Starting phenix.real_space_refine on Sun Mar 24 21:54:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6did_7896/03_2024/6did_7896.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6did_7896/03_2024/6did_7896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6did_7896/03_2024/6did_7896.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6did_7896/03_2024/6did_7896.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6did_7896/03_2024/6did_7896.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6did_7896/03_2024/6did_7896.pdb" } resolution = 4.71 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= 0.004 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9762 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 162 5.16 5 C 15699 2.51 5 N 4089 2.21 5 O 5259 1.98 5 H 9465 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 32": "OE1" <-> "OE2" Residue "C ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 174": "OE1" <-> "OE2" Residue "C ARG 234": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 24": "OE1" <-> "OE2" Residue "D TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D ARG 187": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 32": "OE1" <-> "OE2" Residue "E ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 174": "OE1" <-> "OE2" Residue "E ARG 234": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 24": "OE1" <-> "OE2" Residue "K TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 171": "OE1" <-> "OE2" Residue "K ARG 187": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 174": "OE1" <-> "OE2" Residue "H ARG 234": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 24": "OE1" <-> "OE2" Residue "L TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 171": "OE1" <-> "OE2" Residue "L ARG 187": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34674 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3493 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 3 Chain: "B" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "F" Number of atoms: 3493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3493 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 3 Chain: "I" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "G" Number of atoms: 3493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3493 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 3 Chain: "J" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "C" Number of atoms: 3258 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 3149 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 204} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 217, 3149 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 204} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 3068 Chain: "D" Number of atoms: 3151 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 213, 3071 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 198} Conformer: "B" Number of residues, atoms: 213, 3071 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 198} bond proxies already assigned to first conformer: 3024 Chain: "E" Number of atoms: 3258 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 3149 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 204} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 217, 3149 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 204} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 3068 Chain: "K" Number of atoms: 3151 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 213, 3071 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 198} Conformer: "B" Number of residues, atoms: 213, 3071 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 198} bond proxies already assigned to first conformer: 3024 Chain: "H" Number of atoms: 3258 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 3149 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 204} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 217, 3149 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 204} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 3068 Chain: "L" Number of atoms: 3151 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 213, 3071 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 198} Conformer: "B" Number of residues, atoms: 213, 3071 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 198} bond proxies already assigned to first conformer: 3024 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: 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "R" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "W" 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "d" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "i" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "j" Number of atoms: 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: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "p" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 90 residue: pdb=" N ACYS C 43 " occ=0.68 ... (18 atoms not shown) pdb=" HB3BCYS C 43 " occ=0.32 residue: pdb=" N ALYS C 65 " occ=0.50 ... (42 atoms not shown) pdb=" HZ3BLYS C 65 " occ=0.50 residue: pdb=" N ALYS C 133 " occ=0.47 ... (42 atoms not shown) pdb=" HZ3BLYS C 133 " occ=0.53 residue: pdb=" N AVAL C 137 " occ=0.81 ... (30 atoms not shown) pdb="HG23BVAL C 137 " occ=0.19 residue: pdb=" N ASER C 140 " occ=0.50 ... (20 atoms not shown) pdb=" HG BSER C 140 " occ=0.50 residue: pdb=" N ATHR C 170 " occ=0.38 ... (26 atoms not shown) pdb="HG23BTHR C 170 " occ=0.62 residue: pdb=" N ATHR C 172 " occ=0.25 ... (26 atoms not shown) pdb="HG23BTHR C 172 " occ=0.75 residue: pdb=" N APHE D 87 " occ=0.56 ... (38 atoms not shown) pdb=" HZ BPHE D 87 " occ=0.44 residue: pdb=" N ACYS D 114 " occ=0.75 ... (18 atoms not shown) pdb=" HB3BCYS D 114 " occ=0.25 residue: pdb=" N ATHR D 174 " occ=0.49 ... (26 atoms not shown) pdb="HG23BTHR D 174 " occ=0.51 residue: pdb=" N AARG D 193 " occ=0.54 ... (46 atoms not shown) pdb="HH22BARG D 193 " occ=0.46 residue: pdb=" N ASER D 211 " occ=0.51 ... (20 atoms not shown) pdb=" HG BSER D 211 " occ=0.49 ... (remaining 78 not shown) Time building chain proxies: 23.52, per 1000 atoms: 0.68 Number of scatterers: 34674 At special positions: 0 Unit cell: (186.3, 195.5, 134.