Starting phenix.real_space_refine on Thu Apr 11 04:38:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n65_24195/04_2024/7n65_24195.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n65_24195/04_2024/7n65_24195.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n65_24195/04_2024/7n65_24195.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n65_24195/04_2024/7n65_24195.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n65_24195/04_2024/7n65_24195.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n65_24195/04_2024/7n65_24195.pdb" } resolution = 4.15 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= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 13365 2.51 5 N 3471 2.21 5 O 4572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 91": "OE1" <-> "OE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A ASP 113": "OD1" <-> "OD2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 624": "OD1" <-> "OD2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "C ARG 31": "NH1" <-> "NH2" Residue "C ASP 54": "OD1" <-> "OD2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C ASP 73": "OD1" <-> "OD2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 107": "OD1" <-> "OD2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "D ARG 26": "NH1" <-> "NH2" Residue "D TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 47": "NH1" <-> "NH2" Residue "D TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E ASP 113": "OD1" <-> "OD2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 268": "OE1" <-> "OE2" Residue "E ASP 368": "OD1" <-> "OD2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 624": "OD1" <-> "OD2" Residue "F GLU 648": "OE1" <-> "OE2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G GLU 16": "OE1" <-> "OE2" Residue "G ARG 30": "NH1" <-> "NH2" Residue "G ARG 31": "NH1" <-> "NH2" Residue "G ASP 54": "OD1" <-> "OD2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G ASP 73": "OD1" <-> "OD2" Residue "G TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 107": "OD1" <-> "OD2" Residue "G ARG 111": "NH1" <-> "NH2" Residue "H ARG 26": "NH1" <-> "NH2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 47": "NH1" <-> "NH2" Residue "H TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 91": "OE1" <-> "OE2" Residue "I GLU 92": "OE1" <-> "OE2" Residue "I ASP 113": "OD1" <-> "OD2" Residue "I PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 268": "OE1" <-> "OE2" Residue "I ASP 368": "OD1" <-> "OD2" Residue "I PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 624": "OD1" <-> "OD2" Residue "J GLU 648": "OE1" <-> "OE2" Residue "K ARG 3": "NH1" <-> "NH2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "K ARG 30": "NH1" <-> "NH2" Residue "K ARG 31": "NH1" <-> "NH2" Residue "K ASP 54": "OD1" <-> "OD2" Residue "K GLU 57": "OE1" <-> "OE2" Residue "K ASP 73": "OD1" <-> "OD2" Residue "K TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 107": "OD1" <-> "OD2" Residue "K ARG 111": "NH1" <-> "NH2" Residue "L ARG 26": "NH1" <-> "NH2" Residue "L TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 21525 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 3522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3522 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 425} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1056 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1015 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "D" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 778 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "E" Number of atoms: 3522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3522 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 425} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1056 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1015 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "H" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 778 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "I" Number of atoms: 3522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3522 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 425} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "J" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1056 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1015 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "L" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 778 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 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: 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: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" 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: "W" 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 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: 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: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 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: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "m" Number of atoms: 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: "n" 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: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "0" 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: "1" 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: "2" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "3" 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: "4" 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: "5" 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: "6" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "7" Number of atoms: 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: "8" 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: "9" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "AA" Number of atoms: 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 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: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "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: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "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: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.64, per 1000 atoms: 0.54 Number of scatterers: 21525 At special positions: 0 Unit cell: (162, 163.35, 141.