Starting phenix.real_space_refine on Fri Jul 26 07:00:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1w_9320/07_2024/6n1w_9320.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1w_9320/07_2024/6n1w_9320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1w_9320/07_2024/6n1w_9320.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1w_9320/07_2024/6n1w_9320.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1w_9320/07_2024/6n1w_9320.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1w_9320/07_2024/6n1w_9320.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.105 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 168 5.16 5 C 20007 2.51 5 N 5295 2.21 5 O 6435 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 13": "NH1" <-> "NH2" Residue "3 ARG 31": "NH1" <-> "NH2" Residue "3 TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 38": "NH1" <-> "NH2" Residue "3 ARG 66": "NH1" <-> "NH2" Residue "3 ARG 81": "NH1" <-> "NH2" Residue "3 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 100": "NH1" <-> "NH2" Residue "4 ARG 24": "NH1" <-> "NH2" Residue "4 ARG 61": "NH1" <-> "NH2" Residue "4 PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 52": "NH1" <-> "NH2" Residue "7 PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 61": "NH1" <-> "NH2" Residue "8 PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 13": "NH1" <-> "NH2" Residue "H ARG 31": "NH1" <-> "NH2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H ARG 81": "NH1" <-> "NH2" Residue "H TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 100": "NH1" <-> "NH2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 61": "NH1" <-> "NH2" Residue "Q TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 52": "NH1" <-> "NH2" Residue "R PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 13": "NH1" <-> "NH2" Residue "h ARG 31": "NH1" <-> "NH2" Residue "h ARG 38": "NH1" <-> "NH2" Residue "h ARG 66": "NH1" <-> "NH2" Residue "h ARG 81": "NH1" <-> "NH2" Residue "h TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 100": "NH1" <-> "NH2" Residue "l ARG 24": "NH1" <-> "NH2" Residue "l ARG 61": "NH1" <-> "NH2" Residue "m TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 61": "NH1" <-> "NH2" Residue "q TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 52": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 31905 Number of models: 1 Model: "" Number of chains: 66 Chain: "2" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "3" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 980 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "4" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 787 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Chain: "5" 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: "6" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "7" 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: "8" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" 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: "C" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "D" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 980 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "L" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 787 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Chain: "M" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "Q" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "R" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "c" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "d" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "h" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 980 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "l" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 787 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Chain: "m" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "n" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "q" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "r" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: 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: "T" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: "e" 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: "f" 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: "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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 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: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 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: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "0" Number of atoms: 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: "1" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "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: 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: "2" 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 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: 17.27, per 1000 atoms: 0.54 Number of scatterers: 31905 At special positions: 0 Unit cell: (159.43, 155.15, 166.92, 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 168 16.00 O 6435 8.00 N 5295 7.00 C 20007 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS 2 119 " - pdb=" SG CYS 2 205 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 131 " - pdb=" SG CYS 2 157 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 201 " - pdb=" SG CYS 2 433 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 218 " - pdb=" SG CYS 2 247 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 228 " - pdb=" SG CYS 2 239 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 296 " - pdb=" SG CYS 2 331 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 378 " - pdb=" SG CYS 2 445 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 385 " - pdb=" SG CYS 2 418 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 22 " - pdb=" SG CYS 3 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 23 " - pdb=" SG CYS 4 88 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 22 " - pdb=" SG CYS 5 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 23 " - pdb=" SG CYS 6 88 " distance=2.03 Simple disulfide: pdb=" SG CYS 8 22 " - pdb=" SG CYS 8 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 8 98 " - pdb=" SG CYS 8 100A" distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 98 " - pdb=" SG CYS Q 100A" distance=2.03 Simple disulfide: pdb=" SG CYS c 119 " - pdb=" SG CYS c 205 " distance=2.03 Simple disulfide: pdb=" SG CYS c 131 " - pdb=" SG CYS c 157 " distance=2.03 Simple disulfide: pdb=" SG CYS c 201 " - pdb=" SG CYS c 433 " distance=2.03 Simple disulfide: pdb=" SG CYS c 218 " - pdb=" SG CYS c 247 " distance=2.03 Simple disulfide: pdb=" SG CYS c 228 " - pdb=" SG CYS c 239 " distance=2.03 Simple disulfide: pdb=" SG CYS c 296 " - pdb=" SG CYS c 331 " distance=2.03 Simple disulfide: pdb=" SG CYS c 378 " - pdb=" SG CYS c 445 " distance=2.03 Simple disulfide: pdb=" SG CYS c 385 " - pdb=" SG CYS c 418 " distance=2.03 Simple disulfide: pdb=" SG CYS d 598 " - pdb=" SG CYS d 604 " distance=2.02 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 92 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.03 Simple disulfide: pdb=" SG CYS m 22 " - pdb=" SG CYS m 92 " distance=2.03 Simple disulfide: pdb=" SG CYS n 23 " - pdb=" SG CYS n 88 " distance=2.03 Simple disulfide: pdb=" SG CYS q 22 " - pdb=" SG CYS q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS q 98 " - pdb=" SG CYS q 100A" distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 1 4 " - " MAN 1 5 " " MAN 1 5 " - " MAN 1 6 " " MAN T 4 " - " MAN T 5 " " MAN T 5 " - " MAN T 6 " " MAN j 4 " - " MAN j 5 " " MAN j 5 " - " MAN j 6 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " BMA 1 3 " - " MAN 1 4 " " MAN 1 7 " - " MAN 1 8 " " BMA E 3 " - " MAN E 4 " " BMA J 3 " - " MAN J 4 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " MAN T 7 " - " MAN T 8 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " BMA b 3 " - " MAN b 4 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 4 " " MAN j 7 " - " MAN j 8 " " BMA o 3 " - " MAN o 4 " " BMA s 3 " - " MAN s 4 " " BMA w 3 " - " MAN w 4 " " BMAAA 3 " - " MANAA 4 " ALPHA1-6 " BMA 1 3 " - " MAN 1 7 " " MAN 1 7 " - " MAN 1 9 " " BMA J 3 " - " MAN J 5 " " BMA T 3 " - " MAN T 7 " " MAN T 7 " - " MAN T 9 " " BMA b 3 " - " MAN b 5 " " BMA j 3 " - " MAN j 7 " " MAN j 7 " - " MAN j 9 " " BMA w 3 " - " MAN w 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 9 1 " - " NAG 9 2 " " NAG B 1 " - " NAG B 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " 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 T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 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 o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " NAG-ASN " NAG 0 1 " - " ASN c 386 " " NAG 1 1 " - " ASN c 332 " " NAG 2 611 " - " ASN 2 197 " " NAG 2 623 " - " ASN 2 355 " " NAG 2 631 " - " ASN 2 392 " " NAG B 1 " - " ASN 2 133 " " NAG C 611 " - " ASN C 197 " " NAG C 623 " - " ASN C 355 " " NAG C 631 " - " ASN C 392 " " NAG E 1 " - " ASN 2 137 " " NAG F 1 " - " ASN 2 156 " " NAG G 1 " - " ASN 2 160 " " NAG I 1 " - " ASN 2 234 " " NAG J 1 " - " ASN 2 262 " " NAG K 1 " - " ASN 2 295 " " NAG O 1 " - " ASN 2 301 " " NAG P 1 " - " ASN 2 363 " " NAG S 1 " - " ASN 2 386 " " NAG T 1 " - " ASN 2 332 " " NAG V 1 " - " ASN 2 276 " " NAG W 1 " - " ASN C 133 " " NAG X 1 " - " ASN C 137 " " NAG Y 1 " - " ASN C 156 " " NAG Z 1 " - " ASN C 160 " " NAG a 1 " - " ASN C 234 " " NAG b 1 " - " ASN C 262 " " NAG c 611 " - " ASN c 197 " " NAG c 623 " - " ASN c 355 " " NAG c 631 " - " ASN c 392 " " NAG e 1 " - " ASN C 295 " " NAG f 1 " - " ASN C 301 " " NAG g 1 " - " ASN C 363 " " NAG i 1 " - " ASN C 386 " " NAG j 1 " - " ASN C 332 " " NAG o 1 " - " ASN C 276 " " NAG p 1 " - " ASN c 133 " " NAG s 1 " - " ASN c 137 " " NAG t 1 " - " ASN c 156 " " NAG u 1 " - " ASN c 160 " " NAG v 1 " - " ASN c 234 " " NAG w 1 " - " ASN c 262 " " NAG x 1 " - " ASN c 295 " " NAG y 1 " - " ASN c 301 " " NAG z 1 " - " ASN c 363 " " NAGAA 1 " - " ASN c 276 " Time building additional restraints: 14.46 Conformation dependent library (CDL) restraints added in 5.4 seconds 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7068 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 79 sheets defined 14.0% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.28 Creating SS restraints... Processing helix chain '2' and resid 58 through 63 removed outlier: 3.779A pdb=" N THR 2 63 " --> pdb=" O LYS 2 59 " (cutoff:3.500A) Processing helix chain '2' and resid 100 through 115 Processing helix chain '2' and resid 122 through 126 removed outlier: 3.992A pdb=" N CYS 2 126 " --> pdb=" O THR 2 123 " (cutoff:3.500A) Processing helix chain '2' and resid 195 through 198 removed outlier: 3.719A pdb=" N THR 2 198 " --> pdb=" O ASN 2 195 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 195 through 198' Processing helix chain '2' and resid 335 through 350 Processing helix chain '2' and resid 368 through 373 removed outlier: 3.974A pdb=" N THR 2 372 " --> pdb=" O ASP 2 368 " (cutoff:3.500A) Processing helix chain '2' and resid 425 through 429 removed outlier: 4.121A pdb=" N ARG 2 429 " --> pdb=" O MET 2 426 " (cutoff:3.500A) Processing helix chain '2' and resid 475 through 480 removed outlier: 3.617A pdb=" N TRP 2 479 " --> pdb=" O MET 2 475 " (cutoff:3.500A) Processing helix chain '3' and resid 61 through 64 Processing helix chain '3' and resid 83 through 87 Processing helix chain '4' and resid 79 through 83 removed outlier: 3.709A pdb=" N VAL 4 83 " --> pdb=" O PRO 4 80 " (cutoff:3.500A) Processing helix chain '5' and resid 83 through 87 removed outlier: 3.708A pdb=" N SER 5 87 " --> pdb=" O ALA 5 84 " (cutoff:3.500A) Processing helix chain '7' and resid 78 through 82 Processing helix chain '8' and resid 61 through 64 removed outlier: 3.578A pdb=" N GLN 8 64 " --> pdb=" O ARG 8 61 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 61 through 64' Processing helix chain '8' and resid 83 through 87 removed outlier: 3.748A pdb=" N THR 8 87 " --> pdb=" O PRO 8 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 543 removed outlier: 4.274A pdb=" N MET A 535 " --> pdb=" O GLY A 531 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N THR A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL A 539 " --> pdb=" O MET A 535 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 595 Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.579A pdb=" N ILE A 635 " --> pdb=" O TRP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 661 Processing helix chain 'C' and resid 58 through 63 removed outlier: 3.786A pdb=" N THR C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 115 Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.907A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 