Starting phenix.real_space_refine on Mon Mar 18 10:52:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rai_24362/03_2024/7rai_24362.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rai_24362/03_2024/7rai_24362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rai_24362/03_2024/7rai_24362.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rai_24362/03_2024/7rai_24362.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rai_24362/03_2024/7rai_24362.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rai_24362/03_2024/7rai_24362.pdb" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.103 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 153 5.16 5 C 12840 2.51 5 N 3429 2.21 5 O 4230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "B ARG 588": "NH1" <-> "NH2" Residue "B GLU 657": "OE1" <-> "OE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 35": "NH1" <-> "NH2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 76": "NH1" <-> "NH2" Residue "H ARG 82": "NH1" <-> "NH2" Residue "L ARG 32": "NH1" <-> "NH2" Residue "L ARG 45": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 95": "NH1" <-> "NH2" Residue "L ARG 103": "NH1" <-> "NH2" Residue "L GLU 107": "OE1" <-> "OE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 87": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C GLU 211": "OE1" <-> "OE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C GLU 275": "OE1" <-> "OE2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C ARG 360": "NH1" <-> "NH2" Residue "C GLU 381": "OE1" <-> "OE2" Residue "C TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "D ARG 588": "NH1" <-> "NH2" Residue "D GLU 657": "OE1" <-> "OE2" Residue "I GLU 10": "OE1" <-> "OE2" Residue "I ARG 19": "NH1" <-> "NH2" Residue "I PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 35": "NH1" <-> "NH2" Residue "I PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 76": "NH1" <-> "NH2" Residue "I ARG 82": "NH1" <-> "NH2" Residue "M ARG 32": "NH1" <-> "NH2" Residue "M ARG 45": "NH1" <-> "NH2" Residue "M ARG 54": "NH1" <-> "NH2" Residue "M PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 95": "NH1" <-> "NH2" Residue "M ARG 103": "NH1" <-> "NH2" Residue "M GLU 107": "OE1" <-> "OE2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 87": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E GLU 102": "OE1" <-> "OE2" Residue "E GLU 153": "OE1" <-> "OE2" Residue "E GLU 164": "OE1" <-> "OE2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E GLU 186": "OE1" <-> "OE2" Residue "E GLU 190": "OE1" <-> "OE2" Residue "E GLU 211": "OE1" <-> "OE2" Residue "E GLU 267": "OE1" <-> "OE2" Residue "E GLU 268": "OE1" <-> "OE2" Residue "E GLU 269": "OE1" <-> "OE2" Residue "E GLU 275": "OE1" <-> "OE2" Residue "E ARG 327": "NH1" <-> "NH2" Residue "E ARG 360": "NH1" <-> "NH2" Residue "E GLU 381": "OE1" <-> "OE2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "F ARG 588": "NH1" <-> "NH2" Residue "F GLU 657": "OE1" <-> "OE2" Residue "J GLU 10": "OE1" <-> "OE2" Residue "J ARG 19": "NH1" <-> "NH2" Residue "J ARG 35": "NH1" <-> "NH2" Residue "J PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 76": "NH1" <-> "NH2" Residue "J ARG 82": "NH1" <-> "NH2" Residue "N ARG 32": "NH1" <-> "NH2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "N ARG 54": "NH1" <-> "NH2" Residue "N PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 95": "NH1" <-> "NH2" Residue "N ARG 103": "NH1" <-> "NH2" Residue "N GLU 107": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20652 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3524 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "B" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1010 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "H" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "C" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3524 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "D" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1010 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "M" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "E" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3524 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "F" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1010 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "J" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "N" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 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: "O" 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: "P" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 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: 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: "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: 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: 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: 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: "b" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "c" 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: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 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: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "o" 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: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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: "L" 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: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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: "M" 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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: "N" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.87, per 1000 atoms: 0.53 Number of scatterers: 20652 At special positions: 0 Unit cell: (135.192, 134.144, 132.048, 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 153 16.00 O 4230 8.00 N 3429 7.00 C 12840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 100B" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 97 " - pdb=" SG CYS I 100B" distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 97 " - pdb=" SG CYS J 100B" distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN P 4 " - " MAN P 5 " " MAN P 5 " - " MAN P 6 " " MAN b 4 " - " MAN b 5 " " MAN b 5 " - " MAN b 6 " " MAN n 4 " - " MAN n 5 " " MAN n 5 " - " MAN n 6 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA P 3 " - " MAN P 4 " " BMA Y 3 " - " MAN Y 4 " " BMA b 3 " - " MAN b 4 " " BMA k 3 " - " MAN k 4 " " BMA n 3 " - " MAN n 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA P 3 " - " MAN P 7 " " BMA Y 3 " - " MAN Y 5 " " BMA b 3 " - " MAN b 7 " " BMA k 3 " - " MAN k 5 " " BMA n 3 " - " MAN n 7 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG 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 h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " 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 m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 137 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 339 " " NAG A 606 " - " ASN A 355 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 137 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 339 " " NAG C 606 " - " ASN C 355 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 137 " " NAG E 604 " - " ASN E 234 " " NAG E 605 " - " ASN E 339 " " NAG E 606 " - " ASN E 355 " " NAG G 1 " - " ASN A 156 " " NAG K 1 " - " ASN A 160 " " NAG L1001 " - " ASN L 18 " " NAG M1001 " - " ASN M 18 " " NAG N1001 " - " ASN N 18 " " NAG O 1 " - " ASN A 197 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 276 " " NAG R 1 " - " ASN A 295 " " NAG S 1 " - " ASN A 301 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 