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 4572 8.00 N 3471 7.00 C 13365 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, 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=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.23 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.02 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.04 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.02 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.04 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.02 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=1.80 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=18, symmetry=0 Links applied ALPHA1-2 " MAN 0 4 " - " MAN 0 5 " " MAN 4 4 " - " MAN 4 5 " " MAN S 4 " - " MAN S 5 " " MAN W 4 " - " MAN W 5 " " MAN j 4 " - " MAN j 5 " " MAN n 4 " - " MAN n 5 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " MAN 0 6 " - " MAN 0 7 " " BMA 2 3 " - " MAN 2 4 " " BMA 3 3 " - " MAN 3 7 " " MAN 3 4 " - " MAN 3 5 " " BMA 4 3 " - " MAN 4 4 " " MAN 4 6 " - " MAN 4 7 " " BMA S 3 " - " MAN S 4 " " MAN S 6 " - " MAN S 7 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 7 " " MAN V 4 " - " MAN V 5 " " BMA W 3 " - " MAN W 4 " " MAN W 6 " - " MAN W 7 " " BMA j 3 " - " MAN j 4 " " MAN j 6 " - " MAN j 7 " " BMA l 3 " - " MAN l 4 " " BMA m 3 " - " MAN m 7 " " MAN m 4 " - " MAN m 5 " " BMA n 3 " - " MAN n 4 " " MAN n 6 " - " MAN n 7 " ALPHA1-6 " BMA 0 3 " - " MAN 0 6 " " BMA 2 3 " - " MAN 2 5 " " BMA 3 3 " - " MAN 3 4 " " MAN 3 4 " - " MAN 3 6 " " BMA 4 3 " - " MAN 4 6 " " MAN 4 6 " - " MAN 4 8 " " BMA S 3 " - " MAN S 6 " " BMA U 3 " - " MAN U 5 " " BMA V 3 " - " MAN V 4 " " MAN V 4 " - " MAN V 6 " " BMA W 3 " - " MAN W 6 " " MAN W 6 " - " MAN W 8 " " BMA j 3 " - " MAN j 6 " " BMA l 3 " - " MAN l 5 " " BMA m 3 " - " MAN m 4 " " MAN m 4 " - " MAN m 6 " " BMA n 3 " - " MAN n 6 " " MAN n 6 " - " MAN n 8 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 7 2 " - " BMA 7 3 " " NAG 8 1 " - " NAG 8 2 " " NAG 9 1 " - " NAG 9 2 " " 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 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 S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " 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 f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " NAGAA 1 " - " NAGAA 2 " NAG-ASN " NAG 0 1 " - " ASN I 262 " " NAG 1 1 " - " ASN I 276 " " NAG 2 1 " - " ASN I 295 " " NAG 3 1 " - " ASN I 301 " " NAG 4 1 " - " ASN I 332 " " NAG 5 1 " - " ASN I 355 " " NAG 6 1 " - " ASN I 363 " " NAG 7 1 " - " ASN I 386 " " NAG 8 1 " - " ASN I 392 " " NAG 9 1 " - " ASN I 448 " " NAG A 601 " - " ASN A 339 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 637 " " NAG E 601 " - " ASN E 339 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG I 601 " - " ASN I 339 " " NAG J 701 " - " ASN J 618 " " NAG J 702 " - " ASN J 637 " " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 133 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 160 " " NAG Q 1 " - " ASN A 197 " " NAG R 1 " - " ASN A 234 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN A 276 " " NAG U 1 " - " ASN A 295 " " NAG V 1 " - " ASN A 301 " " NAG W 1 " - " ASN A 332 " " NAG X 1 " - " ASN A 355 " " NAG Y 1 " - " ASN A 363 " " NAG Z 1 " - " ASN A 386 " " NAG a 1 " - " ASN A 392 " " NAG b 1 " - " ASN A 448 " " NAG c 1 " - " ASN B 611 " " NAG d 1 " - " ASN E 88 " " NAG e 1 " - " ASN E 133 " " NAG f 1 " - " ASN E 156 " " NAG g 1 " - " ASN E 160 " " NAG h 1 " - " ASN E 197 " " NAG i 1 " - " ASN E 234 " " NAG j 1 " - " ASN E 262 " " NAG k 1 " - " ASN E 276 " " NAG l 1 " - " ASN E 295 " " NAG m 1 " - " ASN E 301 " " NAG n 1 " - " ASN E 332 " " NAG o 1 " - " ASN E 355 " " NAG p 1 " - " ASN E 363 " " NAG q 1 " - " ASN E 386 " " NAG r 1 " - " ASN E 392 " " NAG s 1 " - " ASN E 448 " " NAG t 1 " - " ASN F 611 " " NAG u 1 " - " ASN I 88 " " NAG v 1 " - " ASN I 133 " " NAG w 1 " - " ASN I 156 " " NAG x 1 " - " ASN I 160 " " NAG y 1 " - " ASN I 197 " " NAG z 1 " - " ASN I 234 " " NAGAA 1 " - " ASN J 611 " Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.97 Conformation dependent library (CDL) restraints added in 3.9 seconds 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4518 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 39 sheets defined 20.8% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.905A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 removed outlier: 4.151A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 removed outlier: 3.663A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 596 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.656A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 655 removed outlier: 3.540A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 662 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.577A pdb=" N ARG C 31 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 28 through 32' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 100 through 104 removed outlier: 4.516A pdb=" N LEU C 103 " --> pdb=" O ALA C 100 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL C 104 " --> pdb=" O TYR C 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 100 through 104' Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 351 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.905A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 484 removed outlier: 4.152A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 543 removed outlier: 3.662A pdb=" N ALA F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 596 Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.657A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 655 removed outlier: 3.540A pdb=" N LEU F 645 " --> pdb=" O ILE F 641 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 662 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.578A pdb=" N ARG G 31 " --> pdb=" O GLY G 28 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 100 through 104 removed outlier: 4.515A pdb=" N LEU G 103 " --> pdb=" O ALA G 100 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL G 104 " --> pdb=" O TYR G 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 100 through 104' Processing helix chain 'I' and resid 99 through 117 Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 177 through 179 No H-bonds generated for 'chain 'I' and resid 177 through 179' Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 335 through 351 Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 387 through 391 Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.905A pdb=" N GLN I 428 " --> pdb=" O ASN I 425 " (cutoff:3.500A) Processing helix chain 'I' and resid 474 through 484 removed outlier: 4.152A pdb=" N ASN I 478 " --> pdb=" O ASP I 474 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 537 through 543 removed outlier: 3.662A pdb=" N ALA J 541 " --> pdb=" O LEU J 537 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN J 543 " --> pdb=" O VAL J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 571 through 596 Processing helix chain 'J' and resid 619 through 