Starting phenix.real_space_refine on Wed Feb 21 06:07:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9j_22750/02_2024/7k9j_22750.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9j_22750/02_2024/7k9j_22750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9j_22750/02_2024/7k9j_22750.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9j_22750/02_2024/7k9j_22750.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9j_22750/02_2024/7k9j_22750.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9j_22750/02_2024/7k9j_22750.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.091 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 117 5.16 5 C 18876 2.51 5 N 4779 2.21 5 O 5994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1139": "OD1" <-> "OD2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 405": "OD1" <-> "OD2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B ASP 614": "OD1" <-> "OD2" Residue "B ARG 646": "NH1" <-> "NH2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1139": "OD1" <-> "OD2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 405": "OD1" <-> "OD2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 574": "OD1" <-> "OD2" Residue "C ASP 614": "OD1" <-> "OD2" Residue "C ARG 646": "NH1" <-> "NH2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 950": "OD1" <-> "OD2" Residue "C ASP 979": "OD1" <-> "OD2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1139": "OD1" <-> "OD2" Residue "H GLU 67": "OE1" <-> "OE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 67": "OE1" <-> "OE2" Residue "I TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 67": "OE1" <-> "OE2" Residue "J TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 45": "NH1" <-> "NH2" Residue "M ARG 45": "NH1" <-> "NH2" Residue "N ARG 45": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29766 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 7680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7680 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 48, 'TRANS': 933} Chain breaks: 8 Chain: "B" Number of atoms: 7680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7680 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 48, 'TRANS': 933} Chain breaks: 8 Chain: "C" Number of atoms: 7680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7680 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 48, 'TRANS': 933} Chain breaks: 8 Chain: "H" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "I" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "J" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "M" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "N" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 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: "K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "O" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "c" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 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: 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: 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 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: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "q" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 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: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 16.01, per 1000 atoms: 0.54 Number of scatterers: 29766 At special positions: 0 Unit cell: (133.1, 147.4, 192.5, 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 117 16.00 O 5994 8.00 N 4779 7.00 C 18876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " BMA S 3 " - " MAN S 4 " " BMA g 3 " - " MAN g 4 " " BMA u 3 " - " MAN u 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " 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 d 1 " - " NAG d 2 " " 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 h 1 " - " NAG h 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 k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " BETA1-6 " NAG K 1 " - " FUC K 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG O 1 " - " FUC O 2 " " NAG b 1 " - " FUC b 4 " " NAG c 1 " - " FUC c 2 " " NAG p 1 " - " FUC p 4 " " NAG q 1 " - " FUC q 2 " NAG-ASN " NAG A1300 " - " ASN A 61 " " NAG B1300 " - " ASN B 61 " " NAG C1300 " - " ASN C 61 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A 331 " " NAG K 1 " - " ASN A 343 " " NAG O 1 " - " ASN A 603 " " NAG P 1 " - " ASN A 616 " " NAG Q 1 " - " ASN A 657 " " NAG R 1 " - " ASN A 709 " " NAG S 1 " - " ASN A 717 " " NAG T 1 " - " ASN A 801 " " NAG U 1 " - " ASN A1074 " " NAG V 1 " - " ASN A1098 " " NAG W 1 " - " ASN A1134 " " NAG X 1 " - " ASN B 165 " " NAG Y 1 " - " ASN B 234 " " NAG Z 1 " - " ASN B 282 " " NAG a 1 " - " ASN B 331 " " NAG b 1 " - " ASN B 343 " " NAG c 1 " - " ASN B 603 " " NAG d 1 " - " ASN B 616 " " NAG e 1 " - " ASN B 657 " " NAG f 1 " - " ASN B 709 " " NAG g 1 " - " ASN B 717 " " NAG h 1 " - " ASN B 801 " " NAG i 1 " - " ASN B1074 " " NAG j 1 " - " ASN B1098 " " NAG k 1 " - " ASN B1134 " " NAG l 1 " - " ASN C 165 " " NAG m 1 " - " ASN C 234 " " NAG n 1 " - " ASN C 282 " " NAG o 1 " - " ASN C 331 " " NAG p 1 " - " ASN C 343 " " NAG q 1 " - " ASN C 603 " " NAG r 1 " - " ASN C 616 " " NAG s 1 " - " ASN C 657 " " NAG t 1 " - " ASN C 709 " " NAG u 1 " - " ASN C 717 " " NAG v 1 " - " ASN C 801 " " NAG w 1 " - " ASN C1074 " " NAG x 1 " - " ASN C1098 " " NAG y 1 " - " ASN C1134 " Time building additional restraints: 12.98 Conformation dependent library (CDL) restraints added in 5.3 seconds 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6774 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 66 sheets defined 