Starting phenix.real_space_refine (version: dev) on Fri Dec 16 22:40:30 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf2_9359/12_2022/6nf2_9359.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf2_9359/12_2022/6nf2_9359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf2_9359/12_2022/6nf2_9359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf2_9359/12_2022/6nf2_9359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf2_9359/12_2022/6nf2_9359.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf2_9359/12_2022/6nf2_9359.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.002 sd= 0.074 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 32": "OE1" <-> "OE2" Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A ASP 141": "OD1" <-> "OD2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A ASP 167": "OD1" <-> "OD2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 474": "OD1" <-> "OD2" Residue "A ASP 477": "OD1" <-> "OD2" Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 584": "OE1" <-> "OE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "B ASP 659": "OD1" <-> "OD2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 61": "NH1" <-> "NH2" Residue "C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D ARG 52": "NH1" <-> "NH2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 81": "OD1" <-> "OD2" Residue "D PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 98": "OE1" <-> "OE2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E ASP 56": "OD1" <-> "OD2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 72": "OD1" <-> "OD2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 79": "OE1" <-> "OE2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "F PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 107": "OD1" <-> "OD2" Residue "G ASP 141": "OD1" <-> "OD2" Residue "G GLU 153": "OE1" <-> "OE2" Residue "G ASP 167": "OD1" <-> "OD2" Residue "G TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 368": "OD1" <-> "OD2" Residue "G PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 474": "OD1" <-> "OD2" Residue "G ASP 477": "OD1" <-> "OD2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H GLU 16": "OE1" <-> "OE2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H ASP 58": "OD1" <-> "OD2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H ARG 75": "NH1" <-> "NH2" Residue "H TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 100": "NH1" <-> "NH2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "I PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 584": "OE1" <-> "OE2" Residue "I GLU 648": "OE1" <-> "OE2" Residue "I ASP 659": "OD1" <-> "OD2" Residue "J GLU 6": "OE1" <-> "OE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J ASP 56": "OD1" <-> "OD2" Residue "J TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 72": "OD1" <-> "OD2" Residue "J TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 79": "OE1" <-> "OE2" Residue "K GLU 83": "OE1" <-> "OE2" Residue "K PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 77": "NH1" <-> "NH2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 107": "NH1" <-> "NH2" Residue "M GLU 17": "OE1" <-> "OE2" Residue "M ARG 52": "NH1" <-> "NH2" Residue "M PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 81": "OD1" <-> "OD2" Residue "M PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 98": "OE1" <-> "OE2" Residue "N PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 61": "NH1" <-> "NH2" Residue "N PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 6": "OE1" <-> "OE2" Residue "O GLU 16": "OE1" <-> "OE2" Residue "O TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "O ASP 58": "OD1" <-> "OD2" Residue "O ARG 66": "NH1" <-> "NH2" Residue "O ARG 75": "NH1" <-> "NH2" Residue "O TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 100": "NH1" <-> "NH2" Residue "O ASP 101": "OD1" <-> "OD2" Residue "P ARG 24": "NH1" <-> "NH2" Residue "P ARG 54": "NH1" <-> "NH2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 77": "NH1" <-> "NH2" Residue "P GLU 81": "OE1" <-> "OE2" Residue "P PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 107": "NH1" <-> "NH2" Residue "Q GLU 32": "OE1" <-> "OE2" Residue "Q TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 107": "OD1" <-> "OD2" Residue "Q ASP 141": "OD1" <-> "OD2" Residue "Q GLU 153": "OE1" <-> "OE2" Residue "Q ASP 167": "OD1" <-> "OD2" Residue "Q TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 368": "OD1" <-> "OD2" Residue "Q PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 474": "OD1" <-> "OD2" Residue "Q ASP 477": "OD1" <-> "OD2" Residue "R PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 584": "OE1" <-> "OE2" Residue "R GLU 648": "OE1" <-> "OE2" Residue "R ASP 659": "OD1" <-> "OD2" Residue "S GLU 6": "OE1" <-> "OE2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S ASP 56": "OD1" <-> "OD2" Residue "S TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 72": "OD1" <-> "OD2" Residue "S TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 79": "OE1" <-> "OE2" Residue "T GLU 83": "OE1" <-> "OE2" Residue "T PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 17": "OE1" <-> "OE2" Residue "U ARG 52": "NH1" <-> "NH2" Residue "U PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 81": "OD1" <-> "OD2" Residue "U PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 98": "OE1" <-> "OE2" Residue "V PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 61": "NH1" <-> "NH2" Residue "V PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 6": "OE1" <-> "OE2" Residue "W GLU 16": "OE1" <-> "OE2" Residue "W TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 38": "NH1" <-> "NH2" Residue "W ASP 58": "OD1" <-> "OD2" Residue "W ARG 66": "NH1" <-> "NH2" Residue "W ARG 75": "NH1" <-> "NH2" Residue "W TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 100": "NH1" <-> "NH2" Residue "W ASP 101": "OD1" <-> "OD2" Residue "X ARG 24": "NH1" <-> "NH2" Residue "X ARG 54": "NH1" <-> "NH2" Residue "X ARG 61": "NH1" <-> "NH2" Residue "X PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 77": "NH1" <-> "NH2" Residue "X GLU 81": "OE1" <-> "OE2" Residue "X PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 107": "NH1" <-> "NH2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 32604 Number of models: 1 Model: "" Number of chains: 78 Chain: "A" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "C" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "D" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "E" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "F" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "G" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "H" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 951 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 115} Chain: "I" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "J" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "K" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "L" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "M" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "N" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "O" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 951 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 115} Chain: "P" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "Q" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "R" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "S" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "T" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "U" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "V" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "W" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 951 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 115} Chain: "X" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} 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 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 chiralities: 2 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 6 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 chiralities: 2 Chain: "i" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 9 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 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 chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "r" 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: 3 Unresolved non-hydrogen chiralities: 5 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "t" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "u" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 6 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 9 Chain: "2" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "3" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "4" 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 chiralities: 2 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 chiralities: 2 Chain: "6" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "7" 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: 3 Unresolved non-hydrogen chiralities: 5 Chain: "8" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "9" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "AA" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "BA" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 6 Chain: "CA" 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 chiralities: 2 Chain: "DA" 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 chiralities: 2 Chain: "EA" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "FA" 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: 3 Unresolved non-hydrogen chiralities: 5 Chain: "GA" 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 chiralities: 2 Chain: "HA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 9 Chain: "IA" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "JA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 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 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 chiralities: 2 Chain: "G" 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 chiralities: 1 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 chiralities: 2 Chain: "Q" 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 chiralities: 1 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 chiralities: 2 Time building chain proxies: 17.65, per 1000 atoms: 0.54 Number of scatterers: 32604 At special positions: 0 Unit cell: (160.988, 152.402, 156.695, 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 171 16.00 O 6672 8.00 N 5331 7.00 C 20430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 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 201 " - pdb=" SG CYS A 433 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 