624 Processing helix chain 'J' and resid 627 through 636 removed outlier: 3.657A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 655 removed outlier: 3.540A pdb=" N LEU J 645 " --> pdb=" O ILE J 641 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN J 650 " --> pdb=" O LEU J 646 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN J 651 " --> pdb=" O GLU J 647 " (cutoff:3.500A) Processing helix chain 'J' and resid 656 through 662 Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.577A pdb=" N ARG K 31 " --> pdb=" O GLY K 28 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 28 through 32' Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'K' and resid 100 through 104 removed outlier: 4.516A pdb=" N LEU K 103 " --> pdb=" O ALA K 100 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL K 104 " --> pdb=" O TYR K 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 100 through 104' 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 removed outlier: 3.592A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.619A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 176 removed outlier: 3.631A pdb=" N CYS A 131 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS A 189 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.557A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 309 removed outlier: 3.706A pdb=" N ASP A 321A" --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ALA A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.234A pdb=" N GLY C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR C 94 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL C 124 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA C 92 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 97 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR C 34 " --> pdb=" O ASP C 50 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ASP C 50 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 17 through 20 Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 4 Processing sheet with id=AB2, first strand: chain 'D' and resid 18 through 21 Processing sheet with id=AB3, first strand: chain 'D' and resid 47 through 48 Processing sheet with id=AB4, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AB5, first strand: chain 'E' and resid 35 through 40 Processing sheet with id=AB6, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.592A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 55 through 56 Processing sheet with id=AB8, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.618A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 170 through 176 removed outlier: 3.631A pdb=" N CYS E 131 " --> pdb=" O LYS E 189 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.558A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 309 removed outlier: 3.705A pdb=" N ASP E 321A" --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ILE E 309 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ALA E 316 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 470 Processing sheet with id=AC3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.234A pdb=" N GLY G 10 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR G 94 " --> pdb=" O THR G 122 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL G 124 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA G 92 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA G 97 " --> pdb=" O THR G 35 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N THR G 34 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ASP G 50 " --> pdb=" O THR G 34 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 17 through 20 Processing sheet with id=AC5, first strand: chain 'H' and resid 3 through 4 Processing sheet with id=AC6, first strand: chain 'H' and resid 18 through 21 Processing sheet with id=AC7, first strand: chain 'H' and resid 47 through 48 Processing sheet with id=AC8, first strand: chain 'H' and resid 50 through 51 Processing sheet with id=AC9, first strand: chain 'I' and resid 35 through 40 Processing sheet with id=AD1, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.592A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 55 through 56 Processing sheet with id=AD3, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.618A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 170 through 176 removed outlier: 3.630A pdb=" N CYS I 131 " --> pdb=" O LYS I 189 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS I 189 " --> pdb=" O CYS I 131 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.558A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 259 through 261 current: chain 'I' and resid 284 through 309 removed outlier: 3.705A pdb=" N ASP I 321A" --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LYS I 305 " --> pdb=" O THR I 320 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N THR I 320 " --> pdb=" O LYS I 305 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE I 307 " --> pdb=" O TYR I 318 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N TYR I 318 " --> pdb=" O ILE I 307 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ILE I 309 " --> pdb=" O ALA I 316 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ALA I 316 " --> pdb=" O ILE I 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 315 through 323 current: chain 'I' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 381 through 385 current: chain 'I' and resid 465 through 470 Processing sheet with id=AD7, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.233A pdb=" N GLY K 10 " --> pdb=" O THR K 125 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR K 94 " --> pdb=" O THR K 122 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL K 124 " --> pdb=" O ALA K 92 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA K 92 " --> pdb=" O VAL K 124 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA K 97 " --> pdb=" O THR K 35 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR K 34 " --> pdb=" O ASP K 50 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ASP K 50 " --> pdb=" O THR K 34 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 17 through 20 Processing sheet with id=AD9, first strand: chain 'L' and resid 3 through 4 Processing sheet with id=AE1, first strand: chain 'L' and resid 18 through 21 Processing sheet with id=AE2, first strand: chain 'L' and resid 47 through 48 Processing sheet with id=AE3, first strand: chain 'L' and resid 50 through 51 516 hydrogen bonds defined for protein. 1341 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: 6.68 Time building geometry restraints manager: 13.