22.5% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.669A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.836A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.442A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.694A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.888A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.919A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.696A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.555A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.537A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.019A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.769A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.605A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.180A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.669A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.836A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.443A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.694A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.888A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.920A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.696A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.555A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.536A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.018A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.768A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.605A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.181A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.669A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.836A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.442A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.693A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 759 through 783 removed outlier: 3.889A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.920A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.695A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.555A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.536A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.019A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.768A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.606A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.180A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'N' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.783A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 52 removed outlier: 7.201A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.686A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 121 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.204A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 595 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.078A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR A 430 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.593A pdb=" N CYS A 525 " --> pdb=" O CYS A 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.544A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 7.014A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.553A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.553A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.606A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.939A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.783A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 52 removed outlier: 7.201A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.685A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 118 through 121 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.204A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 595 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.078A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 3.593A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.544A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.981A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.553A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.553A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.606A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.938A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.784A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 52 removed outlier: 7.200A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.686A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE2, first strand: chain 'C' and resid 118 through 121 Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.203A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 595 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.079A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ASN C 437 " --> pdb=" O PHE C 374 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE C 374 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 3.593A pdb=" N CYS C 525 " --> pdb=" O CYS C 361 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.543A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.553A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.553A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.606A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.938A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF5, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.082A pdb=" N VAL H 12 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE H 34 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS H 59 " --> pdb=" O ASP H 50 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.082A pdb=" N VAL H 12 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR H 109 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AF8, first strand: chain 'I' and resid 11 through 12 removed outlier: 4.081A pdb=" N VAL I 12 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE I 34 " --> pdb=" O ASP I 50 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS I 59 " --> pdb=" O ASP I 50 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 11 through 12 removed outlier: 4.081A pdb=" N VAL I 12 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR I 109 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AG2, first strand: chain 'J' and resid 11 through 12 removed outlier: 4.081A pdb=" N VAL J 12 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE J 34 " --> pdb=" O ASP J 50 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASP J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS J 59 " --> pdb=" O ASP J 50 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 11 through 12 removed outlier: 4.081A pdb=" N VAL J 12 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR J 109 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.961A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER L 63 " --> pdb=" O SER L 74 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.537A pdb=" N LEU L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'L' and resid 44 through 48 removed outlier: 3.512A pdb=" N ARG L 45 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN L 37 " --> pdb=" O ARG L 45 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR L 36 " --> pdb=" O TYR L 87 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 5 through 6 removed outlier: 3.961A pdb=" N VAL M 19 " --> pdb=" O ILE M 75 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER M 63 " --> pdb=" O SER M 74 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.537A pdb=" N LEU M 11 " --> pdb=" O LYS M 103 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU M 105 " --> pdb=" O LEU M 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'M' and resid 44 through 48 removed outlier: 3.511A pdb=" N ARG M 45 " --> pdb=" O GLN M 37 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN M 37 " --> pdb=" O ARG M 45 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR M 36 " --> pdb=" O TYR M 87 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 5 through 6 removed outlier: 3.961A pdb=" N VAL N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER N 63 " --> pdb=" O SER N 74 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.536A pdb=" N LEU N 11 " --> pdb=" O LYS N 103 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU N 105 " --> pdb=" O LEU N 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'N' and resid 44 through 48 removed outlier: 3.511A pdb=" N ARG N 45 " --> pdb=" O GLN N 37 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN N 37 " --> pdb=" O ARG N 45 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR N 36 " --> pdb=" O TYR N 87 " (cutoff:3.500A) 1093 hydrogen bonds defined for protein. 2943 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: 13.75 Time building geometry restraints manager: 13.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4774 1.32 - 1.45: 8759 1.45 - 1.57: 16725 1.57 - 1.70: 3 1.70 - 1.82: 147 Bond restraints: 30408 Sorted by residual: bond pdb=" C PHE A 377 " pdb=" O PHE A 377 " ideal model delta sigma weight residual 1.236 1.194 0.042 1.14e-02 7.69e+03 1.37e+01 bond pdb=" C PRO B 384 " pdb=" O PRO B 384 " ideal model delta sigma weight residual 1.238 1.194 0.044 1.33e-02 5.65e+03 1.11e+01 bond pdb=" C1 NAG X 2 " pdb=" O5 NAG X 2 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C1 NAG l 2 " pdb=" O5 NAG l 2 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.09e+01 ... (remaining 30403 not shown) Histogram of bond angle deviations from ideal: 100.02 - 106.85: 928 106.85 - 113.68: 17360 113.68 - 120.50: 11268 120.50 - 127.33: 11563 127.33 - 134.15: 242 Bond angle restraints: 41361 Sorted by residual: angle pdb=" CA ALA C 520 " pdb=" C ALA C 520 " pdb=" N PRO C 521 " ideal model delta sigma weight residual 117.96 122.84 -4.88 8.10e-01 1.52e+00 3.63e+01 angle pdb=" CA ALA B 520 " pdb=" C ALA B 520 " pdb=" N PRO B 521 " ideal model delta sigma weight residual 117.96 122.64 -4.68 8.10e-01 1.52e+00 3.34e+01 angle pdb=" N ALA C 520 " pdb=" CA ALA C 520 " pdb=" C ALA C 520 " ideal model delta sigma weight residual 108.22 103.06 5.16 9.00e-01 1.23e+00 3.29e+01 angle pdb=" CA ALA A 520 " pdb=" C ALA A 520 " pdb=" N PRO A 521 " ideal model delta sigma weight residual 117.96 122.47 -4.51 8.10e-01 1.52e+00 3.10e+01 angle pdb=" N ILE C 434 " pdb=" CA ILE C 434 " pdb=" CB ILE C 434 " ideal model delta sigma weight residual 111.90 105.73 6.17 1.26e+00 6.30e-01 2.40e+01 ... (remaining 41356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.69: 17874 22.69 - 45.39: 960 45.39 - 68.08: 249 68.08 - 90.77: 192 90.77 - 113.46: 186 Dihedral angle restraints: 19461 sinusoidal: 8928 harmonic: 10533 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -176.00 90.00 1 1.00e+01 1.00e-02 9.60e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -175.99 89.99 1 1.00e+01 1.00e-02 9.60e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -175.96 89.96 1 1.00e+01 1.00e-02 9.59e+01 ... (remaining 19458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 4494 0.090 - 0.180: 467 0.180 - 0.270: 32 0.270 - 0.360: 19 0.360 - 0.451: 10 Chirality restraints: 5022 Sorted by residual: chirality pdb=" C1 NAG A1300 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1300 " pdb=" O5 NAG A1300 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" C1 NAG B1300 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1300 " pdb=" O5 NAG B1300 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" C1 NAG C1300 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1300 " pdb=" O5 NAG C1300 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 4.99e+00 ... (remaining 5019 not shown) Planarity restraints: 5202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 81 " -0.055 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO C 82 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO C 82 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 82 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 81 " 0.055 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO A 82 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 81 " -0.055 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO B 82 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " -0.046 5.00e-02 4.00e+02 ... (remaining 5199 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 526 2.65 - 3.21: 27487 3.21 - 3.77: 43017 