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 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 98 " - pdb=" SG CYS C 100A" distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.05 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.02 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 98 " - pdb=" SG CYS N 100A" distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 54 " - pdb=" SG CYS Q 74 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 119 " - pdb=" SG CYS Q 205 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 126 " - pdb=" SG CYS Q 196 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 131 " - pdb=" SG CYS Q 157 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 201 " - pdb=" SG CYS Q 433 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 218 " - pdb=" SG CYS Q 247 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 228 " - pdb=" SG CYS Q 239 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 296 " - pdb=" SG CYS Q 331 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 378 " - pdb=" SG CYS Q 445 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 385 " - pdb=" SG CYS Q 418 " distance=2.03 Simple disulfide: pdb=" SG CYS R 598 " - pdb=" SG CYS R 604 " distance=2.02 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.04 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 92 " distance=2.03 Simple disulfide: pdb=" SG CYS V 98 " - pdb=" SG CYS V 100A" distance=2.03 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 92 " distance=2.04 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 1 4 " - " MAN 1 5 " " MAN 1 5 " - " MAN 1 6 " " MAN f 4 " - " MAN f 5 " " MAN l 4 " - " MAN l 5 " " MAN l 5 " - " MAN l 6 " " MAN v 4 " - " MAN v 5 " " MANBA 4 " - " MANBA 5 " " MANHA 4 " - " MANHA 5 " " MANHA 5 " - " MANHA 6 " ALPHA1-3 " BMA 1 3 " - " MAN 1 4 " " MAN 1 7 " - " MAN 1 8 " " BMA 3 3 " - " MAN 3 4 " " BMA 6 3 " - " MAN 6 4 " " BMA 7 3 " - " MAN 7 4 " " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 4 " " BMA f 3 " - " MAN f 4 " " BMA j 3 " - " MAN j 4 " " BMA l 3 " - " MAN l 4 " " MAN l 7 " - " MAN l 8 " " BMA n 3 " - " MAN n 4 " " BMA q 3 " - " MAN q 4 " " BMA r 3 " - " MAN r 4 " " BMA v 3 " - " MAN v 4 " " BMA z 3 " - " MAN z 4 " " BMABA 3 " - " MANBA 4 " " BMAFA 3 " - " MANFA 4 " " BMAHA 3 " - " MANHA 4 " " MANHA 7 " - " MANHA 8 " " BMAJA 3 " - " MANJA 4 " ALPHA1-6 " BMA 1 3 " - " MAN 1 7 " " MAN 1 7 " - " MAN 1 9 " " BMA 7 3 " - " MAN 7 5 " " BMA 9 3 " - " MAN 9 4 " " BMA b 3 " - " MAN b 5 " " BMA d 3 " - " MAN d 4 " " BMA f 3 " - " MAN f 6 " " BMA j 3 " - " MAN j 5 " " BMA l 3 " - " MAN l 7 " " MAN l 7 " - " MAN l 9 " " BMA r 3 " - " MAN r 5 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 6 " " BMA z 3 " - " MAN z 5 " " BMABA 3 " - " MANBA 6 " " BMAFA 3 " - " MANFA 5 " " BMAHA 3 " - " MANHA 7 " " MANHA 7 " - " MANHA 9 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " 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 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 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG 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 q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG 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 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 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGDA 1 " - " NAGDA 2 " " NAGEA 1 " - " NAGEA 2 " " NAGEA 2 " - " BMAEA 3 " " NAGFA 1 " - " NAGFA 2 " " NAGFA 2 " - " BMAFA 3 " " NAGGA 1 " - " NAGGA 2 " " NAGHA 1 " - " NAGHA 2 " " NAGHA 2 " - " BMAHA 3 " " NAGIA 1 " - " NAGIA 2 " " NAGIA 2 " - " BMAIA 3 " " NAGJA 1 " - " NAGJA 2 " " NAGJA 2 " - " BMAJA 3 " NAG-ASN " NAG 0 1 " - " ASN G 392 " " NAG 1 1 " - " ASN G 332 " " NAG 2 1 " - " ASN G 448 " " NAG 3 1 " - " ASN G 276 " " NAG 4 1 " - " ASN Q 88 " " NAG 5 1 " - " ASN Q 133 " " NAG 6 1 " - " ASN Q 137 " " NAG 7 1 " - " ASN Q 156 " " NAG 8 1 " - " ASN Q 160 " " NAG 9 1 " - " ASN Q 197 " " NAG A 634 " - " ASN A 355 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 611 " " NAG G 634 " - " ASN G 355 " " NAG I 701 " - " ASN I 637 " " NAG I 702 " - " ASN I 611 " " NAG Q 634 " - " ASN Q 355 " " NAG R 701 " - " ASN R 637 " " NAG R 702 " - " ASN R 611 " " NAG Y 1 " - " ASN A 88 " " NAG Z 1 " - " ASN A 133 " " NAG a 1 " - " ASN A 137 " " NAG b 1 " - " ASN A 156 " " NAG c 1 " - " ASN A 160 " " NAG d 1 " - " ASN A 197 " " NAG e 1 " - " ASN A 234 " " NAG f 1 " - " ASN A 262 " " NAG g 1 " - " ASN A 295 " " NAG h 1 " - " ASN A 301 " " NAG i 1 " - " ASN A 363 " " NAG j 1 " - " ASN A 386 " " NAG k 1 " - " ASN A 392 " " NAG l 1 " - " ASN A 332 " " NAG m 1 " - " ASN A 448 " " NAG n 1 " - " ASN A 276 " " NAG o 1 " - " ASN G 88 " " NAG p 1 " - " ASN G 133 " " NAG q 1 " - " ASN G 137 " " NAG r 1 " - " ASN G 156 " " NAG s 1 " - " ASN G 160 " " NAG t 1 " - " ASN G 197 " " NAG u 1 " - " ASN G 234 " " NAG v 1 " - " ASN G 262 " " NAG w 1 " - " ASN G 295 " " NAG x 1 " - " ASN G 301 " " NAG y 1 " - " ASN G 363 " " NAG z 1 " - " ASN G 386 " " NAGAA 1 " - " ASN Q 234 " " NAGBA 1 " - " ASN Q 262 " " NAGCA 1 " - " ASN Q 295 " " NAGDA 1 " - " ASN Q 301 " " NAGEA 1 " - " ASN Q 363 " " NAGFA 1 " - " ASN Q 386 " " NAGGA 1 " - " ASN Q 392 " " NAGHA 1 " - " ASN Q 332 " " NAGIA 1 " - " ASN Q 448 " " NAGJA 1 " - " ASN Q 276 " Time building additional restraints: 16.08 Conformation dependent library (CDL) restraints added in 4.8 seconds 