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 162 16.00 O 5259 8.00 N 4089 7.00 C 15699 6.00 H 9465 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=60, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.19 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.11 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.19 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.11 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.02 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.04 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.04 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.04 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.04 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS I 605 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.19 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.11 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.04 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.04 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.04 Simple disulfide: pdb=" SG ACYS C 43 " - pdb=" SG CYS C 108 " distance=2.04 Simple disulfide: pdb=" SG CYS C 100 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG BCYS C 43 " distance=2.01 Simple disulfide: pdb=" SG CYS C 160 " - pdb=" SG CYS C 219 " distance=2.03 Simple disulfide: pdb=" SG CYS C 237 " - pdb=" SG CYS D 150 " distance=2.02 Simple disulfide: pdb=" SG CYS D 40 " - pdb=" SG ACYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 40 " - pdb=" SG BCYS D 114 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 69 " distance=2.07 Simple disulfide: pdb=" SG CYS D 163 " - pdb=" SG CYS D 216 " distance=2.04 Simple disulfide: pdb=" SG ACYS E 43 " - pdb=" SG CYS E 108 " distance=2.04 Simple disulfide: pdb=" SG CYS E 100 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG BCYS E 43 " distance=2.01 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 237 " - pdb=" SG CYS K 150 " distance=2.02 Simple disulfide: pdb=" SG CYS K 40 " - pdb=" SG ACYS K 114 " distance=2.03 Simple disulfide: pdb=" SG CYS K 40 " - pdb=" SG BCYS K 114 " distance=2.02 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 69 " distance=2.07 Simple disulfide: pdb=" SG CYS K 163 " - pdb=" SG CYS K 216 " distance=2.04 Simple disulfide: pdb=" SG ACYS H 43 " - pdb=" SG CYS H 108 " distance=2.04 Simple disulfide: pdb=" SG CYS H 100 " - pdb=" SG CYS H 196 " distance=2.04 Simple disulfide: pdb=" SG CYS H 108 " - pdb=" SG BCYS H 43 " distance=2.01 Simple disulfide: pdb=" SG CYS H 160 " - pdb=" SG CYS H 219 " distance=2.03 Simple disulfide: pdb=" SG CYS H 237 " - pdb=" SG CYS L 150 " distance=2.02 Simple disulfide: pdb=" SG CYS L 40 " - pdb=" SG ACYS L 114 " distance=2.03 Simple disulfide: pdb=" SG CYS L 40 " - pdb=" SG BCYS L 114 " distance=2.02 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 69 " distance=2.06 Simple disulfide: pdb=" SG CYS L 163 " - pdb=" SG CYS L 216 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN Q 4 " - " MAN Q 5 " " MAN R 4 " - " MAN R 5 " " MAN c 4 " - " MAN c 5 " " MAN d 4 " - " MAN d 5 " " MAN o 4 " - " MAN o 5 " " MAN p 4 " - " MAN p 5 " ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " MAN Q 6 " - " MAN Q 7 " " BMA R 3 " - " MAN R 4 " " MAN R 6 " - " MAN R 7 " " BMA V 3 " - " MAN V 6 " " MAN V 4 " - " MAN V 5 " " BMA c 3 " - " MAN c 4 " " MAN c 6 " - " MAN c 7 " " BMA d 3 " - " MAN d 4 " " MAN d 6 " - " MAN d 7 " " BMA h 3 " - " MAN h 6 " " MAN h 4 " - " MAN h 5 " " BMA o 3 " - " MAN o 4 " " MAN o 6 " - " MAN o 7 " " BMA p 3 " - " MAN p 4 " " MAN p 6 " - " MAN p 7 " " BMA t 3 " - " MAN t 6 " " MAN t 4 " - " MAN t 5 " ALPHA1-6 " BMA Q 3 " - " MAN Q 6 " " BMA R 3 " - " MAN R 6 " " MAN R 6 " - " MAN R 8 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA c 3 " - " MAN c 6 " " BMA d 3 " - " MAN d 6 " " MAN d 6 " - " MAN d 8 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 4 " " BMA o 3 " - " MAN o 6 " " BMA p 3 " - " MAN p 6 " " MAN p 6 " - " MAN p 8 " " BMA t 3 " - " MAN t 4 " " BMA u 3 " - " MAN u 4 " BETA1-4 " 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 Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 604 " - " ASN A 133 " " NAG A 611 " - " ASN A 234 " " NAG A 633 " - " ASN A 339 " " NAG A 634 " - " ASN A 355 " " NAG A 645 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG F 604 " - " ASN F 133 " " NAG F 611 " - " ASN F 234 " " NAG F 631 " - " ASN F 355 " " NAG F 634 " - " ASN F 339 " " NAG F 645 " - " ASN F 392 " " NAG G 604 " - " ASN G 133 " " NAG G 611 " - " ASN G 234 " " NAG G 633 " - " ASN G 339 " " NAG G 634 " - " ASN G 355 " " NAG G 645 " - " ASN G 392 " " NAG I 701 " - " ASN I 611 " " NAG I 702 " - " ASN I 637 " " NAG J 701 " - " ASN J 611 " " NAG J 702 " - " ASN J 637 " " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 156 " " NAG O 1 " - " ASN A 160 " " NAG P 1 " - " ASN A 197 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 276 " " NAG S 1 " - " ASN A 295 " " NAG T 1 " - " ASN A 301 " " NAG U 1 " - " ASN A 332 " " NAG V 1 " - " ASN A 363 " " NAG W 1 " - " ASN A 386 " " NAG X 1 " - " ASN A 448 " " NAG Y 1 " - " ASN F 88 " " NAG Z 1 " - " ASN F 156 " " NAG a 1 " - " ASN F 160 " " NAG b 1 " - " ASN F 197 " " NAG c 1 " - " ASN F 262 " " NAG d 1 " - " ASN F 276 " " NAG e 1 " - " ASN F 295 " " NAG f 1 " - " ASN F 301 " " NAG g 1 " - " ASN F 332 " " NAG h 1 " - " ASN F 363 " " NAG i 1 " - " ASN F 386 " " NAG j 1 " - " ASN F 448 " " NAG k 1 " - " ASN G 88 " " NAG l 1 " - " ASN G 156 " " NAG m 1 " - " ASN G 160 " " NAG n 1 " - " ASN G 197 " " NAG o 1 " - " ASN G 262 " " NAG p 1 " - " ASN G 276 " " NAG q 1 " - " ASN G 295 " " NAG r 1 " - " ASN G 301 " " NAG s 1 " - " ASN G 332 " " NAG t 1 " - " ASN G 363 " " NAG u 1 " - " ASN G 386 " " NAG v 1 " - " ASN G 448 " Time building additional restraints: 24.40 Conformation dependent library (CDL) restraints added in 6.7 seconds 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5628 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 60 sheets defined 20.3% alpha, 38.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.823A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.864A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 381 removed outlier: 3.500A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.966A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.744A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.581A pdb=" N ARG B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 597 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 649 Processing helix chain 'B' and resid 650 through 663 Processing helix chain 'F' and resid 99 through 117 removed outlier: 3.825A pdb=" N ILE F 109 " --> pdb=" O HIS F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 127 removed outlier: 3.864A pdb=" N VAL F 127 " --> pdb=" O PRO F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 151 Processing helix chain 'F' and resid 335 through 350 Processing helix chain 'F' and resid 351 through 353 No H-bonds generated for 'chain 'F' and resid 351 through 353' Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 377 through 381 removed outlier: 3.501A pdb=" N GLU F 381 " --> pdb=" O CYS F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 392 Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.968A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 523 through 528 Processing helix chain 'I' and resid 529 through 534 removed outlier: 3.745A pdb=" N SER I 534 " --> pdb=" O MET I 530 " (cutoff:3.500A) Processing helix chain 'I' and resid 536 through 542 removed outlier: 3.581A pdb=" N ARG I 542 " --> pdb=" O THR I 538 " (cutoff:3.500A) Processing helix chain 'I' and resid 571 through 597 Processing helix chain 'I' and resid 611 through 615 Processing helix chain 'I' and resid 618 through 624 Processing helix chain 'I' and resid 627 through 636 Processing helix chain 'I' and resid 638 through 649 Processing helix chain 'I' and resid 650 through 663 Processing helix chain 'G' and resid 99 through 117 removed outlier: 3.824A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 127 removed outlier: 3.865A pdb=" N VAL G 127 " --> pdb=" O PRO G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 151 Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 377 through 381 removed outlier: 3.500A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 392 Processing helix chain 'G' and resid 475 through 484 removed outlier: 3.966A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 523 through 528 Processing helix chain 'J' and resid 529 through 534 removed outlier: 3.745A pdb=" N SER J 534 " --> pdb=" O MET J 530 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 542 removed outlier: 3.581A pdb=" N ARG J 542 " --> pdb=" O THR J 538 " (cutoff:3.500A) Processing helix chain 'J' and resid 571 through 597 Processing helix chain 'J' and resid 611 through 615 Processing helix chain 'J' and resid 618 through 624 Processing helix chain 'J' and resid 627 through 636 Processing helix chain 'J' and resid 638 through 649 Processing helix chain 'J' and resid 650 through 663 Processing helix chain 'C' and resid 99 through 103 Processing helix chain 'C' and resid 147 through 153 removed outlier: 4.063A pdb=" N VAL C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR C 153 " --> pdb=" O ASP C 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 147 through 153' Processing helix chain 'C' and resid 208 through 214 removed outlier: 3.529A pdb=" N HIS C 214 " --> pdb=" O GLN C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 237 No H-bonds generated for 'chain 'C' and resid 235 through 237' Processing helix chain 'D' and resid 105 through 109 Processing helix chain 'D' and resid 179 through 181 No H-bonds generated for 'chain 'D' and resid 179 through 181' Processing helix chain 'D' and resid 221 through 224 Processing helix chain 'E' and resid 99 through 103 Processing helix chain 'E' and resid 147 through 153 removed outlier: 4.063A pdb=" N VAL E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA E 152 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR E 153 " --> pdb=" O ASP E 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 147 through 153' Processing helix chain 'E' and resid 208 through 214 removed outlier: 3.529A pdb=" N HIS E 214 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 237 No H-bonds generated for 'chain 'E' and resid 235 through 237' Processing helix chain 'K' and resid 105 through 109 Processing helix chain 'K' and resid 179 through 181 No H-bonds generated for 'chain 'K' and resid 179 through 181' Processing helix chain 'K' and resid 221 through 224 Processing helix chain 'H' and resid 99 through 103 Processing helix chain 'H' and resid 147 through 153 removed outlier: 4.063A pdb=" N VAL H 151 " --> pdb=" O ALA H 147 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA H 152 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR H 153 " --> pdb=" O ASP H 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 147 through 153' Processing helix chain 'H' and resid 208 through 214 removed outlier: 3.529A pdb=" N HIS H 214 " --> pdb=" O GLN H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 237 No H-bonds generated for 'chain 'H' and resid 235 through 237' Processing helix chain 'L' and resid 105 through 109 Processing helix chain 'L' and resid 179 through 181 No H-bonds generated for 'chain 'L' and resid 179 through 181' Processing helix chain 'L' and resid 221 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.863A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA8, first strand: chain 'A' and resid 394 through 395 removed outlier: 6.669A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.057A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 10.324A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.198A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.513A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 316 through 323 removed outlier: 4.410A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 35 through 40 Processing sheet with id=AB3, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AB4, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.863A pdb=" N VAL F 75 " --> pdb=" O CYS F 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 91 through 92 Processing sheet with id=AB6, first strand: chain 'F' and resid 130 through 133 Processing sheet with id=AB7, first strand: chain 'F' and resid 181 through 183 Processing sheet with id=AB8, first strand: chain 'F' and resid 201 through 202 Processing sheet with id=AB9, first strand: chain 'F' and resid 394 through 395 removed outlier: 6.668A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.055A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N VAL F 442 " --> pdb=" O CYS F 296 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N CYS F 296 " --> pdb=" O VAL F 442 " (cutoff:3.500A) removed outlier: 9.990A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.198A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 9.752A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 316 through 323 removed outlier: 4.411A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE F 322 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN F 301 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 35 through 40 Processing sheet with id=AC4, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AC5, first strand: chain 'G' and resid 75 through 76 removed outlier: 3.863A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 91 through 92 Processing sheet with id=AC7, first strand: chain 'G' and resid 130 through 133 Processing sheet with id=AC8, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AC9, first strand: chain 'G' and resid 201 through 202 Processing sheet with id=AD1, first strand: chain 'G' and resid 394 through 395 removed outlier: 6.669A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.056A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 