3.77 - 4.34: 61555 4.34 - 4.90: 100880 Nonbonded interactions: 233465 Sorted by model distance: nonbonded pdb=" O ARG J 105 " pdb=" NE2 HIS N 34 " model vdw 2.084 2.520 nonbonded pdb=" OG1 THR A 29 " pdb=" OD2 ASP A 215 " model vdw 2.154 2.440 nonbonded pdb=" OG1 THR B 29 " pdb=" OD2 ASP B 215 " model vdw 2.154 2.440 nonbonded pdb=" OG1 THR C 29 " pdb=" OD2 ASP C 215 " model vdw 2.155 2.440 nonbonded pdb=" OD1 ASP I 90 " pdb=" OH TYR I 94 " model vdw 2.162 2.440 ... (remaining 233460 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'x' selection = chain 'y' } ncs_group { reference = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'e' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'h' and resid 1) selection = (chain 'i' and resid 1) selection = (chain 'n' and resid 1) selection = (chain 'o' and resid 1) selection = (chain 'q' and resid 1) selection = (chain 'r' and resid 1) selection = (chain 's' and resid 1) selection = (chain 't' and resid 1) selection = (chain 'v' and resid 1) selection = (chain 'w' and resid 1) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'K' and resid 1 through 3) selection = (chain 'S' and resid 1 through 3) selection = (chain 'b' and resid 1 through 3) selection = (chain 'g' and resid 1 through 3) selection = (chain 'p' and resid 1 through 3) selection = (chain 'u' and resid 1 through 3) } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.570 Check model and map are aligned: 0.410 Set scattering table: 0.270 Process input model: 81.400 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.550 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:13.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 : 0.005 0.067 30408 Z= 0.336 Angle : 0.844 11.303 41361 Z= 0.444 Chirality : 0.058 0.451 5022 Planarity : 0.005 0.084 5157 Dihedral : 20.825 113.464 12561 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.57 % Allowed : 0.54 % Favored : 98.89 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.79 % 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: -0.88 (0.13), residues: 3561 helix: -0.06 (0.18), residues: 648 sheet: 0.40 (0.16), residues: 942 loop : -1.29 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 353 HIS 0.006 0.001 HIS B1048 PHE 0.029 0.002 PHE C 58 TYR 0.030 0.002 TYR A 904 ARG 0.054 0.002 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 268 time to evaluate : 3.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8064 (mm-30) REVERT: A 365 TYR cc_start: 0.8032 (m-80) cc_final: 0.7662 (m-80) REVERT: B 988 GLU cc_start: 0.7362 (mp0) cc_final: 0.6995 (mp0) REVERT: C 306 PHE cc_start: 0.8426 (m-10) cc_final: 0.8062 (m-10) REVERT: C 902 MET cc_start: 0.8180 (mmm) cc_final: 0.7957 (mmt) REVERT: H 10 GLU cc_start: 0.5054 (OUTLIER) cc_final: 0.3902 (tm-30) REVERT: I 50 ASP cc_start: 0.7790 (p0) cc_final: 0.7535 (p0) REVERT: I 81 MET cc_start: 0.5984 (tmm) cc_final: 0.5525 (tmm) REVERT: I 109 TYR cc_start: 0.6535 (m-80) cc_final: 0.6327 (m-80) REVERT: J 50 ASP cc_start: 0.7445 (p0) cc_final: 0.7210 (p0) REVERT: J 81 MET cc_start: 0.5790 (tmm) cc_final: 0.5476 (tmm) REVERT: M 3 VAL cc_start: 0.8740 (t) cc_final: 0.8506 (p) outliers start: 18 outliers final: 6 residues processed: 282 average time/residue: 1.0651 time to fit residues: 369.8388 Evaluate side-chains 207 residues out of total 3162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 200 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain J residue 10 GLU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain M residue 13 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 9.9990 chunk 272 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 282 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 326 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN A 762 GLN A 804 GLN A 935 GLN A1005 GLN B 196 ASN C1002 GLN L 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 30408 Z= 0.322 Angle : 0.724 10.144 41361 Z= 0.357 Chirality : 0.051 0.441 5022 Planarity : 0.005 0.056 5157 Dihedral : 17.871 93.312 6162 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.95 % Allowed : 6.48 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.66 (0.14), residues: 3561 helix: 0.99 (0.20), residues: 651 sheet: 0.10 (0.16), residues: 984 loop : -1.25 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 436 HIS 0.007 0.001 HIS B 207 PHE 0.020 0.002 PHE I 64 TYR 0.028 0.002 TYR B 265 ARG 0.006 0.001 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 219 time to evaluate : 3.501 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7873 (t0) cc_final: 0.7660 (t0) REVERT: A 100 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.8047 (mp) REVERT: A 170 TYR cc_start: 0.6681 (t80) cc_final: 0.6437 (t80) REVERT: A 237 ARG cc_start: 0.7451 (tmt170) cc_final: 0.7196 (tmt-80) REVERT: A 571 ASP cc_start: 0.8245 (t0) cc_final: 0.8023 (t0) REVERT: A 902 MET cc_start: 0.7958 (mmt) cc_final: 0.7750 (tpt) REVERT: B 170 TYR cc_start: 0.6713 (t80) cc_final: 0.6396 (t80) REVERT: B 237 ARG cc_start: 0.7463 (tmt170) cc_final: 0.6972 (tmt-80) REVERT: B 646 ARG cc_start: 0.7299 (tmt170) cc_final: 0.7092 (tpt170) REVERT: B 988 GLU cc_start: 0.7466 (mp0) cc_final: 0.7152 (mp0) REVERT: C 99 ASN cc_start: 0.7818 (t0) cc_final: 0.7615 (t0) REVERT: C 140 PHE cc_start: 0.7766 (p90) cc_final: 0.7513 (p90) REVERT: C 237 ARG cc_start: 0.7472 (tmt170) cc_final: 0.7116 (tmt-80) REVERT: C 306 PHE cc_start: 0.8375 (m-10) cc_final: 0.7970 (m-10) REVERT: C 571 ASP cc_start: 0.8196 (t0) cc_final: 0.7763 (t0) REVERT: C 936 ASP cc_start: 0.8047 (t0) cc_final: 0.7793 (t0) REVERT: I 50 ASP cc_start: 0.8046 (p0) cc_final: 0.7835 (p0) REVERT: J 81 MET cc_start: 0.6486 (tmm) cc_final: 0.6116 (tmm) REVERT: M 3 VAL cc_start: 0.8743 (t) cc_final: 0.8498 (p) REVERT: N 37 GLN cc_start: 0.6379 (pm20) cc_final: 0.5773 (pm20) REVERT: N 90 GLN cc_start: 0.8008 (pp30) cc_final: 0.7357 (pp30) outliers start: 30 outliers final: 16 residues processed: 239 average time/residue: 