 0.8371 (mmmm) cc_final: 0.8089 (mppt) REVERT: q 76 ASP cc_start: 0.7958 (t0) cc_final: 0.7646 (t0) REVERT: q 100 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.7737 (t80) REVERT: r 17 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7972 (mt-10) REVERT: r 91 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7703 (pm20) REVERT: O 663 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8728 (pp) REVERT: C 50 GLU cc_start: 0.5151 (mt-10) cc_final: 0.4822 (mm-30) REVERT: F 103 LYS cc_start: 0.8518 (mmmm) cc_final: 0.8203 (mppt) REVERT: I 54 ARG cc_start: 0.8647 (ptt-90) cc_final: 0.8208 (ptt180) REVERT: K 1 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7609 (pt0) REVERT: D 519 PHE cc_start: 0.8399 (m-10) cc_final: 0.8172 (m-10) REVERT: P 255 VAL cc_start: 0.9031 (OUTLIER) cc_final: 0.8805 (m) REVERT: N 50 GLU cc_start: 0.4859 (mt-10) cc_final: 0.4587 (mm-30) REVERT: Q 32 ASN cc_start: 0.8559 (m-40) cc_final: 0.8286 (m110) REVERT: S 100 TYR cc_start: 0.8678 (OUTLIER) cc_final: 0.7780 (t80) REVERT: T 78 ASP cc_start: 0.8666 (t70) cc_final: 0.8443 (t70) outliers start: 115 outliers final: 61 residues processed: 403 average time/residue: 0.4601 time to fit residues: 300.0493 Evaluate side-chains 356 residues out of total 3345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 289 time to evaluate : 4.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain n residue 53 ASP Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 46 GLU Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain q residue 100 TYR Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain r residue 91 GLU Chi-restraints excluded: chain O residue 536 THR Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain O residue 663 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain P residue 496 VAL Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain S residue 42 ASP Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 98 CYS Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain T residue 42 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 9.9990 chunk 258 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 345 optimal weight: 0.7980 chunk 365 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 327 optimal weight: 20.0000 chunk 98 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 32946 Z= 0.296 Angle : 0.696 11.031 44790 Z= 0.340 Chirality : 0.047 0.275 5445 Planarity : 0.004 0.053 5490 Dihedral : 11.090 73.020 7341 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.95 % Allowed : 18.06 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.81 (0.13), residues: 3801 helix: -2.13 (0.23), residues: 396 sheet: -1.43 (0.14), residues: 1239 loop : -2.10 (0.12), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 36 HIS 0.006 0.001 HIS F 3 PHE 0.039 0.002 PHE C 98 TYR 0.016 0.001 TYR A 59 ARG 0.011 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 296 time to evaluate : 3.773 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: B 519 PHE cc_start: 0.8335 (m-80) cc_final: 0.8078 (m-10) REVERT: B 654 GLU cc_start: 0.8519 (tp30) cc_final: 0.8169 (tp30) REVERT: B 657 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8294 (tm-30) REVERT: G 272 ILE cc_start: 0.8935 (pt) cc_final: 0.8617 (mt) REVERT: L 50 GLU cc_start: 0.5071 (mt-10) cc_final: 0.4835 (mm-30) REVERT: m 32 ASN cc_start: 0.8585 (m-40) cc_final: 0.8324 (m110) REVERT: m 103 LYS cc_start: 0.8399 (mmmm) cc_final: 0.8121 (mppt) REVERT: q 100 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.7939 (t80) REVERT: r 17 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7973 (mt-10) REVERT: O 519 PHE cc_start: 0.8337 (m-10) cc_final: 0.8109 (m-10) REVERT: O 663 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8744 (pp) REVERT: C 50 GLU cc_start: 0.5018 (mt-10) cc_final: 0.4721 (mm-30) REVERT: F 43 LYS cc_start: 0.9402 (mmmm) cc_final: 0.9050 (mtmt) REVERT: F 103 LYS cc_start: 0.8495 (mmmm) cc_final: 0.8192 (mppt) REVERT: I 54 ARG cc_start: 0.8615 (ptt-90) cc_final: 0.8211 (ptt90) REVERT: J 100 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.8112 (t80) REVERT: K 1 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7566 (pt0) REVERT: P 255 VAL cc_start: 0.9080 (OUTLIER) cc_final: 0.8868 (m) REVERT: Q 32 ASN cc_start: 0.8543 (m-40) cc_final: 0.8232 (m110) REVERT: S 100 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.7784 (t80) outliers start: 132 outliers final: 81 residues processed: 403 average time/residue: 0.4535 time to fit residues: 297.7553 Evaluate side-chains 366 residues out of total 3345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 279 time to evaluate : 3.