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7080 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 78 sheets defined 13.7% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.548A pdb=" N TYR A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR A 63 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 115 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.952A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.826A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.960A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 Processing helix chain 'B' and resid 570 through 596 removed outlier: 4.187A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 616 removed outlier: 4.310A pdb=" N SER B 615 " --> pdb=" O ASN B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.578A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 663 removed outlier: 3.549A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.904A pdb=" N GLN C 64 " --> pdb=" O ARG C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 83 through 87 removed outlier: 4.112A pdb=" N THR C 87 " --> pdb=" O PRO C 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 100D through 100H Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'G' and resid 57 through 63 removed outlier: 3.548A pdb=" N TYR G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR G 63 " --> pdb=" O LYS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 115 Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.952A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.827A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 480 removed outlier: 3.959A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 537 through 543 Processing helix chain 'I' and resid 570 through 596 removed outlier: 4.186A pdb=" N LEU I 581 " --> pdb=" O GLN I 577 " (cutoff:3.500A) Processing helix chain 'I' and resid 611 through 616 removed outlier: 4.310A pdb=" N SER I 615 " --> pdb=" O ASN I 611 " (cutoff:3.500A) Processing helix chain 'I' and resid 618 through 623 Processing helix chain 'I' and resid 627 through 636 removed outlier: 3.579A pdb=" N LYS I 633 " --> pdb=" O LEU I 629 " (cutoff:3.500A) Processing helix chain 'I' and resid 641 through 663 removed outlier: 3.550A pdb=" N LEU I 663 " --> pdb=" O ASP I 659 " (cutoff:3.500A) Processing helix chain 'J' and resid 100D through 100H Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'N' and resid 61 through 64 removed outlier: 3.905A pdb=" N GLN N 64 " --> pdb=" O ARG N 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 61 through 64' Processing helix chain 'N' and resid 83 through 87 removed outlier: 4.112A pdb=" N THR N 87 " --> pdb=" O PRO N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 Processing helix chain 'Q' and resid 57 through 63 removed outlier: 3.547A pdb=" N TYR Q 61 " --> pdb=" O ASP Q 57 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR Q 63 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 115 Processing helix chain 'Q' and resid 122 through 126 removed outlier: 3.952A pdb=" N CYS Q 126 " --> pdb=" O THR Q 123 " (cutoff:3.500A) Processing helix chain 'Q' and resid 335 through 350 Processing helix chain 'Q' and resid 351 through 353 No H-bonds generated for 'chain 'Q' and resid 351 through 353' Processing helix chain 'Q' and resid 368 through 373 removed outlier: 3.828A pdb=" N THR Q 373 " --> pdb=" O LEU Q 369 " (cutoff:3.500A) Processing helix chain 'Q' and resid 475 through 480 removed outlier: 3.958A pdb=" N TRP Q 479 " --> pdb=" O MET Q 475 " (cutoff:3.500A) Processing helix chain 'R' and resid 529 through 534 Processing helix chain 'R' and resid 537 through 543 Processing helix chain 'R' and resid 570 through 596 removed outlier: 4.185A pdb=" N LEU R 581 " --> pdb=" O GLN R 577 " (cutoff:3.500A) Processing helix chain 'R' and resid 611 through 616 removed outlier: 4.310A pdb=" N SER R 615 " --> pdb=" O ASN R 611 " (cutoff:3.500A) Processing helix chain 'R' and resid 618 through 623 Processing helix chain 'R' and resid 627 through 636 removed outlier: 3.578A pdb=" N LYS R 633 " --> pdb=" O LEU R 629 " (cutoff:3.500A) Processing helix chain 'R' and resid 641 through 663 removed outlier: 3.548A pdb=" N LEU R 663 " --> pdb=" O ASP R 659 " (cutoff:3.500A) Processing helix chain 'S' and resid 100D through 100H Processing helix chain 'T' and resid 79 through 83 Processing helix chain 'V' and resid 61 through 64 removed outlier: 3.905A pdb=" N GLN V 64 " --> pdb=" O ARG V 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 61 through 64' Processing helix chain 'V' and resid 83 through 87 removed outlier: 4.113A pdb=" N THR V 87 " --> pdb=" O PRO V 84 " (cutoff:3.500A) Processing helix chain 'W' and resid 61 through 64 Processing helix chain 'W' and resid 83 through 87 Processing helix chain 'X' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.610A pdb=" N VAL I 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N VAL A 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N THR I 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 47 removed outlier: 4.001A pdb=" N VAL A 44 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.513A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 7.382A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.068A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.590A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.992A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.945A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 