Starting phenix.real_space_refine on Fri Feb 23 03:51:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1v_9319/02_2024/6n1v_9319_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1v_9319/02_2024/6n1v_9319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1v_9319/02_2024/6n1v_9319.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1v_9319/02_2024/6n1v_9319.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1v_9319/02_2024/6n1v_9319_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1v_9319/02_2024/6n1v_9319_neut.pdb" } resolution = 4.0 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= 0.012 sd= 0.109 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 177 5.16 5 C 22872 2.51 5 N 6054 2.21 5 O 7395 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "3 ARG 45": "NH1" <-> "NH2" Residue "3 TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 99": "NH1" <-> "NH2" Residue "3 ARG 219": "NH1" <-> "NH2" Residue "4 TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 55": "NH1" <-> "NH2" Residue "4 ARG 62": "NH1" <-> "NH2" Residue "4 TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "B PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 62": "NH1" <-> "NH2" Residue "g PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 53": "NH1" <-> "NH2" Residue "i ASP 79": "OD1" <-> "OD2" Residue "i TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 45": "NH1" <-> "NH2" Residue "1 TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 99": "NH1" <-> "NH2" Residue "1 ARG 219": "NH1" <-> "NH2" Residue "2 TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 55": "NH1" <-> "NH2" Residue "2 ARG 62": "NH1" <-> "NH2" Residue "2 TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 62": "NH1" <-> "NH2" Residue "f PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 53": "NH1" <-> "NH2" Residue "h ASP 79": "OD1" <-> "OD2" Residue "h TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 370": "OE1" <-> "OE2" Residue "C PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 45": "NH1" <-> "NH2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 99": "NH1" <-> "NH2" Residue "H ARG 219": "NH1" <-> "NH2" Residue "L TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 55": "NH1" <-> "NH2" Residue "L ARG 62": "NH1" <-> "NH2" Residue "L TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 62": "NH1" <-> "NH2" Residue "Q PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 53": "NH1" <-> "NH2" Residue "R ASP 79": "OD1" <-> "OD2" Residue "R TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36498 Number of models: 1 Model: "" Number of chains: 69 Chain: "3" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1669 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 209} Chain: "4" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1612 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 201} Chain: "B" Number of atoms: 3565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3565 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "F" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "Y" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "a" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 787 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "g" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 121} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "i" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "1" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1669 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 209} Chain: "2" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1612 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 201} Chain: "A" Number of atoms: 3565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3565 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "E" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "X" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "Z" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 787 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "f" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 121} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "h" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "C" Number of atoms: 3565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3565 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "D" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "H" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1669 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 209} Chain: "L" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1612 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 201} Chain: "M" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "N" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 787 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "Q" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 121} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 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: "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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 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: 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: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: "j" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 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: "m" 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: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 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: "t" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "u" Number of atoms: 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: "v" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "w" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "x" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "y" 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: "z" 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: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "5" 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: "6" 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: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "8" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "9" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "AA" Number of atoms: 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: "BA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "CA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "DA" Number of atoms: 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 18.35, per 1000 atoms: 0.50 Number of scatterers: 36498 At special positions: 0 Unit cell: (190.4, 185.92, 157.92, 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 177 16.00 O 7395 8.00 N 6054 7.00 C 22872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS 3 22 " - pdb=" SG CYS 3 97 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 149 " - pdb=" SG CYS 3 205 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 225 " - pdb=" SG CYS 4 215 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 22 " - pdb=" SG CYS 4 89 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 138 " - pdb=" SG CYS 4 197 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.04 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.01 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 92 " distance=2.03 Simple disulfide: pdb=" SG CYS a 23 " - pdb=" SG CYS a 88 " distance=2.03 Simple disulfide: pdb=" SG CYS g 22 " - pdb=" SG CYS g 103 " distance=2.04 Simple disulfide: pdb=" SG CYS g 109 " - pdb=" SG CYS g 112 " distance=2.03 Simple disulfide: pdb=" SG CYS 1 22 " - pdb=" SG CYS 1 97 " distance=2.03 Simple disulfide: pdb=" SG CYS 1 149 " - pdb=" SG CYS 1 205 " distance=2.03 Simple disulfide: pdb=" SG CYS 1 225 " - pdb=" SG CYS 2 215 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 22 " - pdb=" SG CYS 2 89 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 138 " - pdb=" SG CYS 2 197 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.01 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 88 " distance=2.03 Simple disulfide: pdb=" SG CYS f 22 " - pdb=" SG CYS f 103 " distance=2.04 Simple disulfide: pdb=" SG CYS f 109 " - pdb=" SG CYS f 112 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.03 Simple disulfide: pdb=" SG CYS H 225 " - pdb=" SG CYS L 215 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 197 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 103 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 109 " - pdb=" SG CYS Q 112 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA W 3 " - " MAN W 4 " " BMA b 3 " - " MAN b 4 " " BMA j 3 " - " MAN j 4 " " BMA l 3 " - " MAN l 4 " " BMA s 3 " - " MAN s 4 " " BMA t 3 " - " MAN t 4 " " BMA x 3 " - " MAN x 4 " " BMA z 3 " - " MAN z 4 " " BMAAA 3 " - " MANAA 4 " " BMABA 3 " - " MANBA 4 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " " BMA W 3 " - " MAN W 5 " " BMA l 3 " - " MAN l 5 " " BMA s 3 " - " MAN s 5 " " BMA z 3 " - " MAN z 5 " " BMAAA 3 " - " MANAA 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 5 2 " - " BMA 5 3 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGCA 2 " - " BMACA 3 " " NAGDA 1 " - " NAGDA 2 " " NAGDA 2 " - " BMADA 3 " NAG-ASN " NAG 0 1 " - " ASN C 133 " " NAG 5 1 " - " ASN C 137 " " NAG 6 1 " - " ASN C 156 " " NAG 7 1 " - " ASN C 301 " " NAG 8 1 " - " ASN C 332 " " NAG 9 1 " - " ASN C 448 " " NAG A 608 " - " ASN A 339 " " NAG A 617 " - " ASN A 392 " " NAG A 623 " - " ASN A 197 " " NAG B 608 " - " ASN B 339 " " NAG B 617 " - " ASN B 392 " " NAG B 623 " - " ASN B 197 " " NAG C 608 " - " ASN C 339 " " NAG C 617 " - " ASN C 392 " " NAG C 623 " - " ASN C 197 " " NAG G 1 " - " ASN B 160 " " NAG I 1 " - " ASN B 295 " " NAG J 1 " - " ASN B 363 " " NAG K 1 " - " ASN B 386 " " NAG O 1 " - " ASN B 133 " " NAG P 1 " - " ASN B 137 " " NAG S 1 " - " ASN B 156 " " NAG T 1 " - " ASN B 301 " " NAG U 1 " - " ASN B 332 " " NAG V 1 " - " ASN B 448 " " NAG W 1 " - " ASN B 262 " " NAG b 1 " - " ASN B 276 " " NAG c 1 " - " ASN B 234 " " NAG d 1 " - " ASN B 88 " " NAG e 1 " - " ASN A 160 " " NAG j 1 " - " ASN A 295 " " NAG k 1 " - " ASN A 363 " " NAG l 1 " - " ASN A 386 " " NAG m 1 " - " ASN A 133 " " NAG n 1 " - " ASN A 137 " " NAG o 1 " - " ASN A 156 " " NAG p 1 " - " ASN A 301 " " NAG q 1 " - " ASN A 332 " " NAG r 1 " - " ASN A 448 " " NAG s 1 " - " ASN A 262 " " NAG t 1 " - " ASN A 276 " " NAG u 1 " - " ASN A 234 " " NAG v 1 " - " ASN A 88 " " NAG w 1 " - " ASN C 160 " " NAG x 1 " - " ASN C 295 " " NAG y 1 " - " ASN C 363 " " NAG z 1 " - " ASN C 386 " " NAGAA 1 " - " ASN C 262 " " NAGBA 1 " - " ASN C 276 " " NAGCA 1 " - " ASN C 234 " " NAGDA 1 " - " ASN C 88 " Time building additional restraints: 15.09 Conformation dependent library (CDL) restraints added in 6.4 seconds 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8208 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 87 sheets defined 14.1% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.47 Creating SS restraints... Processing helix chain '3' and resid 63 through 66 Processing helix chain '3' and resid 88 through 92 removed outlier: 3.752A pdb=" N THR 3 92 " --> pdb=" O ALA 3 89 " (cutoff:3.500A) Processing helix chain '3' and resid 140 through 142 No H-bonds generated for 'chain '3' and resid 140 through 142' Processing helix chain '3' and resid 196 through 199 removed outlier: 4.006A pdb=" N GLY 3 199 " --> pdb=" O SER 3 196 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 196 through 199' Processing helix chain '4' and resid 80 through 84 removed outlier: 3.761A pdb=" N GLU 4 84 " --> pdb=" O SER 4 81 " (cutoff:3.500A) Processing helix chain '4' and resid 125 through 131 Processing helix chain '4' and resid 186 through 190 Processing helix chain '4' and resid 211 through 215 Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 100 through 115 removed outlier: 3.726A pdb=" N ILE B 109 " --> pdb=" O HIS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.733A pdb=" N LEU B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.647A pdb=" N THR B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 373' Processing helix chain 'B' and resid 475 through 481 removed outlier: 4.147A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 528 removed outlier: 4.456A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 543 removed outlier: 3.575A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 595 removed outlier: 3.745A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 616 removed outlier: 4.440A pdb=" N SER F 615 " --> pdb=" O ASN F 611 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 removed outlier: 3.851A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 618 through 623' Processing helix chain 'F' and resid 627 through 635 removed outlier: 4.034A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 664 Processing helix chain 'Y' and resid 83 through 87 removed outlier: 3.711A pdb=" N SER Y 87 " --> pdb=" O ALA Y 84 " (cutoff:3.500A) Processing helix chain 'a' and resid 79 through 83 Processing helix chain 'g' and resid 28 through 32 removed outlier: 3.563A pdb=" N ASP g 31 " --> pdb=" O ASN g 28 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR g 32 " --> pdb=" O PHE g 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 28 through 32' Processing helix chain 'g' and resid 94 through 98 removed outlier: 3.708A pdb=" N THR g 98 " --> pdb=" O PRO g 95 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 83 Processing helix chain '1' and resid 63 through 66 Processing helix chain '1' and resid 88 through 92 removed outlier: 3.752A pdb=" N THR 1 92 " --> pdb=" O ALA 1 89 " (cutoff:3.500A) Processing helix chain '1' and resid 140 through 142 No H-bonds generated for 'chain '1' and resid 140 through 142' Processing helix chain '1' and resid 196 through 199 removed outlier: 4.007A pdb=" N GLY 1 199 " --> pdb=" O SER 1 196 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 196 through 199' Processing helix chain '2' and resid 80 through 84 removed outlier: 3.761A pdb=" N GLU 2 84 " --> pdb=" O SER 2 81 " (cutoff:3.500A) Processing helix chain '2' and resid 125 through 131 Processing helix chain '2' and resid 186 through 190 Processing helix chain '2' and resid 211 through 215 Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 100 through 115 removed outlier: 3.726A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.733A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.647A pdb=" N THR A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 373' Processing helix chain 'A' and resid 475 through 481 removed outlier: 4.147A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 528 removed outlier: 4.456A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 537 through 543 removed outlier: 3.575A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 595 removed outlier: 3.744A pdb=" N LYS E 574 " --> pdb=" O VAL E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 616 removed outlier: 4.441A pdb=" N SER E 615 " --> pdb=" O ASN E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 623 removed outlier: 3.850A pdb=" N ILE E 622 " --> pdb=" O ASN E 618 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TRP E 623 " --> pdb=" O LEU E 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 618 through 623' Processing helix chain 'E' and resid 627 through 635 removed outlier: 4.034A pdb=" N LYS E 633 " --> pdb=" O LEU E 629 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 641 through 664 Processing helix chain 'X' and resid 83 through 87 removed outlier: 3.711A pdb=" N SER X 87 " --> pdb=" O ALA X 84 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 83 Processing helix chain 'f' and resid 28 through 32 removed outlier: 3.562A pdb=" N ASP f 31 " --> pdb=" O ASN f 28 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR f 32 " --> pdb=" O PHE f 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 28 through 32' Processing helix chain 'f' and resid 94 through 98 removed outlier: 3.708A pdb=" N THR f 98 " --> pdb=" O PRO f 95 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 83 Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 100 through 115 removed outlier: 3.726A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.733A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.647A pdb=" N THR C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 373' Processing helix chain 'C' and resid 475 through 481 removed outlier: 4.146A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 528 removed outlier: 4.456A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.575A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 595 removed outlier: 3.745A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 616 removed outlier: 4.440A pdb=" N SER D 615 " --> pdb=" O ASN D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 removed outlier: 3.850A pdb=" N ILE D 622 " --> pdb=" O ASN D 618 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TRP D 623 " --> pdb=" O LEU D 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 618 through 623' Processing helix chain 'D' and resid 627 through 635 removed outlier: 4.033A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 664 Processing helix chain 'H' and resid 63 through 66 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.752A pdb=" N THR H 92 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 142 No H-bonds generated for 'chain 'H' and resid 140 through 142' Processing helix chain 'H' and resid 196 through 199 removed outlier: 4.007A pdb=" N GLY H 199 " --> pdb=" O SER H 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 196 through 199' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.762A pdb=" N GLU L 84 " --> pdb=" O SER L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 131 Processing helix chain 'L' and resid 186 through 190 Processing helix chain 'L' and resid 211 through 215 Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.711A pdb=" N SER M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'Q' and resid 28 through 32 removed outlier: 3.563A pdb=" N ASP Q 31 " --> pdb=" O ASN Q 28 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR Q 32 " --> pdb=" O PHE Q 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 28 through 32' Processing helix chain 'Q' and resid 94 through 98 removed outlier: 3.708A pdb=" N THR Q 98 " --> pdb=" O PRO Q 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain '3' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain '3' and resid 11 through 12 removed outlier: 3.773A pdb=" N GLY 3 50 " --> pdb=" O TRP 3 37 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG 3 39 " --> pdb=" O TRP 3 48 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N TRP 3 48 " --> pdb=" O ARG 3 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 129 through 133 removed outlier: 6.020A pdb=" N TYR 3 185 " --> pdb=" O ASP 3 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '3' and resid 129 through 133 removed outlier: 6.020A pdb=" N TYR 3 185 " --> pdb=" O ASP 3 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '3' and resid 159 through 163 removed outlier: 4.364A pdb=" N TYR 3 203 " --> pdb=" O VAL 3 220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '4' and resid 9 through 12 removed outlier: 6.570A pdb=" N MET 4 10 " --> pdb=" O THR 4 108 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP 4 36 " --> pdb=" O LEU 4 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '4' and resid 9 through 12 removed outlier: 6.570A pdb=" N MET 4 10 " --> pdb=" O THR 4 108 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '4' and resid 18 through 23 Processing sheet with id=AA9, first strand: chain '4' and resid 118 through 122 removed outlier: 5.821A pdb=" N TYR 4 176 " --> pdb=" O ASP 4 142 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER 4 179 " --> pdb=" O LYS 4 167 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LYS 4 167 " --> pdb=" O SER 4 179 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N TYR 4 181 " --> pdb=" O THR 4 165 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N THR 4 165 " --> pdb=" O TYR 4 181 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER 4 183 " --> pdb=" O VAL 4 163 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N VAL 4 163 " --> pdb=" O SER 4 183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '4' and resid 148 through 153 Processing sheet with id=AB2, first strand: chain 'B' and resid 35 through 39 Processing sheet with id=AB3, first strand: chain 'B' and resid 45 through 47 Processing sheet with id=AB4, first strand: chain 'B' and resid 75 through 76 removed outlier: 4.079A pdb=" N VAL B 75 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.697A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 169 through 177 Processing sheet with id=AB7, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.551A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 271 through 273 removed outlier: 7.682A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 271 through 273 removed outlier: 11.364A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 10.950A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.773A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 11.467A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 10.789A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 359 " --> pdb=" O TRP B 395 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER B 393 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 304 through 312 removed outlier: 3.777A pdb=" N LYS B 305 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Y' and resid 5 through 7 Processing sheet with id=AC3, first strand: chain 'Y' and resid 11 through 12 removed outlier: 4.320A pdb=" N TYR Y 33 " --> pdb=" O THR Y 95 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TRP Y 34 " --> pdb=" O TYR Y 50 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TYR Y 50 " --> pdb=" O TRP Y 34 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP Y 36 " --> pdb=" O ILE Y 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Y' and resid 11 through 12 Processing sheet with id=AC5, first strand: chain 'a' and resid 19 through 20 Processing sheet with id=AC6, first strand: chain 'a' and resid 44 through 48 removed outlier: 6.736A pdb=" N TRP a 35 " --> pdb=" O ILE a 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'g' and resid 3 through 5 Processing sheet with id=AC8, first strand: chain 'g' and resid 10 through 12 removed outlier: 6.332A pdb=" N ARG g 38 " --> pdb=" O TRP g 47 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N TRP g 47 " --> pdb=" O ARG g 38 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE g 40 " --> pdb=" O PHE g 45 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N PHE g 45 " --> pdb=" O ILE g 40 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'g' and resid 10 through 12 Processing sheet with id=AD1, first strand: chain 'i' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'i' and resid 10 through 13 removed outlier: 6.382A pdb=" N TRP i 35 " --> pdb=" O LEU i 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '1' and resid 3 through 7 Processing sheet with id=AD4, first strand: chain '1' and resid 11 through 12 removed outlier: 3.774A pdb=" N GLY 1 50 " --> pdb=" O TRP 1 37 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG 1 39 " --> pdb=" O TRP 1 48 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N TRP 1 48 " --> pdb=" O ARG 1 39 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '1' and resid 129 through 133 removed outlier: 6.020A pdb=" N TYR 1 185 " --> pdb=" O ASP 1 153 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '1' and resid 129 through 133 removed outlier: 6.020A pdb=" N TYR 1 185 " --> pdb=" O ASP 1 153 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '1' and resid 159 through 163 removed outlier: 4.364A pdb=" N TYR 1 203 " --> pdb=" O VAL 1 220 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '2' and resid 9 through 12 removed outlier: 6.569A pdb=" N MET 2 10 " --> pdb=" O THR 2 108 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP 2 36 " --> pdb=" O LEU 2 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '2' and resid 9 through 12 removed outlier: 6.569A pdb=" N MET 2 10 " --> pdb=" O THR 2 108 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '2' and resid 18 through 23 Processing sheet with id=AE2, first strand: chain '2' and resid 118 through 122 removed outlier: 5.822A pdb=" N TYR 2 176 " --> pdb=" O ASP 2 142 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N SER 2 179 " --> pdb=" O LYS 2 167 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LYS 2 167 " --> pdb=" O SER 2 179 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N TYR 2 181 " --> pdb=" O THR 2 165 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N THR 2 165 " --> pdb=" O TYR 2 181 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER 2 183 " --> pdb=" O VAL 2 163 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N VAL 2 163 " --> pdb=" O SER 2 183 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '2' and resid 148 through 153 Processing sheet with id=AE4, first strand: chain 'A' and resid 35 through 39 Processing sheet with id=AE5, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AE6, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.079A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.697A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AE9, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.551A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'A' and resid 271 through 273 removed outlier: 7.682A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.363A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.949A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.772A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.467A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.789A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 359 " --> pdb=" O TRP A 395 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 304 through 312 removed outlier: 3.778A pdb=" N LYS A 305 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'X' and resid 5 through 7 Processing sheet with id=AF5, first strand: chain 'X' and resid 11 through 12 removed outlier: 4.320A pdb=" N TYR X 33 " --> pdb=" O THR X 95 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TRP X 34 " --> pdb=" O TYR X 50 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TYR X 50 " --> pdb=" O TRP X 34 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP X 36 " --> pdb=" O ILE X 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'X' and resid 11 through 12 Processing sheet with id=AF7, first strand: chain 'Z' and resid 19 through 20 Processing sheet with id=AF8, first strand: chain 'Z' and resid 44 through 48 removed outlier: 6.736A pdb=" N TRP Z 35 " --> pdb=" O ILE Z 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'f' and resid 3 through 5 Processing sheet with id=AG1, first strand: chain 'f' and resid 10 through 12 removed outlier: 6.332A pdb=" N ARG f 38 " --> pdb=" O TRP f 47 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N TRP f 47 " --> pdb=" O ARG f 38 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE f 40 " --> pdb=" O PHE f 45 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N PHE f 45 " --> pdb=" O ILE f 40 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'f' and resid 10 through 12 Processing sheet with id=AG3, first strand: chain 'h' and resid 4 through 7 Processing sheet with id=AG4, first strand: chain 'h' and resid 10 through 13 removed outlier: 6.382A pdb=" N TRP h 35 " --> pdb=" O LEU h 47 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 35 through 39 Processing sheet with id=AG6, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AG7, first strand: chain 'C' and resid 75 through 76 removed outlier: 4.080A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.697A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AH1, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.551A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.682A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 271 through 273 removed outlier: 11.364A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.950A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.773A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.467A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.788A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 359 " --> pdb=" O TRP C 395 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 304 through 312 removed outlier: 3.777A pdb=" N LYS C 305 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AH6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.773A pdb=" N GLY H 50 " --> pdb=" O TRP H 37 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG H 39 " --> pdb=" O TRP H 48 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N TRP H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 129 through 133 removed outlier: 6.020A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'H' and resid 129 through 133 removed outlier: 6.020A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 159 through 163 removed outlier: 4.364A pdb=" N TYR H 203 " --> pdb=" O VAL H 220 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.570A pdb=" N MET L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.570A pdb=" N MET L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AI4, first strand: chain 'L' and resid 118 through 122 removed outlier: 5.820A pdb=" N TYR L 176 " --> pdb=" O ASP L 142 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N SER L 179 " --> pdb=" O LYS L 167 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LYS L 167 " --> pdb=" O SER L 179 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N TYR L 181 " --> pdb=" O THR L 165 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N THR L 165 " --> pdb=" O TYR L 181 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER L 183 " --> pdb=" O VAL L 163 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N VAL L 163 " --> pdb=" O SER L 183 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'L' and resid 148 through 153 Processing sheet with id=AI6, first strand: chain 'M' and resid 5 through 7 Processing sheet with id=AI7, first strand: chain 'M' and resid 11 through 12 removed outlier: 4.320A pdb=" N TYR M 33 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AI9, first strand: chain 'N' and resid 19 through 20 Processing sheet with id=AJ1, first strand: chain 'N' and resid 44 through 48 removed outlier: 6.736A pdb=" N TRP N 35 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'Q' and resid 3 through 5 Processing sheet with id=AJ3, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.333A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE Q 40 " --> pdb=" O PHE Q 45 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N PHE Q 45 " --> pdb=" O ILE Q 40 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'Q' and resid 10 through 12 Processing sheet with id=AJ5, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AJ6, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.382A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) 1347 hydrogen bonds defined for protein. 3384 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: 16.82 Time building geometry restraints manager: 15.98 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: 11253 1.34 - 1.46: 8475 1.46 - 1.57: 17346 1.57 - 1.69: 3 1.69 - 1.81: 228 Bond restraints: 37305 Sorted by residual: bond pdb=" C THR C 123 " pdb=" N PRO C 124 " ideal model delta sigma weight residual 1.334 1.373 -0.040 8.40e-03 1.42e+04 2.22e+01 bond pdb=" C THR B 123 " pdb=" N PRO B 124 " ideal model delta sigma weight residual 1.334 1.372 -0.039 8.40e-03 1.42e+04 2.14e+01 bond pdb=" C THR A 123 " pdb=" N PRO A 124 " ideal model delta sigma weight residual 1.334 1.372 -0.038 8.40e-03 1.42e+04 2.10e+01 bond pdb=" N PHE i 91 " pdb=" CA PHE i 91 " ideal model delta sigma weight residual 1.457 1.504 -0.046 1.29e-02 6.01e+03 1.29e+01 bond pdb=" N PHE h 91 " pdb=" CA PHE h 91 " ideal model delta sigma weight residual 1.457 1.503 -0.046 1.29e-02 6.01e+03 1.27e+01 ... (remaining 37300 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.30: 1069 106.30 - 113.36: 21622 113.36 - 120.41: 13183 120.41 - 127.47: 14383 127.47 - 134.53: 497 Bond angle restraints: 50754 Sorted by residual: angle pdb=" C GLN h 90 " pdb=" N PHE h 91 " pdb=" CA PHE h 91 " ideal model delta sigma weight residual 121.54 134.53 -12.99 1.91e+00 2.74e-01 4.62e+01 angle pdb=" C GLN i 90 " pdb=" N PHE i 91 " pdb=" CA PHE i 91 " ideal model delta sigma weight residual 121.54 134.51 -12.97 1.91e+00 2.74e-01 4.61e+01 angle pdb=" C GLN R 90 " pdb=" N PHE R 91 " pdb=" CA PHE R 91 " ideal model delta sigma weight residual 121.54 134.50 -12.96 1.91e+00 2.74e-01 4.60e+01 angle pdb=" N GLN h 90 " pdb=" CA GLN h 90 " pdb=" C GLN h 90 " ideal model delta sigma weight residual 110.36 101.36 9.00 1.55e+00 4.16e-01 3.37e+01 angle pdb=" N GLN i 90 " pdb=" CA GLN i 90 " pdb=" C GLN i 90 " ideal model delta sigma weight residual 110.36 101.38 8.98 1.55e+00 4.16e-01 3.36e+01 ... (remaining 