1.0044 time to fit residues: 300.8161 Evaluate side-chains 210 residues out of total 3162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 193 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain N residue 3 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 272 optimal weight: 0.9980 chunk 222 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 327 optimal weight: 30.0000 chunk 353 optimal weight: 30.0000 chunk 291 optimal weight: 1.9990 chunk 324 optimal weight: 20.0000 chunk 111 optimal weight: 8.9990 chunk 262 optimal weight: 0.6980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1005 GLN B 49 HIS B 196 ASN B 440 ASN B 804 GLN B 935 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30408 Z= 0.273 Angle : 0.660 9.434 41361 Z= 0.321 Chirality : 0.049 0.423 5022 Planarity : 0.005 0.050 5157 Dihedral : 14.025 88.594 6153 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.04 % Allowed : 9.52 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.56 (0.14), residues: 3561 helix: 1.19 (0.20), residues: 678 sheet: 0.09 (0.16), residues: 984 loop : -1.23 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 99 HIS 0.007 0.001 HIS C 49 PHE 0.021 0.002 PHE I 64 TYR 0.023 0.002 TYR B 265 ARG 0.009 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 206 time to evaluate : 3.394 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7419 (t0) cc_final: 0.7131 (t0) REVERT: A 571 ASP cc_start: 0.8347 (t0) cc_final: 0.8062 (t0) REVERT: A 574 ASP cc_start: 0.7694 (t0) cc_final: 0.7406 (t0) REVERT: A 988 GLU cc_start: 0.7190 (mp0) cc_final: 0.6943 (mp0) REVERT: B 140 PHE cc_start: 0.7913 (p90) cc_final: 0.7566 (p90) REVERT: B 988 GLU cc_start: 0.7426 (mp0) cc_final: 0.7142 (mp0) REVERT: B 995 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7580 (mtt-85) REVERT: B 1107 ARG cc_start: 0.7338 (mmm-85) cc_final: 0.7055 (mmt-90) REVERT: C 306 PHE cc_start: 0.8391 (m-80) cc_final: 0.8010 (m-10) REVERT: C 571 ASP cc_start: 0.8160 (t0) cc_final: 0.7716 (t0) REVERT: C 936 ASP cc_start: 0.7949 (t0) cc_final: 0.7660 (t0) REVERT: I 108 ASP cc_start: 0.7217 (m-30) cc_final: 0.6563 (p0) REVERT: J 81 MET cc_start: 0.6194 (tmm) cc_final: 0.5755 (tmm) REVERT: M 3 VAL cc_start: 0.8740 (t) cc_final: 0.8498 (p) REVERT: N 37 GLN cc_start: 0.6404 (pm20) cc_final: 0.5914 (pm20) outliers start: 33 outliers final: 15 residues processed: 227 average time/residue: 1.0070 time to fit residues: 289.5618 Evaluate side-chains 202 residues out of total 3162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 186 time to evaluate : 3.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 29 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 20.0000 chunk 246 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 219 optimal weight: 3.9990 chunk 328 optimal weight: 10.0000 chunk 347 optimal weight: 30.0000 chunk 171 optimal weight: 1.9990 chunk 311 optimal weight: 20.0000 chunk 93 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 ASN B 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 30408 Z= 0.293 Angle : 0.647 11.605 41361 Z= 0.316 Chirality : 0.048 0.419 5022 Planarity : 0.004 0.051 5157 Dihedral : 11.446 81.428 6153 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.42 % Allowed : 11.67 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.59 (0.14), residues: 3561 helix: 1.25 (0.21), residues: 672 sheet: -0.05 (0.16), residues: 987 loop : -1.19 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 99 HIS 0.006 0.001 HIS B 207 PHE 0.022 0.002 PHE A 140 TYR 0.025 0.001 TYR B 265 ARG 0.006 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 207 time to evaluate : 3.158 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7410 (t0) cc_final: 0.7113 (t0) REVERT: A 196 ASN cc_start: 0.6372 (OUTLIER) cc_final: 0.5885 (m-40) REVERT: A 237 ARG cc_start: 0.7147 (tpt-90) cc_final: 0.6704 (tmt-80) REVERT: A 357 ARG cc_start: 0.7560 (tpp80) cc_final: 0.7181 (tpp80) REVERT: A 571 ASP cc_start: 0.8335 (t0) cc_final: 0.8041 (t0) REVERT: A 574 ASP cc_start: 0.7687 (t0) cc_final: 0.7397 (t0) REVERT: A 988 GLU cc_start: 0.7216 (mp0) cc_final: 0.6991 (mp0) REVERT: B 140 PHE cc_start: 0.7923 (p90) cc_final: 0.7563 (p90) REVERT: B 237 ARG cc_start: 0.7482 (tmt90) cc_final: 0.6995 (tpt-90) REVERT: B 988 GLU cc_start: 0.7565 (mp0) cc_final: 0.7209 (mp0) REVERT: C 306 PHE cc_start: 0.8431 (m-80) cc_final: 0.8015 (m-10) REVERT: C 571 ASP cc_start: 0.8121 (t0) cc_final: 0.7606 (t0) REVERT: I 48 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7556 (pp) REVERT: J 50 ASP cc_start: 0.7848 (p0) cc_final: 0.7100 (t0) REVERT: J 81 MET cc_start: 0.6246 (tmm) cc_final: 0.5781 (tmm) REVERT: M 3 VAL cc_start: 0.8738 (t) cc_final: 0.8497 (p) REVERT: N 37 GLN cc_start: 0.6440 (pm20) cc_final: 0.5888 (pm20) REVERT: N 90 GLN cc_start: 0.7884 (pp30) cc_final: 0.6976 (pp30) outliers start: 45 outliers final: 17 residues processed: 242 average time/residue: 0.9360 time to fit residues: 288.7021 Evaluate side-chains 210 residues out of total 3162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 191 time to evaluate : 2.