363 " " NAG V 1 " - " ASN A 386 " " NAG W 1 " - " ASN A 392 " " NAG X 1 " - " ASN A 448 " " NAG Y 1 " - " ASN C 156 " " NAG Z 1 " - " ASN C 160 " " NAG a 1 " - " ASN C 197 " " NAG b 1 " - " ASN C 262 " " NAG c 1 " - " ASN C 276 " " NAG d 1 " - " ASN C 295 " " NAG e 1 " - " ASN C 301 " " NAG f 1 " - " ASN C 332 " " NAG g 1 " - " ASN C 363 " " NAG h 1 " - " ASN C 386 " " NAG i 1 " - " ASN C 392 " " NAG j 1 " - " ASN C 448 " " NAG k 1 " - " ASN E 156 " " NAG l 1 " - " ASN E 160 " " NAG m 1 " - " ASN E 197 " " NAG n 1 " - " ASN E 262 " " NAG o 1 " - " ASN E 276 " " NAG p 1 " - " ASN E 295 " " NAG q 1 " - " ASN E 301 " " NAG r 1 " - " ASN E 332 " " NAG s 1 " - " ASN E 363 " " NAG t 1 " - " ASN E 386 " " NAG u 1 " - " ASN E 392 " " NAG v 1 " - " ASN E 448 " Time building additional restraints: 9.45 Conformation dependent library (CDL) restraints added in 3.3 seconds 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4452 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 50 sheets defined 15.3% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 99 through 114 removed outlier: 3.577A pdb=" N HIS A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 349 removed outlier: 3.802A pdb=" N THR A 341 " --> pdb=" O THR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.800A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.803A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 521 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 removed outlier: 3.822A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 583 Processing helix chain 'B' and resid 583 through 596 removed outlier: 3.693A pdb=" N ARG B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.627A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 663 Processing helix chain 'H' and resid 61 through 65 removed outlier: 4.327A pdb=" N ALA H 65 " --> pdb=" O LYS H 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 114 removed outlier: 3.603A pdb=" N HIS C 105 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 349 removed outlier: 3.804A pdb=" N THR C 341 " --> pdb=" O THR C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.808A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 425 through 429' Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.779A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 521 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.833A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 583 Processing helix chain 'D' and resid 583 through 596 removed outlier: 3.691A pdb=" N ARG D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.597A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 663 Processing helix chain 'I' and resid 61 through 65 removed outlier: 4.373A pdb=" N ALA I 65 " --> pdb=" O LYS I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 4.064A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 114 removed outlier: 3.543A pdb=" N HIS E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 349 removed outlier: 3.806A pdb=" N THR E 341 " --> pdb=" O THR E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.837A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 425 through 429' Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.788A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 through 521 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 543 removed outlier: 3.882A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 575 through 583 Processing helix chain 'F' and resid 583 through 596 removed outlier: 3.699A pdb=" N ARG F 588 " --> pdb=" O GLU F 584 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.603A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 663 Processing helix chain 'J' and resid 61 through 65 removed outlier: 4.348A pdb=" N ALA J 65 " --> pdb=" O LYS J 62 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.152A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.430A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 4.065A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 162 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.648A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.133A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.695A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.236A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.020A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 333 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 315 through 320 removed outlier: 7.047A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER H 100A" --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 393 through 395 removed outlier: 3.662A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.034A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.034A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 6 removed outlier: 4.009A pdb=" N ILE L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR L 72 " --> pdb=" O GLY L 65 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.553A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.553A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE L 86 " --> pdb=" O SER L 102 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.151A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.433A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'C' and resid 91 through 94 removed outlier: 4.071A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 154 through 162 Processing sheet with id=AC5, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC6, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.622A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 9.814A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.191A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 333 " --> pdb=" O ILE C 414 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 315 through 320 removed outlier: 7.042A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER I 100A" --> pdb=" O ALA I 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 393 through 395 removed outlier: 3.627A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 423 through 424 Processing sheet with id=AD1, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AD2, first strand: chain 'I' and resid 10 through 11 removed outlier: 7.023A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 10 through 11 removed outlier: 7.023A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N CYS I 92 " --> pdb=" O TRP I 103 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TRP I 103 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARG I 94 " --> pdb=" O ASP I 101 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AD5, first strand: chain 'M' and resid 4 through 6 removed outlier: 4.005A pdb=" N ILE M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR M 72 " --> pdb=" O GLY M 65 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 53 through 54 removed outlier: 6.513A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU M 33 " --> pdb=" O SER M 49 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR M 97 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 495 through 499 removed outlier: 5.157A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.436A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AE1, first strand: chain 'E' and resid 91 through 94 removed outlier: 4.120A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 154 through 162 Processing sheet with