50749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.40: 21651 22.40 - 44.79: 1563 44.79 - 67.19: 450 67.19 - 89.58: 213 89.58 - 111.98: 126 Dihedral angle restraints: 24003 sinusoidal: 11184 harmonic: 12819 Sorted by residual: dihedral pdb=" CA SER R 7 " pdb=" C SER R 7 " pdb=" N PRO R 8 " pdb=" CA PRO R 8 " ideal model delta harmonic sigma weight residual -180.00 -98.58 -81.42 0 5.00e+00 4.00e-02 2.65e+02 dihedral pdb=" CA SER i 7 " pdb=" C SER i 7 " pdb=" N PRO i 8 " pdb=" CA PRO i 8 " ideal model delta harmonic sigma weight residual 180.00 -98.59 -81.41 0 5.00e+00 4.00e-02 2.65e+02 dihedral pdb=" CA SER h 7 " pdb=" C SER h 7 " pdb=" N PRO h 8 " pdb=" CA PRO h 8 " ideal model delta harmonic sigma weight residual -180.00 -98.63 -81.37 0 5.00e+00 4.00e-02 2.65e+02 ... (remaining 24000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 5875 0.133 - 0.267: 173 0.267 - 0.400: 39 0.400 - 0.533: 6 0.533 - 0.666: 3 Chirality restraints: 6096 Sorted by residual: chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN B 156 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" C1 NAG 6 1 " pdb=" ND2 ASN C 156 " pdb=" C2 NAG 6 1 " pdb=" O5 NAG 6 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" C1 NAG o 1 " pdb=" ND2 ASN A 156 " pdb=" C2 NAG o 1 " pdb=" O5 NAG o 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.10e+01 ... (remaining 6093 not shown) Planarity restraints: 6327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE i 91 " 0.034 2.00e-02 2.50e+03 6.50e-02 4.23e+01 pdb=" C PHE i 91 " -0.113 2.00e-02 2.50e+03 pdb=" O PHE i 91 " 0.041 2.00e-02 2.50e+03 pdb=" N GLU i 96 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 91 " -0.034 2.00e-02 2.50e+03 6.50e-02 4.23e+01 pdb=" C PHE R 91 " 0.113 2.00e-02 2.50e+03 pdb=" O PHE R 91 " -0.041 2.00e-02 2.50e+03 pdb=" N GLU R 96 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE h 91 " -0.034 2.00e-02 2.50e+03 6.49e-02 4.21e+01 pdb=" C PHE h 91 " 0.112 2.00e-02 2.50e+03 pdb=" O PHE h 91 " -0.041 2.00e-02 2.50e+03 pdb=" N GLU h 96 " -0.037 2.00e-02 2.50e+03 ... (remaining 6324 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 6844 2.76 - 3.30: 31701 3.30 - 3.83: 60920 3.83 - 4.37: 64905 4.37 - 4.90: 113565 Nonbonded interactions: 277935 Sorted by model distance: nonbonded pdb=" O THR A 387 " pdb=" OG1 THR A 387 " model vdw 2.226 2.440 nonbonded pdb=" O THR B 387 " pdb=" OG1 THR B 387 " model vdw 2.226 2.440 nonbonded pdb=" O THR C 387 " pdb=" OG1 THR C 387 " model vdw 2.226 2.440 nonbonded pdb=" OD1 ASN F 611 " pdb=" OG SER F 613 " model vdw 2.260 2.440 nonbonded pdb=" OD1 ASN D 611 " pdb=" OG SER D 613 " model vdw 2.260 2.440 ... (remaining 277930 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '7' selection = chain '9' selection = chain 'O' selection = chain 'T' selection = chain 'V' selection = chain 'm' selection = chain 'p' selection = chain 'r' } ncs_group { reference = chain '1' selection = chain '3' selection = chain 'H' } ncs_group { reference = chain '2' selection = chain '4' selection = chain 'L' } ncs_group { reference = chain '5' selection = chain '6' selection = chain '8' selection = chain 'CA' selection = chain 'DA' selection = chain 'G' selection = chain 'J' selection = chain 'P' selection = chain 'S' selection = chain 'U' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'k' selection = chain 'n' selection = chain 'o' selection = chain 'q' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'y' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'AA' selection = chain 'K' selection = chain 'W' selection = chain 'l' selection = chain 's' selection = chain 'z' } ncs_group { reference = chain 'BA' selection = chain 'I' selection = chain 'b' selection = chain 'j' selection = chain 't' selection = chain 'x' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'M' selection = chain 'X' selection = chain 'Y' } ncs_group { reference = chain 'N' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'Q' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'R' selection = chain 'h' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.330 Check model and map are aligned: 0.530 Set scattering table: 0.320 Process input model: 96.830 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.910 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 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 0.067 37305 Z= 0.538 Angle : 1.046 14.311 50754 Z= 0.537 Chirality : 0.065 0.666 6096 Planarity : 0.008 0.089 6276 Dihedral : 20.265 111.976 15633 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.68 % Favored : 93.12 % Rotamer: Outliers : 10.74 % Allowed : 13.07 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.07 % 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: -2.97 (0.11), residues: 4404 helix: -2.46 (0.18), residues: 435 sheet: -1.23 (0.12), residues: 1611 loop : -2.44 (0.11), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP X 36 HIS 0.008 0.002 HIS A 374 PHE 0.035 0.003 PHE A 288 TYR 0.021 0.002 TYR X 100B ARG 0.004 0.001 ARG Q 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 414 poor density : 306 time to evaluate : 3.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 265 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8436 (pp) REVERT: B 374 HIS cc_start: 0.9343 (OUTLIER) cc_final: 0.7952 (p90) REVERT: B 377 ASN cc_start: 0.8742 (t0) cc_final: 0.8349 (p0) REVERT: B 480 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8155 (mtt90) REVERT: Y 57 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8034 (t) REVERT: g 70 MET cc_start: 0.8352 (mtt) cc_final: 0.8012 (mtt) REVERT: g 122 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8543 (pt0) REVERT: 2 184 LEU cc_start: 0.5405 (OUTLIER) cc_final: 0.4740 (mp) REVERT: A 265 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8331 (pp) REVERT: A 480 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8654 (mtt90) REVERT: X 57 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.8045 (t) REVERT: Z 93 SER cc_start: 0.8478 (OUTLIER) cc_final: 0.8179 (t) REVERT: f 122 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8650 (pt0) REVERT: C 265 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8251 (pp) REVERT: C 480 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.8714 (mtt90) REVERT: H 208 ASN cc_start: 0.4587 (OUTLIER) cc_final: 0.4078 (t0) REVERT: M 57 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8187 (t) REVERT: M 95 THR cc_start: 0.7983 (OUTLIER) cc_final: 0.6568 (t) REVERT: N 93 SER cc_start: 0.8886 (OUTLIER) cc_final: 0.8605 (t) outliers start: 414 outliers final: 131 residues processed: 689 average time/residue: 0.5073 time to fit residues: 554.3685 Evaluate side-chains 295 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 147 time to evaluate : 4.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 178 VAL Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 28 ASN Chi-restraints excluded: chain 4 residue 95 SER Chi-restraints excluded: chain 4 residue 148 VAL Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 183 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 480 ARG Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 44 GLN Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain a residue 63 SER Chi-restraints excluded: chain a residue 93 SER Chi-restraints excluded: chain g residue 33 SER Chi-restraints excluded: chain g residue 79 ASP Chi-restraints excluded: chain g residue 122 GLN Chi-restraints excluded: chain i residue 7 SER Chi-restraints excluded: chain i residue 82 ASP Chi-restraints excluded: chain 1 residue 116 VAL Chi-restraints excluded: chain 1 residue 172 VAL Chi-restraints excluded: chain 1 residue 178 VAL Chi-restraints excluded: chain 1 residue 191 VAL Chi-restraints excluded: chain 1 residue 210 LYS Chi-restraints excluded: chain 2 residue 20 ILE Chi-restraints excluded: chain 2 residue 28 ASN Chi-restraints excluded: chain 2 residue 141 SER Chi-restraints excluded: chain 2 residue 148 VAL Chi-restraints excluded: chain 2 residue 179 SER Chi-restraints excluded: chain 2 residue 183 SER Chi-restraints excluded: chain 2 residue 184 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 480 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 26 GLU Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain Z residue 93 SER Chi-restraints excluded: chain f residue 33 SER Chi-restraints excluded: chain f residue 79 ASP Chi-restraints excluded: chain f residue 122 GLN Chi-restraints excluded: chain h residue 7 SER Chi-restraints excluded: chain h residue 90 GLN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 480 ARG Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 44 GLN Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 79 ASP Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 82 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 369 optimal weight: 8.9990 chunk 331 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 113 optimal weight: 20.0000 chunk 223 optimal weight: 0.8980 chunk 177 optimal weight: 0.8980 chunk 343 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 208 optimal weight: 5.9990 chunk 255 optimal weight: 10.0000 chunk 397 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 111 HIS 3 180 GLN 4 99 HIS 4 112 GLN ** 4 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 ASN B 432 GLN F 575 GLN F 607 ASN ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 6 GLN g 65 GLN 1 111 HIS 1 180 GLN 2 99 HIS 2 112 GLN ** 2 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 ASN A 103 GLN A 246 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN A 432 GLN E 575 GLN E 607 ASN ** Z 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 6 GLN f 65 GLN C 80 ASN C 103 GLN C 246 GLN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN C 432 GLN D 575 GLN D 607 ASN H 111 HIS H 180 GLN ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 HIS L 112 GLN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN Q 65 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37305 Z= 0.225 Angle : 0.749 13.155 50754 Z= 0.360 Chirality : 0.049 0.456 6096 Planarity : 0.005 0.071 6276 Dihedral : 15.496 89.456 7968 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.11 % Favored : 93.69 % Rotamer: Outliers : 5.63 % Allowed : 18.26 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 1.37 % 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: -2.08 (0.12), residues: 4404 helix: -0.83 (0.23), residues: 438 sheet: -0.81 (0.12), residues: 1632 loop : -1.91 (0.12), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 4 189 HIS 0.004 0.001 HIS B 85 PHE 0.021 0.001 PHE F 522 TYR 0.014 0.001 TYR 1 154 ARG 0.011 0.001 ARG D 588 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 183 time to evaluate : 4.