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain m residue 2 VAL Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain m residue 78 VAL Chi-restraints excluded: chain n residue 53 ASP Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain q residue 18 VAL Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain q residue 100 TYR Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain O residue 536 THR Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain O residue 663 LEU Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 193 LEU Chi-restraints excluded: chain P residue 213 ILE Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 434 MET Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain P residue 496 VAL Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain T residue 42 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 0.9990 chunk 207 optimal weight: 30.0000 chunk 5 optimal weight: 0.7980 chunk 272 optimal weight: 0.7980 chunk 150 optimal weight: 0.5980 chunk 311 optimal weight: 10.0000 chunk 252 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 186 optimal weight: 0.0020 chunk 327 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 203 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 3 GLN K 27 GLN ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 32946 Z= 0.157 Angle : 0.632 10.816 44790 Z= 0.307 Chirality : 0.045 0.263 5445 Planarity : 0.004 0.055 5490 Dihedral : 9.716 65.994 7341 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.17 % Allowed : 19.61 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.55 (0.13), residues: 3801 helix: -1.86 (0.24), residues: 414 sheet: -1.32 (0.14), residues: 1257 loop : -1.89 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 36 HIS 0.006 0.001 HIS m 3 PHE 0.037 0.001 PHE C 98 TYR 0.017 0.001 TYR A 59 ARG 0.010 0.000 ARG H 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 330 time to evaluate : 3.822 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: B 519 PHE cc_start: 0.8323 (m-80) cc_final: 0.8037 (m-10) REVERT: G 272 ILE cc_start: 0.8916 (pt) cc_final: 0.8610 (mt) REVERT: H 32 PHE cc_start: 0.7215 (m-80) cc_final: 0.6786 (m-10) REVERT: L 50 GLU cc_start: 0.4970 (mt-10) cc_final: 0.4762 (mm-30) REVERT: m 32 ASN cc_start: 0.8523 (m-40) cc_final: 0.8236 (m110) REVERT: m 43 LYS cc_start: 0.9279 (mmmm) cc_final: 0.8972 (mtpt) REVERT: m 103 LYS cc_start: 0.8378 (mmmm) cc_final: 0.8118 (mppt) REVERT: q 100 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7846 (t80) REVERT: A 4 LEU cc_start: 0.5070 (tp) cc_final: 0.4798 (tp) REVERT: C 50 GLU cc_start: 0.5099 (mt-10) cc_final: 0.4840 (mm-30) REVERT: F 43 LYS cc_start: 0.9353 (mmmm) cc_final: 0.9031 (mtmt) REVERT: F 103 LYS cc_start: 0.8480 (mmmm) cc_final: 0.8196 (mppt) REVERT: I 54 ARG cc_start: 0.8671 (ptt-90) cc_final: 0.8325 (ptt90) REVERT: J 100 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.8112 (t80) REVERT: K 1 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7449 (pt0) REVERT: K 78 ASP cc_start: 0.8466 (t70) cc_final: 0.8252 (t70) REVERT: D 657 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8390 (pp20) REVERT: Q 32 ASN cc_start: 0.8601 (m-40) cc_final: 0.8245 (m110) REVERT: Q 43 LYS cc_start: 0.9300 (mmmm) cc_final: 0.8928 (mtpt) REVERT: S 100 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.7793 (t80) outliers start: 106 outliers final: 57 residues processed: 419 average time/residue: 0.4474 time to fit residues: 305.3307 Evaluate side-chains 351 residues out of total 3345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 290 time to evaluate : 3.