301 through 308 removed outlier: 7.368A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.656A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TRP H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 31 through 31B Processing sheet with id=AB3, first strand: chain 'B' and resid 603 through 609 removed outlier: 7.871A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.521A pdb=" N THR C 70 " --> pdb=" O TYR C 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.764A pdb=" N VAL C 10 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE C 40 " --> pdb=" O PHE C 45 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N PHE C 45 " --> pdb=" O ILE C 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.764A pdb=" N VAL C 10 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.535A pdb=" N THR D 5 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.391A pdb=" N LEU D 11 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN D 36 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU D 45 " --> pdb=" O GLN D 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.624A pdb=" N SER E 70 " --> pdb=" O SER E 79 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.834A pdb=" N TYR E 33 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TRP E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR E 50 " --> pdb=" O TRP E 34 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.753A pdb=" N TYR E 100O" --> pdb=" O LYS E 96 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 99 through 100A Processing sheet with id=AC4, first strand: chain 'F' and resid 11 through 13 removed outlier: 6.089A pdb=" N VAL F 11 " --> pdb=" O ILE F 105 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR F 86 " --> pdb=" O THR F 102 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP F 35 " --> pdb=" O ILE F 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 19 through 23 Processing sheet with id=AC6, first strand: chain 'G' and resid 44 through 47 removed outlier: 4.001A pdb=" N VAL G 44 " --> pdb=" O GLU G 492 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.512A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 130 through 133 Processing sheet with id=AC9, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AD1, first strand: chain 'G' and resid 271 through 273 removed outlier: 7.385A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 271 through 273 removed outlier: 11.068A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 10.589A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.992A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.946A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 301 through 308 removed outlier: 7.369A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 423 through 424 Processing sheet with id=AD5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD6, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.656A pdb=" N VAL O 12 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TRP O 34 " --> pdb=" O GLY O 50 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 30 through 31B Processing sheet with id=AD8, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.623A pdb=" N SER J 70 " --> pdb=" O SER J 79 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.833A pdb=" N TYR J 33 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TRP J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR J 50 " --> pdb=" O TRP J 34 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.751A pdb=" N TYR J 100O" --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 99 through 100A Processing sheet with id=AE3, first strand: chain 'K' and resid 11 through 13 removed outlier: 6.089A pdb=" N VAL K 11 " --> pdb=" O ILE K 105 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR K 86 " --> pdb=" O THR K 102 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP K 35 " --> pdb=" O ILE K 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE6, first strand: chain 'L' and resid 44 through 48 removed outlier: 5.712A pdb=" N LEU L 46 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 44 through 48 removed outlier: 5.712A pdb=" N LEU L 46 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 5 through 6 removed outlier: 3.536A pdb=" N THR M 5 " --> pdb=" O LYS M 24 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.391A pdb=" N LEU M 11 " --> pdb=" O GLU M 100 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN M 36 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU M 45 " --> pdb=" O GLN M 36 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.522A pdb=" N THR N 70 " --> pdb=" O TYR N 79 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.762A pdb=" N VAL N 10 " --> pdb=" O VAL N 110 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE N 40 " --> pdb=" O PHE N 45 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE N 45 " --> pdb=" O ILE N 40 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.762A pdb=" N VAL N 10 " --> pdb=" O VAL N 110 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'P' and resid 4 through 7 Processing sheet with id=AF6, first strand: chain 'P' and resid 44 through 48 removed outlier: 5.711A pdb=" N LEU P 46 " --> pdb=" O LEU P 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR P 97 " --> pdb=" O GLN