removed outlier: 3.628A pdb=" N THR C 198 " --> pdb=" O ASN C 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 195 through 198' Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.912A pdb=" N THR C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.103A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.593A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 543 removed outlier: 4.214A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR D 536 " --> pdb=" O ALA D 532 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N THR D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL D 539 " --> pdb=" O MET D 535 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 595 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.570A pdb=" N ILE D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.679A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.728A pdb=" N SER M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 64 removed outlier: 3.500A pdb=" N GLN Q 64 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 61 through 64' Processing helix chain 'Q' and resid 83 through 87 removed outlier: 3.836A pdb=" N THR Q 87 " --> pdb=" O PRO Q 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 82 removed outlier: 3.507A pdb=" N PHE R 82 " --> pdb=" O ARG R 79 " (cutoff:3.500A) Processing helix chain 'c' and resid 58 through 63 removed outlier: 3.803A pdb=" N THR c 63 " --> pdb=" O LYS c 59 " (cutoff:3.500A) Processing helix chain 'c' and resid 100 through 115 Processing helix chain 'c' and resid 122 through 126 removed outlier: 4.049A pdb=" N CYS c 126 " --> pdb=" O THR c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 195 through 198 removed outlier: 3.660A pdb=" N THR c 198 " --> pdb=" O ASN c 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 195 through 198' Processing helix chain 'c' and resid 335 through 350 Processing helix chain 'c' and resid 368 through 373 removed outlier: 3.865A pdb=" N THR c 372 " --> pdb=" O ASP c 368 " (cutoff:3.500A) Processing helix chain 'c' and resid 425 through 429 removed outlier: 4.151A pdb=" N ARG c 429 " --> pdb=" O MET c 426 " (cutoff:3.500A) Processing helix chain 'c' and resid 475 through 480 removed outlier: 3.617A pdb=" N TRP c 479 " --> pdb=" O MET c 475 " (cutoff:3.500A) Processing helix chain 'd' and resid 529 through 543 removed outlier: 4.287A pdb=" N MET d 535 " --> pdb=" O GLY d 531 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR d 536 " --> pdb=" O ALA d 532 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N THR d 538 " --> pdb=" O SER d 534 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL d 539 " --> pdb=" O MET d 535 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN d 540 " --> pdb=" O THR d 536 " (cutoff:3.500A) Processing helix chain 'd' and resid 570 through 595 Processing helix chain 'd' and resid 618 through 625 removed outlier: 3.503A pdb=" N ILE d 622 " --> pdb=" O ASN d 618 " (cutoff:3.500A) Processing helix chain 'd' and resid 627 through 635 removed outlier: 3.600A pdb=" N ILE d 635 " --> pdb=" O TRP d 631 " (cutoff:3.500A) Processing helix chain 'd' and resid 638 through 661 Processing helix chain 'h' and resid 61 through 64 Processing helix chain 'h' and resid 83 through 87 Processing helix chain 'l' and resid 79 through 83 removed outlier: 3.699A pdb=" N VAL l 83 " --> pdb=" O PRO l 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 83 through 87 removed outlier: 3.659A pdb=" N SER m 87 " --> pdb=" O ALA m 84 " (cutoff:3.500A) Processing helix chain 'q' and resid 61 through 64 removed outlier: 3.632A pdb=" N GLN q 64 " --> pdb=" O ARG q 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 61 through 64' Processing helix chain 'q' and resid 83 through 87 removed outlier: 3.710A pdb=" N THR q 87 " --> pdb=" O PRO q 84 " (cutoff:3.500A) Processing helix chain 'r' and resid 78 through 82 Processing sheet with id=AA1, first strand: chain '2' and resid 495 through 499 removed outlier: 5.927A pdb=" N VAL A 608 " --> pdb=" O VAL 2 36 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N VAL 2 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N THR A 606 " --> pdb=" O VAL 2 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 45 through 47 removed outlier: 3.602A pdb=" N ILE 2 225 " --> pdb=" O VAL 2 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain '2' and resid 91 through 94 removed outlier: 3.627A pdb=" N GLU 2 91 " --> pdb=" O CYS 2 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain '2' and resid 202 through 203 removed outlier: 6.669A pdb=" N THR 2 202 " --> pdb=" O TYR 2 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 271 through 273 removed outlier: 7.583A pdb=" N GLN 2 293 " --> pdb=" O SER 2 334 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER 2 334 " --> pdb=" O GLN 2 293 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS 2 421 " --> pdb=" O PHE 2 382 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N PHE 2 382 " --> pdb=" O LYS 2 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '2' and resid 271 through 273 removed outlier: 11.252A pdb=" N VAL 2 286 " --> pdb=" O THR 2 455 " (cutoff:3.500A) removed outlier: 10.788A pdb=" N THR 2 455 " --> pdb=" O VAL 2 286 " (cutoff:3.500A) removed outlier: 12.358A pdb=" N PHE 2 288 " --> pdb=" O ILE 2 453 " (cutoff:3.500A) removed outlier: 11.916A pdb=" N ILE 2 453 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) removed outlier: 11.143A pdb=" N THR 2 290 " --> pdb=" O GLY 2 451 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY 2 451 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE 2 358 " --> pdb=" O GLU 2 466 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N PHE 2 468 " --> pdb=" O ILE 2 358 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARG 2 360 " --> pdb=" O PHE 2 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '2' and resid 304 through 312 removed outlier: 6.780A pdb=" N GLN 2 315 " --> pdb=" O ILE 2 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 6 through 7 Processing sheet with id=AB2, first strand: chain '3' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain '3' and resid 57 through 59 removed outlier: 6.456A pdb=" N TRP 3 36 " --> pdb=" O ILE 3 48 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY 3 50 " --> pdb=" O TRP 3 34 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP 3 34 " --> pdb=" O GLY 3 50 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N VAL A 518 " --> pdb=" O ARG 3 95 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LYS 3 97 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '4' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain '4' and resid 10 through 12 removed outlier: 6.962A pdb=" N LEU 4 33 " --> pdb=" O TYR 4 49 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N TYR 4 49 " --> pdb=" O LEU 4 33 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TRP 4 35 " --> pdb=" O LEU 4 47 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR 4 49 " --> pdb=" O THR 4 53 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '5' and resid 5 through 7 removed outlier: 3.833A pdb=" N GLN 5 5 " --> pdb=" O ASN 5 23 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '5' and resid 11 through 12 removed outlier: 3.525A pdb=" N THR 5 105 " --> pdb=" O TYR 5 90 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR 5 90 " --> pdb=" O THR 5 105 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP 5 34 " --> pdb=" O TYR 5 50 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TYR 5 50 " --> pdb=" O TRP 5 34 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TRP 5 36 " --> pdb=" O ILE 5 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '5' and resid 95 through 96 Processing sheet with id=AB9, first strand: chain '5' and resid 99 through 100A Processing sheet with id=AC1, first strand: chain '6' and resid 9 through 12 removed outlier: 6.155A pdb=" N VAL 6 11 " --> pdb=" O ILE 6 105 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP 6 35 " --> pdb=" O ILE 6 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '6' and resid 18 through 23 removed outlier: 3.859A pdb=" N ALA 6 71 " --> pdb=" O CYS 6 23 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '7' and resid 4 through 6 Processing sheet with id=AC4, first strand: chain '7' and resid 10 through 13 removed outlier: 6.452A pdb=" N TRP 7 34 " --> pdb=" O LEU 7 46 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '7' and resid 10 through 13 removed outlier: 3.640A pdb=" N GLN 7 89 " --> pdb=" O PHE 7 92 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '8' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain '8' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain '8' and resid 10 through 11 removed outlier: 3.598A pdb=" N GLY 8 49 " --> pdb=" O TRP 8 36 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG 8 38 " --> pdb=" O TRP 8 47 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N TRP 8 47 " --> pdb=" O ARG 8 38 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE 8 40 " --> pdb=" O PHE 8 45 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N PHE 8 45 " --> pdb=" O ILE 8 40 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '8' and resid 10 through 11 Processing sheet with id=AD1, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.862A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.617A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AD4, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.651A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AD6, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.664A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.490A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.809A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.547A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.376A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.937A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.772A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 518 through 519 removed outlier: 3.936A pdb=" N TYR H 99 " --> pdb=" O VAL D 518 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AE3, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AE4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.949A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR L 49 " --> pdb=" O THR L 53 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 5 through 7 removed outlier: 3.997A pdb=" N GLN M 5 " --> pdb=" O ASN M 23 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.532A pdb=" N THR M 105 " --> pdb=" O TYR M 90 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR M 95 " --> pdb=" O TYR M 33 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR M 33 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 99 through 100A Processing sheet with id=AE9, first strand: chain 'N' and resid 9 through 12 removed outlier: 6.123A pdb=" N VAL N 11 " --> pdb=" O ILE N 105 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP N 35 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 19 through 26 removed outlier: 3.925A pdb=" N ALA N 71 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 3 through 6 Processing sheet with id=AF3, first strand: chain 'Q' and resid 3 through 6 Processing sheet with id=AF4, first strand: chain 'Q' and resid 10 through 11 removed outlier: 3.602A pdb=" N GLY Q 49 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE Q 40 " --> pdb=" O PHE Q 45 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N PHE Q 45 " --> pdb=" O ILE Q 40 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 10 through 11 Processing sheet with id=AF6, first strand: chain 'R' and resid 4 through 6 Processing sheet with id=AF7, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.427A pdb=" N TRP R 34 " --> pdb=" O LEU R 46 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 10 through 13 removed outlier: 3.578A pdb=" N GLN R 89 " --> pdb=" O PHE R 92 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'c' and resid 495 through 499 removed outlier: 5.913A pdb=" N VAL d 608 " --> pdb=" O VAL c 36 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N VAL c 38 " --> pdb=" O THR d 606 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N THR d 606 " --> pdb=" O VAL c 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'c' and resid 45 through 47 removed outlier: 3.607A pdb=" N ILE c 225 " --> pdb=" O VAL c 245 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'c' and resid 53 through 56 Processing sheet with id=AG3, first strand: chain 'c' and resid 91 through 94 removed outlier: 3.675A pdb=" N GLU c 91 " --> pdb=" O CYS c 239 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'c' and resid 169 through 177 Processing sheet with id=AG5, first strand: chain 