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain m residue 2 VAL Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain n residue 53 ASP Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 46 GLU Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain q residue 100 TYR Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 208 VAL Chi-restraints excluded: chain P residue 213 ILE Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain T residue 42 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 3.9990 chunk 329 optimal weight: 10.0000 chunk 72 optimal weight: 50.0000 chunk 214 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 365 optimal weight: 2.9990 chunk 303 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 120 optimal weight: 0.4980 chunk 192 optimal weight: 0.0020 overall best weight: 1.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN L 30EHIS n 51 ASN ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 1 GLN I 51 ASN ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30EHIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 32946 Z= 0.229 Angle : 0.652 10.263 44790 Z= 0.315 Chirality : 0.046 0.270 5445 Planarity : 0.004 0.054 5490 Dihedral : 9.552 67.595 7339 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.77 % Allowed : 19.97 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.38 (0.13), residues: 3801 helix: -1.78 (0.24), residues: 420 sheet: -1.16 (0.15), residues: 1173 loop : -1.80 (0.12), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 36 HIS 0.005 0.001 HIS m 3 PHE 0.026 0.001 PHE C 98 TYR 0.017 0.001 TYR A 59 ARG 0.008 0.000 ARG Q 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 299 time to evaluate : 4.035 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: B 519 PHE cc_start: 0.8354 (m-80) cc_final: 0.8060 (m-10) REVERT: G 272 ILE cc_start: 0.8882 (pt) cc_final: 0.8609 (mt) REVERT: G 482 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7558 (mm-30) REVERT: H 32 PHE cc_start: 0.7187 (m-80) cc_final: 0.6595 (m-10) REVERT: L 30 HIS cc_start: 0.5651 (OUTLIER) cc_final: 0.5348 (m90) REVERT: L 50 GLU cc_start: 0.5045 (mt-10) cc_final: 0.4842 (mm-30) REVERT: m 32 ASN cc_start: 0.8559 (m-40) cc_final: 0.8267 (m110) REVERT: m 103 LYS cc_start: 0.8408 (mmmm) cc_final: 0.8170 (mppt) REVERT: q 100 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.7847 (t80) REVERT: E 95 MET cc_start: 0.8410 (ptm) cc_final: 0.7681 (ttp) REVERT: C 50 GLU cc_start: 0.5014 (mt-10) cc_final: 0.4742 (mm-30) REVERT: F 103 LYS cc_start: 0.8471 (mmmm) cc_final: 0.8193 (mppt) REVERT: I 54 ARG cc_start: 0.8697 (ptt-90) cc_final: 0.8329 (ptt90) REVERT: J 100 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.8004 (t80) REVERT: K 1 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7440 (pt0) REVERT: K 78 ASP cc_start: 0.8471 (t70) cc_final: 0.8263 (t70) REVERT: M 4 LEU cc_start: 0.7342 (mp) cc_final: 0.6881 (tp) REVERT: Q 32 ASN cc_start: 0.8565 (m-40) cc_final: 0.8213 (m110) REVERT: S 100 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.7888 (t80) outliers start: 126 outliers final: 85 residues processed: 399 average time/residue: 0.4456 time to fit residues: 289.2324 Evaluate side-chains 376 residues out of total 3345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 285 time to evaluate : 4.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 482 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 30 HIS Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain m residue 2 VAL Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 51 ASN Chi-restraints excluded: chain n residue 53 ASP Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain q residue 100 TYR Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain O residue 536 THR Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain O residue 624 ASP Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 125 LEU Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 208 VAL Chi-restraints excluded: chain P residue 213 ILE Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 434 MET Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 76 ASP Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 74 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 208 optimal weight: 8.9990 chunk 267 optimal weight: 3.9990 chunk 206 optimal weight: 7.9990 chunk 307 optimal weight: 3.9990 chunk 204 optimal weight: 7.9990 chunk 364 optimal weight: 0.9990 chunk 228 optimal weight: 0.4980 chunk 222 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 30EHIS ** n 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN I 51 ASN K 27 GLN ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 32946 Z= 0.249 Angle : 0.664 10.014 44790 Z= 0.323 Chirality : 0.046 0.273 5445 Planarity : 0.004 0.054 5490 Dihedral : 9.421 67.282 7339 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.65 % Allowed : 20.93 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.28 (0.13), residues: 3801 helix: -1.52 (0.25), residues: 402 sheet: -1.07 (0.15), residues: 1173 loop : -1.79 (0.12), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 36 HIS 0.005 0.001 HIS L 30E PHE 0.018 0.001 PHE J 100D TYR 0.018 0.001 TYR m 100O ARG 0.005 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 294 time to evaluate : 4.386 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: B 519 PHE cc_start: 0.8373 (m-80) cc_final: 0.8079 (m-10) REVERT: G 161 MET cc_start: 0.7663 (tpp) cc_final: 0.7436 (ttm) REVERT: G 272 ILE cc_start: 0.8911 (pt) cc_final: 0.8654 (mt) REVERT: G 482 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7591 (mm-30) REVERT: L 30 HIS cc_start: 0.5702 (OUTLIER) cc_final: 0.5451 (m170) REVERT: m 32 ASN cc_start: 0.8616 (m-40) cc_final: 0.8268 (m110) REVERT: m 43 LYS cc_start: 0.9214 (mmmm) cc_final: 0.8917 (mtpt) REVERT: m 103 LYS cc_start: 0.8402 (mmmm) cc_final: 0.8165 (mppt) REVERT: q 100 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.7838 (t80) REVERT: O 622 ILE cc_start: 0.9470 (pt) cc_final: 0.9252 (mt) REVERT: E 95 MET cc_start: 0.8481 (ptm) cc_final: 0.7847 (ttp) REVERT: C 50 GLU cc_start: 0.5012 (mt-10) cc_final: 0.4730 (mm-30) REVERT: C 90 GLN cc_start: 0.4369 (OUTLIER) cc_final: 0.4046 (pp30) REVERT: F 43 LYS cc_start: 0.9318 (mmmm) cc_final: 0.8991 (mtmt) REVERT: F 103 LYS cc_start: 0.8501 (mmmm) cc_final: 0.8216 (mppt) REVERT: I 51 ASN cc_start: 0.9009 (OUTLIER) cc_final: 0.8551 (t0) REVERT: I 54 ARG cc_start: 0.8746 (ptt-90) cc_final: 0.8291 (ptt90) REVERT: J 100 TYR cc_start: 0.8625 (OUTLIER) cc_final: 0.8264 (t80) REVERT: K 1 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7421 (pt0) REVERT: K 78 ASP cc_start: 0.8484 (t70) cc_final: 0.8279 (t70) REVERT: M 4 LEU cc_start: 0.7195 (mp) cc_final: 0.6764 (tp) REVERT: Q 30 ARG cc_start: 0.8635 (mmt-90) cc_final: 0.8374 (mmt180) REVERT: Q 32 ASN cc_start: 0.8567 (m-40) cc_final: 0.8201 (m110) REVERT: Q 43 LYS cc_start: 0.9246 (mmmm) cc_final: 0.8866 (mtpt) REVERT: S 100 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.7961 (t80) outliers start: 122 outliers final: 100 residues processed: 392 average time/residue: 0.4556 time to fit residues: 295.1064 Evaluate side-chains 392 residues out of total 3345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 284 time to evaluate : 3.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 482 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 30 HIS Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain m residue 2 VAL Chi-restraints excluded: chain m residue 78 VAL Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 53 ASP Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 46 GLU Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain q residue 100 TYR Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain O residue 570 VAL Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain O residue 624 ASP Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 258 GLN Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 95 MET Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 125 LEU Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 208 VAL Chi-restraints excluded: chain P residue 213 ILE Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 433 CYS Chi-restraints excluded: chain P residue 434 MET Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 76 ASP Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 74 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 chunk 109 optimal weight: 0.0570 chunk 71 optimal weight: 0.0060 chunk 70 optimal weight: 30.0000 chunk 231 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 180 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 286 optimal weight: 0.5980 overall best weight: 0.5314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: n 51 ASN C 30EHIS C 34 HIS F 1 GLN I 51 ASN ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 32946 Z= 0.152 Angle : 0.632 9.968 44790 Z= 0.306 Chirality : 0.045 0.264 5445 Planarity : 0.004 0.056 5490 Dihedral : 9.059 63.733 7339 