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 100 VAL cc_start: 0.8749 (OUTLIER) cc_final: 0.8501 (t) REVERT: B 265 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8428 (pp) REVERT: B 377 ASN cc_start: 0.8682 (t0) cc_final: 0.8278 (p0) REVERT: F 601 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7501 (ttpp) REVERT: Y 57 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.7783 (t) REVERT: i 33 MET cc_start: 0.7981 (tpp) cc_final: 0.7487 (tpt) REVERT: 2 100 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8191 (p) REVERT: A 265 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8318 (pp) REVERT: E 629 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8601 (tt) REVERT: X 57 THR cc_start: 0.8396 (OUTLIER) cc_final: 0.8126 (t) REVERT: f 122 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8660 (pt0) REVERT: C 161 MET cc_start: 0.7792 (tpt) cc_final: 0.7354 (tpt) REVERT: C 265 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8310 (pp) REVERT: H 208 ASN cc_start: 0.4572 (OUTLIER) cc_final: 0.3939 (t0) REVERT: L 100 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8371 (p) REVERT: L 179 SER cc_start: 0.1772 (OUTLIER) cc_final: 0.0697 (m) REVERT: M 57 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.8182 (t) REVERT: N 93 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8521 (t) outliers start: 217 outliers final: 139 residues processed: 390 average time/residue: 0.4533 time to fit residues: 295.2738 Evaluate side-chains 293 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 139 time to evaluate : 4.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 178 VAL Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 28 ASN Chi-restraints excluded: chain 4 residue 100 VAL Chi-restraints excluded: chain 4 residue 141 SER Chi-restraints excluded: chain 4 residue 148 VAL Chi-restraints excluded: chain 4 residue 184 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain F residue 515 ILE Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 44 GLN Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 45 SER Chi-restraints excluded: chain a residue 63 SER Chi-restraints excluded: chain a residue 93 SER Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 79 ASP Chi-restraints excluded: chain g residue 122 GLN Chi-restraints excluded: chain i residue 7 SER Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 116 VAL Chi-restraints excluded: chain 1 residue 178 VAL Chi-restraints excluded: chain 1 residue 210 LYS Chi-restraints excluded: chain 2 residue 20 ILE Chi-restraints excluded: chain 2 residue 28 ASN Chi-restraints excluded: chain 2 residue 95 SER Chi-restraints excluded: chain 2 residue 100 VAL Chi-restraints excluded: chain 2 residue 141 SER Chi-restraints excluded: chain 2 residue 148 VAL Chi-restraints excluded: chain 2 residue 206 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 45 SER Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain f residue 11 ILE Chi-restraints excluded: chain f residue 79 ASP Chi-restraints excluded: chain f residue 122 GLN Chi-restraints excluded: chain h residue 7 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 44 GLN Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 79 ASP Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain R residue 7 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 331 optimal weight: 4.9990 chunk 270 optimal weight: 0.8980 chunk 109 optimal weight: 20.0000 chunk 398 optimal weight: 9.9990 chunk 430 optimal weight: 5.9990 chunk 354 optimal weight: 2.9990 chunk 395 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 319 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 65 GLN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 37305 Z= 0.245 Angle : 0.699 11.774 50754 Z= 0.334 Chirality : 0.048 0.436 6096 Planarity : 0.005 0.072 6276 Dihedral : 12.388 89.995 7892 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.81 % Favored : 92.98 % Rotamer: Outliers : 5.73 % Allowed : 18.88 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 1.37 % 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: -1.70 (0.12), residues: 4404 helix: 0.09 (0.26), residues: 417 sheet: -0.57 (0.12), residues: 1620 loop : -1.78 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 4 189 HIS 0.005 0.001 HIS 1 209 PHE 0.018 0.001 PHE A 288 TYR 0.016 0.001 TYR 3 154 ARG 0.009 0.000 ARG B 504 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 151 time to evaluate : 4.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 100 VAL cc_start: 0.8738 (OUTLIER) cc_final: 0.8487 (t) REVERT: 4 179 SER cc_start: 0.2530 (OUTLIER) cc_final: 0.2072 (m) REVERT: B 65 LYS cc_start: 0.6707 (OUTLIER) cc_final: 0.6328 (tppt) REVERT: B 265 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8445 (pp) REVERT: B 480 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8707 (mtt90) REVERT: F 601 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7407 (ttpp) REVERT: Y 57 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.7948 (t) REVERT: g 70 MET cc_start: 0.8362 (mtt) cc_final: 0.7963 (mtt) REVERT: g 72 ARG cc_start: 0.9215 (OUTLIER) cc_final: 0.7310 (pmt-80) REVERT: A 265 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8359 (pp) REVERT: E 629 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8705 (tt) REVERT: X 57 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8192 (t) REVERT: f 65 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7557 (tt0) REVERT: f 72 ARG cc_start: 0.9258 (OUTLIER) cc_final: 0.8112 (pmt-80) REVERT: f 122 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8629 (pt0) REVERT: C 161 MET cc_start: 0.7782 (tpt) cc_final: 0.7312 (tpt) REVERT: C 265 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8330 (pp) REVERT: C 480 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8874 (mtt90) REVERT: H 208 ASN cc_start: 0.4475 (OUTLIER) cc_final: 0.4020 (t0) REVERT: L 100 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8272 (t) REVERT: L 179 SER cc_start: 0.1915 (OUTLIER) cc_final: 0.1238 (m) REVERT: M 57 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8255 (t) REVERT: Q 72 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.7296 (pmt-80) outliers start: 221 outliers final: 153 residues processed: 365 average time/residue: 0.4916 time to fit residues: 300.3471 Evaluate side-chains 302 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 128 time to evaluate : 3.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 178 VAL Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 23 THR Chi-restraints excluded: chain 4 residue 28 ASN Chi-restraints excluded: chain 4 residue 52 ASN Chi-restraints excluded: chain 4 residue 100 VAL Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 184 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 480 ARG Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 44 GLN Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 45 SER Chi-restraints excluded: chain a residue 63 SER Chi-restraints excluded: chain a residue 93 SER Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 72 ARG Chi-restraints excluded: chain g residue 79 ASP Chi-restraints excluded: chain g residue 122 GLN Chi-restraints excluded: chain i residue 7 SER Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 116 VAL Chi-restraints excluded: chain 1 residue 178 VAL Chi-restraints excluded: chain 2 residue 20 ILE Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 28 ASN Chi-restraints excluded: chain 2 residue 95 SER Chi-restraints excluded: chain 2 residue 141 SER Chi-restraints excluded: chain 2 residue 148 VAL Chi-restraints excluded: chain 2 residue 184 LEU Chi-restraints excluded: chain 2 residue 206 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 664 ASP Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 45 SER Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain f residue 11 ILE Chi-restraints excluded: chain f residue 65 GLN Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 72 ARG Chi-restraints excluded: chain f residue 79 ASP Chi-restraints excluded: chain f residue 122 GLN Chi-restraints excluded: chain h residue 7 SER Chi-restraints excluded: chain h residue 90 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 480 ARG Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 44 GLN Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 72 ARG Chi-restraints excluded: chain Q residue 79 ASP Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 72 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 393 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 267 optimal weight: 8.9990 chunk 399 optimal weight: 10.0000 chunk 423 optimal weight: 6.9990 chunk 208 optimal weight: 0.0870 chunk 379 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 GLN ** Z 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 65 GLN C 130 GLN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37305 Z= 0.171 Angle : 0.648 11.594 50754 Z= 0.309 Chirality : 0.047 0.420 6096 Planarity : 0.005 0.067 6276 Dihedral : 10.704 89.735 7873 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.49 % Favored : 93.32 % Rotamer: Outliers : 4.82 % Allowed : 20.00 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 1.37 % 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: -1.44 (0.12), residues: 4404 helix: 0.36 (0.26), residues: 417 sheet: -0.37 (0.13), residues: 1644 loop : -1.66 (0.12), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 36 HIS 0.003 0.001 HIS 1 209 PHE 0.014 0.001 PHE D 522 TYR 0.010 0.001 TYR 1 203 ARG 0.008 0.000 ARG h 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 153 time to evaluate : 4.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 100 VAL cc_start: 0.8730 (OUTLIER) cc_final: 0.8458 (t) REVERT: 4 179 SER cc_start: 0.2294 (OUTLIER) cc_final: 0.1976 (m) REVERT: B 65 LYS cc_start: 0.6455 (OUTLIER) cc_final: 0.6010 (tptt) REVERT: B 95 MET cc_start: 0.8210 (ppp) cc_final: 0.7949 (ppp) REVERT: B 265 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8383 (pp) REVERT: B 480 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8701 (mtt90) REVERT: Y 57 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.7872 (t) REVERT: g 70 MET cc_start: 0.8363 (mtt) cc_final: 0.7964 (mtt) REVERT: g 72 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.7307 (pmt-80) REVERT: 2 100 VAL cc_start: 0.8470 (OUTLIER) cc_final: 0.8174 (p) REVERT: A 265 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8239 (pp) REVERT: A 426 MET cc_start: 0.7288 (tpp) cc_final: 0.6947 (tpp) REVERT: X 44 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7581 (pm20) REVERT: X 57 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.8006 (t) REVERT: f 72 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.8085 (pmt-80) REVERT: f 122 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8629 (pt0) REVERT: C 104 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7230 (tpt) REVERT: C 161 MET cc_start: 0.7870 (tpt) cc_final: 0.7427 (tpt) REVERT: C 265 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8290 (pp) REVERT: H 208 ASN cc_start: 0.4486 (OUTLIER) cc_final: 0.4101 (t0) REVERT: L 100 VAL cc_start: 0.8597 (OUTLIER) cc_final: 0.8351 (p) REVERT: L 179 SER cc_start: 0.1821 (OUTLIER) cc_final: 0.1169 (m) REVERT: M 57 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8228 (t) REVERT: Q 72 ARG cc_start: 0.9243 (OUTLIER) cc_final: 0.7303 (pmt-80) outliers start: 186 outliers final: 127 residues processed: 334 average time/residue: 0.4471 time to fit residues: 250.6268 Evaluate side-chains 273 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 126 time to evaluate : 4.