'c' and resid 202 through 203 removed outlier: 6.697A pdb=" N THR c 202 " --> pdb=" O TYR c 435 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'c' and resid 271 through 273 removed outlier: 7.410A pdb=" N GLN c 293 " --> pdb=" O SER c 334 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER c 334 " --> pdb=" O GLN c 293 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'c' and resid 271 through 273 removed outlier: 11.241A pdb=" N VAL c 286 " --> pdb=" O THR c 455 " (cutoff:3.500A) removed outlier: 10.741A pdb=" N THR c 455 " --> pdb=" O VAL c 286 " (cutoff:3.500A) removed outlier: 12.239A pdb=" N PHE c 288 " --> pdb=" O ILE c 453 " (cutoff:3.500A) removed outlier: 11.783A pdb=" N ILE c 453 " --> pdb=" O PHE c 288 " (cutoff:3.500A) removed outlier: 11.056A pdb=" N THR c 290 " --> pdb=" O GLY c 451 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLY c 451 " --> pdb=" O THR c 290 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE c 358 " --> pdb=" O GLU c 466 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE c 468 " --> pdb=" O ILE c 358 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG c 360 " --> pdb=" O PHE c 468 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'c' and resid 304 through 312 removed outlier: 6.743A pdb=" N GLN c 315 " --> pdb=" O ILE c 309 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'd' and resid 518 through 519 removed outlier: 3.969A pdb=" N TYR h 99 " --> pdb=" O VAL d 518 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TRP h 34 " --> pdb=" O GLY h 50 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY h 50 " --> pdb=" O TRP h 34 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TRP h 36 " --> pdb=" O ILE h 48 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'h' and resid 11 through 12 Processing sheet with id=AH2, first strand: chain 'h' and resid 6 through 7 Processing sheet with id=AH3, first strand: chain 'l' and resid 4 through 7 Processing sheet with id=AH4, first strand: chain 'l' and resid 10 through 12 removed outlier: 6.954A pdb=" N LEU l 33 " --> pdb=" O TYR l 49 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR l 49 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TRP l 35 " --> pdb=" O LEU l 47 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'm' and resid 5 through 7 removed outlier: 3.980A pdb=" N GLN m 5 " --> pdb=" O ASN m 23 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'm' and resid 11 through 12 removed outlier: 3.518A pdb=" N THR m 105 " --> pdb=" O TYR m 90 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR m 90 " --> pdb=" O THR m 105 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TRP m 34 " --> pdb=" O TYR m 50 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR m 50 " --> pdb=" O TRP m 34 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP m 36 " --> pdb=" O ILE m 48 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'm' and resid 99 through 100A Processing sheet with id=AH8, first strand: chain 'n' and resid 9 through 12 removed outlier: 6.198A pdb=" N VAL n 11 " --> pdb=" O ILE n 105 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP n 35 " --> pdb=" O ILE n 47 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'n' and resid 18 through 26 removed outlier: 3.956A pdb=" N ALA n 71 " --> pdb=" O CYS n 23 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'q' and resid 3 through 6 Processing sheet with id=AI2, first strand: chain 'q' and resid 3 through 6 Processing sheet with id=AI3, first strand: chain 'q' and resid 10 through 11 removed outlier: 3.586A pdb=" N GLY q 49 " --> pdb=" O TRP q 36 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ARG q 38 " --> pdb=" O TRP q 47 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N TRP q 47 " --> pdb=" O ARG q 38 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE q 40 " --> pdb=" O PHE q 45 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N PHE q 45 " --> pdb=" O ILE q 40 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'q' and resid 10 through 11 Processing sheet with id=AI5, first strand: chain 'r' and resid 4 through 6 Processing sheet with id=AI6, first strand: chain 'r' and resid 10 through 13 removed outlier: 6.495A pdb=" N TRP r 34 " --> pdb=" O LEU r 46 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'r' and resid 10 through 13 removed outlier: 3.633A pdb=" N GLN r 89 " --> pdb=" O PHE r 92 " (cutoff:3.500A) 1124 hydrogen bonds defined for protein. 2832 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: 13.03 Time building geometry restraints manager: 15.67 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: 9967 1.34 - 1.46: 8344 1.46 - 1.58: 14064 1.58 - 1.70: 1 1.70 - 1.82: 222 Bond restraints: 32598 Sorted by residual: bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.32e+00 bond pdb=" C1 MANAA 4 " pdb=" C2 MANAA 4 " ideal model delta sigma weight residual 1.526 1.583 -0.057 2.00e-02 2.50e+03 8.08e+00 bond pdb=" C1 MAN T 5 " pdb=" O5 MAN T 5 " ideal model delta sigma weight residual 1.399 1.456 -0.057 2.00e-02 2.50e+03 8.06e+00 bond pdb=" C1 NAG 0 2 " pdb=" O5 NAG 0 2 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.03e+00 bond pdb=" C1 NAG i 2 " pdb=" O5 NAG i 2 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.92e+00 ... (remaining 32593 not shown) Histogram of bond angle deviations from ideal: 98.31 - 105.49: 643 105.49 - 112.67: 17998 112.67 - 119.85: 10300 119.85 - 127.03: 14871 127.03 - 134.21: 480 Bond angle restraints: 44292 Sorted by residual: angle pdb=" N PHE 8 100D" pdb=" CA PHE 8 100D" pdb=" C PHE 8 100D" ideal model delta sigma weight residual 109.81 119.66 -9.85 2.21e+00 2.05e-01 1.99e+01 angle pdb=" N PHE Q 100D" pdb=" CA PHE Q 100D" pdb=" C PHE Q 100D" ideal model delta sigma weight residual 109.81 119.48 -9.67 2.21e+00 2.05e-01 1.92e+01 angle pdb=" N PHE q 100D" pdb=" CA PHE q 100D" pdb=" C PHE q 100D" ideal model delta sigma weight residual 109.81 118.81 -9.00 2.21e+00 2.05e-01 1.66e+01 angle pdb=" C ILE 4 29 " pdb=" N ASP 4 30 " pdb=" CA ASP 4 30 " ideal model delta sigma weight residual 121.54 129.10 -7.56 1.91e+00 2.74e-01 1.57e+01 angle pdb=" C ILE l 29 " pdb=" N ASP l 30 " pdb=" CA ASP l 30 " ideal model delta sigma weight residual 121.54 128.95 -7.41 1.91e+00 2.74e-01 1.51e+01 ... (remaining 44287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.91: 19597 21.91 - 43.82: 1033 43.82 - 65.74: 256 65.74 - 87.65: 115 87.65 - 109.56: 65 Dihedral angle restraints: 21066 sinusoidal: 10041 harmonic: 11025 Sorted by residual: dihedral pdb=" CA GLN 7 89 " pdb=" C GLN 7 89 " pdb=" N PHE 7 90 " pdb=" CA PHE 7 90 " ideal model delta harmonic sigma weight residual -180.00 -133.96 -46.04 0 5.00e+00 4.00e-02 8.48e+01 dihedral pdb=" CA GLN r 89 " pdb=" C GLN r 89 " pdb=" N PHE r 90 " pdb=" CA PHE r 90 " ideal model delta harmonic sigma weight residual -180.00 -134.52 -45.48 0 5.00e+00 4.00e-02 8.27e+01 dihedral pdb=" CA GLN R 89 " pdb=" C GLN R 89 " pdb=" N PHE R 90 " pdb=" CA PHE R 90 " ideal model delta harmonic sigma weight residual -180.00 -135.68 -44.32 0 5.00e+00 4.00e-02 7.86e+01 ... (remaining 21063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 4368 0.071 - 0.143: 864 0.143 - 0.214: 52 0.214 - 0.286: 20 0.286 - 0.357: 18 Chirality restraints: 5322 Sorted by residual: chirality pdb=" C1 NAG v 1 " pdb=" ND2 ASN c 234 " pdb=" C2 NAG v 1 " pdb=" O5 NAG v 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.60 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" C5 BMA w 3 " pdb=" C4 BMA w 3 " pdb=" C6 BMA w 3 " pdb=" O5 BMA w 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.60 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 5319 not shown) Planarity restraints: 5499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE Q 100D" -0.048 5.00e-02 4.00e+02 7.27e-02 8.47e+00 pdb=" N PRO Q 100E" 0.126 5.00e-02 4.00e+02 pdb=" CA PRO Q 100E" -0.037 5.00e-02 4.00e+02 pdb=" CD PRO Q 100E" -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE q 100D" 0.048 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO q 100E" -0.125 5.00e-02 4.00e+02 pdb=" CA PRO q 100E" 0.036 5.00e-02 4.00e+02 pdb=" CD PRO q 100E" 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE 8 100D" 0.046 5.00e-02 4.00e+02 6.91e-02 7.65e+00 pdb=" N PRO 8 100E" -0.120 5.00e-02 4.00e+02 pdb=" CA PRO 8 100E" 0.035 5.00e-02 4.00e+02 pdb=" CD PRO 8 100E" 0.039 5.00e-02 4.00e+02 ... (remaining 5496 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 10252 2.83 - 3.35: 26578 3.35 - 3.87: 53550 3.87 - 4.38: 58404 4.38 - 4.90: 100651 Nonbonded interactions: 249435 Sorted by model distance: nonbonded pdb=" O ASP 7 81 " pdb=" OH TYR 7 85 " model vdw 2.314 2.440 nonbonded pdb=" N ASN c 195 " pdb=" OD1 ASN c 195 " model vdw 2.317 2.520 nonbonded pdb=" OE1 GLN 7 6 " pdb=" OG SER 7 97 " model vdw 2.323 2.440 nonbonded pdb=" N ASP 8 76E" pdb=" OD1 ASP 8 76E" model vdw 2.325 2.520 nonbonded pdb=" OG SER m 7 " pdb=" OG1 THR m 21 " model vdw 2.333 2.440 ... (remaining 249430 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 'AA' selection = chain 'E' selection = chain 'S' selection = chain 'V' selection = chain 'X' selection = chain 'i' selection = chain 'o' selection = chain 's' } ncs_group { reference = chain '1' selection = chain 'T' selection = chain 'j' } ncs_group { reference = chain '2' selection = chain 'C' selection = chain 'c' } ncs_group { reference = chain '3' selection = chain 'H' selection = chain 'h' } ncs_group { reference = chain '4' selection = chain 'L' selection = chain 'l' } ncs_group { reference = chain '5' selection = chain 'M' selection = chain 'm' } ncs_group { reference = chain '6' selection = chain 'N' selection = chain 'n' } ncs_group { reference = chain '7' selection = chain 'R' selection = chain 'r' } ncs_group { reference = chain '8' selection = chain 'Q' selection = chain 'q' } ncs_group { reference = chain '9' selection = chain 'B' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'O' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'e' selection = chain 'f' selection = chain 'k' selection = chain 'p' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'J' selection = chain 'b' selection = chain 'w' } ncs_group { reference = chain 'P' selection = chain 'g' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.570 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: 0.020 Extract box with map and model: 1.230 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 85.720 Find NCS groups from input model: 4.020 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 32598 Z= 0.391 Angle : 0.928 10.009 44292 Z= 0.474 Chirality : 0.058 0.357 5322 Planarity : 0.006 0.073 5454 Dihedral : 16.198 109.561 13863 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 7.06 % Allowed : 6.94 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.12), residues: 3786 helix: -1.82 (0.21), residues: 387 sheet: -1.65 (0.13), residues: 1317 loop : -2.34 (0.12), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 571 HIS 0.011 0.002 HIS C 374 PHE 0.025 0.002 PHE 2 288 TYR 0.018 0.002 TYR 3 99 ARG 0.009 0.001 ARG q 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1134 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 898 time to evaluate : 3.