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.29 % Allowed : 21.70 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.19 (0.13), residues: 3801 helix: -1.52 (0.24), residues: 420 sheet: -0.91 (0.15), residues: 1176 loop : -1.78 (0.12), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP M 36 HIS 0.014 0.001 HIS L 30E PHE 0.018 0.001 PHE H 32 TYR 0.018 0.001 TYR A 59 ARG 0.008 0.000 ARG M 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 315 time to evaluate : 3.685 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: B 519 PHE cc_start: 0.8338 (m-80) cc_final: 0.8008 (m-10) REVERT: G 272 ILE cc_start: 0.8894 (pt) cc_final: 0.8650 (mt) REVERT: G 482 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7540 (mm-30) REVERT: m 32 ASN cc_start: 0.8502 (m-40) cc_final: 0.8241 (m110) REVERT: m 43 LYS cc_start: 0.9228 (mmmm) cc_final: 0.8923 (mtpt) REVERT: m 103 LYS cc_start: 0.8432 (mmmm) cc_final: 0.8183 (mppt) REVERT: n 49 TYR cc_start: 0.8451 (p90) cc_final: 0.8213 (p90) REVERT: q 100 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.7893 (t80) REVERT: E 95 MET cc_start: 0.8459 (ptm) cc_final: 0.7885 (ttp) REVERT: E 433 CYS cc_start: 0.7457 (OUTLIER) cc_final: 0.6899 (p) REVERT: C 50 GLU cc_start: 0.5010 (mt-10) cc_final: 0.4755 (mm-30) REVERT: F 43 LYS cc_start: 0.9307 (mmmm) cc_final: 0.9001 (mtmt) REVERT: F 103 LYS cc_start: 0.8496 (mmmm) cc_final: 0.8207 (mppt) REVERT: I 49 TYR cc_start: 0.8411 (p90) cc_final: 0.8082 (p90) REVERT: I 51 ASN cc_start: 0.9099 (OUTLIER) cc_final: 0.8751 (t0) REVERT: I 54 ARG cc_start: 0.8664 (ptt-90) cc_final: 0.8430 (ptt90) REVERT: J 100 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.7827 (t80) REVERT: D 657 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8319 (pp20) REVERT: M 4 LEU cc_start: 0.7142 (mp) cc_final: 0.6591 (mt) REVERT: M 32 PHE cc_start: 0.7353 (m-10) cc_final: 0.7150 (m-10) REVERT: Q 13 LYS cc_start: 0.8294 (mmmt) cc_final: 0.8086 (mmmt) REVERT: Q 32 ASN cc_start: 0.8523 (m-40) cc_final: 0.8161 (m110) REVERT: Q 43 LYS cc_start: 0.9271 (mmmm) cc_final: 0.8876 (mtpt) REVERT: S 99 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8457 (p0) REVERT: S 100 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.7797 (t80) outliers start: 110 outliers final: 84 residues processed: 403 average time/residue: 0.4259 time to fit residues: 281.8533 Evaluate side-chains 377 residues out of total 3345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 286 time to evaluate : 3.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 482 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain m residue 2 VAL Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain m residue 78 VAL Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 51 ASN Chi-restraints excluded: chain n residue 53 ASP Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 46 GLU Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain q residue 100 TYR Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain O residue 570 VAL Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain O residue 624 ASP Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 95 MET Chi-restraints excluded: chain P residue 125 LEU Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 193 LEU Chi-restraints excluded: chain P residue 208 VAL Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 433 CYS Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 91 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 9.9990 chunk 349 optimal weight: 20.0000 chunk 318 optimal weight: 50.0000 chunk 339 optimal weight: 2.9990 chunk 348 optimal weight: 2.9990 chunk 204 optimal weight: 20.0000 chunk 147 optimal weight: 8.9990 chunk 266 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 306 optimal weight: 0.9990 chunk 321 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 203 GLN ** n 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 27 GLN C 34 HIS C 90 GLN I 51 ASN K 27 GLN ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 32946 Z= 0.314 Angle : 0.685 10.096 44790 Z= 0.332 Chirality : 0.046 0.278 5445 Planarity : 0.004 0.053 5490 Dihedral : 9.197 67.476 7339 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.65 % Allowed : 21.76 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 3801 helix: -1.41 (0.25), residues: 