P 90 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'P' and resid 44 through 48 removed outlier: 5.711A pdb=" N LEU P 46 " --> pdb=" O LEU P 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Q' and resid 495 through 499 removed outlier: 5.614A pdb=" N VAL R 608 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N VAL Q 38 " --> pdb=" O THR R 606 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N THR R 606 " --> pdb=" O VAL Q 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 44 through 47 removed outlier: 4.001A pdb=" N VAL Q 44 " --> pdb=" O GLU Q 492 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE Q 225 " --> pdb=" O VAL Q 245 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Q' and resid 91 through 94 removed outlier: 3.511A pdb=" N GLU Q 91 " --> pdb=" O CYS Q 239 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Q' and resid 130 through 133 Processing sheet with id=AG3, first strand: chain 'Q' and resid 181 through 183 Processing sheet with id=AG4, first strand: chain 'Q' and resid 271 through 273 removed outlier: 7.385A pdb=" N GLN Q 293 " --> pdb=" O SER Q 334 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER Q 334 " --> pdb=" O GLN Q 293 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Q' and resid 271 through 273 removed outlier: 11.067A pdb=" N VAL Q 286 " --> pdb=" O THR Q 455 " (cutoff:3.500A) removed outlier: 10.586A pdb=" N THR Q 455 " --> pdb=" O VAL Q 286 " (cutoff:3.500A) removed outlier: 11.992A pdb=" N PHE Q 288 " --> pdb=" O ILE Q 453 " (cutoff:3.500A) removed outlier: 11.649A pdb=" N ILE Q 453 " --> pdb=" O PHE Q 288 " (cutoff:3.500A) removed outlier: 10.945A pdb=" N THR Q 290 " --> pdb=" O GLY Q 451 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLY Q 451 " --> pdb=" O THR Q 290 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 301 through 308 removed outlier: 7.368A pdb=" N ASN Q 301 " --> pdb=" O ILE Q 322 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ILE Q 322 " --> pdb=" O ASN Q 301 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N THR Q 303 " --> pdb=" O GLY Q 321 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 423 through 424 Processing sheet with id=AG8, first strand: chain 'W' and resid 11 through 12 removed outlier: 3.657A pdb=" N VAL W 12 " --> pdb=" O THR W 110 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TRP W 34 " --> pdb=" O GLY W 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY W 50 " --> pdb=" O TRP W 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP W 36 " --> pdb=" O ILE W 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'W' and resid 30 through 31B removed outlier: 6.312A pdb=" N GLY R 516 " --> pdb=" O LYS W 97 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'S' and resid 5 through 7 removed outlier: 3.624A pdb=" N SER S 70 " --> pdb=" O SER S 79 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.834A pdb=" N TYR S 33 " --> pdb=" O THR S 95 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TRP S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TYR S 50 " --> pdb=" O TRP S 34 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TRP S 36 " --> pdb=" O ILE S 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.751A pdb=" N TYR S 100O" --> pdb=" O LYS S 96 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'S' and resid 99 through 100A Processing sheet with id=AH5, first strand: chain 'T' and resid 11 through 13 removed outlier: 6.089A pdb=" N VAL T 11 " --> pdb=" O ILE T 105 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR T 86 " --> pdb=" O THR T 102 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP T 35 " --> pdb=" O ILE T 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'T' and resid 19 through 23 Processing sheet with id=AH7, first strand: chain 'U' and resid 5 through 6 removed outlier: 3.535A pdb=" N THR U 5 " --> pdb=" O LYS U 24 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'U' and resid 10 through 13 removed outlier: 6.391A pdb=" N LEU U 11 " --> pdb=" O GLU U 100 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN U 36 " --> pdb=" O LEU U 45 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU U 45 " --> pdb=" O GLN U 36 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'V' and resid 3 through 6 removed outlier: 3.523A pdb=" N THR V 70 " --> pdb=" O TYR V 79 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'V' and resid 10 through 11 removed outlier: 6.763A pdb=" N VAL V 10 " --> pdb=" O VAL V 110 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ARG V 38 " --> pdb=" O TRP V 47 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TRP V 47 " --> pdb=" O ARG V 38 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE V 40 " --> pdb=" O PHE V 45 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE V 45 " --> pdb=" O ILE V 40 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'V' and resid 10 through 11 removed outlier: 6.763A pdb=" N VAL V 10 " --> pdb=" O VAL V 110 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'W' and resid 3 through 7 Processing sheet with id=AI4, first strand: chain 'X' and resid 4 through 7 Processing sheet with id=AI5, first strand: chain 'X' and resid 44 through 48 removed outlier: 5.714A pdb=" N LEU X 46 " --> pdb=" O LEU X 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU X 37 " --> pdb=" O LEU X 46 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR X 97 " --> pdb=" O GLN X 90 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'X' and resid 44 through 48 removed outlier: 5.714A pdb=" N LEU X 46 " --> pdb=" O LEU X 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU X 37 " --> pdb=" O LEU X 46 " (cutoff:3.500A) 1116 hydrogen bonds defined for protein. 