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 29 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 259 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 296 optimal weight: 10.0000 chunk 240 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 0.6980 chunk 312 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 ASN B 196 ASN C1002 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30408 Z= 0.289 Angle : 0.632 9.722 41361 Z= 0.311 Chirality : 0.047 0.408 5022 Planarity : 0.004 0.051 5157 Dihedral : 9.899 73.445 6151 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.96 % Allowed : 12.52 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.58 (0.14), residues: 3561 helix: 1.34 (0.21), residues: 672 sheet: -0.14 (0.16), residues: 990 loop : -1.16 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 99 HIS 0.006 0.001 HIS B 207 PHE 0.024 0.002 PHE C 192 TYR 0.025 0.001 TYR B 265 ARG 0.007 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 205 time to evaluate : 3.154 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7423 (t0) cc_final: 0.7103 (t0) REVERT: A 196 ASN cc_start: 0.6431 (OUTLIER) cc_final: 0.5976 (m-40) REVERT: A 233 ILE cc_start: 0.2323 (OUTLIER) cc_final: 0.1837 (mt) REVERT: A 571 ASP cc_start: 0.8385 (t0) cc_final: 0.8082 (t0) REVERT: A 574 ASP cc_start: 0.7617 (t0) cc_final: 0.7322 (t0) REVERT: A 651 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8203 (mt) REVERT: A 995 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7602 (mtt-85) REVERT: B 140 PHE cc_start: 0.7949 (p90) cc_final: 0.7620 (p90) REVERT: B 988 GLU cc_start: 0.7552 (mp0) cc_final: 0.7196 (mp0) REVERT: C 306 PHE cc_start: 0.8429 (m-80) cc_final: 0.8020 (m-10) REVERT: C 440 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7940 (OUTLIER) REVERT: C 571 ASP cc_start: 0.8096 (t0) cc_final: 0.7579 (t0) REVERT: C 578 ASP cc_start: 0.8101 (t0) cc_final: 0.7767 (t0) REVERT: H 48 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7376 (pp) REVERT: I 50 ASP cc_start: 0.7780 (p0) cc_final: 0.7328 (t0) REVERT: I 81 MET cc_start: 0.5161 (tmm) cc_final: 0.4954 (tmm) REVERT: J 48 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7668 (pp) REVERT: J 50 ASP cc_start: 0.7936 (p0) cc_final: 0.7193 (t0) REVERT: J 81 MET cc_start: 0.6041 (tmm) cc_final: 0.5625 (tmm) REVERT: M 3 VAL cc_start: 0.8759 (t) cc_final: 0.8534 (p) REVERT: M 90 GLN cc_start: 0.7766 (pp30) cc_final: 0.7528 (pp30) outliers start: 62 outliers final: 26 residues processed: 251 average time/residue: 0.8768 time to fit residues: 284.6238 Evaluate side-chains 222 residues out of total 3162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 190 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 29 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 1.9990 chunk 313 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 204 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 348 optimal weight: 8.9990 chunk 289 optimal weight: 0.6980 chunk 161 optimal weight: 3.9990 chunk 28 optimal weight: 0.0270 chunk 115 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 overall best weight: 1.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 519 HIS ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30408 Z= 0.247 Angle : 0.609 11.493 41361 Z= 0.299 Chirality : 0.046 0.399 5022 Planarity : 0.004 0.053 5157 Dihedral : 9.085 69.207 6151 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.02 % Allowed : 13.57 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.49 (0.14), residues: 3561 helix: 1.48 (0.21), residues: 672 sheet: -0.11 (0.16), residues: 999 loop : -1.12 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 99 HIS 0.005 0.001 HIS B 207 PHE 0.024 0.002 PHE C 201 TYR 0.024 0.001 TYR C 265 ARG 0.007 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 205 time to evaluate : 3.143 Fit side-chains revert: symmetry clash REVERT: A 58 PHE cc_start: 0.6442 (OUTLIER) cc_final: 0.4894 (m-80) REVERT: A 99 ASN cc_start: 0.7338 (t0) cc_final: 0.7039 (t0) REVERT: A 196 ASN cc_start: 0.6484 (OUTLIER) cc_final: 0.5989 (m-40) REVERT: A 357 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7188 (tpp80) REVERT: A 571 ASP cc_start: 0.8373 (t0) cc_final: 0.8026 (t0) REVERT: A 574 ASP cc_start: 0.7591 (t0) cc_final: 0.7326 (t0) REVERT: A 988 GLU cc_start: 0.7130 (mp0) cc_final: 0.6910 (mp0) REVERT: B 140 PHE cc_start: 0.7991 (p90) cc_final: 0.7722 (p90) REVERT: B 988 GLU cc_start: 0.7564 (mp0) cc_final: 0.7203 (mp0) REVERT: C 306 PHE cc_start: 0.8419 (m-80) cc_final: 0.7978 (m-10) REVERT: C 440 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.7905 (OUTLIER) REVERT: C 571 ASP cc_start: 0.8211 (t0) cc_final: 0.7690 (t0) REVERT: C 578 ASP cc_start: 0.8104 (t0) cc_final: 0.7759 (t0) REVERT: C 740 MET cc_start: 0.7342 (tpt) cc_final: 0.7039 (tpt) REVERT: C 988 GLU cc_start: 0.7404 (mp0) cc_final: 0.7198 (mp0) REVERT: H 99 TRP cc_start: 0.5433 (t60) cc_final: 0.5104 (t60) REVERT: I 50 ASP cc_start: 0.7784 (p0) cc_final: 0.7352 (t0) REVERT: I 108 ASP cc_start: 0.6850 (m-30) cc_final: 0.6219 (p0) REVERT: J 48 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7691 (pp) REVERT: J 81 MET cc_start: 0.6095 (tmm) cc_final: 0.5700 (tmm) REVERT: M 3 VAL cc_start: 0.8757 (t) cc_final: 0.8535 (p) REVERT: M 90 GLN cc_start: 0.7817 (pp30) cc_final: 0.7547 (pp30) REVERT: N 37 GLN cc_start: 0.6536 (pm20) cc_final: 0.5934 (pm20) REVERT: N 90 GLN cc_start: 0.7941 (pp30) cc_final: 0.6978 (pp30) outliers start: 64 outliers final: 33 residues processed: 253 average time/residue: 0.8875 time to fit residues: 298.9861 Evaluate side-chains 225 residues out of total 3162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 188 time to evaluate : 2.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 29 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 20.0000 chunk 39 optimal weight: 0.5980 chunk 198 optimal weight: 5.9990 chunk 254 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 293 optimal weight: 0.4980 chunk 194 optimal weight: 3.9990 chunk 346 optimal weight: 50.0000 chunk 217 optimal weight: 1.9990 chunk 211 optimal weight: 8.9990 chunk 160 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 460 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30408 Z= 0.210 Angle : 0.591 10.433 41361 Z= 0.289 Chirality : 0.045 0.391 5022 Planarity : 0.004 0.055 5157 Dihedral : 8.523 65.983 6151 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.49 % Allowed : 14.42 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.39 (0.14), residues: 3561 helix: 1.68 (0.21), residues: 669 sheet: -0.09 (0.16), residues: 1011 loop : -1.08 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 99 HIS 0.005 0.001 HIS B 207 PHE 0.037 0.001 PHE A 168 TYR 0.027 0.001 TYR B 453 ARG 0.006 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 203 time to evaluate : 3.