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3418 1.32 - 1.44: 6285 1.44 - 1.57: 12047 1.57 - 1.69: 15 1.69 - 1.82: 156 Bond restraints: 21921 Sorted by residual: bond pdb=" C CYS I 218 " pdb=" N ALA I 219 " ideal model delta sigma weight residual 1.335 1.190 0.145 3.59e-02 7.76e+02 1.63e+01 bond pdb=" C CYS A 218 " pdb=" N ALA A 219 " ideal model delta sigma weight residual 1.335 1.190 0.145 3.59e-02 7.76e+02 1.63e+01 bond pdb=" C CYS E 218 " pdb=" N ALA E 219 " ideal model delta sigma weight residual 1.335 1.191 0.144 3.59e-02 7.76e+02 1.61e+01 bond pdb=" C5 BMA V 3 " pdb=" C6 BMA V 3 " ideal model delta sigma weight residual 1.526 1.455 0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C5 BMA 3 3 " pdb=" C6 BMA 3 3 " ideal model delta sigma weight residual 1.526 1.456 0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 21916 not shown) Histogram of bond angle deviations from ideal: 97.08 - 104.53: 330 104.53 - 111.99: 12015 111.99 - 119.44: 7238 119.44 - 126.90: 9892 126.90 - 134.35: 306 Bond angle restraints: 29781 Sorted by residual: angle pdb=" N ALA E 70 " pdb=" CA ALA E 70 " pdb=" C ALA E 70 " ideal model delta sigma weight residual 114.75 104.06 10.69 1.26e+00 6.30e-01 7.19e+01 angle pdb=" N ALA A 70 " pdb=" CA ALA A 70 " pdb=" C ALA A 70 " ideal model delta sigma weight residual 114.75 104.11 10.64 1.26e+00 6.30e-01 7.14e+01 angle pdb=" N ALA I 70 " pdb=" CA ALA I 70 " pdb=" C ALA I 70 " ideal model delta sigma weight residual 114.75 104.11 10.64 1.26e+00 6.30e-01 7.13e+01 angle pdb=" N LYS E 65 " pdb=" CA LYS E 65 " pdb=" C LYS E 65 " ideal model delta sigma weight residual 110.80 127.13 -16.33 2.13e+00 2.20e-01 5.87e+01 angle pdb=" N LYS A 65 " pdb=" CA LYS A 65 " pdb=" C LYS A 65 " ideal model delta sigma weight residual 110.80 127.10 -16.30 2.13e+00 2.20e-01 5.86e+01 ... (remaining 29776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.62: 14045 23.62 - 47.23: 1002 47.23 - 70.85: 202 70.85 - 94.46: 186 94.46 - 118.08: 102 Dihedral angle restraints: 15537 sinusoidal: 8508 harmonic: 7029 Sorted by residual: dihedral pdb=" CA CYS E 501 " pdb=" C CYS E 501 " pdb=" N LYS E 502 " pdb=" CA LYS E 502 " ideal model delta harmonic sigma weight residual -180.00 -131.54 -48.46 0 5.00e+00 4.00e-02 9.39e+01 dihedral pdb=" CA CYS I 501 " pdb=" C CYS I 501 " pdb=" N LYS I 502 " pdb=" CA LYS I 502 " ideal model delta harmonic sigma weight residual -180.00 -131.55 -48.45 0 5.00e+00 4.00e-02 9.39e+01 dihedral pdb=" CA CYS A 501 " pdb=" C CYS A 501 " pdb=" N LYS A 502 " pdb=" CA LYS A 502 " ideal model delta harmonic sigma weight residual 180.00 -131.55 -48.45 0 5.00e+00 4.00e-02 9.39e+01 ... (remaining 15534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 3578 0.104 - 0.208: 256 0.208 - 0.311: 54 0.311 - 0.415: 9 0.415 - 0.519: 12 Chirality restraints: 3909 Sorted by residual: chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 8.86e+00 chirality pdb=" C1 NAG 3 2 " pdb=" O4 NAG 3 1 " pdb=" C2 NAG 3 2 " pdb=" O5 NAG 3 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 8.57e+00 chirality pdb=" C1 NAG m 2 " pdb=" O4 NAG m 1 " pdb=" C2 NAG m 2 " pdb=" O5 NAG m 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 8.47e+00 ... (remaining 3906 not shown) Planarity restraints: 3591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 205 " -0.062 5.00e-02 4.00e+02 9.35e-02 1.40e+01 pdb=" N PRO A 206 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS I 205 " -0.062 5.00e-02 4.00e+02 9.33e-02 1.39e+01 pdb=" N PRO I 206 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO I 206 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO I 206 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS E 205 " 0.062 5.00e-02 4.00e+02 9.33e-02 1.39e+01 pdb=" N PRO E 206 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO E 206 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 206 " 0.050 5.00e-02 4.00e+02 ... (remaining 3588 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 542 2.53 - 3.12: 19669 3.12 - 3.71: 33779 3.71 - 4.31: 47794 4.31 - 4.90: 72597 Nonbonded interactions: 174381 Sorted by model distance: nonbonded pdb=" OE2 GLU B 647 " pdb=" NH1 ARG F 542 " model vdw 1.935 2.520 nonbonded pdb=" O LEU C 27 " pdb=" O2 BMA V 3 " model vdw 2.001 2.432 nonbonded pdb=" O LEU G 27 " pdb=" O2 BMA m 3 " model vdw 2.005 2.432 nonbonded pdb=" OG SER I 274 " pdb=" O ASN I 283 " model vdw 2.091 2.440 nonbonded pdb=" OG SER A 274 " pdb=" O ASN A 283 " model vdw 2.092 2.440 ... (remaining 174376 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '0' and (resid 1 or resid 4 through 7)) selection = (chain '3' and (resid 1 or resid 4 through 7)) selection = (chain '4' and (resid 2 or resid 5 through 8)) selection = (chain 'S' and (resid 1 or resid 4 through 7)) selection = (chain 'V' and (resid 1 or resid 4 through 7)) selection = (chain 'W' and (resid 2 or resid 5 through 8)) selection = (chain 'j' and (resid 1 or resid 4 through 7)) selection = (chain 'm' and (resid 1 or resid 4 through 7)) selection = (chain 'n' and (resid 2 or resid 5 through 8)) } ncs_group { reference = chain '1' selection = chain '6' selection = chain '7' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'T' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'k' selection = chain 'p' selection = chain 'q' selection = chain 'u' selection = chain 'w' selection = chain 'x' } ncs_group { reference = chain '2' selection = chain 'U' selection = chain 'l' } ncs_group { reference = chain '5' selection = chain '8' selection = chain '9' selection = chain 'AA' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'X' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'h' selection = chain 'i' selection = chain 'o' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'v' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 15.130 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 60.310 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.550 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 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 : 0.011 0.145 21921 Z= 0.715 Angle : 1.358 16.325 29781 Z= 0.693 Chirality : 0.071 0.519 3909 Planarity : 0.007 0.093 3531 Dihedral : 20.892 118.077 10902 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 36.