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 159 VAL Chi-restraints excluded: chain 3 residue 178 VAL Chi-restraints excluded: chain 3 residue 203 TYR Chi-restraints excluded: chain 3 residue 206 ASN Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 28 ASN Chi-restraints excluded: chain 4 residue 100 VAL Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 184 LEU Chi-restraints excluded: chain 4 residue 206 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 480 ARG Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain F residue 515 ILE Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 44 GLN Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 45 SER Chi-restraints excluded: chain a residue 93 SER Chi-restraints excluded: chain g residue 72 ARG Chi-restraints excluded: chain g residue 79 ASP Chi-restraints excluded: chain g residue 122 GLN Chi-restraints excluded: chain i residue 7 SER Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 116 VAL Chi-restraints excluded: chain 1 residue 178 VAL Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 206 ASN Chi-restraints excluded: chain 2 residue 20 ILE Chi-restraints excluded: chain 2 residue 28 ASN Chi-restraints excluded: chain 2 residue 52 ASN Chi-restraints excluded: chain 2 residue 100 VAL Chi-restraints excluded: chain 2 residue 184 LEU Chi-restraints excluded: chain 2 residue 206 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL 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 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 664 ASP Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain f residue 65 GLN Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 72 ARG Chi-restraints excluded: chain f residue 79 ASP Chi-restraints excluded: chain f residue 122 GLN Chi-restraints excluded: chain h residue 7 SER Chi-restraints excluded: chain h residue 72 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 190 LYS Chi-restraints excluded: chain M residue 44 GLN Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 72 ARG Chi-restraints excluded: chain Q residue 79 ASP Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 72 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 352 optimal weight: 0.0270 chunk 240 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 315 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 361 optimal weight: 0.8980 chunk 292 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 216 optimal weight: 6.9990 chunk 380 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 65 GLN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37305 Z= 0.169 Angle : 0.636 14.664 50754 Z= 0.302 Chirality : 0.047 0.414 6096 Planarity : 0.004 0.066 6276 Dihedral : 9.904 88.475 7849 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.61 % Favored : 93.26 % Rotamer: Outliers : 4.90 % Allowed : 20.10 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 1.37 % 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: -1.24 (0.13), residues: 4404 helix: 0.49 (0.26), residues: 417 sheet: -0.21 (0.13), residues: 1614 loop : -1.53 (0.12), residues: 2373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 36 HIS 0.007 0.001 HIS H 209 PHE 0.013 0.001 PHE D 522 TYR 0.013 0.001 TYR H 154 ARG 0.008 0.000 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 150 time to evaluate : 4.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 179 SER cc_start: 0.2297 (OUTLIER) cc_final: 0.1968 (m) REVERT: B 65 LYS cc_start: 0.6403 (OUTLIER) cc_final: 0.6026 (tptt) REVERT: B 95 MET cc_start: 0.8198 (ppp) cc_final: 0.7922 (ppp) REVERT: B 265 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8388 (pp) REVERT: B 480 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8705 (mtt90) REVERT: Y 44 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7358 (pm20) REVERT: Y 57 THR cc_start: 0.8257 (OUTLIER) cc_final: 0.7899 (t) REVERT: g 70 MET cc_start: 0.8422 (mtt) cc_final: 0.8025 (mtt) REVERT: g 72 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.7347 (pmt-80) REVERT: 2 100 VAL cc_start: 0.8461 (OUTLIER) cc_final: 0.8175 (p) REVERT: A 67 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8182 (p0) REVERT: A 265 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8267 (pp) REVERT: E 629 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8630 (tt) REVERT: X 44 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7557 (pm20) REVERT: X 57 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.8034 (t) REVERT: f 72 ARG cc_start: 0.9240 (OUTLIER) cc_final: 0.7980 (pmt-80) REVERT: f 122 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8669 (pt0) REVERT: C 104 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7031 (tpt) REVERT: C 161 MET cc_start: 0.7841 (tpt) cc_final: 0.7381 (tpt) REVERT: C 265 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8287 (pp) REVERT: H 208 ASN cc_start: 0.4458 (OUTLIER) cc_final: 0.4143 (t0) REVERT: L 100 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8353 (p) REVERT: L 179 SER cc_start: 0.2136 (OUTLIER) cc_final: 0.1575 (m) REVERT: M 57 THR cc_start: 0.8509 (OUTLIER) cc_final: 0.8256 (t) REVERT: Q 72 ARG cc_start: 0.9259 (OUTLIER) cc_final: 0.7324 (pmt-80) outliers start: 189 outliers final: 133 residues processed: 329 average time/residue: 0.4721 time to fit residues: 263.6138 Evaluate side-chains 285 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 130 time to evaluate : 4.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 159 VAL Chi-restraints excluded: chain 3 residue 203 TYR Chi-restraints excluded: chain 3 residue 206 ASN Chi-restraints excluded: chain 4 residue 28 ASN Chi-restraints excluded: chain 4 residue 52 ASN Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 206 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 480 ARG Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain F residue 515 ILE Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain Y residue 44 GLN Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 45 SER Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 72 ARG Chi-restraints excluded: chain g residue 79 ASP Chi-restraints excluded: chain g residue 122 GLN Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 116 VAL Chi-restraints excluded: chain 1 residue 159 VAL Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 206 ASN Chi-restraints excluded: chain 2 residue 20 ILE Chi-restraints excluded: chain 2 residue 28 ASN Chi-restraints excluded: chain 2 residue 52 ASN Chi-restraints excluded: chain 2 residue 100 VAL Chi-restraints excluded: chain 2 residue 148 VAL Chi-restraints excluded: chain 2 residue 184 LEU Chi-restraints excluded: chain 2 residue 206 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 45 SER Chi-restraints excluded: chain f residue 11 ILE Chi-restraints excluded: chain f residue 65 GLN Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 72 ARG Chi-restraints excluded: chain f residue 79 ASP Chi-restraints excluded: chain f residue 122 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain M residue 44 GLN Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 72 ARG Chi-restraints excluded: chain Q residue 79 ASP Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain R residue 72 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 142 optimal weight: 10.0000 chunk 381 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 423 optimal weight: 6.9990 chunk 351 optimal weight: 20.0000 chunk 196 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 140 optimal weight: 0.7980 chunk 222 optimal weight: 0.0670 overall best weight: 2.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 GLN ** Z 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 37305 Z= 0.260 Angle : 0.674 14.705 50754 Z= 0.321 Chirality : 0.047 0.423 6096 Planarity : 0.005 0.083 6276 Dihedral : 9.689 87.829 7828 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.02 % Favored : 92.78 % Rotamer: Outliers : 5.45 % Allowed : 20.34 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 1.37 % 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: -1.20 (0.13), residues: 4404 helix: 0.59 (0.27), residues: 417 sheet: -0.18 (0.13), residues: 1620 loop : -1.52 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 83 HIS 0.006 0.001 HIS 1 209 PHE 0.015 0.001 PHE B 288 TYR 0.012 0.001 TYR 1 154 ARG 0.009 0.000 ARG h 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 130 time to evaluate : 3.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 179 SER cc_start: 0.2422 (OUTLIER) cc_final: 0.2165 (m) REVERT: B 65 LYS cc_start: 0.6436 (OUTLIER) cc_final: 0.5992 (tptt) REVERT: B 265 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8390 (pp) REVERT: B 480 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.8760 (mtt90) REVERT: Y 44 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7351 (pm20) REVERT: Y 57 THR cc_start: 0.8264 (OUTLIER) cc_final: 0.7950 (t) REVERT: g 70 MET cc_start: 0.8407 (mtt) cc_final: 0.7964 (mtt) REVERT: g 72 ARG cc_start: 0.9246 (OUTLIER) cc_final: 0.7327 (pmt-80) REVERT: 2 100 VAL cc_start: 0.8544 (OUTLIER) cc_final: 0.8284 (p) REVERT: A 265 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8298 (pp) REVERT: E 629 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8697 (tt) REVERT: X 44 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7651 (pm20) REVERT: X 57 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7969 (t) REVERT: f 65 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7918 (tt0) REVERT: f 72 ARG cc_start: 0.9278 (OUTLIER) cc_final: 0.7929 (pmt-80) REVERT: f 122 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8683 (pt0) REVERT: C 161 MET cc_start: 0.7800 (tpt) cc_final: 0.7382 (tpt) REVERT: C 265 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8298 (pp) REVERT: L 100 VAL cc_start: 0.8637 (OUTLIER) cc_final: 0.8411 (p) REVERT: L 179 SER cc_start: 0.1974 (OUTLIER) cc_final: 0.1545 (m) REVERT: M 57 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.8168 (t) REVERT: Q 72 ARG cc_start: 0.9294 (OUTLIER) cc_final: 0.7319 (pmt-80) outliers start: 210 outliers final: 152 residues processed: 329 average time/residue: 0.4470 time to fit residues: 250.4709 Evaluate side-chains 290 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 118 time to evaluate : 3.