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 83 GLU cc_start: 0.8793 (pt0) cc_final: 0.8561 (pm20) REVERT: 2 100 MET cc_start: 0.9182 (ptt) cc_final: 0.8926 (ptt) REVERT: 2 138 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8329 (mt) REVERT: 2 207 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8876 (tppt) REVERT: 2 260 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8029 (pp) REVERT: 2 321 ASP cc_start: 0.8596 (t0) cc_final: 0.8336 (t0) REVERT: 2 425 ASN cc_start: 0.8628 (t0) cc_final: 0.8126 (t0) REVERT: 2 443 ILE cc_start: 0.8809 (mm) cc_final: 0.8326 (tt) REVERT: 2 479 TRP cc_start: 0.9279 (m100) cc_final: 0.9013 (m100) REVERT: 2 492 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8452 (mp0) REVERT: 3 23 GLU cc_start: 0.9133 (tp30) cc_final: 0.8893 (tp30) REVERT: 3 53 ASN cc_start: 0.8554 (m-40) cc_final: 0.8242 (p0) REVERT: 3 55 GLU cc_start: 0.6060 (mm-30) cc_final: 0.5625 (mm-30) REVERT: 3 68 ILE cc_start: 0.8598 (mm) cc_final: 0.8361 (mm) REVERT: 6 78 VAL cc_start: 0.9085 (m) cc_final: 0.8756 (p) REVERT: 6 85 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8530 (t0) REVERT: 6 105 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6875 (tt) REVERT: 6 106 VAL cc_start: 0.7400 (OUTLIER) cc_final: 0.6111 (p) REVERT: 7 1 GLU cc_start: 0.7928 (pt0) cc_final: 0.7336 (pm20) REVERT: 7 33 THR cc_start: 0.9215 (m) cc_final: 0.8912 (m) REVERT: 7 48 TYR cc_start: 0.8717 (p90) cc_final: 0.8301 (p90) REVERT: 7 77 LEU cc_start: 0.9303 (mt) cc_final: 0.9062 (tp) REVERT: 7 78 ASP cc_start: 0.9284 (t70) cc_final: 0.8911 (t70) REVERT: 7 81 ASP cc_start: 0.9234 (m-30) cc_final: 0.8976 (m-30) REVERT: 8 30 ARG cc_start: 0.9090 (mtt90) cc_final: 0.8738 (mtt90) REVERT: 8 47 TRP cc_start: 0.8940 (t60) cc_final: 0.8287 (t60) REVERT: 8 48 ILE cc_start: 0.8464 (mt) cc_final: 0.7047 (mp) REVERT: 8 72 GLN cc_start: 0.9521 (tt0) cc_final: 0.9009 (tm-30) REVERT: 8 89 GLU cc_start: 0.7624 (tt0) cc_final: 0.7347 (tt0) REVERT: 8 100 TYR cc_start: 0.8448 (m-80) cc_final: 0.8105 (m-10) REVERT: A 539 VAL cc_start: 0.9490 (OUTLIER) cc_final: 0.9270 (t) REVERT: A 588 ARG cc_start: 0.9100 (mtt180) cc_final: 0.8535 (ttm110) REVERT: A 589 ASP cc_start: 0.8728 (m-30) cc_final: 0.8501 (m-30) REVERT: A 592 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8765 (tt) REVERT: C 45 TRP cc_start: 0.8799 (p90) cc_final: 0.8597 (p90) REVERT: C 83 GLU cc_start: 0.8882 (pt0) cc_final: 0.8509 (pm20) REVERT: C 100 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8567 (ptt) REVERT: C 138 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8493 (tt) REVERT: C 207 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8846 (tptp) REVERT: C 279 ASN cc_start: 0.9273 (t0) cc_final: 0.8930 (t0) REVERT: C 492 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8637 (mp0) REVERT: D 592 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8665 (tp) REVERT: D 601 LYS cc_start: 0.8081 (mtpp) cc_final: 0.7802 (mtpt) REVERT: D 622 ILE cc_start: 0.9621 (pt) cc_final: 0.9384 (pt) REVERT: D 638 TYR cc_start: 0.8996 (OUTLIER) cc_final: 0.8709 (m-80) REVERT: H 23 GLU cc_start: 0.9142 (tp30) cc_final: 0.8934 (tp30) REVERT: H 53 ASN cc_start: 0.8562 (m-40) cc_final: 0.8203 (p0) REVERT: L 95 PRO cc_start: 0.8884 (Cg_endo) cc_final: 0.8661 (Cg_exo) REVERT: M 90 TYR cc_start: 0.8660 (m-10) cc_final: 0.8003 (m-10) REVERT: M 100 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7879 (mt-10) REVERT: M 105 THR cc_start: 0.7357 (m) cc_final: 0.7135 (p) REVERT: N 85 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8403 (t0) REVERT: N 106 VAL cc_start: 0.7466 (OUTLIER) cc_final: 0.6678 (p) REVERT: Q 5 VAL cc_start: 0.9241 (t) cc_final: 0.8865 (p) REVERT: Q 30 ARG cc_start: 0.9134 (mtt90) cc_final: 0.8791 (mtt90) REVERT: Q 72 GLN cc_start: 0.9397 (tt0) cc_final: 0.9001 (tm-30) REVERT: Q 73 LEU cc_start: 0.8308 (mt) cc_final: 0.7739 (mt) REVERT: Q 89 GLU cc_start: 0.7607 (tt0) cc_final: 0.7300 (tt0) REVERT: Q 108 VAL cc_start: 0.9623 (t) cc_final: 0.9391 (p) REVERT: R 33 THR cc_start: 0.9147 (m) cc_final: 0.8755 (m) REVERT: R 77 LEU cc_start: 0.9052 (mt) cc_final: 0.8728 (tp) REVERT: c 100 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8064 (ppp) REVERT: c 256 SER cc_start: 0.9264 (p) cc_final: 0.8966 (t) REVERT: c 321 ASP cc_start: 0.8716 (t0) cc_final: 0.8343 (t0) REVERT: c 334 SER cc_start: 0.8655 (OUTLIER) cc_final: 0.8124 (p) REVERT: c 425 ASN cc_start: 0.8732 (t0) cc_final: 0.8116 (t0) REVERT: c 475 MET cc_start: 0.8856 (mmm) cc_final: 0.8531 (mmm) REVERT: c 479 TRP cc_start: 0.9172 (m100) cc_final: 0.8798 (m100) REVERT: c 491 ILE cc_start: 0.9341 (mm) cc_final: 0.9040 (mp) REVERT: c 492 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8521 (mm-30) REVERT: d 539 VAL cc_start: 0.9517 (OUTLIER) cc_final: 0.9160 (t) REVERT: d 579 ARG cc_start: 0.8787 (ttp-170) cc_final: 0.8549 (ttp-170) REVERT: d 588 ARG cc_start: 0.9047 (mtt180) cc_final: 0.8756 (ttm-80) REVERT: d 592 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8763 (tt) REVERT: d 593 LEU cc_start: 0.9213 (tp) cc_final: 0.9005 (tp) REVERT: d 596 TRP cc_start: 0.8843 (m-10) cc_final: 0.8121 (m-10) REVERT: d 619 LEU cc_start: 0.9286 (tp) cc_final: 0.9081 (mm) REVERT: d 638 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.8640 (m-80) REVERT: h 55 GLU cc_start: 0.5439 (mm-30) cc_final: 0.4996 (mm-30) REVERT: h 95 ARG cc_start: 0.4065 (OUTLIER) cc_final: 0.3818 (ttp-170) REVERT: m 90 TYR cc_start: 0.8555 (m-10) cc_final: 0.8037 (m-10) REVERT: m 100 LYS cc_start: 0.9085 (mptt) cc_final: 0.8794 (tmtt) REVERT: n 13 VAL cc_start: 0.8772 (OUTLIER) cc_final: 0.8542 (t) REVERT: n 78 VAL cc_start: 0.8752 (m) cc_final: 0.8434 (p) REVERT: n 85 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8050 (t0) REVERT: q 28 ASN cc_start: 0.8589 (t0) cc_final: 0.8362 (t0) REVERT: q 69 MET cc_start: 0.9302 (mtt) cc_final: 0.9079 (mtm) REVERT: q 72 GLN cc_start: 0.9430 (tt0) cc_final: 0.9137 (tm-30) REVERT: q 73 LEU cc_start: 0.8520 (mt) cc_final: 0.8154 (mt) REVERT: q 82 PHE cc_start: 0.8480 (t80) cc_final: 0.8149 (t80) REVERT: r 27 GLN cc_start: 0.8774 (mt0) cc_final: 0.8526 (mp10) REVERT: r 45 LEU cc_start: 0.9285 (tt) cc_final: 0.9002 (tt) REVERT: r 57 VAL cc_start: 0.8888 (t) cc_final: 0.8440 (t) REVERT: r 77 LEU cc_start: 0.9216 (mt) cc_final: 0.8926 (tp) REVERT: r 84 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8363 (m) outliers start: 236 outliers final: 67 residues processed: 1064 average time/residue: 0.4837 time to fit residues: 780.2978 Evaluate side-chains 561 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 470 time to evaluate : 3.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 9.9990 chunk 284 optimal weight: 0.0970 chunk 157 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 293 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 178 optimal weight: 0.9980 chunk 218 optimal weight: 7.9990 chunk 340 optimal weight: 1.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 72 HIS 2 80 ASN 2 315 GLN ** 2 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 377 ASN 2 448 ASN 3 60 ASN ** 4 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 23 ASN ** 5 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 51 ASN 7 27 GLN 8 6 GLN 8 101 GLN A 611 ASN ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 GLN C 72 HIS C 80 ASN C 85 HIS C 293 GLN C 315 GLN ** C 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN D 577 GLN ** D 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 35 HIS Q 101 GLN R 27 GLN c 72 HIS c 80 ASN c 315 GLN ** c 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 377 ASN ** d 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 611 ASN ** d 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 60 ASN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 23 ASN ** m 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 42 GLN q 6 GLN q 101 GLN r 30 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 32598 Z= 0.256 Angle : 0.713 12.937 44292 Z= 0.357 Chirality : 0.048 0.268 5322 Planarity : 0.006 0.136 5454 Dihedral : 12.393 75.114 6945 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.21 % Allowed : 3.14 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.13), residues: 3786 helix: -0.09 (0.24), residues: 393 sheet: -1.11 (0.13), residues: 1266 loop : -1.76 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP q 100F HIS 0.006 0.001 HIS c 374 PHE 0.025 0.002 PHE Q 100D TYR 0.019 0.002 TYR q 102 ARG 0.019 0.001 ARG 4 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 623 time to evaluate : 3.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 83 GLU cc_start: 0.8769 (pt0) cc_final: 0.8375 (pm20) REVERT: 2 95 MET cc_start: 0.8630 (pmm) cc_final: 0.8189 (pmm) REVERT: 2 100 MET cc_start: 0.9159 (ptt) cc_final: 0.8897 (ptp) REVERT: 2 190 GLU cc_start: 0.8623 (pt0) cc_final: 0.8260 (pm20) REVERT: 2 321 ASP cc_start: 0.8407 (t0) cc_final: 0.8182 (t0) REVERT: 2 425 ASN cc_start: 0.8618 (t0) cc_final: 0.8235 (t0) REVERT: 2 492 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8381 (mp0) REVERT: 3 23 GLU cc_start: 0.9162 (tp30) cc_final: 0.8956 (tp30) REVERT: 3 51 MET cc_start: 0.3232 (ttp) cc_final: 0.2188 (ttm) REVERT: 3 53 ASN cc_start: 0.8557 (m-40) cc_final: 0.8259 (p0) REVERT: 3 55 GLU cc_start: 0.6194 (mm-30) cc_final: 0.5576 (mm-30) REVERT: 3 71 LYS cc_start: 0.5666 (pttp) cc_final: 0.5453 (ptmm) REVERT: 3 81 ARG cc_start: 0.8705 (ttp-110) cc_final: 0.7925 (mtt90) REVERT: 6 85 ASP cc_start: 0.8797 (m-30) cc_final: 0.8536 (t0) REVERT: 7 32 MET cc_start: 0.8718 (tpt) cc_final: 0.8511 (tpt) REVERT: 7 33 THR cc_start: 0.9207 (m) cc_final: 0.8815 (p) REVERT: 7 48 TYR cc_start: 0.8596 (p90) cc_final: 0.8218 (p90) REVERT: 7 70 PHE cc_start: 0.8514 (m-10) cc_final: 0.8254 (m-10) REVERT: 7 77 LEU cc_start: 0.9293 (mt) cc_final: 0.9066 (tp) REVERT: 7 78 ASP cc_start: 0.9257 (t70) cc_final: 0.8732 (t70) REVERT: 7 80 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8541 (mm-30) REVERT: 7 81 ASP cc_start: 0.9530 (m-30) cc_final: 0.9033 (m-30) REVERT: 8 27 TYR cc_start: 0.8429 (p90) cc_final: 0.8126 (p90) REVERT: 8 47 TRP cc_start: 0.8931 (t60) cc_final: 0.8215 (t60) REVERT: 8 48 ILE cc_start: 0.8241 (mt) cc_final: 0.6909 (mp) REVERT: 8 52 LYS cc_start: 0.9257 (mtmm) cc_final: 0.8546 (mtmm) REVERT: 8 89 GLU cc_start: 0.7537 (tt0) cc_final: 0.7322 (tt0) REVERT: 8 100 TYR cc_start: 0.8449 (m-80) cc_final: 0.8128 (m-10) REVERT: A 588 ARG cc_start: 0.9073 (mtt180) cc_final: 0.8610 (ttm110) REVERT: A 589 ASP cc_start: 0.8693 (m-30) cc_final: 0.8447 (m-30) REVERT: A 591 GLN cc_start: 0.9357 (tm-30) cc_final: 0.8880 (tm-30) REVERT: A 632 ASP cc_start: 0.8965 (t0) cc_final: 0.8683 (t70) REVERT: C 45 TRP cc_start: 0.8977 (p90) cc_final: 0.8310 (p90) REVERT: C 83 GLU cc_start: 0.8967 (pt0) cc_final: 0.8427 (pm20) REVERT: C 95 MET cc_start: 0.8886 (pmm) cc_final: 0.8412 (pmm) REVERT: C 492 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8501 (mp0) REVERT: D 584 GLU cc_start: 0.8780 (mt-10) cc_final: 0.7336 (mt-10) REVERT: D 601 LYS cc_start: 0.8086 (mtpp) cc_final: 0.7783 (mtpt) REVERT: D 647 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8437 (mt-10) REVERT: H 53 ASN cc_start: 0.8510 (m-40) cc_final: 0.8146 (p0) REVERT: L 4 MET cc_start: 0.5236 (mmm) cc_final: 0.4471 (mtp) REVERT: L 92 PHE cc_start: 0.8135 (t80) cc_final: 0.7888 (t80) REVERT: M 105 THR cc_start: 0.8019 (m) cc_final: 0.7644 (p) REVERT: N 36 TYR cc_start: 0.8160 (m-10) cc_final: 0.7872 (m-10) REVERT: Q 19 LYS cc_start: 0.8576 (tptm) cc_final: 0.8359 (tptm) REVERT: Q 52 LYS cc_start: 0.9289 (mtmm) cc_final: 0.8664 (mtmm) REVERT: Q 69 MET cc_start: 0.9362 (mtt) cc_final: 0.9097 (mtp) REVERT: Q 76 ASP cc_start: 0.7825 (m-30) cc_final: 0.7618 (m-30) REVERT: R 27 GLN cc_start: 0.7724 (mp10) cc_final: 0.7258 (mp10) REVERT: R 38 ARG cc_start: 0.8641 (mtp85) cc_final: 0.8382 (mtp180) REVERT: R 53 ARG cc_start: 0.8416 (mtm-85) cc_final: 0.8145 (ttm110) REVERT: c 83 GLU cc_start: 0.8863 (pt0) cc_final: 0.8530 (pm20) REVERT: c 97 LYS cc_start: 0.9358 (mmtt) cc_final: 0.8993 (mmmm) REVERT: c 100 MET cc_start: 0.9005 (ptt) cc_final: 0.8589 (ptp) REVERT: c 321 ASP cc_start: 0.8524 (t0) cc_final: 0.8011 (t0) REVERT: c 423 ILE cc_start: 0.8711 (pt) cc_final: 0.8416 (pt) REVERT: c 425 ASN cc_start: 0.8686 (t0) cc_final: 0.8202 (t0) REVERT: c 492 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8318 (mp0) REVERT: d 574 LYS cc_start: 0.9299 (pttt) cc_final: 0.9057 (pttt) REVERT: d 588 ARG cc_start: 0.9085 (mtt180) cc_final: 0.8801 (ttm-80) REVERT: d 589 ASP cc_start: 0.8780 (m-30) cc_final: 0.8557 (m-30) REVERT: d 591 GLN cc_start: 0.9288 (tm-30) cc_final: 0.8981 (tm-30) REVERT: d 655 LYS cc_start: 0.9619 (mmmm) cc_final: 0.9051 (pttp) REVERT: h 51 MET cc_start: 0.4094 (ttp) cc_final: 0.2805 (ttm) REVERT: h 55 GLU cc_start: 0.5490 (mm-30) cc_final: 0.5050 (mm-30) REVERT: h 97 LYS cc_start: 0.9086 (mtmt) cc_final: 0.8878 (mtpp) REVERT: l 4 MET cc_start: 0.3831 (mmt) cc_final: 0.2312 (mtp) REVERT: l 82 ASP cc_start: 0.5153 (p0) cc_final: 0.2562 (p0) REVERT: m 90 TYR cc_start: 0.8526 (m-10) cc_final: 0.8208 (m-10) REVERT: m 100 LYS cc_start: 0.9080 (mptt) cc_final: 0.8755 (tmtt) REVERT: n 85 ASP cc_start: 0.8737 (m-30) cc_final: 0.8221 (t0) REVERT: q 28 ASN cc_start: 0.8867 (t0) cc_final: 0.8429 (t0) REVERT: q 52 LYS cc_start: 0.9199 (mtmm) cc_final: 0.8335 (mtmm) REVERT: q 69 MET cc_start: 0.9192 (mtt) cc_final: 0.8969 (mtm) REVERT: q 72 GLN cc_start: 0.9229 (tt0) cc_final: 0.8770 (tm-30) REVERT: q 73 LEU cc_start: 0.8988 (mt) cc_final: 0.8314 (tp) REVERT: q 80 MET cc_start: 0.8085 (tmm) cc_final: 0.7873 (tmm) REVERT: q 82 PHE cc_start: 0.8472 (t80) cc_final: 0.7984 (t80) REVERT: q 105 GLN cc_start: 0.9001 (pp30) cc_final: 0.8750 (pp30) REVERT: r 33 THR cc_start: 0.9049 (m) cc_final: 0.8784 (p) REVERT: r 59 ASP cc_start: 0.9057 (t0) cc_final: 0.8742 (t0) REVERT: r 77 LEU cc_start: 0.9194 (mt) cc_final: 0.8982 (tp) REVERT: r 80 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8421 (mm-30) REVERT: r 81 ASP cc_start: 0.9508 (m-30) cc_final: 0.8825 (m-30) outliers start: 7 outliers final: 3 residues processed: 629 average time/residue: 0.4807 time to fit residues: 467.9471 Evaluate side-chains 444 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 441 time to evaluate : 3.