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 15.22 % Favored : 84.58 % Rotamer: Outliers : 4.29 % Allowed : 11.29 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (0.14), residues: 2412 helix: -2.71 (0.20), residues: 375 sheet: -2.06 (0.21), residues: 579 loop : -3.58 (0.13), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP F 610 HIS 0.006 0.002 HIS G 102 PHE 0.024 0.004 PHE I 159 TYR 0.024 0.003 TYR L 93 ARG 0.019 0.001 ARG A 503 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 305 time to evaluate : 2.348 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: A 47 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8114 (p0) REVERT: A 115 SER cc_start: 0.8979 (OUTLIER) cc_final: 0.8640 (t) REVERT: A 116 LEU cc_start: 0.8672 (mt) cc_final: 0.8284 (tp) REVERT: A 377 ASN cc_start: 0.8323 (t0) cc_final: 0.8005 (t0) REVERT: B 530 MET cc_start: 0.8106 (mtm) cc_final: 0.7716 (mtt) REVERT: B 545 LEU cc_start: 0.7295 (tp) cc_final: 0.6642 (tp) REVERT: B 624 ASP cc_start: 0.8366 (t70) cc_final: 0.7762 (t70) REVERT: B 643 TYR cc_start: 0.8597 (m-10) cc_final: 0.8351 (m-80) REVERT: C 37 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8676 (p) REVERT: C 53 GLU cc_start: 0.7638 (pp20) cc_final: 0.7001 (pp20) REVERT: D 72 SER cc_start: 0.9083 (t) cc_final: 0.8746 (p) REVERT: D 88 TYR cc_start: 0.8482 (m-80) cc_final: 0.8221 (m-80) REVERT: E 116 LEU cc_start: 0.8714 (mt) cc_final: 0.8317 (tp) REVERT: E 391 PHE cc_start: 0.8215 (m-80) cc_final: 0.7683 (m-80) REVERT: G 53 GLU cc_start: 0.7411 (pp20) cc_final: 0.6841 (pp20) REVERT: H 81 GLN cc_start: 0.9195 (mm110) cc_final: 0.8745 (mm-40) REVERT: I 161 MET cc_start: 0.7763 (tpt) cc_final: 0.7394 (tpt) REVERT: I 251 ILE cc_start: 0.8853 (mt) cc_final: 0.8479 (mt) REVERT: I 377 ASN cc_start: 0.8414 (t0) cc_final: 0.8174 (t0) REVERT: J 530 MET cc_start: 0.8084 (mtm) cc_final: 0.7187 (mtt) outliers start: 90 outliers final: 22 residues processed: 382 average time/residue: 0.3641 time to fit residues: 209.0833 Evaluate side-chains 206 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 181 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 188 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 114 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS D 16 GLN D 81 GLN E 82 GLN ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 625 ASN G 52 ASN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 HIS H 16 GLN I 82 GLN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 GLN ** I 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 422 GLN ** I 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21921 Z= 0.263 Angle : 0.935 17.036 29781 Z= 0.452 Chirality : 0.057 0.425 3909 Planarity : 0.006 0.087 3531 Dihedral : 16.720 89.631 6459 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 22.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.32 % Favored : 88.68 % Rotamer: Outliers : 0.38 % Allowed : 6.05 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.15), residues: 2412 helix: -1.46 (0.22), residues: 417 sheet: -1.73 (0.21), residues: 567 loop : -3.23 (0.13), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 610 HIS 0.006 0.001 HIS C 102 PHE 0.024 0.002 PHE E 159 TYR 0.016 0.002 TYR I 40 ARG 0.008 0.001 ARG D 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 308 time to evaluate : 2.567 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: A 317 PHE cc_start: 0.7811 (t80) cc_final: 0.7302 (t80) REVERT: A 377 ASN cc_start: 0.7911 (t0) cc_final: 0.7458 (t0) REVERT: A 391 PHE cc_start: 0.8284 (m-80) cc_final: 0.7519 (m-10) REVERT: A 434 MET cc_start: 0.7200 (tmm) cc_final: 0.6930 (tmm) REVERT: B 543 ASN cc_start: 0.8449 (m110) cc_final: 0.7493 (t0) REVERT: B 624 ASP cc_start: 0.8323 (t70) cc_final: 0.7767 (t70) REVERT: C 53 GLU cc_start: 0.7203 (pp20) cc_final: 0.6744 (pp20) REVERT: C 72 ARG cc_start: 0.4717 (ptp-170) cc_final: 0.4255 (ptm160) REVERT: D 72 SER cc_start: 0.8904 (t) cc_final: 0.8656 (p) REVERT: D 88 TYR cc_start: 0.8590 (m-80) cc_final: 0.8127 (m-80) REVERT: E 52 LEU cc_start: 0.9149 (mt) cc_final: 0.8863 (mt) REVERT: E 377 ASN cc_start: 0.7698 (t0) cc_final: 0.7403 (t0) REVERT: E 391 PHE cc_start: 0.8297 (m-80) cc_final: 0.8041 (m-80) REVERT: F 530 MET cc_start: 0.7942 (mtt) cc_final: 0.7701 (mtt) REVERT: G 53 GLU cc_start: 0.7276 (pp20) cc_final: 0.6764 (pp20) REVERT: G 59 LYS cc_start: 0.7909 (tttm) cc_final: 0.7604 (tttm) REVERT: G 83 MET cc_start: 0.8873 (mpp) cc_final: 0.8645 (mpp) REVERT: H 89 TYR cc_start: 0.7734 (m-80) cc_final: 0.7249 (m-80) REVERT: I 317 PHE cc_start: 0.7942 (t80) cc_final: 0.7533 (t80) REVERT: J 543 ASN cc_start: 0.8507 (m-40) cc_final: 0.8223 (p0) REVERT: J 591 GLN cc_start: 0.8682 (mt0) cc_final: 0.8157 (mt0) outliers start: 8 outliers final: 3 residues processed: 316 average time/residue: 0.3619 time to fit residues: 174.6278 Evaluate side-chains 193 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 190 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 218 optimal weight: 9.9990 chunk 235 optimal weight: 0.0970 chunk 194 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 175 optimal weight: 0.8980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN A 352 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 21921 Z= 0.363 Angle : 0.965 16.892 29781 Z= 0.463 Chirality : 0.057 0.398 3909 Planarity : 0.006 0.082 3531 Dihedral : 14.214 78.150 6459 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 25.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.18 % Favored : 86.69 % Rotamer: Outliers : 0.57 % Allowed : 5.86 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.15), residues: 2412 helix: -0.72 (0.25), residues: 384 sheet: -1.80 (0.20), residues: 636 loop : -3.11 (0.14), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 610 HIS 0.003 0.001 HIS A 352 PHE 0.022 0.002 PHE I 159 TYR 0.017 0.002 TYR C 101 ARG 0.005 0.001 ARG E 503 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 275 time to evaluate : 2.500 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: A 251 ILE cc_start: 0.8991 (mp) cc_final: 0.8673 (mp) REVERT: A 377 ASN cc_start: 0.8305 (t0) cc_final: 0.8088 (t0) REVERT: A 391 PHE cc_start: 0.8308 (m-80) cc_final: 0.8038 (m-10) REVERT: B 530 MET cc_start: 0.7509 (mtt) cc_final: 0.7163 (mtt) REVERT: B 624 ASP cc_start: 0.8219 (t70) cc_final: 0.7893 (t70) REVERT: C 53 GLU cc_start: 0.7377 (pp20) cc_final: 0.6981 (pp20) REVERT: D 88 TYR cc_start: 0.8625 (m-80) cc_final: 0.8205 (m-80) REVERT: E 150 MET cc_start: 0.2802 (ttt) cc_final: 0.2584 (ttm) REVERT: E 251 ILE cc_start: 0.8713 (mt) cc_final: 0.8364 (mp) REVERT: E 377 ASN cc_start: 0.8055 (t0) cc_final: 0.7734 (t0) REVERT: E 378 CYS cc_start: 0.4248 (t) cc_final: 0.3572 (t) REVERT: E 391 PHE cc_start: 0.8296 (m-80) cc_final: 0.8012 (m-80) REVERT: F 530 MET cc_start: 0.8083 (mtt) cc_final: 0.7736 (mtt) REVERT: F 545 LEU cc_start: 0.7103 (mt) cc_final: 0.6830 (tp) REVERT: F 567 LYS cc_start: 0.5790 (mttm) cc_final: 0.5517 (mtpt) REVERT: G 53 GLU cc_start: 0.7355 (pp20) cc_final: 0.6777 (pp20) REVERT: G 59 LYS cc_start: 0.7988 (tttm) cc_final: 0.7630 (tttm) REVERT: H 89 TYR cc_start: 0.7828 (m-80) cc_final: 0.7421 (m-80) REVERT: I 80 ASN cc_start: 0.8525 (t0) cc_final: 0.8217 (t0) REVERT: I 161 MET cc_start: 0.7734 (tpt) cc_final: 0.7510 (tpt) REVERT: I 251 ILE cc_start: 0.8687 (mt) cc_final: 0.8356 (mm) REVERT: I 377 ASN cc_start: 0.7875 (t0) cc_final: 0.7535 (m-40) REVERT: I 378 CYS cc_start: 0.3674 (t) cc_final: 0.2594 (t) REVERT: J 530 MET cc_start: 0.7628 (mtt) cc_final: 0.7267 (mtt) REVERT: J 543 ASN cc_start: 0.8359 (m-40) cc_final: 0.7750 (t0) REVERT: K 53 GLU cc_start: 0.7588 (pp20) cc_final: 0.7142 (pp20) outliers start: 12 outliers final: 8 residues processed: 286 average time/residue: 0.3608 time to fit residues: 157.2547 Evaluate side-chains 190 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 182 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.9980 chunk 164 optimal weight: 8.9990 chunk 113 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 219 optimal weight: 9.9990 chunk 231 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 HIS ** I 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 616 ASN ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21921 Z= 0.238 Angle : 0.883 16.835 29781 Z= 0.423 Chirality : 0.055 0.414 3909 Planarity : 0.005 0.077 3531 Dihedral : 12.188 69.320 6459 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 0.24 % Allowed : 5.52 % Favored : 94.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.15), residues: 2412 helix: -0.62 (0.24), residues: 420 sheet: -1.91 (0.20), residues: 588 loop : -2.89 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 35 HIS 0.002 0.001 HIS H 36 PHE 0.015 0.001 PHE A 382 TYR 0.035 0.002 TYR B 643 ARG 0.007 0.001 ARG G 3 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 286 time to evaluate : 2.307 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: A 391 PHE cc_start: 0.8233 (m-80) cc_final: 0.7985 (m-10) REVERT: B 624 ASP cc_start: 0.8104 (t70) cc_final: 0.7817 (t70) REVERT: C 53 GLU cc_start: 0.7265 (pp20) cc_final: 0.6852 (pp20) REVERT: D 88 TYR cc_start: 0.8565 (m-80) cc_final: 0.8128 (m-80) REVERT: E 251 ILE cc_start: 0.8685 (mt) cc_final: 0.8370 (mp) REVERT: E 317 PHE cc_start: 0.8293 (t80) cc_final: 0.8064 (t80) REVERT: E 377 ASN cc_start: 0.7963 (t0) cc_final: 0.7680 (t0) REVERT: E 391 PHE cc_start: 0.8282 (m-80) cc_final: 0.8009 (m-80) REVERT: F 530 MET cc_start: 0.7957 (mtt) cc_final: 0.7688 (mtt) REVERT: F 543 ASN cc_start: 0.8713 (m110) cc_final: 0.7764 (t0) REVERT: F 545 LEU cc_start: 0.7183 (mt) cc_final: 0.6736 (tp) REVERT: F 567 LYS cc_start: 0.5410 (mttm) cc_final: 0.5082 (mtpt) REVERT: F 591 GLN cc_start: 0.8789 (tp40) cc_final: 0.8513 (tp40) REVERT: G 2 ILE cc_start: 0.8981 (pt) cc_final: 0.8402 (tt) REVERT: G 53 GLU cc_start: 0.7195 (pp20) cc_final: 0.6736 (pp20) REVERT: G 59 LYS cc_start: 0.8178 (tttm) cc_final: 0.7884 (tttm) REVERT: H 89 TYR cc_start: 0.7738 (m-80) cc_final: 0.7362 (m-80) REVERT: I 80 ASN cc_start: 0.8461 (t0) cc_final: 0.8162 (t0) REVERT: I 208 VAL cc_start: 0.7469 (OUTLIER) cc_final: 0.7212 (p) REVERT: I 251 ILE cc_start: 0.8618 (mt) cc_final: 0.8317 (mm) REVERT: I 377 ASN cc_start: 0.7700 (t0) cc_final: 0.7228 (m-40) REVERT: J 530 MET cc_start: 0.7970 (mtt) cc_final: 0.7478 (mtt) REVERT: J 543 ASN cc_start: 0.8188 (m-40) cc_final: 0.7073 (t0) REVERT: J 591 GLN cc_start: 0.8543 (mt0) cc_final: 0.8068 (pt0) REVERT: J 595 ILE cc_start: 0.9086 (mt) cc_final: 0.8683 (mt) REVERT: J 616 ASN cc_start: 0.7421 (OUTLIER) cc_final: 0.7002 (m-40) REVERT: K 53 GLU cc_start: 0.7483 (pp20) cc_final: 0.7132 (pp20) outliers start: 5 outliers final: 0 residues processed: 291 average time/residue: 0.3692 time to fit residues: 161.6298 Evaluate side-chains 196 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 194 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 172 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 208 optimal weight: 0.0060 chunk 58 optimal weight: 8.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 ASN ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 428 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21921 Z= 0.226 Angle : 0.865 16.847 29781 Z= 0.418 Chirality : 0.055 0.414 3909 Planarity : 0.005 0.072 3531 Dihedral : 10.907 61.566 6459 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 0.14 % Allowed : 4.24 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.16), residues: 2412 helix: -0.23 (0.26), residues: 402 sheet: -1.95 (0.19), residues: 654 loop : -2.80 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 610 HIS 0.009 0.001 HIS I 374 PHE 0.013 0.001 PHE G 68 TYR 0.038 0.002 TYR B 643 ARG 0.008 0.001 ARG K 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 305 time to evaluate : 2.467 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: A 377 ASN cc_start: 0.8115 (t0) cc_final: 0.7772 (m-40) REVERT: A 391 PHE cc_start: 0.8189 (m-80) cc_final: 0.7902 (m-10) REVERT: B 624 ASP cc_start: 0.8147 (t70) cc_final: 0.7828 (t70) REVERT: C 53 GLU cc_start: 0.7263 (pp20) cc_final: 0.6863 (pp20) REVERT: D 88 TYR cc_start: 0.8550 (m-80) cc_final: 0.8121 (m-10) REVERT: E 378 CYS cc_start: 0.3952 (t) cc_final: 0.2965 (t) REVERT: E 391 PHE cc_start: 0.8436 (m-80) cc_final: 0.8151 (m-80) REVERT: F 530 MET cc_start: 0.7879 (mtt) cc_final: 0.7595 (mtt) REVERT: F 543 ASN cc_start: 0.8733 (m110) cc_final: 0.7732 (t0) REVERT: F 545 LEU cc_start: 0.7184 (mt) cc_final: 0.6895 (tp) REVERT: F 591 GLN cc_start: 0.8735 (tp40) cc_final: 0.8452 (tp40) REVERT: F 616 ASN cc_start: 0.6378 (OUTLIER) cc_final: 0.5965 (m-40) REVERT: G 2 ILE cc_start: 0.9052 (pt) cc_final: 0.8414 (tt) REVERT: G 30 ARG cc_start: 0.7669 (mpp80) cc_final: 0.7232 (mpp80) REVERT: G 53 GLU cc_start: 0.7231 (pp20) cc_final: 0.6713 (pp20) REVERT: G 59 LYS cc_start: 0.8000 (tttm) cc_final: 0.7734 (tttm) REVERT: I 161 MET cc_start: 0.7717 (mmp) cc_final: 0.7174 (tpp) REVERT: I 251 ILE cc_start: 0.8794 (mt) cc_final: 0.8538 (mm) REVERT: I 378 CYS cc_start: 0.3185 (t) cc_final: 0.2748 (t) REVERT: I 391 PHE cc_start: 0.8473 (m-80) cc_final: 0.8208 (m-10) REVERT: J 530 MET cc_start: 0.7920 (mtt) cc_final: 0.7426 (mtt) REVERT: J 543 ASN cc_start: 0.8242 (m-40) cc_final: 0.7151 (t0) REVERT: J 655 LYS cc_start: 0.8166 (tppt) cc_final: 0.7356 (mtmt) REVERT: L 88 TYR cc_start: 0.8863 (m-10) cc_final: 0.8552 (m-10) outliers start: 3 outliers final: 0 residues processed: 308 average time/residue: 0.3440 time to fit residues: 162.5790 Evaluate side-chains 215 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 214 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 9.9990 chunk 208 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 ASN I 82 GLN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 ASN ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 ASN ** I 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 21921 Z= 0.376 Angle : 0.958 17.011 29781 Z= 0.461 Chirality : 0.057 0.383 3909 Planarity : 0.006 0.138 3531 Dihedral : 10.743 59.585 6459 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 25.