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 12 VAL Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 159 VAL Chi-restraints excluded: chain 3 residue 178 VAL Chi-restraints excluded: chain 3 residue 203 TYR Chi-restraints excluded: chain 3 residue 206 ASN Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 23 THR Chi-restraints excluded: chain 4 residue 28 ASN Chi-restraints excluded: chain 4 residue 49 ILE Chi-restraints excluded: chain 4 residue 52 ASN Chi-restraints excluded: chain 4 residue 100 VAL Chi-restraints excluded: chain 4 residue 132 ASN Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 480 ARG Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain Y residue 44 GLN Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 45 SER Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 72 ARG Chi-restraints excluded: chain g residue 79 ASP Chi-restraints excluded: chain g residue 122 GLN Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 116 VAL Chi-restraints excluded: chain 1 residue 159 VAL Chi-restraints excluded: chain 1 residue 178 VAL Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 206 ASN Chi-restraints excluded: chain 2 residue 20 ILE Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 28 ASN Chi-restraints excluded: chain 2 residue 52 ASN Chi-restraints excluded: chain 2 residue 95 SER Chi-restraints excluded: chain 2 residue 100 VAL Chi-restraints excluded: chain 2 residue 148 VAL Chi-restraints excluded: chain 2 residue 184 LEU Chi-restraints excluded: chain 2 residue 206 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain f residue 11 ILE Chi-restraints excluded: chain f residue 65 GLN Chi-restraints excluded: chain f residue 70 MET Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 72 ARG Chi-restraints excluded: chain f residue 79 ASP Chi-restraints excluded: chain f residue 122 GLN Chi-restraints excluded: chain h residue 72 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 190 LYS Chi-restraints excluded: chain M residue 44 GLN Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 72 ARG Chi-restraints excluded: chain Q residue 79 ASP Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain R residue 72 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 241 optimal weight: 3.9990 chunk 309 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 356 optimal weight: 10.0000 chunk 236 optimal weight: 0.8980 chunk 422 optimal weight: 5.9990 chunk 264 optimal weight: 0.3980 chunk 257 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 38 GLN ** g 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 GLN Z 38 GLN f 65 GLN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Q 3 GLN Q 65 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37305 Z= 0.170 Angle : 0.633 14.957 50754 Z= 0.301 Chirality : 0.046 0.402 6096 Planarity : 0.004 0.082 6276 Dihedral : 9.110 87.438 7824 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.45 % Favored : 93.46 % Rotamer: Outliers : 4.28 % Allowed : 21.63 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 1.37 % 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: -1.03 (0.13), residues: 4404 helix: 0.76 (0.28), residues: 399 sheet: -0.06 (0.13), residues: 1614 loop : -1.40 (0.13), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 36 HIS 0.003 0.001 HIS 1 209 PHE 0.012 0.001 PHE B 288 TYR 0.010 0.001 TYR 1 154 ARG 0.008 0.000 ARG h 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 143 time to evaluate : 4.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 179 SER cc_start: 0.2312 (OUTLIER) cc_final: 0.2040 (m) REVERT: B 65 LYS cc_start: 0.6249 (OUTLIER) cc_final: 0.5756 (tppt) REVERT: B 265 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8324 (pp) REVERT: B 480 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8633 (mtt90) REVERT: Y 57 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8067 (t) REVERT: g 70 MET cc_start: 0.8402 (mtt) cc_final: 0.8021 (mtt) REVERT: g 72 ARG cc_start: 0.9237 (OUTLIER) cc_final: 0.7332 (pmt-80) REVERT: 2 100 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8203 (p) REVERT: A 34 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7493 (mm) REVERT: A 67 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.8168 (p0) REVERT: A 265 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8257 (pp) REVERT: E 629 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8592 (tt) REVERT: X 57 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.8027 (t) REVERT: f 65 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7744 (tt0) REVERT: f 72 ARG cc_start: 0.9250 (OUTLIER) cc_final: 0.7841 (pmt-80) REVERT: C 161 MET cc_start: 0.7834 (tpt) cc_final: 0.7381 (tpt) REVERT: C 265 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8285 (pp) REVERT: C 478 ASN cc_start: 0.8985 (OUTLIER) cc_final: 0.8605 (m-40) REVERT: M 57 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.8093 (t) REVERT: M 100 MET cc_start: 0.6882 (mmm) cc_final: 0.6458 (mmm) REVERT: Q 72 ARG cc_start: 0.9280 (OUTLIER) cc_final: 0.7267 (pmt-80) outliers start: 165 outliers final: 125 residues processed: 305 average time/residue: 0.4676 time to fit residues: 239.4597 Evaluate side-chains 268 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 125 time to evaluate : 4.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 12 VAL Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 159 VAL Chi-restraints excluded: chain 3 residue 178 VAL Chi-restraints excluded: chain 3 residue 203 TYR Chi-restraints excluded: chain 3 residue 206 ASN Chi-restraints excluded: chain 4 residue 28 ASN Chi-restraints excluded: chain 4 residue 52 ASN Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 206 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 480 ARG Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain g residue 72 ARG Chi-restraints excluded: chain g residue 79 ASP Chi-restraints excluded: chain g residue 122 GLN Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 116 VAL Chi-restraints excluded: chain 1 residue 159 VAL Chi-restraints excluded: chain 1 residue 178 VAL Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 206 ASN Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 28 ASN Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 52 ASN Chi-restraints excluded: chain 2 residue 95 SER Chi-restraints excluded: chain 2 residue 100 VAL Chi-restraints excluded: chain 2 residue 206 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain f residue 65 GLN Chi-restraints excluded: chain f residue 70 MET Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 72 ARG Chi-restraints excluded: chain f residue 79 ASP Chi-restraints excluded: chain f residue 122 GLN Chi-restraints excluded: chain h residue 46 LEU Chi-restraints excluded: chain h residue 72 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain M residue 44 GLN Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 99 ARG Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 72 ARG Chi-restraints excluded: chain Q residue 79 ASP Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain R residue 72 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 261 optimal weight: 3.9990 chunk 168 optimal weight: 20.0000 chunk 252 optimal weight: 9.9990 chunk 127 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 268 optimal weight: 3.9990 chunk 287 optimal weight: 4.9990 chunk 208 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 331 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN ** g 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 122 GLN ** 2 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 GLN f 65 GLN f 122 GLN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 GLN Q 122 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 37305 Z= 0.321 Angle : 0.712 15.199 50754 Z= 0.339 Chirality : 0.047 0.437 6096 Planarity : 0.005 0.086 6276 Dihedral : 9.119 87.687 7807 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.95 % Favored : 91.92 % Rotamer: Outliers : 5.08 % Allowed : 21.17 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 1.37 % 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: -1.12 (0.13), residues: 4404 helix: 0.69 (0.27), residues: 417 sheet: -0.06 (0.13), residues: 1593 loop : -1.52 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP Y 100J HIS 0.006 0.001 HIS C 85 PHE 0.017 0.001 PHE A 288 TYR 0.011 0.001 TYR 1 96 ARG 0.011 0.000 ARG Y 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 116 time to evaluate : 4.069 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: 4 179 SER cc_start: 0.2511 (OUTLIER) cc_final: 0.2286 (m) REVERT: B 65 LYS cc_start: 0.6405 (OUTLIER) cc_final: 0.5950 (tppt) REVERT: B 265 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8358 (pp) REVERT: B 480 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8939 (ttp-170) REVERT: Y 57 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8070 (t) REVERT: g 70 MET cc_start: 0.8437 (mtt) cc_final: 0.8075 (mtt) REVERT: g 72 ARG cc_start: 0.9259 (OUTLIER) cc_final: 0.7541 (pmt-80) REVERT: 2 100 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8303 (p) REVERT: A 34 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7566 (mm) REVERT: A 265 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8316 (pp) REVERT: E 629 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8662 (tt) REVERT: X 44 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7683 (pm20) REVERT: f 72 ARG cc_start: 0.9300 (OUTLIER) cc_final: 0.7820 (pmt-80) REVERT: C 265 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8312 (pp) REVERT: C 478 ASN cc_start: 0.9041 (OUTLIER) cc_final: 0.8646 (m-40) REVERT: L 100 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8377 (p) REVERT: Q 72 ARG cc_start: 0.9276 (OUTLIER) cc_final: 0.7490 (pmt-80) outliers start: 196 outliers final: 148 residues processed: 307 average time/residue: 0.4518 time to fit residues: 237.4885 Evaluate side-chains 276 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 112 time to evaluate : 4.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 12 VAL Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 159 VAL Chi-restraints excluded: chain 3 residue 178 VAL Chi-restraints excluded: chain 3 residue 206 ASN Chi-restraints excluded: chain 4 residue 23 THR Chi-restraints excluded: chain 4 residue 28 ASN Chi-restraints excluded: chain 4 residue 49 ILE Chi-restraints excluded: chain 4 residue 52 ASN Chi-restraints excluded: chain 4 residue 100 VAL Chi-restraints excluded: chain 4 residue 132 ASN Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 206 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 480 ARG Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 72 ARG Chi-restraints excluded: chain g residue 79 ASP Chi-restraints excluded: chain g residue 122 GLN Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 116 VAL Chi-restraints excluded: chain 1 residue 159 VAL Chi-restraints excluded: chain 1 residue 178 VAL Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 206 ASN Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 28 ASN Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 52 ASN Chi-restraints excluded: chain 2 residue 95 SER Chi-restraints excluded: chain 2 residue 100 VAL Chi-restraints excluded: chain 2 residue 148 VAL Chi-restraints excluded: chain 2 residue 206 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain f residue 11 ILE Chi-restraints excluded: chain f residue 70 MET Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 72 ARG Chi-restraints excluded: chain f residue 79 ASP Chi-restraints excluded: chain f residue 122 GLN Chi-restraints excluded: chain h residue 46 LEU Chi-restraints excluded: chain h residue 72 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 72 ARG Chi-restraints excluded: chain Q residue 79 ASP Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain R residue 72 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 384 optimal weight: 30.0000 chunk 404 optimal weight: 1.9990 chunk 368 optimal weight: 20.0000 chunk 393 optimal weight: 20.0000 chunk 236 optimal weight: 7.9990 chunk 171 optimal weight: 10.0000 chunk 308 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 355 optimal weight: 7.9990 chunk 372 optimal weight: 20.0000 chunk 392 optimal weight: 30.