id=AE3, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AE4, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.623A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.843A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.224A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.717A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.235A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.178A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.043A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL E 333 " --> pdb=" O ILE E 414 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS E 385 " --> pdb=" O HIS E 374 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 315 through 320 removed outlier: 7.052A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER J 100A" --> pdb=" O ALA J 98 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 393 through 395 removed outlier: 3.610A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AE8, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 11 removed outlier: 7.028A pdb=" N GLU J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 10 through 11 removed outlier: 7.028A pdb=" N GLU J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N CYS J 92 " --> pdb=" O TRP J 103 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N TRP J 103 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ARG J 94 " --> pdb=" O ASP J 101 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AF3, first strand: chain 'N' and resid 19 through 20 Processing sheet with id=AF4, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.524A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.524A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE N 86 " --> pdb=" O SER N 102 " (cutoff:3.500A) 599 hydrogen bonds defined for protein. 1557 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: 7.92 Time building geometry restraints manager: 10.14 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: 6407 1.34 - 1.46: 5219 1.46 - 1.58: 9203 1.58 - 1.70: 0 1.70 - 1.82: 216 Bond restraints: 21045 Sorted by residual: bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.20e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.95e+00 bond pdb=" C1 NAG E 601 " pdb=" O5 NAG E 601 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" C5 MAN P 7 " pdb=" O5 MAN P 7 " ideal model delta sigma weight residual 1.418 1.452 -0.034 2.00e-02 2.50e+03 2.81e+00 bond pdb=" C5 MAN b 7 " pdb=" O5 MAN b 7 " ideal model delta sigma weight residual 1.418 1.451 -0.033 2.00e-02 2.50e+03 2.67e+00 ... (remaining 21040 not shown) Histogram of bond angle deviations from ideal: 99.01 - 106.01: 436 106.01 - 113.02: 12290 113.02 - 120.02: 6599 120.02 - 127.03: 8898 127.03 - 134.03: 286 Bond angle restraints: 28509 Sorted by residual: angle pdb=" N LEU B 545 " pdb=" CA LEU B 545 " pdb=" C LEU B 545 " ideal model delta sigma weight residual 114.62 110.64 3.98 1.14e+00 7.69e-01 1.22e+01 angle pdb=" N LEU D 545 " pdb=" CA LEU D 545 " pdb=" C LEU D 545 " ideal model delta sigma weight residual 114.62 110.66 3.96 1.14e+00 7.69e-01 1.20e+01 angle pdb=" C CYS E 119 " pdb=" N VAL E 120 " pdb=" CA VAL E 120 " ideal model delta sigma weight residual 120.35 124.55 -4.20 1.39e+00 5.18e-01 9.14e+00 angle pdb=" C CYS C 119 " pdb=" N VAL C 120 " pdb=" CA VAL C 120 " ideal model delta sigma weight residual 120.35 124.39 -4.04 1.39e+00 5.18e-01 8.43e+00 angle pdb=" CA LEU D 545 " pdb=" C LEU D 545 " pdb=" N SER D 546 " ideal model delta sigma weight residual 119.71 116.41 3.30 1.17e+00 7.31e-01 7.98e+00 ... (remaining 28504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 12930 21.85 - 43.70: 904 43.70 - 65.56: 244 65.56 - 87.41: 150 87.41 - 109.26: 94 Dihedral angle restraints: 14322 sinusoidal: 7407 harmonic: 6915 Sorted by residual: 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 -121.00 35.00 1 1.00e+01 1.00e-02 1.74e+01 dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -120.95 34.95 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -120.81 34.81 1 1.00e+01 1.00e-02 1.72e+01 ... (remaining 14319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2736 0.059 - 0.117: 659 0.117 - 0.175: 111 0.175 - 0.234: 16 0.234 - 0.292: 24 Chirality restraints: 3546 Sorted by residual: chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 2.36e+00 chirality pdb=" C5 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C6 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C5 BMA b 3 " pdb=" C4 BMA b 3 " pdb=" C6 BMA b 3 " pdb=" O5 BMA b 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 3543 not shown) Planarity restraints: 3531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 42 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 43 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 42 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO E 43 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 42 " -0.025 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO C 43 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 43 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 43 " -0.022 5.00e-02 4.00e+02 ... (remaining 3528 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2485 2.74 - 3.28: 19799 3.28 - 3.82: 32058 3.82 - 4.36: 39270 4.36 - 4.90: 69655 Nonbonded interactions: 163267 Sorted by model distance: nonbonded pdb=" N ASP A 167 " pdb=" OD1 ASP A 167 " model vdw 2.199 2.520 nonbonded pdb=" N ASP E 167 " pdb=" OD1 ASP E 167 " model vdw 2.200 2.520 nonbonded pdb=" NE2 GLN C 258 " pdb=" OG1 THR C 387 " model vdw 2.201 2.520 nonbonded pdb=" N ASP C 167 " pdb=" OD1 ASP C 167 " model vdw 2.209 2.520 nonbonded pdb=" NE2 GLN A 258 " pdb=" OG1 THR A 387 " model vdw 2.210 2.520 ... (remaining 163262 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 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'Y' selection = chain 'k' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' } ncs_group { reference = chain 'P' selection = chain 'b' selection = chain 'n' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.330 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: 0.010 Extract box with map and model: 6.640 Check model and map are aligned: 0.320 Set scattering table: 0.210 Process input model: 55.750 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.460 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 : 0.008 0.064 21045 Z= 0.523 Angle : 0.878 8.098 28509 Z= 0.421 Chirality : 0.056 0.292 3546 Planarity : 0.004 0.040 3474 Dihedral : 19.829 109.262 9744 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 7.69 % Allowed : 12.27 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.72 (0.14), residues: 2376 helix: -2.98 (0.20), residues: 432 sheet: -2.86 (0.16), residues: 750 loop : -3.38 (0.14), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 112 HIS 0.005 0.001 HIS A 249 PHE 0.015 0.002 PHE M 98 TYR 0.024 0.002 TYR L 91 ARG 0.004 0.001 ARG E 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 331 time to evaluate : 2.