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.18 % Favored : 86.82 % Rotamer: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.16), residues: 2412 helix: -0.14 (0.26), residues: 384 sheet: -1.75 (0.20), residues: 615 loop : -2.82 (0.15), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 427 HIS 0.003 0.001 HIS A 374 PHE 0.029 0.002 PHE I 159 TYR 0.030 0.002 TYR K 101 ARG 0.019 0.001 ARG H 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 2.307 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: A 377 ASN cc_start: 0.8501 (t0) cc_final: 0.8042 (t0) REVERT: A 391 PHE cc_start: 0.8280 (m-80) cc_final: 0.7960 (m-10) REVERT: B 530 MET cc_start: 0.7961 (mpp) cc_final: 0.7630 (mpp) REVERT: B 545 LEU cc_start: 0.7681 (tp) cc_final: 0.7231 (tp) REVERT: B 624 ASP cc_start: 0.8264 (t70) cc_final: 0.7975 (t70) REVERT: C 30 ARG cc_start: 0.7548 (mtm180) cc_final: 0.6850 (mpp80) REVERT: C 53 GLU cc_start: 0.7377 (pp20) cc_final: 0.6944 (pp20) REVERT: D 88 TYR cc_start: 0.8581 (m-80) cc_final: 0.8195 (m-10) REVERT: E 378 CYS cc_start: 0.4082 (t) cc_final: 0.3179 (t) REVERT: E 445 CYS cc_start: 0.3819 (t) cc_final: 0.3385 (t) REVERT: F 530 MET cc_start: 0.7975 (mtt) cc_final: 0.7631 (mtt) REVERT: F 591 GLN cc_start: 0.8878 (tp40) cc_final: 0.8640 (tp-100) REVERT: G 2 ILE cc_start: 0.9019 (pt) cc_final: 0.8442 (tt) REVERT: G 53 GLU cc_start: 0.7379 (pp20) cc_final: 0.6870 (pp20) REVERT: G 59 LYS cc_start: 0.7864 (tttm) cc_final: 0.7581 (tttm) REVERT: H 88 TYR cc_start: 0.9046 (m-10) cc_final: 0.8649 (m-10) REVERT: I 378 CYS cc_start: 0.2734 (t) cc_final: 0.2319 (t) REVERT: J 543 ASN cc_start: 0.8205 (m-40) cc_final: 0.7164 (t0) REVERT: J 591 GLN cc_start: 0.8665 (mt0) cc_final: 0.8086 (mt0) REVERT: K 30 ARG cc_start: 0.7449 (mpp80) cc_final: 0.7096 (mpp80) REVERT: K 53 GLU cc_start: 0.7794 (pp20) cc_final: 0.7437 (pp20) REVERT: L 88 TYR cc_start: 0.8864 (m-10) cc_final: 0.8519 (m-10) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.3381 time to fit residues: 142.2477 Evaluate side-chains 186 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 169 optimal weight: 0.9980 chunk 131 optimal weight: 0.0980 chunk 195 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 231 optimal weight: 0.5980 chunk 144 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21921 Z= 0.234 Angle : 0.864 16.712 29781 Z= 0.416 Chirality : 0.054 0.399 3909 Planarity : 0.005 0.071 3531 Dihedral : 10.027 59.131 6459 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.16), residues: 2412 helix: -0.38 (0.25), residues: 405 sheet: -1.74 (0.20), residues: 600 loop : -2.64 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP I 35 HIS 0.006 0.001 HIS I 374 PHE 0.018 0.001 PHE I 382 TYR 0.018 0.002 TYR L 88 ARG 0.007 0.001 ARG K 3 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 2.476 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: A 377 ASN cc_start: 0.8395 (t0) cc_final: 0.7843 (t0) REVERT: A 391 PHE cc_start: 0.8386 (m-80) cc_final: 0.8035 (m-10) REVERT: B 530 MET cc_start: 0.7939 (mpp) cc_final: 0.7569 (mpp) REVERT: B 586 TYR cc_start: 0.8471 (t80) cc_final: 0.8224 (t80) REVERT: B 624 ASP cc_start: 0.8229 (t70) cc_final: 0.7899 (t70) REVERT: C 30 ARG cc_start: 0.7589 (mtm180) cc_final: 0.6762 (mpp80) REVERT: C 53 GLU cc_start: 0.7200 (pp20) cc_final: 0.6558 (pp20) REVERT: C 72 ARG cc_start: 0.4724 (ptp-170) cc_final: 0.4292 (ptm160) REVERT: D 88 TYR cc_start: 0.8558 (m-80) cc_final: 0.8115 (m-10) REVERT: E 377 ASN cc_start: 0.7838 (t0) cc_final: 0.7449 (m-40) REVERT: E 378 CYS cc_start: 0.3335 (t) cc_final: 0.3030 (t) REVERT: F 530 MET cc_start: 0.7876 (mtt) cc_final: 0.7581 (mtt) REVERT: F 543 ASN cc_start: 0.8639 (m110) cc_final: 0.7721 (t0) REVERT: F 545 LEU cc_start: 0.7242 (mt) cc_final: 0.6884 (tp) REVERT: F 652 GLN cc_start: 0.8361 (pp30) cc_final: 0.8130 (pp30) REVERT: G 2 ILE cc_start: 0.8999 (pt) cc_final: 0.8306 (tt) REVERT: G 53 GLU cc_start: 0.7327 (pp20) cc_final: 0.6854 (pp20) REVERT: H 88 TYR cc_start: 0.8919 (m-10) cc_final: 0.8324 (m-10) REVERT: I 378 CYS cc_start: 0.2503 (t) cc_final: 0.2283 (t) REVERT: I 445 CYS cc_start: 0.4118 (t) cc_final: 0.3796 (t) REVERT: J 530 MET cc_start: 0.8127 (mmp) cc_final: 0.7791 (mmp) REVERT: J 543 ASN cc_start: 0.8131 (m-40) cc_final: 0.7097 (t0) REVERT: K 53 GLU cc_start: 0.7644 (pp20) cc_final: 0.7327 (pp20) REVERT: L 88 TYR cc_start: 0.8753 (m-10) cc_final: 0.8282 (m-10) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.3436 time to fit residues: 149.9103 Evaluate side-chains 198 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.2980 chunk 92 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 157 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 21 optimal weight: 0.0770 chunk 181 optimal weight: 0.1980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN E 425 ASN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 HIS ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21921 Z= 0.202 Angle : 0.821 16.444 29781 Z= 0.397 Chirality : 0.053 0.412 3909 Planarity : 0.005 0.074 3531 Dihedral : 9.168 58.072 6459 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.16), residues: 2412 helix: -0.02 (0.26), residues: 402 sheet: -1.70 (0.19), residues: 642 loop : -2.61 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 35 HIS 0.006 0.001 HIS I 374 PHE 0.011 0.001 PHE I 159 TYR 0.022 0.002 TYR A 217 ARG 0.006 0.001 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 2.292 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: A 100 MET cc_start: 0.8570 (mtm) cc_final: 0.8317 (mpp) REVERT: A 377 ASN cc_start: 0.8282 (t0) cc_final: 0.7747 (t0) REVERT: A 391 PHE cc_start: 0.8401 (m-80) cc_final: 0.8075 (m-10) REVERT: B 530 MET cc_start: 0.7974 (mpp) cc_final: 0.7681 (mpp) REVERT: B 543 ASN cc_start: 0.8622 (m110) cc_final: 0.7469 (t0) REVERT: B 624 ASP cc_start: 0.8216 (t70) cc_final: 0.7874 (t70) REVERT: C 53 GLU cc_start: 0.7227 (pp20) cc_final: 0.6754 (pp20) REVERT: C 72 ARG cc_start: 0.4490 (ptp-170) cc_final: 0.4167 (ptm160) REVERT: D 88 TYR cc_start: 0.8574 (m-80) cc_final: 0.8091 (m-80) REVERT: E 217 TYR cc_start: 0.8475 (m-80) cc_final: 0.8230 (m-80) REVERT: E 377 ASN cc_start: 0.7673 (t0) cc_final: 0.7237 (m-40) REVERT: F 530 MET cc_start: 0.7763 (mtt) cc_final: 0.7545 (mtt) REVERT: F 543 ASN cc_start: 0.8741 (m110) cc_final: 0.7800 (t0) REVERT: F 545 LEU cc_start: 0.7257 (mt) cc_final: 0.6859 (tp) REVERT: G 2 ILE