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 283 optimal weight: 3.9990 chunk 231 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 341 optimal weight: 5.9990 chunk 368 optimal weight: 0.9980 chunk 303 optimal weight: 8.9990 chunk 338 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 273 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 85 HIS 2 98 ASN ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 103 GLN 2 293 GLN 2 352 HIS ** 4 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN C 352 HIS D 611 ASN ** D 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 80 ASN c 85 HIS c 98 ASN c 352 HIS ** d 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 658 GLN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 GLN ** m 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 97 HIS ** n 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 32598 Z= 0.290 Angle : 0.697 12.910 44292 Z= 0.348 Chirality : 0.047 0.243 5322 Planarity : 0.005 0.114 5454 Dihedral : 10.623 71.143 6945 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.15 % Allowed : 3.95 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.13), residues: 3786 helix: 0.55 (0.27), residues: 384 sheet: -0.91 (0.14), residues: 1275 loop : -1.59 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP m 34 HIS 0.005 0.001 HIS c 374 PHE 0.016 0.002 PHE Q 91 TYR 0.018 0.002 TYR D 638 ARG 0.012 0.001 ARG 4 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 552 time to evaluate : 3.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 52 LEU cc_start: 0.9448 (mt) cc_final: 0.9195 (mm) REVERT: 2 83 GLU cc_start: 0.8871 (pt0) cc_final: 0.8348 (pm20) REVERT: 2 95 MET cc_start: 0.8820 (pmm) cc_final: 0.8395 (pmm) REVERT: 2 97 LYS cc_start: 0.9334 (mttt) cc_final: 0.8924 (mttt) REVERT: 2 100 MET cc_start: 0.9391 (ptt) cc_final: 0.8968 (ptp) REVERT: 2 119 CYS cc_start: 0.6756 (m) cc_final: 0.6418 (m) REVERT: 2 190 GLU cc_start: 0.8677 (pt0) cc_final: 0.8298 (pm20) REVERT: 2 211 GLU cc_start: 0.8671 (tt0) cc_final: 0.8457 (tt0) REVERT: 2 321 ASP cc_start: 0.8424 (t0) cc_final: 0.8210 (t0) REVERT: 2 425 ASN cc_start: 0.8823 (t0) cc_final: 0.8300 (t0) REVERT: 2 492 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8398 (mp0) REVERT: 3 23 GLU cc_start: 0.9135 (tp30) cc_final: 0.8912 (tp30) REVERT: 3 51 MET cc_start: 0.3272 (ttp) cc_final: 0.1607 (ttm) REVERT: 3 53 ASN cc_start: 0.8520 (m-40) cc_final: 0.8183 (p0) REVERT: 3 55 GLU cc_start: 0.6161 (mm-30) cc_final: 0.5471 (mm-30) REVERT: 6 85 ASP cc_start: 0.8821 (m-30) cc_final: 0.8547 (t0) REVERT: 7 48 TYR cc_start: 0.8609 (p90) cc_final: 0.8316 (p90) REVERT: 7 78 ASP cc_start: 0.9242 (t70) cc_final: 0.9008 (t0) REVERT: 7 81 ASP cc_start: 0.9504 (m-30) cc_final: 0.9050 (m-30) REVERT: 8 47 TRP cc_start: 0.8949 (t60) cc_final: 0.8227 (t60) REVERT: 8 48 ILE cc_start: 0.8295 (mt) cc_final: 0.6848 (mp) REVERT: 8 76 ASP cc_start: 0.5587 (p0) cc_final: 0.5226 (p0) REVERT: 8 89 GLU cc_start: 0.7480 (tt0) cc_final: 0.7271 (tt0) REVERT: 8 100 TYR cc_start: 0.8503 (m-80) cc_final: 0.8194 (m-10) REVERT: A 588 ARG cc_start: 0.9124 (mtt180) cc_final: 0.8631 (ttm110) REVERT: A 589 ASP cc_start: 0.8789 (m-30) cc_final: 0.8548 (m-30) REVERT: A 591 GLN cc_start: 0.9402 (tm-30) cc_final: 0.8963 (tm-30) REVERT: A 632 ASP cc_start: 0.9027 (t0) cc_final: 0.8793 (t70) REVERT: C 45 TRP cc_start: 0.9047 (p90) cc_final: 0.8178 (p90) REVERT: C 83 GLU cc_start: 0.9023 (pt0) cc_final: 0.8439 (pm20) REVERT: C 161 MET cc_start: 0.9190 (tpp) cc_final: 0.8468 (tpp) REVERT: C 321 ASP cc_start: 0.8797 (m-30) cc_final: 0.8581 (t0) REVERT: C 492 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8430 (mp0) REVERT: D 530 MET cc_start: 0.8108 (mmm) cc_final: 0.7771 (mmt) REVERT: D 601 LYS cc_start: 0.8027 (mtpp) cc_final: 0.7683 (mtpt) REVERT: H 53 ASN cc_start: 0.8399 (m-40) cc_final: 0.8056 (p0) REVERT: L 4 MET cc_start: 0.5246 (mmm) cc_final: 0.4652 (mtp) REVERT: L 92 PHE cc_start: 0.8167 (t80) cc_final: 0.7894 (t80) REVERT: M 105 THR cc_start: 0.8062 (m) cc_final: 0.7697 (p) REVERT: Q 19 LYS cc_start: 0.8615 (tptm) cc_final: 0.8186 (tptm) REVERT: R 32 MET cc_start: 0.9130 (tpt) cc_final: 0.8854 (tpt) REVERT: R 38 ARG cc_start: 0.8724 (mtp85) cc_final: 0.8467 (mtp180) REVERT: R 53 ARG cc_start: 0.8610 (mtm-85) cc_final: 0.8054 (ttm110) REVERT: R 77 LEU cc_start: 0.9175 (mt) cc_final: 0.8943 (tp) REVERT: c 83 GLU cc_start: 0.8920 (pt0) cc_final: 0.8547 (pm20) REVERT: c 97 LYS cc_start: 0.9382 (mmtt) cc_final: 0.9064 (mmmm) REVERT: c 100 MET cc_start: 0.9179 (ptt) cc_final: 0.8847 (ptp) REVERT: c 104 MET cc_start: 0.9261 (tmm) cc_final: 0.8742 (tmm) REVERT: c 123 THR cc_start: 0.9200 (p) cc_final: 0.8891 (t) REVERT: c 321 ASP cc_start: 0.8617 (t0) cc_final: 0.8112 (t0) REVERT: c 425 ASN cc_start: 0.8758 (t0) cc_final: 0.8385 (t0) REVERT: c 492 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8435 (mp0) REVERT: d 574 LYS cc_start: 0.9380 (pttt) cc_final: 0.8995 (pttt) REVERT: d 588 ARG cc_start: 0.9056 (mtt180) cc_final: 0.8790 (ttm-80) REVERT: d 589 ASP cc_start: 0.8863 (m-30) cc_final: 0.8605 (m-30) REVERT: d 591 GLN cc_start: 0.9353 (tm-30) cc_final: 0.9030 (tm-30) REVERT: d 601 LYS cc_start: 0.8102 (mtpp) cc_final: 0.7755 (mtpt) REVERT: d 632 ASP cc_start: 0.8752 (t70) cc_final: 0.8536 (t70) REVERT: h 51 MET cc_start: 0.3144 (ttp) cc_final: 0.2625 (ttm) REVERT: h 55 GLU cc_start: 0.5295 (mm-30) cc_final: 0.5054 (mm-30) REVERT: l 90 GLN cc_start: 0.5901 (OUTLIER) cc_final: 0.4179 (pp30) REVERT: n 85 ASP cc_start: 0.8764 (m-30) cc_final: 0.8276 (t0) REVERT: q 28 ASN cc_start: 0.8891 (t0) cc_final: 0.8438 (t0) REVERT: q 32 TYR cc_start: 0.8874 (m-80) cc_final: 0.8673 (m-80) REVERT: q 52 LYS cc_start: 0.9220 (mtmm) cc_final: 0.8529 (mtmm) REVERT: q 80 MET cc_start: 0.8138 (tmm) cc_final: 0.7675 (tmm) REVERT: q 100 TYR cc_start: 0.8225 (m-80) cc_final: 0.7710 (m-80) REVERT: r 32 MET cc_start: 0.9086 (tpt) cc_final: 0.8615 (tpt) REVERT: r 33 THR cc_start: 0.9044 (m) cc_final: 0.8748 (p) REVERT: r 81 ASP cc_start: 0.9529 (m-30) cc_final: 0.9272 (m-30) outliers start: 5 outliers final: 1 residues processed: 556 average time/residue: 0.4496 time to fit residues: 386.4099 Evaluate side-chains 406 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 404 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 10.0000 chunk 256 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 229 optimal weight: 3.9990 chunk 342 optimal weight: 9.9990 chunk 362 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 324 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 27 GLN ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** D 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN c 80 ASN c 103 GLN c 377 ASN ** d 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 89 GLN ** m 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 68 HIS n 51 ASN r 30 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 32598 Z= 0.206 Angle : 0.650 13.441 44292 Z= 0.324 Chirality : 0.046 0.228 5322 Planarity : 0.005 0.108 5454 Dihedral : 9.351 69.335 6945 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.18 % Allowed : 2.69 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.13), residues: 3786 helix: 0.93 (0.27), residues: 381 sheet: -0.78 (0.14), residues: 1254 loop : -1.46 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP d 631 HIS 0.004 0.001 HIS C 374 PHE 0.026 0.002 PHE Q 100D TYR 0.030 0.001 TYR Q 100 ARG 0.009 0.001 ARG 3 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 545 time to evaluate : 3.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 52 LEU cc_start: 0.9414 (mt) cc_final: 0.9182 (mt) REVERT: 2 83 GLU cc_start: 0.8848 (pt0) cc_final: 0.8336 (pm20) REVERT: 2 97 LYS cc_start: 0.9322 (mttt) cc_final: 0.9013 (mttt) REVERT: 2 100 MET cc_start: 0.9404 (ptt) cc_final: 0.8980 (ptp) REVERT: 2 119 CYS cc_start: 0.6705 (m) cc_final: 0.6339 (m) REVERT: 2 190 GLU cc_start: 0.8692 (pt0) cc_final: 0.8304 (pm20) REVERT: 2 425 ASN cc_start: 0.8823 (t0) cc_final: 0.8333 (t0) REVERT: 2 492 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8518 (mm-30) REVERT: 3 23 GLU cc_start: 0.9141 (tp30) cc_final: 0.8915 (tp30) REVERT: 3 51 MET cc_start: 0.1422 (ttp) cc_final: 0.0847 (ttm) REVERT: 3 53 ASN cc_start: 0.8425 (m-40) cc_final: 0.8176 (p0) REVERT: 3 55 GLU cc_start: 0.5570 (mm-30) cc_final: 0.5106 (mm-30) REVERT: 6 85 ASP cc_start: 0.8822 (m-30) cc_final: 0.8542 (t0) REVERT: 7 1 GLU cc_start: 0.8216 (pm20) cc_final: 0.7996 (pm20) REVERT: 7 11 LEU cc_start: 0.9239 (tp) cc_final: 0.8989 (mt) REVERT: 7 48 TYR cc_start: 0.8655 (p90) cc_final: 0.8415 (p90) REVERT: 7 78 ASP cc_start: 0.9343 (t70) cc_final: 0.9038 (t70) REVERT: 7 81 ASP cc_start: 0.9493 (m-30) cc_final: 0.9191 (m-30) REVERT: 8 47 TRP cc_start: 0.8937 (t60) cc_final: 0.8329 (t60) REVERT: 8 48 ILE cc_start: 0.8158 (mt) cc_final: 0.6754 (mp) REVERT: 8 76 ASP cc_start: 0.7681 (p0) cc_final: 0.7346 (p0) REVERT: 8 80 MET cc_start: 0.7978 (tmm) cc_final: 0.7400 (tmm) REVERT: 8 89 GLU cc_start: 0.7546 (tt0) cc_final: 0.7345 (tt0) REVERT: 8 100 TYR cc_start: 0.8449 (m-80) cc_final: 0.8196 (m-10) REVERT: A 588 ARG cc_start: 0.9099 (mtt180) cc_final: 0.8618 (ttm110) REVERT: A 589 ASP cc_start: 0.8771 (m-30) cc_final: 0.8478 (m-30) REVERT: A 591 GLN cc_start: 0.9391 (tm-30) cc_final: 0.9052 (tm-30) REVERT: A 632 ASP cc_start: 0.8985 (t0) cc_final: 0.8764 (t70) REVERT: C 45 TRP cc_start: 0.8907 (p90) cc_final: 0.8105 (p90) REVERT: C 83 GLU cc_start: 0.9025 (pt0) cc_final: 0.8468 (pm20) REVERT: C 161 MET cc_start: 0.9199 (tpp) cc_final: 0.8469 (tpp) REVERT: C 479 TRP cc_start: 0.9348 (m100) cc_final: 0.9014 (m100) REVERT: C 492 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8400 (mp0) REVERT: D 601 LYS cc_start: 0.8226 (mtpp) cc_final: 0.7875 (mtpt) REVERT: H 55 GLU cc_start: 0.5877 (mm-30) cc_final: 0.5443 (mm-30) REVERT: L 4 MET cc_start: 0.5348 (mmm) cc_final: 0.4788 (mtp) REVERT: L 92 PHE cc_start: 0.8214 (t80) cc_final: 0.7897 (t80) REVERT: M 105 THR cc_start: 0.8010 (m) cc_final: 0.7647 (p) REVERT: Q 69 MET cc_start: 0.9395 (mtt) cc_final: 0.9029 (mtp) REVERT: Q 75 GLN cc_start: 0.8598 (mp10) cc_final: 0.8079 (mp10) REVERT: Q 76 ASP cc_start: 0.6086 (p0) cc_final: 0.5548 (p0) REVERT: Q 76 ASP cc_start: 0.8617 (m-30) cc_final: 0.8201 (p0) REVERT: Q 80 MET cc_start: 0.8516 (tmm) cc_final: 0.7548 (tmm) REVERT: R 38 ARG cc_start: 0.8701 (mtp85) cc_final: 0.8404 (mtp180) REVERT: R 53 ARG cc_start: 0.8376 (mtm-85) cc_final: 0.7554 (mtm-85) REVERT: R 77 LEU cc_start: 0.9169 (mt) cc_final: 0.8898 (tp) REVERT: c 83 GLU cc_start: 0.8941 (pt0) cc_final: 0.8435 (pm20) REVERT: c 97 LYS cc_start: 0.9408 (mmtt) cc_final: 0.9070 (mmmm) REVERT: c 123 THR cc_start: 0.9218 (p) cc_final: 0.8808 (t) REVERT: c 321 ASP cc_start: 0.8587 (t0) cc_final: 0.8092 (t0) REVERT: c 425 ASN cc_start: 0.8802 (t0) cc_final: 0.8438 (t0) REVERT: c 492 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8472 (mm-30) REVERT: d 574 LYS cc_start: 0.9394 (pttt) cc_final: 0.8936 (ptpp) REVERT: d 588 ARG cc_start: 0.9041 (mtt180) cc_final: 0.8797 (ttm-80) REVERT: d 589 ASP cc_start: 0.8857 (m-30) cc_final: 0.8566 (m-30) REVERT: d 591 GLN cc_start: 0.9349 (tm-30) cc_final: 0.9050 (tm-30) REVERT: d 626 MET cc_start: 0.8411 (mtt) cc_final: 0.8148 (mtt) REVERT: d 633 LYS cc_start: 0.9285 (mmmm) cc_final: 0.9055 (mmmm) REVERT: d 655 LYS cc_start: 0.9564 (mmmm) cc_final: 0.9056 (pttp) REVERT: h 55 GLU cc_start: 0.5589 (mm-30) cc_final: 0.5350 (mm-30) REVERT: l 4 MET cc_start: 0.3337 (mmt) cc_final: 0.2447 (mtp) REVERT: m 100 LYS cc_start: 0.9282 (mmmm) cc_final: 0.8612 (tmtt) REVERT: n 85 ASP cc_start: 0.8648 (m-30) cc_final: 0.8302 (t0) REVERT: q 28 ASN cc_start: 0.8867 (t0) cc_final: 0.8391 (t0) REVERT: q 32 TYR cc_start: 0.8877 (m-80) cc_final: 0.8442 (m-80) REVERT: q 52 LYS cc_start: 0.9210 (mtmm) cc_final: 0.8484 (mtmm) REVERT: q 100 ASP cc_start: 0.6872 (t70) cc_final: 0.6661 (t70) REVERT: r 33 THR cc_start: 0.8976 (m) cc_final: 0.8676 (p) REVERT: r 78 ASP cc_start: 0.9319 (t70) cc_final: 0.8938 (t70) REVERT: r 81 ASP cc_start: 0.9532 (m-30) cc_final: 0.9329 (m-30) outliers start: 6 outliers final: 1 residues processed: 551 average time/residue: 0.4559 time to fit residues: 390.5038 Evaluate side-chains 392 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 391 time to evaluate : 3.