10.324A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.197A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 9.752A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 316 through 323 removed outlier: 4.410A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 24 through 27 removed outlier: 3.831A pdb=" N GLN C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 30 through 34 removed outlier: 6.336A pdb=" N VAL C 31 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALYS C 133 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA C 33 " --> pdb=" O ALYS C 133 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU C 53 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N TYR C 69 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP C 55 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 140 through 144 removed outlier: 6.101A pdb=" N TYR C 198 " --> pdb=" O LYS C 164 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 178 through 179 Processing sheet with id=AD8, first strand: chain 'D' and resid 23 through 25 removed outlier: 6.176A pdb=" N THR D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 28 through 30 removed outlier: 6.089A pdb=" N GLY D 28 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N MET D 53 " --> pdb=" O CYS D 69 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N CYS D 69 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP D 55 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 28 through 30 removed outlier: 6.089A pdb=" N GLY D 28 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 125 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 143 through 147 removed outlier: 5.559A pdb=" N TYR D 199 " --> pdb=" O GLY D 167 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 143 through 147 removed outlier: 5.559A pdb=" N TYR D 199 " --> pdb=" O GLY D 167 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 174 through 177 Processing sheet with id=AE5, first strand: chain 'E' and resid 24 through 27 removed outlier: 3.831A pdb=" N GLN E 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 30 through 34 removed outlier: 6.337A pdb=" N VAL E 31 " --> pdb=" O VAL E 131 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALYS E 133 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA E 33 " --> pdb=" O ALYS E 133 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU E 53 " --> pdb=" O TYR E 69 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR E 69 " --> pdb=" O LEU E 53 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP E 55 " --> pdb=" O LEU E 67 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 140 through 144 removed outlier: 6.101A pdb=" N TYR E 198 " --> pdb=" O LYS E 164 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 178 through 179 Processing sheet with id=AE9, first strand: chain 'K' and resid 23 through 25 removed outlier: 6.176A pdb=" N THR K 96 " --> pdb=" O THR K 92 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 28 through 30 removed outlier: 6.090A pdb=" N GLY K 28 " --> pdb=" O THR K 133 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N MET K 53 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N CYS K 69 " --> pdb=" O MET K 53 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP K 55 " --> pdb=" O ILE K 67 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 28 through 30 removed outlier: 6.090A pdb=" N GLY K 28 " --> pdb=" O THR K 133 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU K 125 " --> pdb=" O ARG K 116 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 143 through 147 removed outlier: 5.559A pdb=" N TYR K 199 " --> pdb=" O GLY K 167 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 143 through 147 removed outlier: 5.559A pdb=" N TYR K 199 " --> pdb=" O GLY K 167 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 174 through 177 Processing sheet with id=AF6, first strand: chain 'H' and resid 24 through 27 removed outlier: 3.832A pdb=" N GLN H 90 " --> pdb=" O SER H 87 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 30 through 34 removed outlier: 6.337A pdb=" N VAL H 31 " --> pdb=" O VAL H 131 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALYS H 133 " --> pdb=" O VAL H 31 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA H 33 " --> pdb=" O ALYS H 133 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU H 53 " --> pdb=" O TYR H 69 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR H 69 " --> pdb=" O LEU H 53 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP H 55 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 140 through 144 removed outlier: 6.101A pdb=" N TYR H 198 " --> pdb=" O LYS H 164 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 178 through 179 Processing sheet with id=AG1, first strand: chain 'L' and resid 23 through 25 removed outlier: 6.176A pdb=" N THR L 96 " --> pdb=" O THR L 92 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 28 through 30 removed outlier: 6.089A pdb=" N GLY L 28 " --> pdb=" O THR L 133 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N MET L 53 " --> pdb=" O CYS L 69 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N CYS L 69 " --> pdb=" O MET L 53 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP L 55 " --> pdb=" O ILE L 67 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 28 through 30 removed outlier: 6.089A pdb=" N GLY L 28 " --> pdb=" O THR L 133 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU L 125 " --> pdb=" O ARG L 116 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 143 through 147 removed outlier: 5.559A pdb=" N TYR L 199 " --> pdb=" O GLY L 167 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 143 through 147 removed outlier: 5.559A pdb=" N TYR L 199 " --> pdb=" O GLY L 167 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 174 through 177 1023 hydrogen bonds defined for protein. 2556 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: 15.40 Time building geometry restraints manager: 25.