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.7345 (ptmt) REVERT: A 271 MET cc_start: 0.7651 (tpt) cc_final: 0.7363 (tpp) REVERT: A 469 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.6588 (mtp85) REVERT: A 475 MET cc_start: 0.8024 (mmm) cc_final: 0.7689 (mmm) REVERT: B 543 ASN cc_start: 0.8804 (m110) cc_final: 0.8444 (m110) REVERT: B 619 LEU cc_start: 0.7980 (mt) cc_final: 0.7757 (mt) REVERT: H 19 ARG cc_start: 0.8272 (ttm170) cc_final: 0.7955 (ttm170) REVERT: H 24 ASP cc_start: 0.8673 (p0) cc_final: 0.8296 (p0) REVERT: H 46 GLU cc_start: 0.8169 (tt0) cc_final: 0.7931 (tt0) REVERT: L 3 GLN cc_start: 0.8093 (mm110) cc_final: 0.7851 (mm-40) REVERT: L 81 ASP cc_start: 0.8002 (t0) cc_final: 0.7739 (t0) REVERT: L 91 TYR cc_start: 0.9152 (OUTLIER) cc_final: 0.8795 (p90) REVERT: L 100 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8265 (pm20) REVERT: C 91 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: C 155 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.7469 (ptmt) REVERT: C 271 MET cc_start: 0.7760 (tpt) cc_final: 0.7499 (tpp) REVERT: C 305 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8120 (ttmm) REVERT: C 475 MET cc_start: 0.8120 (mmm) cc_final: 0.7674 (mmm) REVERT: D 543 ASN cc_start: 0.8847 (m110) cc_final: 0.8469 (m110) REVERT: D 544 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8896 (tt) REVERT: D 654 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7200 (mt-10) REVERT: I 24 ASP cc_start: 0.8753 (p0) cc_final: 0.8503 (p0) REVERT: M 50 ARG cc_start: 0.8245 (mmm-85) cc_final: 0.7978 (mtp85) REVERT: M 100 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8275 (pm20) REVERT: E 155 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.7455 (ptmt) REVERT: E 271 MET cc_start: 0.7691 (tpt) cc_final: 0.7336 (mmp) REVERT: E 475 MET cc_start: 0.8034 (mmm) cc_final: 0.7399 (mmm) REVERT: F 543 ASN cc_start: 0.8888 (m110) cc_final: 0.8505 (m110) REVERT: F 601 LYS cc_start: 0.8445 (ttmt) cc_final: 0.8210 (mtpp) REVERT: F 632 ASP cc_start: 0.8944 (t0) cc_final: 0.8717 (t0) REVERT: F 654 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7105 (mt-10) REVERT: J 23 LYS cc_start: 0.9294 (tttm) cc_final: 0.9041 (tttt) REVERT: J 24 ASP cc_start: 0.8719 (p0) cc_final: 0.8345 (p0) REVERT: J 67 MET cc_start: 0.8695 (ptm) cc_final: 0.8241 (ptm) REVERT: N 61 ARG cc_start: 0.8507 (ptp90) cc_final: 0.8304 (ptt-90) REVERT: N 79 GLN cc_start: 0.8176 (mt0) cc_final: 0.7948 (mt0) outliers start: 161 outliers final: 83 residues processed: 464 average time/residue: 0.3640 time to fit residues: 245.8187 Evaluate side-chains 349 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 256 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 108 GLN Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 370 GLU Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 91 TYR Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 94 optimal weight: 0.0980 chunk 183 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 111 optimal weight: 0.0570 chunk 136 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 249 HIS A 258 GLN A 293 GLN A 302 ASN B 540 GLN B 607 ASN B 618 ASN H 3 GLN H 6 GLN H 108 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN C 66 HIS C 114 GLN C 249 HIS C 258 GLN C 302 ASN ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN D 607 ASN D 618 ASN I 3 GLN I 6 GLN I 108 GLN M 6 GLN M 79 GLN M 89 GLN E 66 HIS E 99 ASN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS E 258 GLN E 302 ASN F 540 GLN F 607 ASN F 618 ASN J 3 GLN J 6 GLN N 6 GLN N 79 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21045 Z= 0.188 Angle : 0.683 9.241 28509 Z= 0.317 Chirality : 0.047 0.264 3546 Planarity : 0.004 0.037 3474 Dihedral : 14.802 76.237 5469 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 5.78 % Allowed : 15.47 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.16), residues: 2376 helix: -1.92 (0.25), residues: 390 sheet: -1.95 (0.18), residues: 735 loop : -2.73 (0.16), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 112 HIS 0.005 0.001 HIS A 249 PHE 0.013 0.001 PHE E 382 TYR 0.016 0.001 TYR L 91 ARG 0.003 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 309 time to evaluate : 1.951 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: A 46 LYS cc_start: 0.8309 (mmtp) cc_final: 0.7467 (mmtm) REVERT: A 91 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: A 111 LEU cc_start: 0.9037 (tp) cc_final: 0.8828 (tp) REVERT: A 244 THR cc_start: 0.9279 (OUTLIER) cc_final: 0.9075 (t) REVERT: A 271 MET cc_start: 0.7817 (tpt) cc_final: 0.7604 (mmm) REVERT: A 469 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.6988 (mtp85) REVERT: A 475 MET cc_start: 0.7841 (mmm) cc_final: 0.7461 (mmm) REVERT: B 543 ASN cc_start: 0.8684 (m110) cc_final: 0.8411 (m-40) REVERT: B 626 MET cc_start: 0.7581 (mtp) cc_final: 0.6901 (ttm) REVERT: B 654 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6963 (mt-10) REVERT: L 81 ASP cc_start: 0.7986 (t0) cc_final: 0.7646 (t70) REVERT: L 100 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8161 (pm20) REVERT: C 271 MET cc_start: 0.7705 (tpt) cc_final: 0.7504 (mmm) REVERT: C 475 MET cc_start: 0.7900 (mmm) cc_final: 0.7589 (mmm) REVERT: D 543 ASN cc_start: 0.8585 (m110) cc_final: 0.8200 (m110) REVERT: D 654 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7144 (mt-10) REVERT: I 24 ASP cc_start: 0.8637 (p0) cc_final: 0.8405 (p0) REVERT: I 43 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7459 (pm20) REVERT: I 80 MET cc_start: 0.8658 (tmm) cc_final: 0.7702 (tmm) REVERT: M 50 ARG cc_start: 0.8279 (mmm-85) cc_final: 0.7934 (mtp85) REVERT: E 35 TRP cc_start: 0.8713 (m100) cc_final: 0.8239 (m-90) REVERT: E 271 MET cc_start: 0.7575 (tpt) cc_final: 0.7289 (mmp) REVERT: E 305 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8150 (ttpp) REVERT: E 370 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7998 (mp0) REVERT: E 373 THR cc_start: 0.9206 (OUTLIER) cc_final: 0.9004 (m) REVERT: E 475 MET cc_start: 0.7819 (mmm) cc_final: 0.7187 (mmm) REVERT: F 543 ASN cc_start: 0.8778 (m110) cc_final: 0.8406 (m110) REVERT: F 632 ASP cc_start: 0.8741 (t0) cc_final: 0.8467 (t0) REVERT: F 654 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7094 (mt-10) REVERT: J 24 ASP cc_start: 0.8648 (p0) cc_final: 0.8265 (p0) REVERT: N 24 ARG cc_start: 0.7645 (mtp-110) cc_final: 0.7392 (ttm110) outliers start: 121 outliers final: 65 residues processed: 403 average time/residue: 0.3260 time to fit residues: 199.4738 Evaluate side-chains 342 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 269 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain I residue 43 GLN Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 370 GLU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 589 ASP Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain N residue 96 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 212 optimal weight: 6.9990 chunk 229 optimal weight: 7.9990 chunk 189 optimal weight: 0.6980 chunk 211 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN B 618 ASN B 625 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 293 GLN D 618 ASN M 6 GLN E 293 GLN F 618 ASN F 625 ASN N 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 21045 Z= 0.415 Angle : 0.743 10.013 28509 Z= 0.347 Chirality : 0.050 0.278 3546 Planarity : 0.004 0.038 3474 Dihedral : 12.341 68.944 5384 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 6.64 % Allowed : 16.91 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.16), residues: 2376 helix: -1.45 (0.26), residues: 390 sheet: -1.76 (0.18), residues: 750 loop : -2.55 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 112 HIS 0.004 0.001 HIS A 249 PHE 0.017 0.002 PHE I 91 TYR 0.028 0.002 TYR L 91 ARG 0.004 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 267 time to evaluate : 2.134 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: A 46 LYS cc_start: 0.8300 (mmtp) cc_final: 0.7486 (mmtm) REVERT: A 271 MET cc_start: 0.7834 (tpt) cc_final: 0.7576 (mmm) REVERT: A 426 MET cc_start: 0.8772 (mmm) cc_final: 0.8493 (mmm) REVERT: A 469 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.6779 (mtp85) REVERT: A 475 MET cc_start: 0.8015 (mmm) cc_final: 0.7654 (mmm) REVERT: B 543 ASN cc_start: 0.8854 (m110) cc_final: 0.8459 (m110) REVERT: B 588 ARG cc_start: 0.7789 (ttm-80) cc_final: 0.7490 (ttm-80) REVERT: B 626 MET cc_start: 0.7415 (mtp) cc_final: 0.7170 (mtp) REVERT: B 654 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7228 (mt-10) REVERT: H 24 ASP cc_start: 0.8586 (p0) cc_final: 0.8362 (p0) REVERT: L 81 ASP cc_start: 0.8117 (t0) cc_final: 0.7822 (t70) REVERT: L 100 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8181 (pm20) REVERT: C 46 LYS cc_start: 0.8287 (mmtm) cc_final: 0.7953 (mmtm) REVERT: C 271 MET cc_start: 0.7762 (tpt) cc_final: 0.7457 (tpp) REVERT: C 475 MET cc_start: 0.8105 (mmm) cc_final: 0.7731 (mmm) REVERT: D 654 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7109 (mt-10) REVERT: I 24 ASP cc_start: 0.8767 (p0) cc_final: 0.8518 (p0) REVERT: I 43 GLN cc_start: 0.7677 (pm20) cc_final: 0.7363 (pm20) REVERT: M 4 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.7597 (mmm) REVERT: M 50 ARG cc_start: 0.8301 (mmm-85) cc_final: 0.8002 (mtp85) REVERT: M 100 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8273 (pm20) REVERT: E 153 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7941 (tp30) REVERT: E 211 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8485 (tp30) REVERT: E 271 MET cc_start: 0.7600 (tpt) cc_final: 0.7295 (mmp) REVERT: E 305 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8263 (ttpp) REVERT: E 469 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.6646 (ptp90) REVERT: E 475 MET cc_start: 0.7995 (mmm) cc_final: 0.7419 (mmm) REVERT: F 543 ASN cc_start: 0.8777 (m110) cc_final: 0.8373 (m110) REVERT: F 632 ASP cc_start: 0.8803 (t0) cc_final: 0.8561 (t0) REVERT: F 654 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7267 (mt-10) REVERT: J 24 ASP cc_start: 0.8677 (p0) cc_final: 0.8360 (p0) outliers start: 139 outliers final: 96 residues processed: 375 average time/residue: 0.3204 time to fit residues: 184.8082 Evaluate side-chains 361 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 257 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain M residue 4 MET Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 589 ASP Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 100 GLN Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 106 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 0.6980 chunk 160 optimal weight: 0.1980 chunk 110 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 142 optimal weight: 6.9990 chunk 213 optimal weight: 7.9990 chunk 226 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 618 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN N 6 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21045 Z= 0.183 Angle : 0.643 10.159 28509 Z= 0.297 Chirality : 0.047 0.266 3546 Planarity : 0.003 0.035 3474 Dihedral : 10.379 60.586 5376 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.87 % Allowed : 19.05 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.74 (0.16), residues: 2376 helix: -1.09 (0.27), residues: 384 sheet: -1.40 (0.18), residues: 744 loop : -2.34 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 112 HIS 0.004 0.001 HIS C 249 PHE 0.012 0.001 PHE E 382 TYR 0.012 0.001 TYR N 91 ARG 0.006 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 287 time to evaluate : 2.076 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: A 46 LYS cc_start: 0.8313 (mmtp) cc_final: 0.7454 (mmtm) REVERT: A 155 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.7234 (ptmt) REVERT: A 271 MET cc_start: 0.7828 (tpt) cc_final: 0.7618 (mmm) REVERT: A 469 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7055 (mtp85) REVERT: A 475 MET cc_start: 0.7867 (mmm) cc_final: 0.7416 (mmm) REVERT: B 543 ASN cc_start: 0.8764 (m110) cc_final: 0.8418 (m110) REVERT: B 588 ARG cc_start: 0.7774 (ttm-80) cc_final: 0.7549 (ttm-80) REVERT: B 654 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7051 (mt-10) REVERT: H 24 ASP cc_start: 0.8539 (p0) cc_final: 0.8337 (p0) REVERT: L 3 GLN cc_start: 0.8119 (mm110) cc_final: 0.7849 (mm-40) REVERT: L 24 ARG cc_start: 0.7550 (mtp-110) cc_final: 0.7345 (ttm110) REVERT: L 50 ARG cc_start: 0.8287 (mtp85) cc_final: 0.8002 (mtp85) REVERT: L 81 ASP cc_start: 0.8046 (t0) cc_final: 0.7752 (t70) REVERT: L 100 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8105 (pm20) REVERT: C 35 TRP cc_start: 0.8694 (m100) cc_final: 0.8312 (m-90) REVERT: C 155 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.7095 (ptmt) REVERT: C 475 MET cc_start: 0.7945 (mmm) cc_final: 0.7655 (mmm) REVERT: D 535 MET cc_start: 0.7630 (mmm) cc_final: 0.7366 (mmm) REVERT: D 654 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7119 (mt-10) REVERT: I 43 GLN cc_start: 0.7669 (pm20) cc_final: 0.7374 (pm20) REVERT: I 100 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7424 (mt-10) REVERT: M 50 ARG cc_start: 0.8249 (mmm-85) cc_final: 0.7913 (mtp85) REVERT: M 100 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8230 (pm20) REVERT: E 155 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.7417 (ptmt) REVERT: E 211 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8485 (tp30) REVERT: E 271 MET cc_start: 0.7607 (tpt) cc_final: 0.7280 (mmp) REVERT: E 305 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8256 (ttpp) REVERT: E 373 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8992 (m) REVERT: E 469 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.6515 (ptp90) REVERT: E 475 MET cc_start: 0.7738 (mmm) cc_final: 0.7166 (mmm) REVERT: F 543 ASN cc_start: 0.8709 (m110) cc_final: 0.8344 (m110) REVERT: F 626 MET cc_start: 0.7256 (mtp) cc_final: 0.6654 (ttm) REVERT: F 632 ASP cc_start: 0.8747 (t0) cc_final: 0.8446 (t0) REVERT: F 654 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7080 (mt-10) REVERT: J 24 ASP cc_start: 0.8612 (p0) cc_final: 0.8305 (p0) REVERT: J 100 GLU cc_start: 0.7887 (mp0) cc_final: 0.7613 (mt-10) REVERT: N 76 LYS cc_start: 0.8290 (mmmm) cc_final: 0.8070 (mmmm) outliers start: 123 outliers final: 70 residues processed: 381 average time/residue: 0.3194 time to fit residues: 186.8388 Evaluate side-chains 356 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 276 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 589 ASP Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 100 GLN Chi-restraints excluded: chain N residue 106 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 0.4980 chunk 128 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 93 optimal weight: 0.0980 chunk 193 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN B 618 ASN B 625 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN D 618 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN F 618 ASN N 6 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 21045 Z= 0.346 Angle : 0.688 10.200 28509 Z= 0.322 Chirality : 0.048 0.279 3546 Planarity : 0.004 0.040 3474 Dihedral : 9.874 59.860 5365 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.73 % Allowed : 19.82 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.67 (0.16), residues: 2376 helix: -1.05 (0.27), residues: 390 sheet: -1.35 (0.19), residues: 750 loop : -2.29 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 112 HIS 0.005 0.001 HIS A 249 PHE 0.015 0.002 PHE A 382 TYR 0.024 0.002 TYR L 91 ARG 0.009 0.000 ARG N 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 263 time to evaluate : 2.410 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: A 46 LYS cc_start: 0.8294 (mmtp) cc_final: 0.7434 (mmtm) REVERT: A 155 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.7548 (ptmt) REVERT: A 271 MET cc_start: 0.7779 (tpt) cc_final: 0.7552 (mmm) REVERT: A 469 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7140 (mtp85) REVERT: A 475 MET cc_start: 0.7939 (mmm) cc_final: 0.7579 (mmm) REVERT: B 543 ASN cc_start: 0.8838 (m110) cc_final: 0.8507 (m110) REVERT: B 626 MET cc_start: 0.7224 (mtp) cc_final: 0.6393 (ttm) REVERT: B 654 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7166 (mt-10) REVERT: H 24 ASP cc_start: 0.8617 (p0) cc_final: 0.8399 (p0) REVERT: L 50 ARG cc_start: 0.8291 (mtp85) cc_final: 0.8010 (mtp85) REVERT: L 81 ASP cc_start: 0.8108 (t0) cc_final: 0.7815 (t70) REVERT: L 100 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8080 (pm20) REVERT: C 46 LYS cc_start: 0.8249 (mmtm) cc_final: 0.7967 (mmtm) REVERT: C 155 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.7223 (ptmt) REVERT: C 475 MET cc_start: 0.8080 (mmm) cc_final: 0.7691 (mmm) REVERT: D 535 MET cc_start: 0.7904 (mmm) cc_final: 0.7561 (mmm) REVERT: D 654 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7135 (mt-10) REVERT: I 43 GLN cc_start: 0.7711 (pm20) cc_final: 0.7405 (pm20) REVERT: M 4 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.7945 (mmm) REVERT: M 50 ARG cc_start: 0.8267 (mmm-85) cc_final: 0.8034 (mtp85) REVERT: M 100 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8243 (pm20) REVERT: E 155 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.7778 (ptmt) REVERT: E 211 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8485 (tp30) REVERT: E 271 MET cc_start: 0.7593 (tpt) cc_final: 0.7254 (mmp) REVERT: E 305 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8167 (ttpp) REVERT: E 373 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.9020 (m) REVERT: E 469 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.6711 (ptp90) REVERT: E 475 MET cc_start: 0.7896 (mmm) cc_final: 0.7350 (mmm) REVERT: F 543 ASN cc_start: 0.8750 (m110) cc_final: 0.8347 (m110) REVERT: F 626 MET cc_start: 0.7348 (mtp) cc_final: 0.6704 (ttm) REVERT: F 632 ASP cc_start: 0.8798 (t0) cc_final: 0.8526 (t0) REVERT: F 654 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7108 (mt-10) REVERT: J 24 ASP cc_start: 0.8632 (p0) cc_final: 0.8352 (p0) REVERT: N 4 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.7606 (mmm) REVERT: N 24 ARG cc_start: 0.7618 (ttm110) cc_final: 0.7314 (mtp-110) outliers start: 120 outliers final: 83 residues processed: 354 average time/residue: 0.3300 time to fit residues: 178.6333 Evaluate side-chains 353 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 258 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain M residue 4 MET Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 100 GLN Chi-restraints excluded: chain N residue 106 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 2.9990 chunk 203 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 226 optimal weight: 6.9990 chunk 187 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 118 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN B 625 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN N 6 GLN N 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21045 Z= 0.181 Angle : 0.632 10.898 28509 Z= 0.294 Chirality : 0.046 0.255 3546 Planarity : 0.003 0.036 3474 Dihedral : 9.218 59.448 5363 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.63 % Allowed : 21.01 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.45 (0.17), residues: 2376 helix: -1.08 (0.26), residues: 408 sheet: -1.11 (0.19), residues: 738 loop : -2.15 (0.16), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 112 HIS 0.005 0.001 HIS A 249 PHE 0.012 0.001 PHE E 382 TYR 0.013 0.001 TYR A 486 ARG 0.007 0.000 ARG N 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 276 time to evaluate : 2.248 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: A 46 LYS cc_start: 0.8292 (mmtp) cc_final: 0.7417 (mmtm) REVERT: A 155 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.7617 (ptmt) REVERT: A 271 MET cc_start: 0.7815 (tpt) cc_final: 0.7477 (tpp) REVERT: A 469 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.6649 (mtp85) REVERT: A 475 MET cc_start: 0.7894 (mmm) cc_final: 0.7396 (mmm) REVERT: B 543 ASN cc_start: 0.8836 (m110) cc_final: 0.8490 (m110) REVERT: B 626 MET cc_start: 0.7176 (mtp) cc_final: 0.6871 (ttm) REVERT: B 654 GLU cc_start: 0.7297 (mm-30) cc_final: 0.7025 (mt-10) REVERT: H 24 ASP cc_start: 0.8581 (p0) cc_final: 0.8371 (p0) REVERT: L 4 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7070 (mmm) REVERT: L 50 ARG cc_start: 0.8264 (mtp85) cc_final: 0.7981 (mtp85) REVERT: L 81 ASP cc_start: 0.8063 (t0) cc_final: 0.7775 (t0) REVERT: L 100 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8064 (pm20) REVERT: C 35 TRP cc_start: 0.8670 (m100) cc_final: 0.8321 (m-90) REVERT: C 46 LYS cc_start: 0.8256 (mmtm) cc_final: 0.7927 (mmtm) REVERT: C 150 MET cc_start: 0.7606 (tpp) cc_final: 0.7222 (ttm) REVERT: C 155 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.7429 (ptmt) REVERT: C 475 MET cc_start: 0.7972 (mmm) cc_final: 0.7645 (mmm) REVERT: D 535 MET cc_start: 0.7860 (mmm) cc_final: 0.7519 (mmm) REVERT: D 626 MET cc_start: 0.7136 (mtp) cc_final: 0.6768 (ttm) REVERT: D 654 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7011 (mt-10) REVERT: I 43 GLN cc_start: 0.7642 (pm20) cc_final: 0.7373 (pm20) REVERT: I 69 MET cc_start: 0.8853 (mtm) cc_final: 0.8580 (mtm) REVERT: I 100 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7462 (mt-10) REVERT: M 24 ARG cc_start: 0.7596 (mtp-110) cc_final: 0.7383 (ttm110) REVERT: M 50 ARG cc_start: 0.8261 (mmm-85) cc_final: 0.7949 (mtp85) REVERT: M 100 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8210 (pm20) REVERT: E 155 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7838 (ptmt) REVERT: E 211 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8499 (tp30) REVERT: E 271 MET cc_start: 0.7564 (tpt) cc_final: 0.7251 (mmp) REVERT: E 305 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8142 (ttpp) REVERT: E 373 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8961 (m) REVERT: E 469 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.6559 (ptp90) REVERT: E 475 MET cc_start: 0.7756 (mmm) cc_final: 0.7212 (mmm) REVERT: F 535 MET cc_start: 0.8000 (mmm) cc_final: 0.7778 (mmm) REVERT: F 543 ASN cc_start: 0.8651 (m110) cc_final: 0.8290 (m110) REVERT: F 626 MET cc_start: 0.7238 (mtp) cc_final: 0.6759 (ttm) REVERT: F 632 ASP cc_start: 0.8771 (t0) cc_final: 0.8499 (t0) REVERT: F 654 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7082 (mt-10) REVERT: J 19 ARG cc_start: 0.8068 (ttm170) cc_final: 0.7857 (ttm170) REVERT: J 24 ASP cc_start: 0.8561 (p0) cc_final: 0.8280 (p0) REVERT: J 52 ILE cc_start: 0.8281 (mp) cc_final: 0.8009 (mt) REVERT: J 100 GLU cc_start: 0.7892 (mp0) cc_final: 0.7612 (mt-10) REVERT: N 24 ARG cc_start: 0.7596 (ttm110) cc_final: 0.7300 (mtp-110) outliers start: 97 outliers final: 69 residues processed: 349 average time/residue: 0.3174 time to fit residues: 169.5247 Evaluate side-chains 349 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 269 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 589 ASP Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 106 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 225 optimal weight: 0.0060 chunk 141 optimal weight: 0.0970 chunk 137 optimal weight: 3.9990 chunk 104 optimal weight: 0.0670 chunk 139 optimal weight: 2.9990 overall best weight: 0.3932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 618 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21045 Z= 0.153 Angle : 0.618 13.761 28509 Z= 0.285 Chirality : 0.046 0.251 3546 Planarity : 0.003 0.035 3474 Dihedral : 8.727 59.926 5357 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.30 % Allowed : 21.54 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.17), residues: 2376 helix: -0.63 (0.28), residues: 384 sheet: -0.93 (0.19), residues: 735 loop : -2.07 (0.16), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 112 HIS 0.005 0.000 HIS A 249 PHE 0.011 0.001 PHE E 382 TYR 0.015 0.001 TYR A 486 ARG 0.010 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 275 time to evaluate : 2.144 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: A 46 LYS cc_start: 0.8267 (mmtp) cc_final: 0.7382 (mmtm) REVERT: A 155 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.7690 (ptmt) REVERT: A 271 MET cc_start: 0.7804 (tpt) cc_final: 0.7478 (tpp) REVERT: A 469 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.6927 (mtp85) REVERT: A 475 MET cc_start: 0.7752 (mmm) cc_final: 0.7358 (mmm) REVERT: B 543 ASN cc_start: 0.8829 (m110) cc_final: 0.8480 (m110) REVERT: L 4 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7160 (mmm) REVERT: L 50 ARG cc_start: 0.8229 (mtp85) cc_final: 0.7935 (mtp85) REVERT: L 81 ASP cc_start: 0.7984 (t0) cc_final: 0.7718 (t0) REVERT: C 35 TRP cc_start: 0.8651 (m100) cc_final: 0.8385 (m-90) REVERT: C 150 MET cc_start: 0.7582 (tpp) cc_final: 0.7346 (ttm) REVERT: C 155 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.7494 (ptmt) REVERT: C 265 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8720 (mt) REVERT: C 475 MET cc_start: 0.7819 (mmm) cc_final: 0.7536 (mmm) REVERT: C 502 LYS cc_start: 0.8806 (tttt) cc_final: 0.8379 (tttp) REVERT: D 535 MET cc_start: 0.7816 (mmm) cc_final: 0.7516 (mmm) REVERT: D 626 MET cc_start: 0.7012 (mtp) cc_final: 0.6724 (ttm) REVERT: D 654 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7062 (mt-10) REVERT: I 43 GLN cc_start: 0.7569 (pm20) cc_final: 0.7287 (pm20) REVERT: I 69 MET cc_start: 0.8824 (mtm) cc_final: 0.8533 (mtm) REVERT: I 100 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7457 (mt-10) REVERT: M 50 ARG cc_start: 0.8237 (mmm-85) cc_final: 0.8003 (mtp85) REVERT: M 100 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8202 (pm20) REVERT: E 155 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7854 (ptmt) REVERT: E 246 GLN cc_start: 0.8236 (pm20) cc_final: 0.7755 (tp-100) REVERT: E 271 MET cc_start: 0.7536 (tpt) cc_final: 0.7254 (mmp) REVERT: E 305 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7987 (ttpp) REVERT: E 373 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8940 (m) REVERT: E 469 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.6473 (ptp90) REVERT: E 475 MET cc_start: 0.7708 (mmm) cc_final: 0.7184 (mmm) REVERT: F 543 ASN cc_start: 0.8622 (m110) cc_final: 0.8282 (m110) REVERT: F 632 ASP cc_start: 0.8763 (t0) cc_final: 0.8456 (t0) REVERT: F 654 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7106 (mt-10) REVERT: J 19 ARG cc_start: 0.8096 (ttm170) cc_final: 0.7893 (ttm170) REVERT: J 24 ASP cc_start: 0.8574 (p0) cc_final: 0.8272 (p0) REVERT: J 52 ILE cc_start: 0.8220 (mp) cc_final: 0.7983 (mt) REVERT: J 100 GLU cc_start: 0.7898 (mp0) cc_final: 0.7624 (mt-10) REVERT: N 76 LYS cc_start: 0.8274 (mmmm) cc_final: 0.7962 (mmmm) outliers start: 90 outliers final: 63 residues processed: 342 average time/residue: 0.3369 time to fit residues: 176.2182 Evaluate side-chains 341 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 268 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 589 ASP Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 106 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21045 Z= 0.276 Angle : 0.663 15.160 28509 Z= 0.306 Chirality : 0.047 0.271 3546 Planarity : 0.003 0.047 3474 Dihedral : 8.556 59.914 5351 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.35 % Allowed : 21.82 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 (0.17), residues: 2376 helix: -0.52 (0.28), residues: 384 sheet: -1.02 (0.19), residues: 720 loop : -2.03 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 112 HIS 0.005 0.001 HIS A 249 PHE 0.013 0.002 PHE H 91 TYR 0.037 0.001 TYR A 486 ARG 0.015 0.000 ARG N 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 264 time to evaluate : 2.347 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: A 46 LYS cc_start: 0.8248 (mmtp) cc_final: 0.7368 (mmtm) REVERT: A 155 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.7812 (ptmt) REVERT: A 161 MET cc_start: 0.8197 (mmm) cc_final: 0.7970 (mmm) REVERT: A 271 MET cc_start: 0.7747 (tpt) cc_final: 0.7545 (mmm) REVERT: A 469 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.6450 (mtp85) REVERT: A 475 MET cc_start: 0.7862 (mmm) cc_final: 0.7497 (mmm) REVERT: B 543 ASN cc_start: 0.8844 (m110) cc_final: 0.8470 (m110) REVERT: L 4 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7141 (mmm) REVERT: L 50 ARG cc_start: 0.8253 (mtp85) cc_final: 0.7969 (mtp85) REVERT: L 81 ASP cc_start: 0.8045 (t0) cc_final: 0.7788 (t0) REVERT: C 150 MET cc_start: 0.7723 (tpp) cc_final: 0.7420 (ttm) REVERT: C 155 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.7842 (ptmt) REVERT: C 265 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8724 (mt) REVERT: C 475 MET cc_start: 0.8010 (mmm) cc_final: 0.7640 (mmm) REVERT: D 535 MET cc_start: 0.7860 (mmm) cc_final: 0.7499 (mmm) REVERT: D 626 MET cc_start: 0.7083 (mtp) cc_final: 0.6698 (ttm) REVERT: D 654 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7275 (mt-10) REVERT: I 43 GLN cc_start: 0.7633 (pm20) cc_final: 0.7360 (pm20) REVERT: I 100 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7480 (mt-10) REVERT: M 24 ARG cc_start: 0.7627 (mtp-110) cc_final: 0.7381 (ttm110) REVERT: M 50 ARG cc_start: 0.8239 (mmm-85) cc_final: 0.8026 (mtp85) REVERT: M 76 LYS cc_start: 0.8340 (mmmm) cc_final: 0.8062 (mmmm) REVERT: M 100 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8161 (pm20) REVERT: E 155 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.7863 (ptmt) REVERT: E 211 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8503 (tp30) REVERT: E 271 MET cc_start: 0.7569 (tpt) cc_final: 0.7247 (mmp) REVERT: E 305 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8197 (ttpp) REVERT: E 373 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8965 (m) REVERT: E 469 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.6681 (ptp90) REVERT: E 475 MET cc_start: 0.7791 (mmm) cc_final: 0.7311 (mmm) REVERT: F 543 ASN cc_start: 0.8654 (m110) cc_final: 0.8270 (m110) REVERT: F 632 ASP cc_start: 0.8810 (t0) cc_final: 0.8534 (t0) REVERT: F 654 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7165 (mt-10) REVERT: J 24 ASP cc_start: 0.8594 (p0) cc_final: 0.8310 (p0) REVERT: J 52 ILE cc_start: 0.8313 (mp) cc_final: 0.8040 (mt) REVERT: N 76 LYS cc_start: 0.8289 (mmmm) cc_final: 0.7946 (mmmm) outliers start: 91 outliers final: 72 residues processed: 329 average time/residue: 0.3332 time to fit residues: 166.9924 Evaluate side-chains 342 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 259 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 589 ASP Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 106 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 7.9990 chunk 197 optimal weight: 1.9990 chunk 210 optimal weight: 4.9990 chunk 126 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 189 optimal weight: 1.9990 chunk 198 optimal weight: 0.9980 chunk 209 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 618 ASN N 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21045 Z= 0.289 Angle : 0.668 13.956 28509 Z= 0.310 Chirality : 0.047 0.274 3546 Planarity : 0.004 0.064 3474 Dihedral : 8.430 59.973 5351 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.58 % Allowed : 21.97 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.17 (0.17), residues: 2376 helix: -0.50 (0.28), residues: 384 sheet: -1.06 (0.19), residues: 732 loop : -1.99 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 112 HIS 0.006 0.001 HIS A 249 PHE 0.013 0.002 PHE J 91 TYR 0.042 0.001 TYR A 486 ARG 0.015 0.000 ARG N 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 260 time to evaluate : 2.226 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: A 46 LYS cc_start: 0.8245 (mmtp) cc_final: 0.7370 (mmtm) REVERT: A 155 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.7814 (ptmt) REVERT: A 