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 0.1980 chunk 205 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 269 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 chunk 309 optimal weight: 20.0000 chunk 250 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 185 optimal weight: 0.9980 chunk 325 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 55 GLN 4 89 GLN ** 5 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 89 GLN ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 GLN H 76 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 HIS N 42 GLN ** N 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 GLN c 80 ASN c 99 ASN ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 577 GLN ** d 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 37 GLN ** n 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 30 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 32598 Z= 0.371 Angle : 0.746 12.922 44292 Z= 0.370 Chirality : 0.047 0.250 5322 Planarity : 0.005 0.083 5454 Dihedral : 9.072 67.156 6945 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.06 % Allowed : 3.38 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.51 (0.13), residues: 3786 helix: 0.51 (0.27), residues: 399 sheet: -0.67 (0.14), residues: 1248 loop : -1.53 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP d 571 HIS 0.005 0.001 HIS 5 52 PHE 0.027 0.002 PHE q 100D TYR 0.041 0.002 TYR A 643 ARG 0.009 0.001 ARG Q 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 483 time to evaluate : 3.455 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: 2 83 GLU cc_start: 0.8901 (pt0) cc_final: 0.8362 (pm20) REVERT: 2 95 MET cc_start: 0.8871 (pmm) cc_final: 0.8532 (pmm) REVERT: 2 100 MET cc_start: 0.9495 (ptt) cc_final: 0.9019 (ptp) REVERT: 2 119 CYS cc_start: 0.6659 (m) cc_final: 0.6344 (m) REVERT: 2 492 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8430 (mp0) REVERT: 4 89 GLN cc_start: 0.6653 (OUTLIER) cc_final: 0.6420 (mp10) REVERT: 6 25 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8877 (mm-30) REVERT: 6 85 ASP cc_start: 0.8937 (m-30) cc_final: 0.8658 (t0) REVERT: 7 27 GLN cc_start: 0.8014 (mp10) cc_final: 0.7779 (mp10) REVERT: 7 48 TYR cc_start: 0.8747 (p90) cc_final: 0.8525 (p90) REVERT: 7 78 ASP cc_start: 0.9370 (t70) cc_final: 0.9069 (t0) REVERT: 7 81 ASP cc_start: 0.9539 (m-30) cc_final: 0.9074 (m-30) REVERT: 8 72 GLN cc_start: 0.9362 (tt0) cc_final: 0.9020 (tp40) REVERT: 8 80 MET cc_start: 0.7969 (tmm) cc_final: 0.7732 (tmm) REVERT: 8 89 GLU cc_start: 0.7475 (tt0) cc_final: 0.7237 (tt0) REVERT: 8 100 TYR cc_start: 0.8527 (m-80) cc_final: 0.8130 (m-10) REVERT: A 542 ARG cc_start: 0.9144 (ttp-110) cc_final: 0.8902 (ttp-110) REVERT: A 574 LYS cc_start: 0.9427 (ptpp) cc_final: 0.9174 (pttm) REVERT: A 588 ARG cc_start: 0.9150 (mtt180) cc_final: 0.8619 (ttm110) REVERT: A 589 ASP cc_start: 0.8852 (m-30) cc_final: 0.8611 (m-30) REVERT: A 632 ASP cc_start: 0.9147 (t0) cc_final: 0.8924 (t70) REVERT: A 655 LYS cc_start: 0.9046 (pttp) cc_final: 0.8837 (pttm) REVERT: C 45 TRP cc_start: 0.9058 (p90) cc_final: 0.8063 (p90) REVERT: C 83 GLU cc_start: 0.9014 (pt0) cc_final: 0.8558 (pm20) REVERT: C 95 MET cc_start: 0.9005 (pmm) cc_final: 0.8560 (pmm) REVERT: C 140 ASP cc_start: 0.8231 (m-30) cc_final: 0.7646 (t0) REVERT: C 161 MET cc_start: 0.9284 (tpp) cc_final: 0.8625 (tpp) REVERT: C 321 ASP cc_start: 0.8845 (m-30) cc_final: 0.8612 (t0) REVERT: C 492 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8537 (mp0) REVERT: D 655 LYS cc_start: 0.9101 (pttp) cc_final: 0.8773 (mmmt) REVERT: H 55 GLU cc_start: 0.5697 (mm-30) cc_final: 0.5185 (mm-30) REVERT: L 4 MET cc_start: 0.5208 (mmm) cc_final: 0.4685 (mtp) REVERT: L 92 PHE cc_start: 0.8248 (t80) cc_final: 0.7965 (t80) REVERT: M 100 MET cc_start: 0.7341 (mmm) cc_final: 0.7091 (mmm) REVERT: M 105 THR cc_start: 0.8036 (m) cc_final: 0.7701 (p) REVERT: Q 20 ILE cc_start: 0.9249 (pt) cc_final: 0.9013 (pt) REVERT: Q 52 LYS cc_start: 0.9290 (mtmm) cc_final: 0.8753 (mtmm) REVERT: Q 76 ASP cc_start: 0.8760 (m-30) cc_final: 0.8180 (m-30) REVERT: Q 80 MET cc_start: 0.8479 (tmm) cc_final: 0.7528 (tmm) REVERT: R 32 MET cc_start: 0.9150 (tpt) cc_final: 0.8867 (tpt) REVERT: R 33 THR cc_start: 0.9039 (m) cc_final: 0.8820 (m) REVERT: R 59 ASP cc_start: 0.9507 (t0) cc_final: 0.9245 (t0) REVERT: c 83 GLU cc_start: 0.8940 (pt0) cc_final: 0.8417 (pm20) REVERT: c 97 LYS cc_start: 0.9449 (mmtt) cc_final: 0.9151 (mmmm) REVERT: c 104 MET cc_start: 0.9345 (tmm) cc_final: 0.8830 (tmm) REVERT: c 123 THR cc_start: 0.9389 (p) cc_final: 0.8993 (t) REVERT: c 321 ASP cc_start: 0.8779 (t0) cc_final: 0.8376 (t0) REVERT: c 425 ASN cc_start: 0.8946 (t0) cc_final: 0.8514 (t0) REVERT: c 492 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8406 (mp0) REVERT: d 530 MET cc_start: 0.7982 (mmp) cc_final: 0.7732 (mmp) REVERT: d 574 LYS cc_start: 0.9557 (pttt) cc_final: 0.9221 (ptpt) REVERT: d 586 TYR cc_start: 0.9554 (t80) cc_final: 0.9326 (t80) REVERT: d 588 ARG cc_start: 0.9088 (mtt180) cc_final: 0.8823 (ttm-80) REVERT: d 589 ASP cc_start: 0.8882 (m-30) cc_final: 0.8621 (m-30) REVERT: d 591 GLN cc_start: 0.9475 (tm-30) cc_final: 0.8905 (tm-30) REVERT: d 595 ILE cc_start: 0.9683 (pt) cc_final: 0.9404 (mt) REVERT: d 626 MET cc_start: 0.8539 (mtt) cc_final: 0.8258 (mtt) REVERT: d 633 LYS cc_start: 0.9350 (mmmm) cc_final: 0.9138 (mmmm) REVERT: d 655 LYS cc_start: 0.9572 (mmmm) cc_final: 0.9165 (pttp) REVERT: h 55 GLU cc_start: 0.5779 (mm-30) cc_final: 0.5550 (mm-30) REVERT: l 4 MET cc_start: 0.3497 (mmt) cc_final: 0.3123 (mtp) REVERT: m 100 LYS cc_start: 0.9366 (mmmm) cc_final: 0.8639 (tmtt) REVERT: m 100 MET cc_start: 0.7355 (mmm) cc_final: 0.6986 (mmm) REVERT: n 85 ASP cc_start: 0.8724 (m-30) cc_final: 0.8461 (t0) REVERT: q 28 ASN cc_start: 0.8934 (t0) cc_final: 0.8504 (t0) REVERT: q 52 LYS cc_start: 0.9251 (mtmm) cc_final: 0.8600 (mtmm) REVERT: q 76 ASP cc_start: 0.8643 (m-30) cc_final: 0.8403 (m-30) REVERT: r 11 LEU cc_start: 0.9241 (tp) cc_final: 0.8989 (tt) REVERT: r 32 MET cc_start: 0.9052 (tpt) cc_final: 0.8635 (tpt) REVERT: r 33 THR cc_start: 0.9010 (m) cc_final: 0.8664 (m) REVERT: r 78 ASP cc_start: 0.9348 (t70) cc_final: 0.8930 (t70) REVERT: r 81 ASP cc_start: 0.9581 (m-30) cc_final: 0.9377 (m-30) outliers start: 2 outliers final: 0 residues processed: 485 average time/residue: 0.4466 time to fit residues: 340.2166 Evaluate side-chains 360 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 359 time to evaluate : 3.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 3.9990 chunk 326 optimal weight: 30.0000 chunk 71 optimal weight: 0.9980 chunk 212 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 362 optimal weight: 3.9990 chunk 301 optimal weight: 0.0470 chunk 167 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 190 optimal weight: 9.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 80 ASN ** 2 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 76 ASN ** 5 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN C 103 GLN ** D 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN Q 35 HIS ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 80 ASN c 88 ASN ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 377 ASN d 575 GLN ** d 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 27 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 32598 Z= 0.196 Angle : 0.648 13.697 44292 Z= 0.323 Chirality : 0.045 0.224 5322 Planarity : 0.004 0.067 5454 Dihedral : 8.361 66.222 6945 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.09 % Allowed : 1.53 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.14), residues: 3786 helix: 0.93 (0.27), residues: 399 sheet: -0.55 (0.14), residues: 1275 loop : -1.37 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP d 631 HIS 0.003 0.001 HIS 2 85 PHE 0.023 0.001 PHE d 519 TYR 0.015 0.001 TYR D 638 ARG 0.012 0.001 ARG 6 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 502 time to evaluate : 3.824 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: 2 52 LEU cc_start: 0.9432 (mt) cc_final: 0.9223 (mt) REVERT: 2 83 GLU cc_start: 0.8863 (pt0) cc_final: 0.8328 (pm20) REVERT: 2 95 MET cc_start: 0.8790 (pmm) cc_final: 0.8474 (pmm) REVERT: 2 100 MET cc_start: 0.9429 (ptt) cc_final: 0.8875 (ptp) REVERT: 2 119 CYS cc_start: 0.6677 (m) cc_final: 0.6405 (m) REVERT: 2 425 ASN cc_start: 0.8811 (t0) cc_final: 0.8335 (t0) REVERT: 2 492 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8448 (mm-30) REVERT: 3 23 GLU cc_start: 0.9161 (tp30) cc_final: 0.8954 (tp30) REVERT: 3 31 ASP cc_start: 0.8121 (t0) cc_final: 0.7772 (m-30) REVERT: 3 51 MET cc_start: 0.1766 (ttp) cc_final: 0.0886 (ttm) REVERT: 3 71 LYS cc_start: 0.6193 (mtmm) cc_final: 0.4905 (mtmt) REVERT: 5 82 LEU cc_start: 0.9222 (tt) cc_final: 0.8530 (mp) REVERT: 5 103 LYS cc_start: 0.8837 (mmmt) cc_final: 0.8354 (mmtm) REVERT: 6 25 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8833 (mm-30) REVERT: 6 85 ASP cc_start: 0.8778 (m-30) cc_final: 0.8557 (t0) REVERT: 7 27 GLN cc_start: 0.8006 (mp10) cc_final: 0.7799 (mp10) REVERT: 7 78 ASP cc_start: 0.9350 (t70) cc_final: 0.9116 (t70) REVERT: 7 81 ASP cc_start: 0.9510 (m-30) cc_final: 0.9106 (m-30) REVERT: 8 47 TRP cc_start: 0.8897 (t60) cc_final: 0.8143 (t60) REVERT: 8 80 MET cc_start: 0.8171 (tmm) cc_final: 0.7742 (tmm) REVERT: 8 89 GLU cc_start: 0.7553 (tt0) cc_final: 0.7344 (tt0) REVERT: 8 100 TYR cc_start: 0.8456 (m-80) cc_final: 0.8198 (m-10) REVERT: A 542 ARG cc_start: 0.9138 (ttp-110) cc_final: 0.8928 (ttp-110) REVERT: A 574 LYS cc_start: 0.9336 (ptpp) cc_final: 0.9064 (pttp) REVERT: A 588 ARG cc_start: 0.9088 (mtt180) cc_final: 0.8611 (ttm110) REVERT: A 589 ASP cc_start: 0.8805 (m-30) cc_final: 0.8499 (m-30) REVERT: A 591 GLN cc_start: 0.9454 (tm-30) cc_final: 0.8874 (tm-30) REVERT: C 45 TRP cc_start: 0.8926 (p90) cc_final: 0.8021 (p90) REVERT: C 83 GLU cc_start: 0.8944 (pt0) cc_final: 0.8438 (pm20) REVERT: C 95 MET cc_start: 0.8967 (pmm) cc_final: 0.8518 (pmm) REVERT: C 104 MET cc_start: 0.9137 (tmm) cc_final: 0.8908 (tmm) REVERT: C 140 ASP cc_start: 0.8167 (m-30) cc_final: 0.7550 (t0) REVERT: C 161 MET cc_start: 0.9245 (tpp) cc_final: 0.8606 (tpp) REVERT: C 425 ASN cc_start: 0.8957 (t0) cc_final: 0.8613 (t0) REVERT: C 479 TRP cc_start: 0.9402 (m100) cc_final: 0.9081 (m100) REVERT: C 492 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8339 (mp0) REVERT: D 530 MET cc_start: 0.7903 (mmm) cc_final: 0.7585 (mmt) REVERT: D 632 ASP cc_start: 0.8876 (t70) cc_final: 0.8647 (t70) REVERT: D 655 LYS cc_start: 0.9065 (pttp) cc_final: 0.8715 (mmmt) REVERT: H 55 GLU cc_start: 0.5695 (mm-30) cc_final: 0.5088 (mm-30) REVERT: L 4 MET cc_start: 0.5141 (mmm) cc_final: 0.4469 (mtp) REVERT: L 92 PHE cc_start: 0.8223 (t80) cc_final: 0.7932 (t80) REVERT: M 100 MET cc_start: 0.7160 (mmm) cc_final: 0.6900 (mmm) REVERT: M 105 THR cc_start: 0.8010 (m) cc_final: 0.7683 (p) REVERT: Q 52 LYS cc_start: 0.9275 (mtmm) cc_final: 0.8731 (mtmm) REVERT: Q 76 ASP cc_start: 0.8819 (m-30) cc_final: 0.8250 (m-30) REVERT: Q 80 MET cc_start: 0.8539 (tmm) cc_final: 0.7629 (tmm) REVERT: Q 82 PHE cc_start: 0.8433 (t80) cc_final: 0.8056 (t80) REVERT: Q 89 GLU cc_start: 0.6757 (tm-30) cc_final: 0.6351 (tm-30) REVERT: R 32 MET cc_start: 0.9154 (tpt) cc_final: 0.8889 (tpt) REVERT: R 77 LEU cc_start: 0.9182 (mt) cc_final: 0.8936 (tp) REVERT: c 83 GLU cc_start: 0.8887 (pt0) cc_final: 0.8361 (pm20) REVERT: c 97 LYS cc_start: 0.9406 (mmtt) cc_final: 0.9113 (mmmm) REVERT: c 123 THR cc_start: 0.9293 (p) cc_final: 0.8855 (t) REVERT: c 321 ASP cc_start: 0.8658 (t0) cc_final: 0.8224 (t0) REVERT: c 370 GLU cc_start: 0.7793 (pm20) cc_final: 0.7426 (pm20) REVERT: c 425 ASN cc_start: 0.8773 (t0) cc_final: 0.8361 (t0) REVERT: c 492 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8363 (mp0) REVERT: d 530 MET cc_start: 0.7842 (mmp) cc_final: 0.7500 (mmp) REVERT: d 586 TYR cc_start: 0.9480 (t80) cc_final: 0.9279 (t80) REVERT: d 588 ARG cc_start: 0.9024 (mtt180) cc_final: 0.8747 (ttm-80) REVERT: d 589 ASP cc_start: 0.8843 (m-30) cc_final: 0.8555 (m-30) REVERT: d 591 GLN cc_start: 0.9443 (tm-30) cc_final: 0.9066 (tm-30) REVERT: d 626 MET cc_start: 0.8589 (mtt) cc_final: 0.8360 (mtt) REVERT: l 4 MET cc_start: 0.3438 (mmt) cc_final: 0.2974 (mtt) REVERT: m 100 LYS cc_start: 0.9370 (mmmm) cc_final: 0.8692 (tmtt) REVERT: m 100 GLU cc_start: 0.8082 (pt0) cc_final: 0.7400 (pt0) REVERT: m 100 MET cc_start: 0.7235 (mmm) cc_final: 0.6993 (mmm) REVERT: q 28 ASN cc_start: 0.8882 (t0) cc_final: 0.8438 (t0) REVERT: q 52 LYS cc_start: 0.9243 (mtmm) cc_final: 0.8642 (mtmm) REVERT: q 76 ASP cc_start: 0.8611 (m-30) cc_final: 0.8378 (m-30) REVERT: r 11 LEU cc_start: 0.9271 (tp) cc_final: 0.9008 (tt) REVERT: r 32 MET cc_start: 0.9020 (tpt) cc_final: 0.8788 (tpt) REVERT: r 78 ASP cc_start: 0.9360 (t70) cc_final: 0.9030 (t70) REVERT: r 81 ASP cc_start: 0.9533 (m-30) cc_final: 0.9307 (m-30) outliers start: 3 outliers final: 2 residues processed: 504 average time/residue: 0.4612 time to fit residues: 361.8386 Evaluate side-chains 386 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 384 time to evaluate : 3.