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 9462 1.04 - 1.25: 3839 1.25 - 1.46: 9907 1.46 - 1.66: 11787 1.66 - 1.87: 207 Bond restraints: 35202 Sorted by residual: bond pdb=" C3 MAN d 5 " pdb=" C4 MAN d 5 " ideal model delta sigma weight residual 1.524 1.615 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C3 MAN p 5 " pdb=" C4 MAN p 5 " ideal model delta sigma weight residual 1.524 1.614 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C3 MAN R 5 " pdb=" C4 MAN R 5 " ideal model delta sigma weight residual 1.524 1.614 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" CA ILE B 641 " pdb=" C ILE B 641 " ideal model delta sigma weight residual 1.524 1.471 0.053 1.23e-02 6.61e+03 1.86e+01 bond pdb=" C4 MAN R 5 " pdb=" C5 MAN R 5 " ideal model delta sigma weight residual 1.533 1.619 -0.086 2.00e-02 2.50e+03 1.86e+01 ... (remaining 35197 not shown) Histogram of bond angle deviations from ideal: 98.12 - 105.35: 720 105.35 - 112.58: 31028 112.58 - 119.81: 11116 119.81 - 127.04: 13324 127.04 - 134.27: 344 Bond angle restraints: 56532 Sorted by residual: angle pdb=" C LYS A 252 " pdb=" N PRO A 253 " pdb=" CA PRO A 253 " ideal model delta sigma weight residual 120.12 131.59 -11.47 1.11e+00 8.12e-01 1.07e+02 angle pdb=" C LYS G 252 " pdb=" N PRO G 253 " pdb=" CA PRO G 253 " ideal model delta sigma weight residual 120.12 131.54 -11.42 1.11e+00 8.12e-01 1.06e+02 angle pdb=" C LYS F 252 " pdb=" N PRO F 253 " pdb=" CA PRO F 253 " ideal model delta sigma weight residual 120.12 131.53 -11.41 1.11e+00 8.12e-01 1.06e+02 angle pdb=" C CYS F 239 " pdb=" N PRO F 240 " pdb=" CA PRO F 240 " ideal model delta sigma weight residual 119.56 129.04 -9.48 1.01e+00 9.80e-01 8.80e+01 angle pdb=" C CYS A 239 " pdb=" N PRO A 240 " pdb=" CA PRO A 240 " ideal model delta sigma weight residual 119.56 129.02 -9.46 1.01e+00 9.80e-01 8.77e+01 ... (remaining 56527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.84: 19716 22.84 - 45.69: 743 45.69 - 68.53: 265 68.53 - 91.38: 106 91.38 - 114.22: 44 Dihedral angle restraints: 20874 sinusoidal: 11490 harmonic: 9384 Sorted by residual: dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 205 " pdb=" CB CYS F 205 " ideal model delta sinusoidal sigma weight residual -86.00 -130.26 44.26 1 1.00e+01 1.00e-02 2.73e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -130.24 44.24 1 1.00e+01 1.00e-02 2.72e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -130.18 44.18 1 1.00e+01 1.00e-02 2.72e+01 ... (remaining 20871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 4170 0.175 - 0.350: 258 0.350 - 0.526: 48 0.526 - 0.701: 3 0.701 - 0.876: 3 Chirality restraints: 4482 Sorted by residual: chirality pdb=" C1 MAN R 6 " pdb=" O6 BMA R 3 " pdb=" C2 MAN R 6 " pdb=" O5 MAN R 6 " both_signs ideal model delta sigma weight residual False 2.40 1.52 0.88 2.00e-02 2.50e+03 1.92e+03 chirality pdb=" C1 MAN d 6 " pdb=" O6 BMA d 3 " pdb=" C2 MAN d 6 " pdb=" O5 MAN d 6 " both_signs ideal model delta sigma weight residual False 2.40 1.52 0.88 2.00e-02 2.50e+03 1.91e+03 chirality pdb=" C1 MAN p 6 " pdb=" O6 BMA p 3 " pdb=" C2 MAN p 6 " pdb=" O5 MAN p 6 " both_signs ideal model delta sigma weight residual False 2.40 1.53 0.87 2.00e-02 2.50e+03 1.91e+03 ... (remaining 4479 not shown) Planarity restraints: 5607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 363 " 0.195 2.00e-02 2.50e+03 2.62e-01 8.61e+02 pdb=" CG ASN G 363 " -0.090 2.00e-02 2.50e+03 pdb=" OD1 ASN G 363 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN G 363 " -0.443 2.00e-02 2.50e+03 pdb=" C1 NAG t 1 " 0.319 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 363 " 0.195 2.00e-02 2.50e+03 2.62e-01 8.61e+02 pdb=" CG ASN A 363 " -0.089 2.00e-02 2.50e+03 pdb=" OD1 ASN A 363 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 363 " -0.443 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.319 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 363 " -0.195 2.00e-02 2.50e+03 2.62e-01 8.60e+02 pdb=" CG ASN F 363 " 0.088 2.00e-02 2.50e+03 pdb=" OD1 ASN F 363 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN F 363 " 0.443 2.00e-02 2.50e+03 pdb=" C1 NAG h 1 " -0.319 2.00e-02 2.50e+03 ... (remaining 5604 not shown) Histogram of nonbonded interaction distances: 0.72 - 1.49: 37 1.49 - 2.27: 3215 2.27 - 3.05: 68487 3.05 - 3.82: 115467 3.82 - 4.60: 187629 Warning: very small nonbonded interaction distances. Nonbonded interactions: 374835 Sorted by model distance: nonbonded pdb=" NZ LYS A 231 " pdb=" OH TYR L 52 " model vdw 0.718 2.350 nonbonded pdb=" NZ LYS F 231 " pdb=" OH TYR D 52 " model vdw 0.726 2.350 nonbonded pdb=" NZ LYS G 231 " pdb=" OH TYR K 52 " model vdw 0.726 2.350 nonbonded pdb=" CA PRO A 240 " pdb="HH22 ARG H 50 " model vdw 0.778 2.750 nonbonded pdb=" CA PRO G 240 " pdb="HH22 ARG E 50 " model vdw 0.791 2.750 ... (remaining 374830 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 'F' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'C' and (resid 21 through 42 or resid 44 through 64 or resid 66 through 1 \ 32 or resid 134 through 136 or resid 138 through 139 or resid 141 through 169 or \ resid 171 or resid 173 through 237)) selection = (chain 'E' and (resid 21 through 42 or resid 44 through 64 or resid 66 through 1 \ 32 or resid 134 through 136 or resid 138 through 139 or resid 141 through 169 or \ resid 171 or resid 173 through 237)) selection = (chain 'H' and (resid 21 through 42 or resid 44 through 64 or resid 66 through 1 \ 32 or resid 134 through 136 or resid 138 through 139 or resid 141 through 169 or \ resid 171 or resid 173 through 237)) } ncs_group { reference = (chain 'D' and (resid 22 through 86 or resid 88 through 113 or resid 115 through \ 173 or resid 175 through 192 or resid 194 through 210 or resid 213 through 234) \ ) selection = (chain 'K' and (resid 22 through 86 or resid 88 through 113 or resid 115 through \ 173 or resid 175 through 192 or resid 194 through 210 or resid 213 through 234) \ ) selection = (chain 'L' and (resid 22 through 86 or resid 88 through 113 or resid 115 through \ 173 or resid 175 through 192 or resid 194 through 210 or resid 213 through 234) \ ) } ncs_group { reference = chain 'M' selection = chain 'Y' selection = chain 'k' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'j' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 'v' } ncs_group { reference = (chain 'Q' and resid 5 through 7) selection = (chain 'R' and resid 6 through 8) selection = (chain 'V' and resid 4 through 6) selection = (chain 'c' and resid 5 through 7) selection = (chain 'd' and resid 6 through 8) selection = (chain 'h' and resid 4 through 6) selection = (chain 'o' and resid 5 through 7) selection = (chain 'p' and resid 6 through 8) selection = (chain 't' and resid 4 through 6) } ncs_group { reference = chain 'W' selection = chain 'i' selection = chain 'u' } 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=0.00 max=1.00 mean=0.97 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.290 Construct map_model_manager: 0.760 Extract box with map and model: 7.730 Check model and map are aligned: 0.560 Set scattering table: 0.330 Process input model: 113.580 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.580 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5412 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 : 0.014 0.132 25737 Z= 0.905 Angle : 1.607 12.653 35118 Z= 0.968 Chirality : 0.102 0.876 4482 Planarity : 0.010 0.087 4272 Dihedral : 15.537 114.220 11523 Min Nonbonded Distance : 0.718 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.83 % Allowed : 2.17 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.15), residues: 3066 helix: -0.71 (0.22), residues: 414 sheet: 0.76 (0.15), residues: 1149 loop : 1.69 (0.17), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.007 TRP F 479 HIS 0.010 0.003 HIS A 72 PHE 0.023 0.005 PHE H 91 TYR 0.036 0.005 TYR G 318 ARG 0.012 0.001 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 333 time to evaluate : 2.