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7257 (t0) cc_final: 0.6976 (t0) REVERT: A 196 ASN cc_start: 0.6498 (OUTLIER) cc_final: 0.6017 (m-40) REVERT: A 233 ILE cc_start: 0.2364 (OUTLIER) cc_final: 0.1804 (mt) REVERT: A 357 ARG cc_start: 0.7487 (ttp80) cc_final: 0.7141 (tpp80) REVERT: A 532 ASN cc_start: 0.8074 (t0) cc_final: 0.7853 (t0) REVERT: A 571 ASP cc_start: 0.8199 (t0) cc_final: 0.7925 (t0) REVERT: A 574 ASP cc_start: 0.7566 (t0) cc_final: 0.7305 (t0) REVERT: B 140 PHE cc_start: 0.8021 (p90) cc_final: 0.7747 (p90) REVERT: B 357 ARG cc_start: 0.7509 (ttp80) cc_final: 0.7185 (tpp80) REVERT: B 985 ASP cc_start: 0.6671 (OUTLIER) cc_final: 0.6414 (p0) REVERT: B 988 GLU cc_start: 0.7575 (mp0) cc_final: 0.7324 (mp0) REVERT: C 306 PHE cc_start: 0.8402 (m-80) cc_final: 0.7943 (m-10) REVERT: C 440 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7867 (OUTLIER) REVERT: C 571 ASP cc_start: 0.8187 (t0) cc_final: 0.7640 (t0) REVERT: C 578 ASP cc_start: 0.8073 (t0) cc_final: 0.7721 (t0) REVERT: I 50 ASP cc_start: 0.7840 (p0) cc_final: 0.7352 (t0) REVERT: I 105 ARG cc_start: 0.6459 (mtm-85) cc_final: 0.5700 (mtm-85) REVERT: I 108 ASP cc_start: 0.7103 (m-30) cc_final: 0.6433 (p0) REVERT: J 50 ASP cc_start: 0.7904 (p0) cc_final: 0.7158 (t0) REVERT: M 3 VAL cc_start: 0.8755 (t) cc_final: 0.8535 (p) REVERT: M 90 GLN cc_start: 0.7834 (pp30) cc_final: 0.7545 (pp30) REVERT: N 37 GLN cc_start: 0.6365 (pm20) cc_final: 0.5817 (pm20) REVERT: N 90 GLN cc_start: 0.7893 (pp30) cc_final: 0.6881 (pp30) outliers start: 47 outliers final: 27 residues processed: 238 average time/residue: 0.9212 time to fit residues: 282.8679 Evaluate side-chains 220 residues out of total 3162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 190 time to evaluate : 3.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain N residue 3 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 207 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 220 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 272 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN B 196 ASN B 460 ASN C 394 ASN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30408 Z= 0.276 Angle : 0.615 11.024 41361 Z= 0.304 Chirality : 0.046 0.386 5022 Planarity : 0.004 0.057 5157 Dihedral : 8.244 63.125 6151 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.61 % Allowed : 14.71 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.50 (0.14), residues: 3561 helix: 1.62 (0.21), residues: 666 sheet: -0.18 (0.16), residues: 990 loop : -1.14 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 99 HIS 0.006 0.001 HIS B 207 PHE 0.032 0.002 PHE A 168 TYR 0.024 0.001 TYR B 265 ARG 0.006 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 200 time to evaluate : 2.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7256 (t0) cc_final: 0.6977 (t0) REVERT: A 196 ASN cc_start: 0.6548 (OUTLIER) cc_final: 0.6077 (m-40) REVERT: A 233 ILE cc_start: 0.2353 (OUTLIER) cc_final: 0.1845 (mt) REVERT: A 357 ARG cc_start: 0.7606 (ttp80) cc_final: 0.7265 (tpp80) REVERT: A 532 ASN cc_start: 0.8108 (t0) cc_final: 0.7906 (t0) REVERT: A 571 ASP cc_start: 0.8402 (t0) cc_final: 0.8115 (t0) REVERT: A 574 ASP cc_start: 0.7597 (t0) cc_final: 0.7317 (t0) REVERT: A 651 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8171 (mt) REVERT: A 936 ASP cc_start: 0.7721 (t0) cc_final: 0.7441 (t0) REVERT: A 988 GLU cc_start: 0.7217 (mp0) cc_final: 0.6845 (mp0) REVERT: B 140 PHE cc_start: 0.8040 (p90) cc_final: 0.7759 (p90) REVERT: B 224 GLU cc_start: 0.5613 (OUTLIER) cc_final: 0.5396 (pm20) REVERT: B 985 ASP cc_start: 0.6697 (OUTLIER) cc_final: 0.6435 (p0) REVERT: B 988 GLU cc_start: 0.7583 (mp0) cc_final: 0.7324 (mp0) REVERT: C 306 PHE cc_start: 0.8428 (m-80) cc_final: 0.7948 (m-10) REVERT: C 440 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7852 (OUTLIER) REVERT: C 571 ASP cc_start: 0.8200 (t0) cc_final: 0.7692 (t0) REVERT: C 578 ASP cc_start: 0.8090 (t0) cc_final: 0.7729 (t0) REVERT: H 99 TRP cc_start: 0.5550 (t60) cc_final: 0.5343 (t60) REVERT: I 50 ASP cc_start: 0.7866 (p0) cc_final: 0.7419 (t0) REVERT: I 108 ASP cc_start: 0.7214 (m-30) cc_final: 0.6517 (p0) REVERT: J 50 ASP cc_start: 0.8020 (p0) cc_final: 0.7273 (t0) REVERT: M 3 VAL cc_start: 0.8753 (t) cc_final: 0.8527 (p) REVERT: N 37 GLN cc_start: 0.6335 (pm20) cc_final: 0.5750 (pm20) REVERT: N 90 GLN cc_start: 0.7864 (pp30) cc_final: 0.7249 (pp30) outliers start: 51 outliers final: 31 residues processed: 241 average time/residue: 0.8637 time to fit residues: 268.6196 Evaluate side-chains 230 residues out of total 3162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 194 time to evaluate : 3.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain N residue 3 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 5.9990 chunk 332 optimal weight: 20.0000 chunk 303 optimal weight: 20.0000 chunk 323 optimal weight: 0.0060 chunk 194 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 253 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 292 optimal weight: 0.9980 chunk 305 optimal weight: 6.9990 chunk 322 optimal weight: 7.9990 overall best weight: 1.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 460 ASN C 394 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30408 Z= 0.266 Angle : 0.612 10.727 41361 Z= 0.302 Chirality : 0.046 0.384 5022 Planarity : 0.004 0.060 5157 Dihedral : 8.064 61.553 6151 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.55 % Allowed : 15.09 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.50 (0.14), residues: 3561 helix: 1.60 (0.21), residues: 669 sheet: -0.19 (0.16), residues: 990 loop : -1.13 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 99 HIS 0.006 0.001 HIS B 207 PHE 0.031 0.002 PHE A 168 TYR 0.026 0.001 TYR B 453 ARG 0.006 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 201 time to evaluate : 2.