2799 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: 12.92 Time building geometry restraints manager: 17.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9457 1.33 - 1.46: 9333 1.46 - 1.59: 14294 1.59 - 1.72: 0 1.72 - 1.85: 225 Bond restraints: 33309 Sorted by residual: bond pdb=" C HIS K 89 " pdb=" N ILE K 90 " ideal model delta sigma weight residual 1.330 1.288 0.041 1.57e-02 4.06e+03 6.96e+00 bond pdb=" C HIS F 89 " pdb=" N ILE F 90 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.57e-02 4.06e+03 6.44e+00 bond pdb=" C HIS T 89 " pdb=" N ILE T 90 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.57e-02 4.06e+03 6.43e+00 bond pdb=" C7 NAG o 2 " pdb=" N2 NAG o 2 " ideal model delta sigma weight residual 1.337 1.364 -0.027 1.10e-02 8.26e+03 5.83e+00 bond pdb=" C7 NAG Y 2 " pdb=" N2 NAG Y 2 " ideal model delta sigma weight residual 1.337 1.362 -0.025 1.10e-02 8.26e+03 5.29e+00 ... (remaining 33304 not shown) Histogram of bond angle deviations from ideal: 98.14 - 106.16: 928 106.16 - 114.18: 20271 114.18 - 122.21: 17794 122.21 - 130.23: 6073 130.23 - 138.26: 222 Bond angle restraints: 45288 Sorted by residual: angle pdb=" C2 NAG 4 2 " pdb=" N2 NAG 4 2 " pdb=" C7 NAG 4 2 " ideal model delta sigma weight residual 123.12 134.12 -11.00 1.28e+00 6.08e-01 7.35e+01 angle pdb=" C2 NAG Y 2 " pdb=" N2 NAG Y 2 " pdb=" C7 NAG Y 2 " ideal model delta sigma weight residual 123.12 133.95 -10.83 1.28e+00 6.08e-01 7.13e+01 angle pdb=" C2 NAG o 2 " pdb=" N2 NAG o 2 " pdb=" C7 NAG o 2 " ideal model delta sigma weight residual 123.12 133.94 -10.82 1.28e+00 6.08e-01 7.12e+01 angle pdb=" C ASN P 53 " pdb=" N ARG P 54 " pdb=" CA ARG P 54 " ideal model delta sigma weight residual 122.09 130.64 -8.55 1.48e+00 4.57e-01 3.34e+01 angle pdb=" C ASN X 53 " pdb=" N ARG X 54 " pdb=" CA ARG X 54 " ideal model delta sigma weight residual 122.09 130.64 -8.55 1.48e+00 4.57e-01 3.33e+01 ... (remaining 45283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.34: 18285 21.34 - 42.69: 1281 42.69 - 64.03: 210 64.03 - 85.38: 30 85.38 - 106.72: 27 Dihedral angle restraints: 19833 sinusoidal: 8778 harmonic: 11055 Sorted by residual: dihedral pdb=" CA ASP L 50 " pdb=" C ASP L 50 " pdb=" N VAL L 51 " pdb=" CA VAL L 51 " ideal model delta harmonic sigma weight residual -180.00 -119.37 -60.63 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA ASP P 50 " pdb=" C ASP P 50 " pdb=" N VAL P 51 " pdb=" CA VAL P 51 " ideal model delta harmonic sigma weight residual -180.00 -119.38 -60.62 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA ASP X 50 " pdb=" C ASP X 50 " pdb=" N VAL X 51 " pdb=" CA VAL X 51 " ideal model delta harmonic sigma weight residual -180.00 -119.47 -60.53 0 5.00e+00 4.00e-02 1.47e+02 ... (remaining 19830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 4599 0.079 - 0.159: 840 0.159 - 0.238: 117 0.238 - 0.318: 21 0.318 - 0.397: 12 Chirality restraints: 5589 Sorted by residual: chirality pdb=" C1 MAN q 4 " pdb=" O3 BMA q 3 " pdb=" C2 MAN q 4 " pdb=" O5 MAN q 4 " both_signs ideal model delta sigma weight residual False 2.40 2.34 0.06 2.00e-02 2.50e+03 8.11e+00 chirality pdb=" C1 MAN 6 4 " pdb=" O3 BMA 6 3 " pdb=" C2 MAN 6 4 " pdb=" O5 MAN 6 4 " both_signs ideal model delta sigma weight residual False 2.40 2.35 0.05 2.00e-02 2.50e+03 6.34e+00 chirality pdb=" C1 MAN a 4 " pdb=" O3 BMA a 3 " pdb=" C2 MAN a 4 " pdb=" O5 MAN a 4 " both_signs ideal model delta sigma weight residual False 2.40 2.35 0.05 2.00e-02 2.50e+03 6.00e+00 ... (remaining 5586 not shown) Planarity restraints: 5565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 28 " 0.091 5.00e-02 4.00e+02 1.40e-01 3.14e+01 pdb=" N PRO H 29 " -0.242 5.00e-02 4.00e+02 pdb=" CA PRO H 29 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO H 29 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR W 28 " -0.091 5.00e-02 4.00e+02 1.40e-01 3.13e+01 pdb=" N PRO W 29 " 0.242 5.00e-02 4.00e+02 pdb=" CA PRO W 29 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO W 29 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR O 28 " 0.091 5.00e-02 4.00e+02 1.40e-01 3.12e+01 pdb=" N PRO O 29 " -0.241 5.00e-02 4.00e+02 pdb=" CA PRO O 29 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO O 29 " 0.071 5.00e-02 4.00e+02 ... (remaining 5562 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 7003 2.77 - 3.31: 28556 3.31 - 3.84: 53775 3.84 - 4.37: 59169 4.37 - 4.90: 103109 Nonbonded interactions: 251612 Sorted by model distance: nonbonded pdb=" NH2 ARG W 100F" pdb=" OD2 ASP X 50 " model vdw 2.242 2.520 nonbonded pdb=" OG SER J 70 " pdb=" OG SER J 79 " model vdw 2.244 2.440 nonbonded pdb=" OG SER E 70 " pdb=" OG SER E 79 " model vdw 2.244 2.440 nonbonded pdb=" OG SER S 70 " pdb=" OG SER S 79 " model vdw 2.245 2.440 nonbonded pdb=" OH TYR G 318 " pdb=" OD2 ASP N 76B" model vdw 2.249 2.440 ... (remaining 251607 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '4' selection = chain '5' selection = chain 'CA' selection = chain 'DA' selection = chain 'GA' selection = chain 'Y' selection = chain 'Z' selection = chain 