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8409 (ttt) cc_final: 0.8171 (ttm) REVERT: A 114 GLN cc_start: 0.9097 (tp40) cc_final: 0.8825 (tm-30) REVERT: A 475 MET cc_start: 0.8893 (mmp) cc_final: 0.8561 (mmm) REVERT: B 530 MET cc_start: 0.8943 (mtp) cc_final: 0.8728 (mtt) REVERT: B 536 THR cc_start: 0.9098 (p) cc_final: 0.8736 (t) REVERT: B 595 ILE cc_start: 0.9700 (mt) cc_final: 0.9500 (mm) REVERT: F 475 MET cc_start: 0.8936 (mmp) cc_final: 0.8461 (mmm) REVERT: I 530 MET cc_start: 0.9011 (mtp) cc_final: 0.8789 (mtt) REVERT: I 536 THR cc_start: 0.9097 (p) cc_final: 0.8765 (t) REVERT: I 595 ILE cc_start: 0.9735 (mt) cc_final: 0.9534 (mm) REVERT: G 475 MET cc_start: 0.8822 (mmp) cc_final: 0.8421 (mmm) REVERT: J 536 THR cc_start: 0.9067 (p) cc_final: 0.8691 (t) REVERT: C 89 THR cc_start: 0.6413 (OUTLIER) cc_final: 0.5958 (t) REVERT: D 70 ILE cc_start: 0.8679 (tt) cc_final: 0.8425 (tt) REVERT: E 89 THR cc_start: 0.6006 (OUTLIER) cc_final: 0.5588 (t) REVERT: E 93 LEU cc_start: 0.7556 (tp) cc_final: 0.7278 (tt) REVERT: K 97 VAL cc_start: 0.7039 (t) cc_final: 0.6811 (t) REVERT: H 89 THR cc_start: 0.6077 (OUTLIER) cc_final: 0.5741 (t) REVERT: H 93 LEU cc_start: 0.7543 (tp) cc_final: 0.7201 (tt) REVERT: H 233 ASN cc_start: 0.5305 (m-40) cc_final: 0.4574 (m110) outliers start: 45 outliers final: 8 residues processed: 376 average time/residue: 0.6035 time to fit residues: 343.3657 Evaluate side-chains 224 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 213 time to evaluate : 3.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 8.9990 chunk 222 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 119 optimal weight: 0.7980 chunk 230 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 171 optimal weight: 10.0000 chunk 266 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 ASN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 ASN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 618 ASN D 194 GLN L 194 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5453 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25737 Z= 0.225 Angle : 0.730 7.142 35118 Z= 0.374 Chirality : 0.047 0.281 4482 Planarity : 0.005 0.069 4272 Dihedral : 13.912 76.891 6252 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.30 % Allowed : 0.72 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.15), residues: 3066 helix: 1.08 (0.26), residues: 414 sheet: 0.60 (0.14), residues: 1230 loop : 1.60 (0.18), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 69 HIS 0.006 0.001 HIS F 85 PHE 0.015 0.002 PHE L 145 TYR 0.020 0.002 TYR G 217 ARG 0.004 0.001 ARG E 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 252 time to evaluate : 3.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8139 (t80) cc_final: 0.7485 (t80) REVERT: A 107 ASP cc_start: 0.8714 (t70) cc_final: 0.8332 (t0) REVERT: B 647 GLU cc_start: 0.7916 (tt0) cc_final: 0.7705 (tt0) REVERT: F 107 ASP cc_start: 0.8621 (t70) cc_final: 0.8333 (t0) REVERT: F 475 MET cc_start: 0.8988 (mmp) cc_final: 0.8783 (mmm) REVERT: G 40 TYR cc_start: 0.7884 (t80) cc_final: 0.7456 (t80) REVERT: G 104 MET cc_start: 0.8292 (mmp) cc_final: 0.8020 (mmt) REVERT: G 475 MET cc_start: 0.8936 (mmp) cc_final: 0.8672 (mmm) REVERT: D 70 ILE cc_start: 0.8760 (tt) cc_final: 0.8555 (tt) outliers start: 5 outliers final: 0 residues processed: 257 average time/residue: 0.6653 time to fit residues: 253.0361 Evaluate side-chains 190 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 3.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 222 optimal weight: 5.9990 chunk 181 optimal weight: 20.0000 chunk 73 optimal weight: 4.9990 chunk 267 optimal weight: 9.9990 chunk 288 optimal weight: 8.9990 chunk 238 optimal weight: 10.0000 chunk 265 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 214 optimal weight: 0.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 GLN E 191 GLN L 194 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5602 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 25737 Z= 0.271 Angle : 0.714 15.276 35118 Z= 0.356 Chirality : 0.048 1.016 4482 Planarity : 0.004 0.038 4272 Dihedral : 11.310 72.011 6252 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 27.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.27 % Allowed : 1.30 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.15), residues: 3066 helix: 1.60 (0.27), residues: 393 sheet: 0.48 (0.14), residues: 1206 loop : 1.36 (0.17), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 395 HIS 0.005 0.002 HIS G 216 PHE 0.024 0.003 PHE F 353 TYR 0.026 0.002 TYR G 217 ARG 0.006 0.001 ARG K 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 208 time to evaluate : 3.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.8906 (ptm) cc_final: 0.8431 (ttp) REVERT: I 626 MET cc_start: 0.8716 (ptm) cc_final: 0.8309 (ttp) REVERT: G 45 TRP cc_start: 0.7619 (m-90) cc_final: 0.7373 (m-90) REVERT: G 434 MET cc_start: 0.9002 (ppp) cc_final: 0.8771 (ppp) REVERT: J 626 MET cc_start: 0.8654 (ptm) cc_final: 0.8405 (ttp) outliers start: 4 outliers final: 4 residues processed: 212 average time/residue: 0.6376 time to fit residues: 202.4006 Evaluate side-chains 164 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 160 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 9.9990 chunk 201 optimal weight: 8.9990 chunk 138 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 179 optimal weight: 5.9990 chunk 268 optimal weight: 20.0000 chunk 284 optimal weight: 20.0000 chunk 140 optimal weight: 0.6980 chunk 254 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 130 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN F 82 GLN F 130 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 640 GLN G 82 GLN G 130 GLN G 170 GLN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 640 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5701 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25737 Z= 0.262 Angle : 0.674 10.066 35118 Z= 0.337 Chirality : 0.046 0.776 4482 Planarity : 0.004 0.041 4272 Dihedral : 9.764 68.839 6252 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 34.