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7268 (t0) cc_final: 0.6996 (t0) REVERT: A 196 ASN cc_start: 0.6575 (OUTLIER) cc_final: 0.6104 (m-40) REVERT: A 233 ILE cc_start: 0.2293 (OUTLIER) cc_final: 0.1806 (mt) REVERT: A 237 ARG cc_start: 0.7429 (tmt90) cc_final: 0.7063 (ttt-90) REVERT: A 357 ARG cc_start: 0.7594 (ttp80) cc_final: 0.7276 (tpp80) REVERT: A 571 ASP cc_start: 0.8196 (t0) cc_final: 0.7932 (t0) REVERT: A 574 ASP cc_start: 0.7544 (t0) cc_final: 0.7263 (t0) REVERT: A 651 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8179 (mt) REVERT: A 936 ASP cc_start: 0.7745 (t0) cc_final: 0.7449 (t0) REVERT: A 988 GLU cc_start: 0.7198 (mp0) cc_final: 0.6839 (mp0) REVERT: B 140 PHE cc_start: 0.8023 (p90) cc_final: 0.7746 (p90) REVERT: B 985 ASP cc_start: 0.6686 (OUTLIER) cc_final: 0.6420 (p0) REVERT: B 988 GLU cc_start: 0.7582 (mp0) cc_final: 0.7322 (mp0) REVERT: C 306 PHE cc_start: 0.8424 (m-80) cc_final: 0.7996 (m-10) REVERT: C 571 ASP cc_start: 0.8189 (t0) cc_final: 0.7649 (t0) REVERT: C 578 ASP cc_start: 0.8090 (t0) cc_final: 0.7732 (t0) REVERT: I 50 ASP cc_start: 0.7825 (p0) cc_final: 0.7283 (t0) REVERT: I 108 ASP cc_start: 0.7410 (m-30) cc_final: 0.6713 (p0) REVERT: J 50 ASP cc_start: 0.8020 (p0) cc_final: 0.7233 (t0) REVERT: L 3 VAL cc_start: 0.8779 (t) cc_final: 0.8387 (p) REVERT: M 3 VAL cc_start: 0.8746 (t) cc_final: 0.8531 (p) REVERT: M 90 GLN cc_start: 0.7658 (pp30) cc_final: 0.7412 (pp30) REVERT: N 37 GLN cc_start: 0.6325 (pm20) cc_final: 0.5753 (pm20) outliers start: 49 outliers final: 35 residues processed: 239 average time/residue: 0.8510 time to fit residues: 263.9197 Evaluate side-chains 233 residues out of total 3162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 194 time to evaluate : 3.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 29 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 0.9990 chunk 341 optimal weight: 50.0000 chunk 208 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 237 optimal weight: 0.2980 chunk 358 optimal weight: 20.0000 chunk 330 optimal weight: 20.0000 chunk 285 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 220 optimal weight: 0.5980 chunk 175 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.350 30408 Z= 0.287 Angle : 0.819 59.176 41361 Z= 0.467 Chirality : 0.047 0.471 5022 Planarity : 0.005 0.166 5157 Dihedral : 8.066 61.555 6149 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.45 % Allowed : 15.40 % Favored : 83.14 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.50 (0.14), residues: 3561 helix: 1.62 (0.21), residues: 669 sheet: -0.20 (0.16), residues: 990 loop : -1.13 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 99 HIS 0.005 0.001 HIS B 207 PHE 0.032 0.002 PHE J 64 TYR 0.303 0.002 TYR B 453 ARG 0.005 0.000 ARG B1107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 195 time to evaluate : 3.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7270 (t0) cc_final: 0.6995 (t0) REVERT: A 196 ASN cc_start: 0.6566 (OUTLIER) cc_final: 0.6102 (m-40) REVERT: A 233 ILE cc_start: 0.2293 (OUTLIER) cc_final: 0.1806 (mt) REVERT: A 237 ARG cc_start: 0.7424 (tmt90) cc_final: 0.6888 (tmt-80) REVERT: A 357 ARG cc_start: 0.7589 (ttp80) cc_final: 0.7272 (tpp80) REVERT: A 571 ASP cc_start: 0.8194 (t0) cc_final: 0.7931 (t0) REVERT: A 574 ASP cc_start: 0.7541 (t0) cc_final: 0.7261 (t0) REVERT: A 651 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8176 (mt) REVERT: A 936 ASP cc_start: 0.7742 (t0) cc_final: 0.7447 (t0) REVERT: A 988 GLU cc_start: 0.7193 (mp0) cc_final: 0.6836 (mp0) REVERT: B 140 PHE cc_start: 0.8022 (p90) cc_final: 0.7743 (p90) REVERT: B 224 GLU cc_start: 0.5613 (OUTLIER) cc_final: 0.5396 (pm20) REVERT: B 453 TYR cc_start: 0.5849 (OUTLIER) cc_final: 0.5459 (p90) REVERT: B 985 ASP cc_start: 0.6683 (OUTLIER) cc_final: 0.6414 (p0) REVERT: B 988 GLU cc_start: 0.7580 (mp0) cc_final: 0.7318 (mp0) REVERT: C 306 PHE cc_start: 0.8422 (m-80) cc_final: 0.7990 (m-10) REVERT: C 571 ASP cc_start: 0.8188 (t0) cc_final: 0.7646 (t0) REVERT: C 578 ASP cc_start: 0.8087 (t0) cc_final: 0.7729 (t0) REVERT: I 50 ASP cc_start: 0.7815 (p0) cc_final: 0.7285 (t0) REVERT: I 105 ARG cc_start: 0.6286 (mtm-85) cc_final: 0.5929 (mtm-85) REVERT: I 108 ASP cc_start: 0.7411 (m-30) cc_final: 0.6712 (p0) REVERT: L 3 VAL cc_start: 0.8779 (t) cc_final: 0.8387 (p) REVERT: M 3 VAL cc_start: 0.8746 (t) cc_final: 0.8531 (p) REVERT: M 90 GLN cc_start: 0.7658 (pp30) cc_final: 0.7411 (pp30) REVERT: N 37 GLN cc_start: 0.6321 (pm20) cc_final: 0.5755 (pm20) outliers start: 46 outliers final: 34 residues processed: 231 average time/residue: 0.8755 time to fit residues: 265.2289 Evaluate side-chains 232 residues out of total 3162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 192 time to evaluate : 3.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 29 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 8.9990 chunk 304 optimal weight: 20.0000 chunk 87 optimal weight: 0.3980 chunk 263 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 286 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 293 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.203749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.138751 restraints weight = 38515.572| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 3.24 r_work: 0.3634 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.350 30408 Z= 0.287 Angle : 0.819 59.176 41361 Z= 0.467 Chirality : 0.047 0.471 5022 Planarity : 0.005 0.166 5157 Dihedral : 8.066 61.555 6149 Min Nonbonded Distance : 1.427 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.33 % Allowed : 15.56 % Favored : 83.11 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.50 (0.14), residues: 3561 helix: 1.62 (0.21), residues: 669 sheet: -0.20 (0.16), residues: 990 loop : -1.13 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 99 HIS 0.005 0.001 HIS B 207 PHE 0.032 0.002 PHE J 64 TYR 0.303 0.002 TYR B 453 ARG 0.005 0.000 ARG B1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6726.54 seconds wall clock time: 123 minutes 21.79 seconds (7401.79 seconds total)