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 206 optimal weight: 0.5980 chunk 264 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 305 optimal weight: 4.9990 chunk 202 optimal weight: 20.0000 chunk 361 optimal weight: 4.9990 chunk 226 optimal weight: 6.9990 chunk 220 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 374 HIS ** 5 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN ** D 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 374 HIS ** d 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 55 GLN ** l 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 32598 Z= 0.230 Angle : 0.653 13.628 44292 Z= 0.324 Chirality : 0.045 0.218 5322 Planarity : 0.005 0.076 5454 Dihedral : 8.070 63.389 6945 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.18 (0.14), residues: 3786 helix: 1.06 (0.27), residues: 402 sheet: -0.54 (0.14), residues: 1305 loop : -1.32 (0.14), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 36 HIS 0.003 0.001 HIS c 85 PHE 0.021 0.002 PHE q 100D TYR 0.020 0.001 TYR q 32 ARG 0.012 0.001 ARG q 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 489 time to evaluate : 3.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 52 LEU cc_start: 0.9449 (mt) cc_final: 0.9199 (mm) REVERT: 2 83 GLU cc_start: 0.8854 (pt0) cc_final: 0.8322 (pm20) REVERT: 2 95 MET cc_start: 0.8773 (pmm) cc_final: 0.8474 (pmm) REVERT: 2 100 MET cc_start: 0.9421 (ptt) cc_final: 0.8904 (ptp) REVERT: 2 119 CYS cc_start: 0.6495 (m) cc_final: 0.6168 (m) REVERT: 2 140 ASP cc_start: 0.7803 (m-30) cc_final: 0.7209 (t0) REVERT: 2 425 ASN cc_start: 0.8845 (t0) cc_final: 0.8360 (t0) REVERT: 2 492 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8480 (mm-30) REVERT: 3 23 GLU cc_start: 0.9176 (tp30) cc_final: 0.8964 (tp30) REVERT: 3 51 MET cc_start: 0.1653 (ttp) cc_final: 0.0658 (ttm) REVERT: 3 71 LYS cc_start: 0.5629 (mtmm) cc_final: 0.3996 (mtmt) REVERT: 5 82 LEU cc_start: 0.9234 (tt) cc_final: 0.8571 (mp) REVERT: 5 100 LYS cc_start: 0.9486 (mmmm) cc_final: 0.8315 (tmtt) REVERT: 5 103 LYS cc_start: 0.8898 (mmmt) cc_final: 0.8385 (mmtm) REVERT: 7 27 GLN cc_start: 0.8061 (mp10) cc_final: 0.7777 (mp10) REVERT: 7 78 ASP cc_start: 0.9356 (t70) cc_final: 0.9118 (t70) REVERT: 7 81 ASP cc_start: 0.9510 (m-30) cc_final: 0.9101 (m-30) REVERT: 8 72 GLN cc_start: 0.9331 (tt0) cc_final: 0.9038 (tp40) REVERT: 8 80 MET cc_start: 0.8168 (tmm) cc_final: 0.7763 (tmm) REVERT: 8 89 GLU cc_start: 0.7544 (tt0) cc_final: 0.7329 (tt0) REVERT: 8 100 TYR cc_start: 0.8457 (m-80) cc_final: 0.8169 (m-10) REVERT: A 542 ARG cc_start: 0.9159 (ttp-110) cc_final: 0.8880 (ttp-110) REVERT: A 574 LYS cc_start: 0.9326 (ptpp) cc_final: 0.9048 (pttp) REVERT: A 588 ARG cc_start: 0.9083 (mtt180) cc_final: 0.8583 (ttm110) REVERT: A 589 ASP cc_start: 0.8799 (m-30) cc_final: 0.8532 (m-30) REVERT: A 632 ASP cc_start: 0.8956 (t70) cc_final: 0.8652 (t70) REVERT: C 45 TRP cc_start: 0.8956 (p90) cc_final: 0.8002 (p90) REVERT: C 83 GLU cc_start: 0.8890 (pt0) cc_final: 0.8644 (mp0) REVERT: C 95 MET cc_start: 0.8937 (pmm) cc_final: 0.8488 (pmm) REVERT: C 104 MET cc_start: 0.9193 (tmm) cc_final: 0.8799 (tmm) REVERT: C 140 ASP cc_start: 0.8265 (m-30) cc_final: 0.7647 (t0) REVERT: C 161 MET cc_start: 0.9313 (tpp) cc_final: 0.8647 (tpp) REVERT: C 425 ASN cc_start: 0.8913 (t0) cc_final: 0.8631 (t0) REVERT: C 492 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8314 (mp0) REVERT: D 530 MET cc_start: 0.7976 (mmm) cc_final: 0.7664 (mmm) REVERT: D 632 ASP cc_start: 0.8910 (t70) cc_final: 0.8644 (t70) REVERT: D 633 LYS cc_start: 0.9293 (mmmm) cc_final: 0.8819 (mmtm) REVERT: D 655 LYS cc_start: 0.9094 (pttp) cc_final: 0.8721 (mmmt) REVERT: H 55 GLU cc_start: 0.5311 (mm-30) cc_final: 0.4821 (mm-30) REVERT: L 4 MET cc_start: 0.5036 (mmm) cc_final: 0.4366 (mtp) REVERT: L 92 PHE cc_start: 0.8275 (t80) cc_final: 0.7939 (t80) REVERT: M 100 LYS cc_start: 0.9450 (mmmm) cc_final: 0.8855 (tmtt) REVERT: M 100 MET cc_start: 0.7143 (mmm) cc_final: 0.6884 (mmm) REVERT: M 105 THR cc_start: 0.8110 (m) cc_final: 0.7760 (p) REVERT: Q 52 LYS cc_start: 0.9359 (mtmm) cc_final: 0.8692 (mtmm) REVERT: Q 76 ASP cc_start: 0.8842 (m-30) cc_final: 0.8256 (m-30) REVERT: Q 82 PHE cc_start: 0.8518 (t80) cc_final: 0.8095 (t80) REVERT: Q 89 GLU cc_start: 0.6700 (tm-30) cc_final: 0.6303 (tm-30) REVERT: R 32 MET cc_start: 0.9131 (tpt) cc_final: 0.8878 (tpt) REVERT: R 53 ARG cc_start: 0.8995 (mpp80) cc_final: 0.8752 (mpp80) REVERT: R 78 ASP cc_start: 0.9295 (t70) cc_final: 0.8938 (t70) REVERT: c 83 GLU cc_start: 0.8869 (pt0) cc_final: 0.8350 (pm20) REVERT: c 97 LYS cc_start: 0.9411 (mmtt) cc_final: 0.9126 (mmmm) REVERT: c 123 THR cc_start: 0.9306 (p) cc_final: 0.8887 (t) REVERT: c 321 ASP cc_start: 0.8705 (t0) cc_final: 0.8260 (t0) REVERT: c 425 ASN cc_start: 0.8899 (t0) cc_final: 0.8464 (t0) REVERT: c 492 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8359 (mp0) REVERT: d 530 MET cc_start: 0.7851 (mmp) cc_final: 0.7575 (mmp) REVERT: d 586 TYR cc_start: 0.9498 (t80) cc_final: 0.9242 (t80) REVERT: d 588 ARG cc_start: 0.9057 (mtt180) cc_final: 0.8733 (ttm-80) REVERT: d 589 ASP cc_start: 0.8866 (m-30) cc_final: 0.8593 (m-30) REVERT: d 632 ASP cc_start: 0.8750 (t70) cc_final: 0.8544 (t70) REVERT: d 655 LYS cc_start: 0.9490 (mmmm) cc_final: 0.9111 (pttp) REVERT: h 55 GLU cc_start: 0.5386 (mm-30) cc_final: 0.5132 (mm-30) REVERT: l 4 MET cc_start: 0.3565 (mmt) cc_final: 0.3191 (mtp) REVERT: m 100 LYS cc_start: 0.9381 (mmmm) cc_final: 0.8712 (tmtt) REVERT: m 100 GLU cc_start: 0.8120 (pt0) cc_final: 0.7469 (pt0) REVERT: m 100 MET cc_start: 0.7226 (mmm) cc_final: 0.6950 (mmm) REVERT: n 25 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8738 (mm-30) REVERT: q 28 ASN cc_start: 0.8920 (t0) cc_final: 0.8614 (t0) REVERT: q 52 LYS cc_start: 0.9279 (mtmm) cc_final: 0.8684 (mtmm) REVERT: q 73 LEU cc_start: 0.8903 (mt) cc_final: 0.8608 (mt) REVERT: q 76 ASP cc_start: 0.8656 (m-30) cc_final: 0.8416 (m-30) REVERT: r 11 LEU cc_start: 0.9270 (tp) cc_final: 0.9000 (mt) REVERT: r 78 ASP cc_start: 0.9388 (t70) cc_final: 0.8997 (t70) REVERT: r 81 ASP cc_start: 0.9547 (m-30) cc_final: 0.9303 (m-30) outliers start: 0 outliers final: 0 residues processed: 489 average time/residue: 0.4573 time to fit residues: 351.1366 Evaluate side-chains 371 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 3.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 229 optimal weight: 3.9990 chunk 246 optimal weight: 8.9990 chunk 178 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 284 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 374 HIS ** 5 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 97 HIS 7 30 ASN ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 30 ASN ** c 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 374 HIS ** d 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.090 32598 Z= 0.615 Angle : 0.959 15.406 44292 Z= 0.472 Chirality : 0.053 0.297 5322 Planarity : 0.006 0.091 5454 Dihedral : 9.548 62.026 6945 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 28.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.96 (0.13), residues: 3786 helix: -0.31 (0.25), residues: 420 sheet: -1.02 (0.14), residues: 1272 loop : -1.69 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP M 36 HIS 0.018 0.002 HIS 2 374 PHE 0.029 0.003 PHE A 519 TYR 0.036 0.003 TYR q 32 ARG 0.011 0.001 ARG 8 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 419 time to evaluate : 3.546 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: 2 52 LEU cc_start: 0.9534 (mt) cc_final: 0.9310 (mm) REVERT: 2 83 GLU cc_start: 0.8883 (pt0) cc_final: 0.8396 (pm20) REVERT: 2 95 MET cc_start: 0.8957 (pmm) cc_final: 0.8667 (pmm) REVERT: 2 100 MET cc_start: 0.9537 (ptt) cc_final: 0.9330 (ptt) REVERT: 2 119 CYS cc_start: 0.6211 (m) cc_final: 0.5818 (m) REVERT: 2 140 ASP cc_start: 0.8126 (m-30) cc_final: 0.7561 (t0) REVERT: 2 321 ASP cc_start: 0.8933 (t0) cc_final: 0.8606 (t0) REVERT: 2 492 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8581 (mp0) REVERT: 3 51 MET cc_start: 0.1950 (ttp) cc_final: 0.1668 (ttm) REVERT: 3 71 LYS cc_start: 0.5629 (mtmm) cc_final: 0.5212 (mtpt) REVERT: 7 27 GLN cc_start: 0.8097 (mp10) cc_final: 0.7838 (mp10) REVERT: 7 49 ASP cc_start: 0.8559 (t0) cc_final: 0.8316 (t0) REVERT: 7 78 ASP cc_start: 0.9379 (t70) cc_final: 0.9076 (t70) REVERT: 7 81 ASP cc_start: 0.9430 (m-30) cc_final: 0.8987 (m-30) REVERT: 8 80 MET cc_start: 0.8307 (tmm) cc_final: 0.7865 (tmm) REVERT: 8 89 GLU cc_start: 0.7529 (tt0) cc_final: 0.7234 (tt0) REVERT: A 574 LYS cc_start: 0.9334 (ptpp) cc_final: 0.9096 (ptpt) REVERT: A 588 ARG cc_start: 0.9148 (mtt180) cc_final: 0.8619 (ttm110) REVERT: A 632 ASP cc_start: 0.9196 (t70) cc_final: 0.8925 (t70) REVERT: A 647 GLU cc_start: 0.8846 (mp0) cc_final: 0.8587 (mp0) REVERT: A 655 LYS cc_start: 0.9135 (pttm) cc_final: 0.8708 (mmmt) REVERT: C 45 TRP cc_start: 0.9178 (p90) cc_final: 0.8182 (p90) REVERT: C 83 GLU cc_start: 0.8893 (pt0) cc_final: 0.8688 (mp0) REVERT: C 95 MET cc_start: 0.8989 (pmm) cc_final: 0.8694 (pmm) REVERT: C 140 ASP cc_start: 0.8409 (m-30) cc_final: 0.7928 (t0) REVERT: C 161 MET cc_start: 0.9350 (tpp) cc_final: 0.8545 (tpp) REVERT: C 492 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8610 (mp0) REVERT: D 603 ILE cc_start: 0.9618 (mm) cc_final: 0.9180 (tt) REVERT: H 55 GLU cc_start: 0.5100 (mm-30) cc_final: 0.4761 (mm-30) REVERT: L 4 MET cc_start: 0.5227 (mmm) cc_final: 0.4759 (mtp) REVERT: L 32 ASP cc_start: 0.6760 (m-30) cc_final: 0.6484 (m-30) REVERT: L 92 PHE cc_start: 0.8254 (t80) cc_final: 0.8002 (t80) REVERT: M 100 LYS cc_start: 0.9460 (mmmm) cc_final: 0.8572 (tmtt) REVERT: M 100 MET cc_start: 0.7515 (mmm) cc_final: 0.7099 (mmm) REVERT: M 103 LYS cc_start: 0.8714 (mmmt) cc_final: 0.8129 (mmtm) REVERT: Q 28 ASN cc_start: 0.8593 (t0) cc_final: 0.8339 (t0) REVERT: Q 52 LYS cc_start: 0.9405 (mtmm) cc_final: 0.8942 (mtmm) REVERT: Q 76 ASP cc_start: 0.8923 (m-30) cc_final: 0.8220 (m-30) REVERT: Q 100 ASP cc_start: 0.7642 (t70) cc_final: 0.7343 (t0) REVERT: R 78 ASP cc_start: 0.9167 (t70) cc_final: 0.8858 (t70) REVERT: c 83 GLU cc_start: 0.8926 (pt0) cc_final: 0.8360 (pm20) REVERT: c 95 MET cc_start: 0.9157 (ptp) cc_final: 0.8864 (pmm) REVERT: c 104 MET cc_start: 0.9010 (tmm) cc_final: 0.8654 (tmm) REVERT: c 123 THR cc_start: 0.9552 (p) cc_final: 0.9227 (t) REVERT: c 140 ASP cc_start: 0.8020 (m-30) cc_final: 0.7494 (t70) REVERT: c 492 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8434 (mp0) REVERT: d 530 MET cc_start: 0.8167 (mmp) cc_final: 0.7954 (mmp) REVERT: d 574 LYS cc_start: 0.9555 (pttt) cc_final: 0.9258 (ptpt) REVERT: d 588 ARG cc_start: 0.9119 (mtt180) cc_final: 0.8786 (ttm-80) REVERT: d 589 ASP cc_start: 0.8996 (m-30) cc_final: 0.8729 (m-30) REVERT: d 632 ASP cc_start: 0.9046 (t70) cc_final: 0.8834 (t70) REVERT: m 100 LYS cc_start: 0.9420 (mmmm) cc_final: 0.8564 (tmtt) REVERT: m 100 GLU cc_start: 0.8470 (pt0) cc_final: 0.7743 (pt0) REVERT: m 100 MET cc_start: 0.7616 (mmm) cc_final: 0.7058 (mmm) REVERT: m 103 LYS cc_start: 0.8832 (mmmt) cc_final: 0.8320 (mmtm) REVERT: n 25 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8853 (mm-30) REVERT: q 28 ASN cc_start: 0.9045 (t0) cc_final: 0.8776 (t0) REVERT: q 52 LYS cc_start: 0.9335 (mtmm) cc_final: 0.8740 (mtmm) REVERT: q 72 GLN cc_start: 0.9128 (tp40) cc_final: 0.8875 (tp40) REVERT: q 73 LEU cc_start: 0.9155 (mt) cc_final: 0.8685 (mt) REVERT: q 76 ASP cc_start: 0.8715 (m-30) cc_final: 0.8194 (m-30) REVERT: r 78 ASP cc_start: 0.9326 (t70) cc_final: 0.8989 (t70) REVERT: r 81 ASP cc_start: 0.9463 (m-30) cc_final: 0.9046 (m-30) outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.4734 time to fit residues: 309.5581 Evaluate side-chains 337 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 3.