271 MET cc_start: 0.7752 (tpt) cc_final: 0.7543 (mmm) REVERT: A 426 MET cc_start: 0.8703 (mmm) cc_final: 0.8409 (mmm) REVERT: A 469 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.6424 (mtp85) REVERT: A 475 MET cc_start: 0.7865 (mmm) cc_final: 0.7509 (mmm) REVERT: B 543 ASN cc_start: 0.8806 (m110) cc_final: 0.8454 (m110) REVERT: H 24 ASP cc_start: 0.8614 (p0) cc_final: 0.8396 (p0) REVERT: L 4 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7199 (mmm) REVERT: L 50 ARG cc_start: 0.8251 (mtp85) cc_final: 0.7964 (mtp85) REVERT: L 81 ASP cc_start: 0.8055 (t0) cc_final: 0.7811 (t0) REVERT: C 46 LYS cc_start: 0.8248 (mmtm) cc_final: 0.7948 (mmtm) REVERT: C 150 MET cc_start: 0.7800 (tpp) cc_final: 0.7567 (ttm) REVERT: C 155 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.7936 (ptmt) REVERT: C 265 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8651 (mt) REVERT: C 475 MET cc_start: 0.8020 (mmm) cc_final: 0.7652 (mmm) REVERT: D 535 MET cc_start: 0.7841 (mmm) cc_final: 0.7543 (mmm) REVERT: D 626 MET cc_start: 0.7185 (mtp) cc_final: 0.6728 (ttm) REVERT: D 654 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7284 (mt-10) REVERT: I 43 GLN cc_start: 0.7633 (pm20) cc_final: 0.7359 (pm20) REVERT: I 100 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7465 (mt-10) REVERT: M 50 ARG cc_start: 0.8230 (mmm-85) cc_final: 0.8015 (mtp85) REVERT: M 76 LYS cc_start: 0.8373 (mmmm) cc_final: 0.8051 (mmmm) REVERT: M 100 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8196 (pm20) REVERT: E 155 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.7938 (ptmt) REVERT: E 211 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8514 (tp30) REVERT: E 271 MET cc_start: 0.7595 (tpt) cc_final: 0.7184 (mmp) REVERT: E 305 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8158 (ttpp) REVERT: E 373 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8974 (m) REVERT: E 469 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.6915 (ptp90) REVERT: E 475 MET cc_start: 0.7785 (mmm) cc_final: 0.7305 (mmm) REVERT: F 543 ASN cc_start: 0.8670 (m110) cc_final: 0.8277 (m110) REVERT: F 632 ASP cc_start: 0.8802 (t0) cc_final: 0.8528 (t0) REVERT: F 654 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7208 (mt-10) REVERT: J 19 ARG cc_start: 0.8046 (ttm170) cc_final: 0.7845 (ttm170) REVERT: J 24 ASP cc_start: 0.8584 (p0) cc_final: 0.8317 (p0) REVERT: J 52 ILE cc_start: 0.8327 (mp) cc_final: 0.8058 (mt) REVERT: J 100 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.6746 (mp0) REVERT: N 76 LYS cc_start: 0.8292 (mmmm) cc_final: 0.7982 (mmmm) outliers start: 96 outliers final: 76 residues processed: 330 average time/residue: 0.3329 time to fit residues: 168.8132 Evaluate side-chains 343 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 255 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 589 ASP Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 106 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 6.9990 chunk 135 optimal weight: 0.3980 chunk 105 optimal weight: 4.9990 chunk 154 optimal weight: 0.6980 chunk 233 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 21045 Z= 0.359 Angle : 0.701 12.785 28509 Z= 0.327 Chirality : 0.048 0.289 3546 Planarity : 0.004 0.063 3474 Dihedral : 8.443 59.648 5349 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.35 % Allowed : 21.97 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.22 (0.17), residues: 2376 helix: -0.65 (0.27), residues: 399 sheet: -1.09 (0.19), residues: 732 loop : -2.00 (0.16), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 112 HIS 0.006 0.001 HIS A 249 PHE 0.015 0.002 PHE E 159 TYR 0.023 0.002 TYR L 91 ARG 0.016 0.000 ARG N 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 250 time to evaluate : 2.530 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: A 46 LYS cc_start: 0.8254 (mmtp) cc_final: 0.7391 (mmtm) REVERT: A 155 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.7808 (ptmt) REVERT: A 271 MET cc_start: 0.7759 (tpt) cc_final: 0.7539 (mmm) REVERT: A 469 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.6457 (mtp85) REVERT: A 475 MET cc_start: 0.7934 (mmm) cc_final: 0.7478 (mmm) REVERT: B 543 ASN cc_start: 0.8801 (m110) cc_final: 0.8425 (m110) REVERT: H 24 ASP cc_start: 0.8640 (p0) cc_final: 0.8425 (p0) REVERT: L 4 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7178 (mmm) REVERT: L 24 ARG cc_start: 0.7417 (ttm110) cc_final: 0.7178 (ttm110) REVERT: L 50 ARG cc_start: 0.8273 (mtp85) cc_final: 0.7976 (mtp85) REVERT: L 81 ASP cc_start: 0.8072 (t0) cc_final: 0.7826 (t0) REVERT: C 46 LYS cc_start: 0.8252 (mmtm) cc_final: 0.7948 (mmtm) REVERT: C 155 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.7988 (ptmt) REVERT: C 265 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8684 (mt) REVERT: C 475 MET cc_start: 0.8079 (mmm) cc_final: 0.7658 (mmm) REVERT: D 535 MET cc_start: 0.7840 (mmm) cc_final: 0.7519 (mmm) REVERT: D 626 MET cc_start: 0.7323 (mtp) cc_final: 0.6814 (ttm) REVERT: D 654 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7280 (mt-10) REVERT: I 43 GLN cc_start: 0.7624 (pm20) cc_final: 0.7348 (pm20) REVERT: M 50 ARG cc_start: 0.8224 (mmm-85) cc_final: 0.8019 (mtp85) REVERT: M 76 LYS cc_start: 0.8442 (mmmm) cc_final: 0.8142 (mmmm) REVERT: M 100 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8175 (pm20) REVERT: E 155 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8005 (ptmt) REVERT: E 211 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8492 (tp30) REVERT: E 271 MET cc_start: 0.7622 (tpt) cc_final: 0.7156 (mmp) REVERT: E 305 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7951 (ttmm) REVERT: E 373 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.8983 (m) REVERT: E 469 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.6915 (ptp90) REVERT: E 475 MET cc_start: 0.7848 (mmm) cc_final: 0.7337 (mmm) REVERT: F 543 ASN cc_start: 0.8693 (m110) cc_final: 0.8291 (m110) REVERT: F 632 ASP cc_start: 0.8899 (t0) cc_final: 0.8628 (t0) REVERT: F 654 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7313 (mt-10) REVERT: J 24 ASP cc_start: 0.8564 (p0) cc_final: 0.8295 (p0) REVERT: J 100 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.6787 (mp0) REVERT: N 76 LYS cc_start: 0.8323 (mmmm) cc_final: 0.8004 (mmmm) outliers start: 91 outliers final: 72 residues processed: 316 average time/residue: 0.3278 time to fit residues: 158.9987 Evaluate side-chains 331 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 247 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 69 MET Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 589 ASP Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 106 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 77 optimal weight: 0.3980 chunk 190 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.112802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.090101 restraints weight = 35447.417| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.70 r_work: 0.3079 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21045 Z= 0.235 Angle : 0.653 12.430 28509 Z= 0.303 Chirality : 0.046 0.268 3546 Planarity : 0.003 0.070 3474 Dihedral : 8.095 59.543 5347 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.11 % Allowed : 22.59 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.09 (0.17), residues: 2376 helix: -0.56 (0.27), residues: 399 sheet: -0.96 (0.19), residues: 747 loop : -1.94 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 112 HIS 0.005 0.001 HIS A 249 PHE 0.013 0.001 PHE C 382 TYR 0.015 0.001 TYR A 486 ARG 0.016 0.000 ARG N 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4625.81 seconds wall clock time: 84 minutes 32.35 seconds (5072.35 seconds total)