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 ASN F 653 GLN ** g 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 653 GLN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN Q 35 HIS Q 65 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.066 37305 Z= 0.605 Angle : 0.934 14.601 50754 Z= 0.449 Chirality : 0.051 0.480 6096 Planarity : 0.006 0.090 6276 Dihedral : 10.152 83.532 7802 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 21.41 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.60 % Favored : 90.17 % Rotamer: Outliers : 5.14 % Allowed : 21.56 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 1.37 % 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: -1.68 (0.12), residues: 4404 helix: -0.15 (0.25), residues: 417 sheet: -0.33 (0.13), residues: 1551 loop : -1.88 (0.12), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP Y 100J HIS 0.008 0.002 HIS C 85 PHE 0.027 0.003 PHE A 288 TYR 0.018 0.002 TYR B 61 ARG 0.012 0.001 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 97 time to evaluate : 4.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 265 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8405 (pp) REVERT: B 480 ARG cc_start: 0.9345 (OUTLIER) cc_final: 0.8874 (mtt90) REVERT: g 70 MET cc_start: 0.8402 (mtt) cc_final: 0.8069 (mtt) REVERT: g 72 ARG cc_start: 0.9235 (OUTLIER) cc_final: 0.8349 (pmt-80) REVERT: 2 100 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8260 (t) REVERT: A 34 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7686 (mm) REVERT: A 265 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8454 (pp) REVERT: X 44 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7817 (pm20) REVERT: f 72 ARG cc_start: 0.9251 (OUTLIER) cc_final: 0.8647 (pmt-80) REVERT: C 265 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8366 (pp) REVERT: C 478 ASN cc_start: 0.9100 (OUTLIER) cc_final: 0.8738 (m-40) REVERT: D 664 ASP cc_start: 0.6549 (p0) cc_final: 0.6344 (p0) REVERT: L 100 VAL cc_start: 0.8633 (OUTLIER) cc_final: 0.8382 (p) REVERT: Q 72 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8326 (pmt-80) outliers start: 198 outliers final: 154 residues processed: 292 average time/residue: 0.4205 time to fit residues: 213.8726 Evaluate side-chains 261 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 95 time to evaluate : 4.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 12 VAL Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 159 VAL Chi-restraints excluded: chain 3 residue 178 VAL Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 23 THR Chi-restraints excluded: chain 4 residue 28 ASN Chi-restraints excluded: chain 4 residue 49 ILE Chi-restraints excluded: chain 4 residue 52 ASN Chi-restraints excluded: chain 4 residue 100 VAL Chi-restraints excluded: chain 4 residue 206 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 480 ARG Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain F residue 515 ILE Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 63 SER Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 72 ARG Chi-restraints excluded: chain g residue 79 ASP Chi-restraints excluded: chain g residue 122 GLN Chi-restraints excluded: chain i residue 69 THR Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 116 VAL Chi-restraints excluded: chain 1 residue 159 VAL Chi-restraints excluded: chain 1 residue 178 VAL Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 206 ASN Chi-restraints excluded: chain 2 residue 20 ILE Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 28 ASN Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 52 ASN Chi-restraints excluded: chain 2 residue 95 SER Chi-restraints excluded: chain 2 residue 100 VAL Chi-restraints excluded: chain 2 residue 142 ASP Chi-restraints excluded: chain 2 residue 148 VAL Chi-restraints excluded: chain 2 residue 206 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain f residue 11 ILE Chi-restraints excluded: chain f residue 70 MET Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 72 ARG Chi-restraints excluded: chain f residue 79 ASP Chi-restraints excluded: chain f residue 122 GLN Chi-restraints excluded: chain h residue 46 LEU Chi-restraints excluded: chain h residue 72 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 72 ARG Chi-restraints excluded: chain Q residue 79 ASP Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 72 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 3.9990 chunk 415 optimal weight: 1.9990 chunk 253 optimal weight: 0.3980 chunk 197 optimal weight: 0.9990 chunk 289 optimal weight: 7.9990 chunk 436 optimal weight: 4.9990 chunk 401 optimal weight: 9.9990 chunk 347 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 268 optimal weight: 10.0000 chunk 213 optimal weight: 2.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 65 GLN ** 2 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 39 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 GLN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 37305 Z= 0.195 Angle : 0.683 15.507 50754 Z= 0.327 Chirality : 0.047 0.405 6096 Planarity : 0.005 0.086 6276 Dihedral : 9.211 81.712 7796 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.27 % Favored : 93.57 % Rotamer: Outliers : 3.63 % Allowed : 23.06 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 1.37 % 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: -1.26 (0.13), residues: 4404 helix: 0.68 (0.26), residues: 417 sheet: -0.19 (0.13), residues: 1572 loop : -1.59 (0.12), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 427 HIS 0.003 0.001 HIS C 85 PHE 0.013 0.001 PHE C 288 TYR 0.014 0.001 TYR B 384 ARG 0.015 0.000 ARG H 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 125 time to evaluate : 4.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 265 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8284 (pp) REVERT: B 426 MET cc_start: 0.7366 (tpp) cc_final: 0.7042 (tpt) REVERT: B 480 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8616 (mtt90) REVERT: g 70 MET cc_start: 0.8395 (mtt) cc_final: 0.8018 (mtt) REVERT: g 72 ARG cc_start: 0.9254 (OUTLIER) cc_final: 0.7375 (pmt-80) REVERT: 1 29 ILE cc_start: 0.7189 (OUTLIER) cc_final: 0.6916 (tp) REVERT: 2 100 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8197 (p) REVERT: A 34 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7468 (mm) REVERT: X 44 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7563 (pm20) REVERT: f 72 ARG cc_start: 0.9266 (OUTLIER) cc_final: 0.8090 (pmt-80) REVERT: C 265 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8301 (pp) REVERT: C 478 ASN cc_start: 0.8949 (OUTLIER) cc_final: 0.8541 (m-40) REVERT: L 100 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8378 (p) REVERT: M 100 MET cc_start: 0.6795 (mmm) cc_final: 0.6491 (mmm) REVERT: Q 72 ARG cc_start: 0.9292 (OUTLIER) cc_final: 0.7260 (pmt-80) outliers start: 140 outliers final: 112 residues processed: 261 average time/residue: 0.4597 time to fit residues: 204.8383 Evaluate side-chains 232 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 108 time to evaluate : 4.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 12 VAL Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 159 VAL Chi-restraints excluded: chain 3 residue 178 VAL Chi-restraints excluded: chain 4 residue 23 THR Chi-restraints excluded: chain 4 residue 28 ASN Chi-restraints excluded: chain 4 residue 52 ASN Chi-restraints excluded: chain 4 residue 206 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 480 ARG Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain F residue 515 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain g residue 65 GLN Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 72 ARG Chi-restraints excluded: chain g residue 79 ASP Chi-restraints excluded: chain g residue 122 GLN Chi-restraints excluded: chain 1 residue 29 ILE Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 116 VAL Chi-restraints excluded: chain 1 residue 159 VAL Chi-restraints excluded: chain 1 residue 178 VAL Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 206 ASN Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 28 ASN Chi-restraints excluded: chain 2 residue 39 GLN Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 52 ASN Chi-restraints excluded: chain 2 residue 95 SER Chi-restraints excluded: chain 2 residue 100 VAL Chi-restraints excluded: chain 2 residue 206 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain f residue 11 ILE Chi-restraints excluded: chain f residue 70 MET Chi-restraints excluded: chain f residue 72 ARG Chi-restraints excluded: chain f residue 79 ASP Chi-restraints excluded: chain f residue 122 GLN Chi-restraints excluded: chain h residue 72 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 72 ARG Chi-restraints excluded: chain Q residue 79 ASP Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain R residue 72 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 276 optimal weight: 8.9990 chunk 370 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 320 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 348 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 357 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 39 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 GLN E 616 ASN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN ** H 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.054985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.036032 restraints weight = 281278.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.036833 restraints weight = 152527.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.037215 restraints weight = 108875.364| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 37305 Z= 0.404 Angle : 0.782 14.565 50754 Z= 0.374 Chirality : 0.048 0.442 6096 Planarity : 0.005 0.092 6276 Dihedral : 9.339 82.287 7788 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.33 % Favored : 91.46 % Rotamer: Outliers : 4.15 % Allowed : 22.70 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 1.37 % 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: -1.44 (0.13), residues: 4404 helix: 0.27 (0.26), residues: 417 sheet: -0.31 (0.13), residues: 1575 loop : -1.66 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP Q 55 HIS 0.012 0.001 HIS 3 209 PHE 0.023 0.002 PHE 2 40 TYR 0.012 0.001 TYR H 154 ARG 0.010 0.001 ARG R 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6462.50 seconds wall clock time: 120 minutes 42.24 seconds (7242.24 seconds total)