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 9.9990 chunk 346 optimal weight: 0.9990 chunk 315 optimal weight: 6.9990 chunk 336 optimal weight: 1.9990 chunk 202 optimal weight: 20.0000 chunk 146 optimal weight: 0.9990 chunk 264 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 304 optimal weight: 0.6980 chunk 318 optimal weight: 0.8980 chunk 335 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 377 ASN ** d 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.5423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 32598 Z= 0.218 Angle : 0.715 14.328 44292 Z= 0.356 Chirality : 0.047 0.346 5322 Planarity : 0.005 0.158 5454 Dihedral : 8.490 61.966 6945 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.03 % Allowed : 0.60 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.51 (0.13), residues: 3786 helix: 0.38 (0.26), residues: 420 sheet: -0.74 (0.14), residues: 1269 loop : -1.46 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP 2 427 HIS 0.005 0.001 HIS N 89 PHE 0.028 0.002 PHE 8 100D TYR 0.036 0.002 TYR A 643 ARG 0.013 0.001 ARG 8 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 464 time to evaluate : 3.941 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: 2 52 LEU cc_start: 0.9414 (mt) cc_final: 0.9133 (mm) REVERT: 2 83 GLU cc_start: 0.8846 (pt0) cc_final: 0.8342 (pm20) REVERT: 2 95 MET cc_start: 0.9040 (pmm) cc_final: 0.8659 (pmm) REVERT: 2 100 MET cc_start: 0.9110 (ptt) cc_final: 0.8290 (ppp) REVERT: 2 119 CYS cc_start: 0.6071 (m) cc_final: 0.5649 (m) REVERT: 2 140 ASP cc_start: 0.7955 (m-30) cc_final: 0.7348 (t0) REVERT: 2 425 ASN cc_start: 0.8770 (t0) cc_final: 0.8280 (t0) REVERT: 2 492 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8312 (mp0) REVERT: 3 23 GLU cc_start: 0.9207 (tp30) cc_final: 0.8995 (tp30) REVERT: 3 51 MET cc_start: 0.1732 (ttp) cc_final: 0.1083 (ttm) REVERT: 3 55 GLU cc_start: 0.5676 (mm-30) cc_final: 0.5460 (mm-30) REVERT: 5 82 LEU cc_start: 0.9211 (tt) cc_final: 0.8595 (mp) REVERT: 5 100 LYS cc_start: 0.9528 (mmmm) cc_final: 0.9113 (tppt) REVERT: 7 27 GLN cc_start: 0.7995 (mp10) cc_final: 0.7751 (mp10) REVERT: 7 49 ASP cc_start: 0.8365 (t0) cc_final: 0.8096 (t0) REVERT: 7 78 ASP cc_start: 0.9376 (t70) cc_final: 0.9140 (t70) REVERT: 7 81 ASP cc_start: 0.9460 (m-30) cc_final: 0.9089 (m-30) REVERT: 8 80 MET cc_start: 0.8325 (tmm) cc_final: 0.7922 (tmm) REVERT: 8 89 GLU cc_start: 0.7470 (tt0) cc_final: 0.7191 (tt0) REVERT: 8 100 TYR cc_start: 0.8560 (m-80) cc_final: 0.8216 (m-10) REVERT: 8 100 PHE cc_start: 0.8137 (m-10) cc_final: 0.7711 (m-10) REVERT: A 542 ARG cc_start: 0.9351 (ttp-110) cc_final: 0.9016 (ttp-110) REVERT: A 588 ARG cc_start: 0.9109 (mtt180) cc_final: 0.8579 (ttm110) REVERT: A 632 ASP cc_start: 0.9049 (t70) cc_final: 0.8829 (t70) REVERT: A 655 LYS cc_start: 0.9134 (pttm) cc_final: 0.8764 (mmmt) REVERT: C 39 TYR cc_start: 0.9266 (m-10) cc_final: 0.9058 (m-80) REVERT: C 45 TRP cc_start: 0.8950 (p90) cc_final: 0.8105 (p90) REVERT: C 83 GLU cc_start: 0.8874 (pt0) cc_final: 0.8654 (mp0) REVERT: C 95 MET cc_start: 0.9035 (pmm) cc_final: 0.8623 (pmm) REVERT: C 140 ASP cc_start: 0.8262 (m-30) cc_final: 0.7705 (t0) REVERT: C 161 MET cc_start: 0.9338 (tpp) cc_final: 0.8769 (tpp) REVERT: C 280 ASN cc_start: 0.9107 (p0) cc_final: 0.8779 (p0) REVERT: C 425 ASN cc_start: 0.8954 (t0) cc_final: 0.8610 (t0) REVERT: C 492 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8348 (mp0) REVERT: D 632 ASP cc_start: 0.8923 (t70) cc_final: 0.8685 (t70) REVERT: D 633 LYS cc_start: 0.9323 (mmmm) cc_final: 0.8740 (mmtm) REVERT: D 655 LYS cc_start: 0.9032 (pttp) cc_final: 0.8531 (mmmt) REVERT: H 55 GLU cc_start: 0.4837 (mm-30) cc_final: 0.4533 (mm-30) REVERT: L 4 MET cc_start: 0.5302 (mmm) cc_final: 0.4651 (mtp) REVERT: L 32 ASP cc_start: 0.6664 (m-30) cc_final: 0.6379 (m-30) REVERT: L 92 PHE cc_start: 0.8276 (t80) cc_final: 0.8007 (t80) REVERT: M 100 LYS cc_start: 0.9462 (mmmm) cc_final: 0.8663 (tmtt) REVERT: M 100 MET cc_start: 0.7311 (mmm) cc_final: 0.6847 (mmm) REVERT: M 103 LYS cc_start: 0.8794 (mmmt) cc_final: 0.8367 (mmtm) REVERT: Q 52 LYS cc_start: 0.9394 (mtmm) cc_final: 0.8664 (mtmm) REVERT: Q 76 ASP cc_start: 0.8879 (m-30) cc_final: 0.8330 (m-30) REVERT: Q 80 MET cc_start: 0.8317 (tmm) cc_final: 0.7611 (tmm) REVERT: R 77 LEU cc_start: 0.9221 (mt) cc_final: 0.8994 (mt) REVERT: R 78 ASP cc_start: 0.9242 (t70) cc_final: 0.8903 (t70) REVERT: R 98 GLU cc_start: 0.8763 (tp30) cc_final: 0.8480 (tp30) REVERT: c 83 GLU cc_start: 0.8878 (pt0) cc_final: 0.8376 (pm20) REVERT: c 97 LYS cc_start: 0.9417 (mttt) cc_final: 0.9058 (mmmm) REVERT: c 104 MET cc_start: 0.8921 (tmm) cc_final: 0.8492 (tmm) REVERT: c 119 CYS cc_start: 0.5853 (m) cc_final: 0.5582 (m) REVERT: c 140 ASP cc_start: 0.7834 (m-30) cc_final: 0.7215 (t70) REVERT: c 321 ASP cc_start: 0.8868 (t0) cc_final: 0.8440 (t0) REVERT: c 425 ASN cc_start: 0.8902 (t0) cc_final: 0.8674 (t0) REVERT: c 434 MET cc_start: 0.8104 (ttm) cc_final: 0.7842 (mtp) REVERT: c 492 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8401 (mp0) REVERT: d 530 MET cc_start: 0.7938 (mmp) cc_final: 0.7600 (mmp) REVERT: d 574 LYS cc_start: 0.9507 (pttt) cc_final: 0.9231 (ptpt) REVERT: d 586 TYR cc_start: 0.9515 (t80) cc_final: 0.9297 (t80) REVERT: d 588 ARG cc_start: 0.9028 (mtt180) cc_final: 0.8772 (ttm170) REVERT: d 589 ASP cc_start: 0.8906 (m-30) cc_final: 0.8622 (m-30) REVERT: d 632 ASP cc_start: 0.8880 (t70) cc_final: 0.8653 (t70) REVERT: d 655 LYS cc_start: 0.9519 (mmmm) cc_final: 0.9100 (pttp) REVERT: m 100 LYS cc_start: 0.9361 (mmmm) cc_final: 0.8586 (tmtt) REVERT: m 100 GLU cc_start: 0.8232 (pt0) cc_final: 0.7605 (pt0) REVERT: m 100 MET cc_start: 0.7442 (mmm) cc_final: 0.6901 (mmm) REVERT: m 103 LYS cc_start: 0.8963 (mmmt) cc_final: 0.8491 (mmtm) REVERT: n 25 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8730 (mm-30) REVERT: q 28 ASN cc_start: 0.9000 (t0) cc_final: 0.8733 (t0) REVERT: q 52 LYS cc_start: 0.9333 (mtmm) cc_final: 0.8695 (mtmm) REVERT: q 76 ASP cc_start: 0.8701 (m-30) cc_final: 0.8286 (m-30) REVERT: r 11 LEU cc_start: 0.8974 (tt) cc_final: 0.8444 (mt) REVERT: r 32 MET cc_start: 0.8659 (tpt) cc_final: 0.8287 (tpt) REVERT: r 78 ASP cc_start: 0.9434 (t70) cc_final: 0.9224 (t70) outliers start: 1 outliers final: 0 residues processed: 465 average time/residue: 0.4729 time to fit residues: 345.1651 Evaluate side-chains 361 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 3.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 0.9990 chunk 356 optimal weight: 4.9990 chunk 217 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 247 optimal weight: 0.9980 chunk 373 optimal weight: 0.6980 chunk 343 optimal weight: 8.9990 chunk 297 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 377 ASN ** d 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 GLN ** m 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 32598 Z= 0.207 Angle : 0.689 20.614 44292 Z= 0.342 Chirality : 0.046 0.236 5322 Planarity : 0.005 0.098 5454 Dihedral : 7.966 59.982 6945 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.06 % Allowed : 0.21 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.30 (0.14), residues: 3786 helix: 0.72 (0.27), residues: 402 sheet: -0.64 (0.14), residues: 1254 loop : -1.31 (0.14), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP 8 100F HIS 0.004 0.001 HIS 2 105 PHE 0.023 0.002 PHE 8 100D TYR 0.034 0.002 TYR h 99 ARG 0.016 0.001 ARG H 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 466 time to evaluate : 3.493 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: 2 52 LEU cc_start: 0.9397 (mt) cc_final: 0.9154 (mm) REVERT: 2 83 GLU cc_start: 0.8850 (pt0) cc_final: 0.8364 (pm20) REVERT: 2 95 MET cc_start: 0.9100 (pmm) cc_final: 0.8645 (pmm) REVERT: 2 100 MET cc_start: 0.9117 (ptt) cc_final: 0.8257 (ppp) REVERT: 2 119 CYS cc_start: 0.6241 (m) cc_final: 0.5814 (m) REVERT: 2 140 ASP cc_start: 0.7908 (m-30) cc_final: 0.7283 (t0) REVERT: 2 492 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8348 (mp0) REVERT: 3 51 MET cc_start: 0.1417 (ttp) cc_final: 0.0731 (ttm) REVERT: 5 82 LEU cc_start: 0.9248 (tt) cc_final: 0.8693 (mp) REVERT: 5 100 LYS cc_start: 0.9503 (mmmm) cc_final: 0.9116 (tppt) REVERT: 7 27 GLN cc_start: 0.7935 (mp10) cc_final: 0.7678 (mp10) REVERT: 7 59 ASP cc_start: 0.9333 (t70) cc_final: 0.9119 (t0) REVERT: 7 78 ASP cc_start: 0.9406 (t70) cc_final: 0.9103 (t70) REVERT: 7 81 ASP cc_start: 0.9436 (m-30) cc_final: 0.9035 (m-30) REVERT: 8 80 MET cc_start: 0.8244 (tmm) cc_final: 0.7941 (tmm) REVERT: 8 89 GLU cc_start: 0.7489 (tt0) cc_final: 0.7237 (tt0) REVERT: 8 100 TYR cc_start: 0.8511 (m-80) cc_final: 0.8282 (m-10) REVERT: A 542 ARG cc_start: 0.9322 (ttp-110) cc_final: 0.8998 (ttp-110) REVERT: A 574 LYS cc_start: 0.9153 (ptpp) cc_final: 0.8823 (pttm) REVERT: A 588 ARG cc_start: 0.9099 (mtt180) cc_final: 0.8559 (ttm110) REVERT: A 626 MET cc_start: 0.8693 (mmm) cc_final: 0.8479 (mmm) REVERT: A 632 ASP cc_start: 0.9084 (t70) cc_final: 0.8847 (t70) REVERT: A 655 LYS cc_start: 0.9111 (pttm) cc_final: 0.8735 (mmmt) REVERT: C 39 TYR cc_start: 0.9327 (m-10) cc_final: 0.9027 (m-80) REVERT: C 45 TRP cc_start: 0.8951 (p90) cc_final: 0.8137 (p90) REVERT: C 95 MET cc_start: 0.9053 (pmm) cc_final: 0.8689 (pmm) REVERT: C 140 ASP cc_start: 0.8233 (m-30) cc_final: 0.7678 (t0) REVERT: C 161 MET cc_start: 0.9344 (tpp) cc_final: 0.8835 (tpp) REVERT: C 425 ASN cc_start: 0.8885 (t0) cc_final: 0.8554 (t0) REVERT: C 479 TRP cc_start: 0.9320 (m100) cc_final: 0.8974 (m100) REVERT: C 492 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8464 (mp0) REVERT: D 632 ASP cc_start: 0.8916 (t70) cc_final: 0.8677 (t70) REVERT: D 633 LYS cc_start: 0.9324 (mmmm) cc_final: 0.8771 (mmtm) REVERT: D 655 LYS cc_start: 0.8971 (pttp) cc_final: 0.8498 (mmmt) REVERT: H 55 GLU cc_start: 0.5390 (mm-30) cc_final: 0.5166 (mm-30) REVERT: L 4 MET cc_start: 0.5070 (mmm) cc_final: 0.4423 (mtp) REVERT: L 32 ASP cc_start: 0.6596 (m-30) cc_final: 0.6384 (m-30) REVERT: L 92 PHE cc_start: 0.8321 (t80) cc_final: 0.8028 (t80) REVERT: M 100 LYS cc_start: 0.9458 (mmmm) cc_final: 0.8638 (tmtt) REVERT: M 100 MET cc_start: 0.7180 (mmm) cc_final: 0.6717 (mmm) REVERT: M 103 LYS cc_start: 0.8912 (mmmt) cc_final: 0.8460 (mmtm) REVERT: Q 52 LYS cc_start: 0.9409 (mtmm) cc_final: 0.8694 (mtmm) REVERT: Q 76 ASP cc_start: 0.8945 (m-30) cc_final: 0.8277 (m-30) REVERT: R 46 LEU cc_start: 0.9639 (mp) cc_final: 0.9414 (mp) REVERT: R 53 ARG cc_start: 0.8817 (mpp80) cc_final: 0.8297 (mtm-85) REVERT: R 77 LEU cc_start: 0.9140 (mt) cc_final: 0.8924 (tp) REVERT: R 98 GLU cc_start: 0.8734 (tp30) cc_final: 0.8395 (tp30) REVERT: c 95 MET cc_start: 0.9079 (pmm) cc_final: 0.8703 (pmm) REVERT: c 97 LYS cc_start: 0.9423 (mttt) cc_final: 0.9111 (mmmm) REVERT: c 100 MET cc_start: 0.9319 (ptp) cc_final: 0.9053 (ptp) REVERT: c 123 THR cc_start: 0.9278 (p) cc_final: 0.8870 (t) REVERT: c 140 ASP cc_start: 0.7809 (m-30) cc_final: 0.7167 (t70) REVERT: c 321 ASP cc_start: 0.8839 (t0) cc_final: 0.8425 (t0) REVERT: c 425 ASN cc_start: 0.8906 (t0) cc_final: 0.8629 (t0) REVERT: c 492 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8390 (mp0) REVERT: d 530 MET cc_start: 0.7855 (mmp) cc_final: 0.7473 (mmp) REVERT: d 586 TYR cc_start: 0.9512 (t80) cc_final: 0.9263 (t80) REVERT: d 588 ARG cc_start: 0.9026 (mtt180) cc_final: 0.8780 (ttm170) REVERT: d 589 ASP cc_start: 0.8880 (m-30) cc_final: 0.8596 (m-30) REVERT: d 632 ASP cc_start: 0.8886 (t70) cc_final: 0.8670 (t70) REVERT: h 4 LEU cc_start: 0.7169 (mt) cc_final: 0.6845 (mt) REVERT: m 100 LYS cc_start: 0.9359 (mmmm) cc_final: 0.8606 (tmtt) REVERT: m 100 GLU cc_start: 0.8201 (pt0) cc_final: 0.7400 (pt0) REVERT: m 100 MET cc_start: 0.7216 (mmm) cc_final: 0.6808 (mmm) REVERT: m 103 LYS cc_start: 0.8966 (mmmt) cc_final: 0.8538 (mmtm) REVERT: n 25 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8725 (mm-30) REVERT: q 28 ASN cc_start: 0.9005 (t0) cc_final: 0.8685 (t0) REVERT: q 30 ARG cc_start: 0.8954 (mtt90) cc_final: 0.8617 (mtt90) REVERT: q 52 LYS cc_start: 0.9338 (mtmm) cc_final: 0.8701 (mtmm) REVERT: q 73 LEU cc_start: 0.8672 (mm) cc_final: 0.8385 (mt) REVERT: q 76 ASP cc_start: 0.8667 (m-30) cc_final: 0.8271 (m-30) REVERT: q 94 ARG cc_start: 0.8355 (ttp80) cc_final: 0.8147 (ttp80) REVERT: r 11 LEU cc_start: 0.8911 (tt) cc_final: 0.8472 (mt) REVERT: r 32 MET cc_start: 0.8616 (tpt) cc_final: 0.8303 (tpt) outliers start: 2 outliers final: 0 residues processed: 468 average time/residue: 0.4717 time to fit residues: 344.5610 Evaluate side-chains 362 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 3.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 236 optimal weight: 0.7980 chunk 316 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 chunk 274 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 297 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 305 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.088048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.061166 restraints weight = 126915.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.063394 restraints weight = 69613.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 78)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.064808 restraints weight = 47237.313| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 32598 Z= 0.249 Angle : 0.695 18.173 44292 Z= 0.348 Chirality : 0.046 0.226 5322 Planarity : 0.005 0.085 5454 Dihedral : 7.953 59.247 6945 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.84 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.14), residues: 3786 helix: 0.80 (0.27), residues: 402 sheet: -0.60 (0.14), residues: 1287 loop : -1.31 (0.14), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP 2 427 HIS 0.003 0.001 HIS c 85 PHE 0.022 0.002 PHE q 100D TYR 0.016 0.002 TYR h 100 ARG 0.014 0.001 ARG H 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7620.85 seconds wall clock time: 137 minutes 11.43 seconds (8231.43 seconds total)