402 sheet: -1.01 (0.15), residues: 1218 loop : -1.70 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP M 36 HIS 0.004 0.001 HIS F 3 PHE 0.021 0.002 PHE J 100D TYR 0.022 0.001 TYR Q 100O ARG 0.007 0.000 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 285 time to evaluate : 3.727 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: B 519 PHE cc_start: 0.8356 (m-80) cc_final: 0.8020 (m-10) REVERT: G 482 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7552 (mm-30) REVERT: m 32 ASN cc_start: 0.8551 (m-40) cc_final: 0.8234 (m110) REVERT: m 103 LYS cc_start: 0.8417 (mmmm) cc_final: 0.8181 (mppt) REVERT: q 100 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.8071 (t80) REVERT: E 95 MET cc_start: 0.8525 (ptm) cc_final: 0.7933 (ttp) REVERT: E 302 ASN cc_start: 0.8495 (t0) cc_final: 0.8174 (t0) REVERT: E 433 CYS cc_start: 0.7310 (OUTLIER) cc_final: 0.6745 (p) REVERT: C 90 GLN cc_start: 0.4686 (OUTLIER) cc_final: 0.4454 (pp30) REVERT: F 43 LYS cc_start: 0.9349 (mmmm) cc_final: 0.9035 (mtmt) REVERT: F 103 LYS cc_start: 0.8490 (mmmm) cc_final: 0.8196 (mppt) REVERT: I 49 TYR cc_start: 0.8439 (p90) cc_final: 0.8117 (p90) REVERT: I 51 ASN cc_start: 0.9198 (OUTLIER) cc_final: 0.8894 (t0) REVERT: I 54 ARG cc_start: 0.8677 (ptt-90) cc_final: 0.8388 (ptt90) REVERT: J 100 TYR cc_start: 0.8412 (OUTLIER) cc_final: 0.7730 (t80) REVERT: K 1 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7371 (pt0) REVERT: D 519 PHE cc_start: 0.7965 (m-10) cc_final: 0.7760 (m-10) REVERT: M 4 LEU cc_start: 0.7144 (mp) cc_final: 0.6601 (mt) REVERT: Q 13 LYS cc_start: 0.8295 (mmmt) cc_final: 0.8058 (mmmt) REVERT: Q 32 ASN cc_start: 0.8547 (m-40) cc_final: 0.8160 (m110) REVERT: Q 43 LYS cc_start: 0.9245 (mmmm) cc_final: 0.8832 (mtpt) REVERT: R 104 LEU cc_start: 0.8198 (tp) cc_final: 0.7716 (tt) REVERT: S 100 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.7850 (t80) REVERT: T 32 MET cc_start: 0.8171 (tpt) cc_final: 0.7450 (tpp) outliers start: 122 outliers final: 93 residues processed: 388 average time/residue: 0.4236 time to fit residues: 268.7136 Evaluate side-chains 378 residues out of total 3345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 277 time to evaluate : 3.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 433 CYS Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 482 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain m residue 2 VAL Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain m residue 78 VAL Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 53 ASP Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 18 VAL Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain q residue 100 TYR Chi-restraints excluded: chain r residue 51 SER Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain O residue 624 ASP Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 95 MET Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 193 LEU Chi-restraints excluded: chain P residue 208 VAL Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 433 CYS Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 76 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 74 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 0.0980 chunk 222 optimal weight: 3.9990 chunk 359 optimal weight: 2.9990 chunk 219 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 376 optimal weight: 2.9990 chunk 346 optimal weight: 20.0000 chunk 299 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 231 optimal weight: 0.4980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 203 GLN r 27 GLN C 53 ASN C 90 GLN F 1 GLN I 51 ASN ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 32946 Z= 0.212 Angle : 0.658 9.998 44790 Z= 0.319 Chirality : 0.045 0.271 5445 Planarity : 0.004 0.054 5490 Dihedral : 9.037 65.205 7339 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.14 % Allowed : 22.36 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.06 (0.13), residues: 3801 helix: -1.37 (0.25), residues: 402 sheet: -0.83 (0.15), residues: 1170 loop : -1.68 (0.13), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP M 36 HIS 0.004 0.001 HIS m 3 PHE 0.044 0.001 PHE M 32 TYR 0.022 0.001 TYR Q 100O ARG 0.010 0.000 ARG H 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 281 time to evaluate : 3.841 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: B 519 PHE cc_start: 0.8337 (m-80) cc_final: 0.8002 (m-10) REVERT: G 482 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7505 (mm-30) REVERT: m 32 ASN cc_start: 0.8533 (m-40) cc_final: 0.8274 (m110) REVERT: m 43 LYS cc_start: 0.9213 (mmmm) cc_final: 0.8890 (mtpt) REVERT: m 103 LYS cc_start: 0.8422 (mmmm) cc_final: 0.8191 (mppt) REVERT: q 100 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.8068 (t80) REVERT: E 95 MET cc_start: 0.8492 (ptm) cc_final: 0.7912 (ttp) REVERT: E 302 ASN cc_start: 0.8442 (t0) cc_final: 0.8137 (t0) REVERT: E 433 CYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6773 (p) REVERT: C 50 GLU cc_start: 0.6143 (tm-30) cc_final: 0.5632 (mm-30) REVERT: C 90 GLN cc_start: 0.4749 (OUTLIER) cc_final: 0.4474 (pp30) REVERT: F 43 LYS cc_start: 0.9326 (mmmm) cc_final: 0.9007 (mtmt) REVERT: F 103 LYS cc_start: 0.8480 (mmmm) cc_final: 0.8207 (mppt) REVERT: I 49 TYR cc_start: 0.8428 (p90) cc_final: 0.8125 (p90) REVERT: I 51 ASN cc_start: 0.9165 (OUTLIER) cc_final: 0.8904 (t0) REVERT: I 54 ARG cc_start: 0.8686 (ptt-90) cc_final: 0.8444 (ptt90) REVERT: K 1 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7284 (pt0) REVERT: M 4 LEU cc_start: 0.7143 (mp) cc_final: 0.6717 (mt) REVERT: Q 13 LYS cc_start: 0.8267 (mmmt) cc_final: 0.8027 (mmmt) REVERT: Q 32 ASN cc_start: 0.8525 (m-40) cc_final: 0.8078 (m110) REVERT: Q 43 LYS cc_start: 0.9241 (mmmm) cc_final: 0.8840 (mtpt) REVERT: R 104 LEU cc_start: 0.8174 (tp) cc_final: 0.7692 (tt) REVERT: S 99 ASP cc_start: 0.8388 (p0) cc_final: 0.7950 (p0) REVERT: S 100 TYR cc_start: 0.8319 (OUTLIER) cc_final: 0.8034 (t80) outliers start: 105 outliers final: 92 residues processed: 368 average time/residue: 0.4517 time to fit residues: 271.6420 Evaluate side-chains 378 residues out of total 3345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 279 time to evaluate : 3.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 433 CYS Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 482 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain m residue 2 VAL Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain m residue 78 VAL Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 53 ASP Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 18 VAL Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain q residue 100 TYR Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain O residue 624 ASP Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 258 GLN Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 95 MET Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 193 LEU Chi-restraints excluded: chain P residue 208 VAL Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 433 CYS Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 25 GLU Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 76 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain T residue 42 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 0.9990 chunk 238 optimal weight: 1.9990 chunk 319 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 chunk 276 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 300 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 308 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: r 27 GLN C 90 GLN I 51 ASN ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.108055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.066269 restraints weight = 80549.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.068324 restraints weight = 46495.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.069631 restraints weight = 34326.192| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32946 Z= 0.205 Angle : 0.652 10.001 44790 Z= 0.316 Chirality : 0.045 0.268 5445 Planarity : 0.004 0.054 5490 Dihedral : 8.926 64.604 7339 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.20 % Allowed : 22.27 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.00 (0.13), residues: 3801 helix: -1.32 (0.25), residues: 402 sheet: -0.80 (0.15), residues: 1170 loop : -1.65 (0.13), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP M 36 HIS 0.005 0.001 HIS F 3 PHE 0.036 0.001 PHE M 32 TYR 0.021 0.001 TYR Q 100O ARG 0.009 0.000 ARG H 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6543.18 seconds wall clock time: 120 minutes 52.13 seconds (7252.13 seconds total)