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.34 % Allowed : 0.99 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.15), residues: 3066 helix: 1.21 (0.26), residues: 411 sheet: 0.40 (0.14), residues: 1209 loop : 1.15 (0.18), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 395 HIS 0.005 0.002 HIS G 85 PHE 0.017 0.002 PHE F 391 TYR 0.024 0.002 TYR G 217 ARG 0.008 0.001 ARG K 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 3.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8474 (mmp) cc_final: 0.7778 (mmm) REVERT: A 434 MET cc_start: 0.8880 (ppp) cc_final: 0.8619 (ppp) REVERT: B 626 MET cc_start: 0.8819 (ptm) cc_final: 0.8215 (ttp) REVERT: F 100 MET cc_start: 0.9108 (ptp) cc_final: 0.8843 (ptp) REVERT: F 175 LEU cc_start: 0.9287 (mt) cc_final: 0.9086 (mt) REVERT: I 626 MET cc_start: 0.8849 (ptm) cc_final: 0.8322 (ttp) REVERT: G 45 TRP cc_start: 0.7737 (m-90) cc_final: 0.7397 (m-90) REVERT: J 626 MET cc_start: 0.8808 (ptm) cc_final: 0.8455 (ptm) REVERT: L 64 LEU cc_start: 0.7933 (mt) cc_final: 0.7710 (mt) REVERT: L 70 ILE cc_start: 0.8668 (tt) cc_final: 0.8381 (tt) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.6660 time to fit residues: 191.8665 Evaluate side-chains 167 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 20.0000 chunk 161 optimal weight: 7.9990 chunk 4 optimal weight: 0.0000 chunk 211 optimal weight: 40.0000 chunk 117 optimal weight: 10.0000 chunk 242 optimal weight: 20.0000 chunk 196 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 145 optimal weight: 8.9990 chunk 255 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 overall best weight: 7.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN B 590 GLN ** F 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 550 GLN I 590 GLN ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 550 GLN H 192 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5951 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 25737 Z= 0.488 Angle : 0.996 15.835 35118 Z= 0.489 Chirality : 0.050 0.515 4482 Planarity : 0.006 0.093 4272 Dihedral : 10.360 66.181 6252 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 66.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.72 % Favored : 93.18 % Rotamer: Outliers : 0.57 % Allowed : 2.17 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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 (0.15), residues: 3066 helix: -1.22 (0.22), residues: 441 sheet: -0.06 (0.14), residues: 1182 loop : -0.24 (0.17), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 45 HIS 0.012 0.004 HIS G 105 PHE 0.037 0.005 PHE A 391 TYR 0.033 0.003 TYR G 217 ARG 0.021 0.001 ARG F 151 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 165 time to evaluate : 3.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9177 (ptp) cc_final: 0.8915 (ptp) REVERT: A 161 MET cc_start: 0.8430 (tmm) cc_final: 0.8213 (tmm) REVERT: B 595 ILE cc_start: 0.9636 (tt) cc_final: 0.9401 (pt) REVERT: I 530 MET cc_start: 0.9419 (mtp) cc_final: 0.9118 (mtm) REVERT: G 150 MET cc_start: 0.8885 (mmm) cc_final: 0.8191 (mmm) outliers start: 3 outliers final: 0 residues processed: 168 average time/residue: 0.6881 time to fit residues: 171.8918 Evaluate side-chains 132 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 6.9990 chunk 255 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 166 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 284 optimal weight: 8.9990 chunk 236 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 287 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 287 GLN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 25737 Z= 0.309 Angle : 0.707 10.776 35118 Z= 0.357 Chirality : 0.046 0.804 4482 Planarity : 0.004 0.044 4272 Dihedral : 9.393 63.276 6252 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 51.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.46 % Allowed : 0.95 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: -0.40 (0.15), residues: 3066 helix: -1.01 (0.22), residues: 438 sheet: 0.03 (0.14), residues: 1197 loop : -0.11 (0.17), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 628 HIS 0.007 0.002 HIS F 374 PHE 0.020 0.003 PHE A 353 TYR 0.027 0.002 TYR G 217 ARG 0.004 0.001 ARG H 234 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 3.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8893 (mmp) cc_final: 0.8341 (mmm) REVERT: B 530 MET cc_start: 0.9554 (mtp) cc_final: 0.8711 (ptt) REVERT: F 150 MET cc_start: 0.8260 (mmt) cc_final: 0.7956 (mmm) REVERT: F 434 MET cc_start: 0.8730 (ppp) cc_final: 0.8469 (ppp) REVERT: I 530 MET cc_start: 0.9488 (mtp) cc_final: 0.9084 (mtm) REVERT: G 150 MET cc_start: 0.9002 (mmm) cc_final: 0.8408 (mmm) REVERT: J 626 MET cc_start: 0.8737 (ptm) cc_final: 0.8206 (ttp) REVERT: K 64 LEU cc_start: 0.7910 (mt) cc_final: 0.7673 (mt) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.7346 time to fit residues: 180.3775 Evaluate side-chains 138 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 20.0000 chunk 32 optimal weight: 0.9980 chunk 162 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 239 optimal weight: 20.0000 chunk 158 optimal weight: 3.9990 chunk 283 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 172 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5857 moved from start: 0.5633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25737 Z= 0.207 Angle : 0.595 7.310 35118 Z= 0.302 Chirality : 0.044 0.713 4482 Planarity : 0.004 0.039 4272 Dihedral : 8.591 60.436 6252 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 45.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.46 % Allowed : 0.76 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: -0.06 (0.15), residues: 3066 helix: -0.31 (0.23), residues: 444 sheet: 0.08 (0.14), residues: 1185 loop : 0.13 (0.18), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 628 HIS 0.005 0.001 HIS F 374 PHE 0.014 0.002 PHE C 166 TYR 0.014 0.001 TYR K 78 ARG 0.003 0.000 ARG C 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 3.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8927 (mmp) cc_final: 0.8424 (mmm) REVERT: B 530 MET cc_start: 0.9588 (mtp) cc_final: 0.8492 (ptp) REVERT: B 626 MET cc_start: 0.8399 (ptm) cc_final: 0.8107 (ppp) REVERT: F 150 MET cc_start: 0.8227 (mmt) cc_final: 0.7910 (mmm) REVERT: F 434 MET cc_start: 0.8755 (ppp) cc_final: 0.8504 (ppp) REVERT: I 626 MET cc_start: 0.8573 (ptm) cc_final: 0.8368 (ppp) REVERT: G 150 MET cc_start: 0.9001 (mmm) cc_final: 0.8434 (mmm) REVERT: J 626 MET cc_start: 0.8862 (ptm) cc_final: 0.7417 (ttp) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.7181 time to fit residues: 175.0146 Evaluate side-chains 138 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 3.