cc_start: 0.8939 (pt) cc_final: 0.8279 (tt) REVERT: G 53 GLU cc_start: 0.7304 (pp20) cc_final: 0.6839 (pp20) REVERT: H 88 TYR cc_start: 0.8861 (m-10) cc_final: 0.8297 (m-10) REVERT: I 47 ASP cc_start: 0.8003 (m-30) cc_final: 0.7760 (p0) REVERT: I 100 MET cc_start: 0.9157 (mmm) cc_final: 0.8617 (mmp) REVERT: I 378 CYS cc_start: 0.2664 (t) cc_final: 0.2451 (t) REVERT: I 445 CYS cc_start: 0.4009 (t) cc_final: 0.3476 (t) REVERT: J 543 ASN cc_start: 0.8132 (m-40) cc_final: 0.7016 (t0) REVERT: K 53 GLU cc_start: 0.7640 (pp20) cc_final: 0.7323 (pp20) REVERT: L 88 TYR cc_start: 0.8583 (m-10) cc_final: 0.8191 (m-10) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.3186 time to fit residues: 141.2489 Evaluate side-chains 212 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 4.9990 chunk 221 optimal weight: 9.9990 chunk 202 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 203 optimal weight: 0.6980 chunk 214 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 ASN ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21921 Z= 0.229 Angle : 0.824 16.380 29781 Z= 0.398 Chirality : 0.053 0.400 3909 Planarity : 0.005 0.068 3531 Dihedral : 8.885 57.413 6459 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.16), residues: 2412 helix: -0.14 (0.26), residues: 405 sheet: -1.56 (0.19), residues: 636 loop : -2.56 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 35 HIS 0.004 0.001 HIS I 374 PHE 0.013 0.001 PHE F 522 TYR 0.020 0.002 TYR J 586 ARG 0.006 0.001 ARG K 3 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 2.301 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: A 377 ASN cc_start: 0.8454 (t0) cc_final: 0.7933 (t0) REVERT: A 391 PHE cc_start: 0.8426 (m-80) cc_final: 0.8202 (m-10) REVERT: B 530 MET cc_start: 0.8060 (mpp) cc_final: 0.7743 (mpp) REVERT: C 2 ILE cc_start: 0.9153 (pt) cc_final: 0.8787 (tt) REVERT: C 53 GLU cc_start: 0.7208 (pp20) cc_final: 0.6660 (pp20) REVERT: C 72 ARG cc_start: 0.4333 (ptp-170) cc_final: 0.3978 (ptm160) REVERT: D 88 TYR cc_start: 0.8526 (m-80) cc_final: 0.8098 (m-80) REVERT: E 377 ASN cc_start: 0.7844 (t0) cc_final: 0.7449 (m-40) REVERT: F 530 MET cc_start: 0.7827 (mtt) cc_final: 0.7570 (mtt) REVERT: F 543 ASN cc_start: 0.8623 (m110) cc_final: 0.8003 (t0) REVERT: F 545 LEU cc_start: 0.7131 (mt) cc_final: 0.6576 (tp) REVERT: G 2 ILE cc_start: 0.8966 (pt) cc_final: 0.8322 (tt) REVERT: G 53 GLU cc_start: 0.7325 (pp20) cc_final: 0.6875 (pp20) REVERT: H 88 TYR cc_start: 0.8854 (m-10) cc_final: 0.8339 (m-10) REVERT: I 80 ASN cc_start: 0.8760 (t0) cc_final: 0.8549 (t0) REVERT: J 543 ASN cc_start: 0.8170 (m-40) cc_final: 0.7050 (t0) REVERT: K 53 GLU cc_start: 0.7685 (pp20) cc_final: 0.7292 (pp20) REVERT: L 88 TYR cc_start: 0.8640 (m-10) cc_final: 0.8286 (m-10) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.3139 time to fit residues: 136.4142 Evaluate side-chains 202 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 4.9990 chunk 227 optimal weight: 0.8980 chunk 139 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 chunk 158 optimal weight: 0.9980 chunk 239 optimal weight: 5.9990 chunk 220 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 19 optimal weight: 0.3980 chunk 147 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN F 543 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21921 Z= 0.208 Angle : 0.817 16.109 29781 Z= 0.396 Chirality : 0.053 0.401 3909 Planarity : 0.005 0.067 3531 Dihedral : 8.641 57.192 6459 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.16), residues: 2412 helix: -0.10 (0.26), residues: 405 sheet: -1.33 (0.20), residues: 642 loop : -2.59 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 610 HIS 0.004 0.001 HIS I 374 PHE 0.013 0.001 PHE L 64 TYR 0.019 0.002 TYR J 586 ARG 0.006 0.000 ARG K 3 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 2.312 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: A 251 ILE cc_start: 0.8830 (mp) cc_final: 0.8460 (mp) REVERT: A 377 ASN cc_start: 0.8435 (t0) cc_final: 0.7918 (t0) REVERT: A 391 PHE cc_start: 0.8513 (m-80) cc_final: 0.8287 (m-10) REVERT: B 530 MET cc_start: 0.8027 (mpp) cc_final: 0.7665 (mpp) REVERT: C 2 ILE cc_start: 0.9125 (pt) cc_final: 0.8788 (tt) REVERT: C 53 GLU cc_start: 0.7174 (pp20) cc_final: 0.6624 (pp20) REVERT: C 72 ARG cc_start: 0.4356 (ptp-170) cc_final: 0.3958 (ptm160) REVERT: D 88 TYR cc_start: 0.8510 (m-80) cc_final: 0.8063 (m-80) REVERT: E 95 MET cc_start: 0.8377 (ppp) cc_final: 0.8051 (ppp) REVERT: E 377 ASN cc_start: 0.7960 (t0) cc_final: 0.7388 (m-40) REVERT: E 378 CYS cc_start: 0.3282 (t) cc_final: 0.2454 (t) REVERT: F 530 MET cc_start: 0.7965 (mtt) cc_final: 0.7741 (mtt) REVERT: F 543 ASN cc_start: 0.8595 (m-40) cc_final: 0.7898 (t0) REVERT: F 545 LEU cc_start: 0.7254 (mt) cc_final: 0.6854 (tp) REVERT: G 2 ILE cc_start: 0.8991 (pt) cc_final: 0.8419 (tt) REVERT: G 53 GLU cc_start: 0.7314 (pp20) cc_final: 0.6863 (pp20) REVERT: H 88 TYR cc_start: 0.8753 (m-10) cc_final: 0.8123 (m-10) REVERT: I 47 ASP cc_start: 0.7752 (m-30) cc_final: 0.7547 (p0) REVERT: J 543 ASN cc_start: 0.8155 (m-40) cc_final: 0.7039 (t0) REVERT: K 53 GLU cc_start: 0.7678 (pp20) cc_final: 0.7295 (pp20) REVERT: L 88 TYR cc_start: 0.8627 (m-10) cc_final: 0.8316 (m-10) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.3119 time to fit residues: 136.3083 Evaluate side-chains 212 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 175 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 190 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS B 591 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 HIS I 80 ASN I 82 GLN ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.092136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.071678 restraints weight = 82209.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.072194 restraints weight = 54419.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.072702 restraints weight = 50539.729| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 21921 Z= 0.399 Angle : 0.952 15.341 29781 Z= 0.460 Chirality : 0.056 0.380 3909 Planarity : 0.006 0.075 3531 Dihedral : 9.385 58.400 6459 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 26.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.14 % Favored : 86.86 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.16), residues: 2412 helix: -0.50 (0.25), residues: 402 sheet: -1.42 (0.20), residues: 636 loop : -2.81 (0.15), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP F 623 HIS 0.010 0.001 HIS A 105 PHE 0.027 0.002 PHE A 159 TYR 0.024 0.003 TYR A 61 ARG 0.007 0.001 ARG L 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4053.97 seconds wall clock time: 76 minutes 26.22 seconds (4586.22 seconds total)