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 20.0000 chunk 113 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 180 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5895 moved from start: 0.5866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 25737 Z= 0.248 Angle : 0.628 7.090 35118 Z= 0.316 Chirality : 0.043 0.663 4482 Planarity : 0.004 0.038 4272 Dihedral : 8.419 59.725 6252 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 50.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.53 % Allowed : 1.07 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: -0.01 (0.16), residues: 3066 helix: -0.19 (0.24), residues: 426 sheet: 0.10 (0.14), residues: 1215 loop : 0.16 (0.18), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 628 HIS 0.005 0.002 HIS F 216 PHE 0.019 0.002 PHE A 353 TYR 0.020 0.002 TYR G 217 ARG 0.003 0.000 ARG H 234 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 3.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8965 (mmp) cc_final: 0.8408 (mmm) REVERT: F 150 MET cc_start: 0.8121 (mmt) cc_final: 0.7822 (mmm) REVERT: F 434 MET cc_start: 0.8742 (ppp) cc_final: 0.8501 (ppp) REVERT: I 626 MET cc_start: 0.8694 (ptm) cc_final: 0.8045 (ptm) REVERT: G 150 MET cc_start: 0.9057 (mmm) cc_final: 0.8504 (mmm) REVERT: J 530 MET cc_start: 0.9054 (mtm) cc_final: 0.8772 (ptp) REVERT: D 70 ILE cc_start: 0.8929 (tt) cc_final: 0.8720 (tt) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.7255 time to fit residues: 160.0436 Evaluate side-chains 136 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 3.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 0.6980 chunk 271 optimal weight: 9.9990 chunk 247 optimal weight: 0.8980 chunk 264 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 238 optimal weight: 9.9990 chunk 249 optimal weight: 4.9990 chunk 263 optimal weight: 0.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5871 moved from start: 0.5964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25737 Z= 0.197 Angle : 0.581 6.918 35118 Z= 0.294 Chirality : 0.044 0.630 4482 Planarity : 0.004 0.038 4272 Dihedral : 8.156 59.441 6252 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 47.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.53 % Allowed : 0.34 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.14 (0.16), residues: 3066 helix: 0.06 (0.24), residues: 429 sheet: 0.14 (0.14), residues: 1209 loop : 0.26 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 628 HIS 0.004 0.001 HIS F 85 PHE 0.014 0.002 PHE A 233 TYR 0.019 0.001 TYR G 217 ARG 0.005 0.000 ARG I 588 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 3.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8992 (mmp) cc_final: 0.8483 (mmm) REVERT: B 530 MET cc_start: 0.8430 (ttp) cc_final: 0.8126 (ptp) REVERT: F 100 MET cc_start: 0.9087 (pmm) cc_final: 0.8784 (pmm) REVERT: F 150 MET cc_start: 0.8203 (mmt) cc_final: 0.7956 (mmm) REVERT: F 434 MET cc_start: 0.8729 (ppp) cc_final: 0.8487 (ppp) REVERT: I 626 MET cc_start: 0.8619 (ptm) cc_final: 0.8226 (ppp) REVERT: G 150 MET cc_start: 0.9068 (mmm) cc_final: 0.8624 (mmm) REVERT: J 530 MET cc_start: 0.9134 (mtm) cc_final: 0.8663 (ptp) REVERT: J 626 MET cc_start: 0.8536 (ptm) cc_final: 0.8279 (ppp) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.7250 time to fit residues: 164.2362 Evaluate side-chains 132 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 2.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 0.0870 chunk 279 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 chunk 132 optimal weight: 0.5980 chunk 194 optimal weight: 4.9990 chunk 292 optimal weight: 20.0000 chunk 269 optimal weight: 6.9990 chunk 233 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 180 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5827 moved from start: 0.6016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 25737 Z= 0.148 Angle : 0.539 6.952 35118 Z= 0.273 Chirality : 0.043 0.596 4482 Planarity : 0.003 0.072 4272 Dihedral : 7.658 59.433 6252 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 43.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.53 % Allowed : 0.30 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.46 (0.16), residues: 3066 helix: 0.84 (0.26), residues: 411 sheet: 0.34 (0.15), residues: 1179 loop : 0.30 (0.18), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 596 HIS 0.007 0.001 HIS G 249 PHE 0.024 0.001 PHE G 233 TYR 0.021 0.001 TYR G 217 ARG 0.009 0.000 ARG L 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 3.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8974 (mmp) cc_final: 0.8596 (mmm) REVERT: F 100 MET cc_start: 0.9053 (pmm) cc_final: 0.8811 (pmm) REVERT: F 150 MET cc_start: 0.8215 (mmt) cc_final: 0.7947 (mmm) REVERT: G 100 MET cc_start: 0.9105 (ptp) cc_final: 0.8774 (ptp) REVERT: G 104 MET cc_start: 0.8535 (mmp) cc_final: 0.8306 (mmp) REVERT: G 150 MET cc_start: 0.9139 (mmm) cc_final: 0.8740 (mmm) REVERT: J 530 MET cc_start: 0.9123 (mtm) cc_final: 0.8285 (ptp) REVERT: J 626 MET cc_start: 0.8459 (ptm) cc_final: 0.8060 (ppp) REVERT: D 70 ILE cc_start: 0.8923 (tt) cc_final: 0.8705 (tt) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.7212 time to fit residues: 162.7581 Evaluate side-chains 128 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 5.9990 chunk 248 optimal weight: 0.2980 chunk 71 optimal weight: 10.0000 chunk 215 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 233 optimal weight: 20.0000 chunk 97 optimal weight: 8.9990 chunk 239 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.082500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.064181 restraints weight = 2143007.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.066376 restraints weight = 492994.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.067342 restraints weight = 209950.435| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 630 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1037 | |-----------------------------------------------------------------------------| r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.6281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25737 Z= 0.227 Angle : 0.599 6.806 35118 Z= 0.302 Chirality : 0.042 0.598 4482 Planarity : 0.004 0.101 4272 Dihedral : 7.439 58.571 6252 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 51.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.53 % Allowed : 0.30 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.29 (0.16), residues: 3066 helix: 0.62 (0.25), residues: 411 sheet: 0.22 (0.15), residues: 1212 loop : 0.22 (0.18), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 596 HIS 0.005 0.001 HIS G 216 PHE 0.020 0.002 PHE A 353 TYR 0.025 0.002 TYR G 217 ARG 0.006 0.000 ARG L 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6017.63 seconds wall clock time: 110 minutes 5.41 seconds (6605.41 seconds total)