'g' selection = chain 'h' selection = chain 'k' selection = chain 'o' selection = chain 'p' selection = chain 'w' selection = chain 'x' } ncs_group { reference = chain '1' selection = chain 'HA' selection = chain 'l' } ncs_group { reference = chain '2' selection = chain '8' selection = chain 'AA' selection = chain 'EA' selection = chain 'IA' selection = chain 'c' selection = chain 'e' selection = chain 'i' selection = chain 'm' selection = chain 's' selection = chain 'u' selection = chain 'y' } ncs_group { reference = chain '3' selection = chain '6' selection = chain '9' selection = chain 'JA' selection = chain 'a' selection = chain 'd' selection = chain 'n' selection = chain 'q' selection = chain 't' } ncs_group { reference = chain '7' selection = chain 'FA' selection = chain 'b' selection = chain 'j' selection = chain 'r' selection = chain 'z' } ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'Q' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'R' } ncs_group { reference = chain 'BA' selection = chain 'f' selection = chain 'v' } ncs_group { reference = chain 'C' selection = chain 'N' selection = chain 'V' } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'U' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'T' } ncs_group { reference = chain 'H' selection = chain 'O' selection = chain 'W' } ncs_group { reference = chain 'L' selection = chain 'P' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 171 5.16 5 C 20430 2.51 5 N 5331 2.21 5 O 6672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 17.020 Check model and map are aligned: 0.460 Convert atoms to be neutral: 0.310 Process input model: 84.990 Find NCS groups from input model: 2.560 Set up NCS constraints: 0.850 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.076 33309 Z= 0.554 Angle : 1.156 19.499 45288 Z= 0.649 Chirality : 0.065 0.397 5589 Planarity : 0.008 0.140 5508 Dihedral : 14.970 106.722 12600 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.16 % Favored : 93.69 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.12), residues: 3801 helix: -2.83 (0.18), residues: 369 sheet: -1.25 (0.13), residues: 1269 loop : -2.22 (0.11), residues: 2163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 445 time to evaluate : 3.841 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 outliers start: 15 outliers final: 2 residues processed: 460 average time/residue: 0.5458 time to fit residues: 383.6458 Evaluate side-chains 223 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 221 time to evaluate : 4.089 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2629 time to fit residues: 5.7785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 6.9990 chunk 286 optimal weight: 0.8980 chunk 158 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 193 optimal weight: 10.0000 chunk 153 optimal weight: 20.0000 chunk 296 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 343 optimal weight: 4.9990 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 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 GLN A 203 GLN A 246 GLN A 328 GLN A 411 ASN B 543 ASN C 64 GLN C 72 GLN D 27 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN F 51 ASN G 72 HIS G 82 GLN G 183 GLN G 203 GLN G 246 GLN G 328 GLN G 411 ASN H 39 GLN I 543 ASN J 5 GLN J 58 ASN K 51 ASN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN M 27 GLN ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 64 GLN N 72 GLN P 27 GLN ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN ** Q 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 82 GLN Q 203 GLN Q 246 GLN Q 328 GLN Q 411 ASN R 543 ASN S 58 ASN T 51 ASN U 27 GLN U 36 GLN V 64 GLN V 72 GLN W 39 GLN ** W 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 27 GLN ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 53 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.067 33309 Z= 0.360 Angle : 0.718 9.845 45288 Z= 0.382 Chirality : 0.047 0.346 5589 Planarity : 0.005 0.079 5508 Dihedral : 10.191 111.973 5613 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.26 % Favored : 94.58 % Rotamer Outliers : 2.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.12), residues: 3801 helix: -0.94 (0.25), residues: 363 sheet: -0.90 (0.14), residues: 1239 loop : -1.83 (0.12), residues: 2199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 247 time to evaluate : 3.828 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 outliers start: 86 outliers final: 34 residues processed: 313 average time/residue: 0.4909 time to fit residues: 240.3589 Evaluate side-chains 228 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 194 time to evaluate : 3.707 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.3239 time to fit residues: 25.7303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 285 optimal weight: 1.9990 chunk 233 optimal weight: 0.1980 chunk 94 optimal weight: 10.0000 chunk 343 optimal weight: 4.9990 chunk 371 optimal weight: 0.9990 chunk 306 optimal weight: 0.9990 chunk 341 optimal weight: 3.9990 chunk 117 optimal weight: 0.1980 chunk 275 optimal weight: 0.4980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN B 543 ASN B 590 GLN C 101 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 HIS ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 411 ASN H 76 ASN I 543 ASN I 577 GLN I 590 GLN J 97 HIS ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 183 GLN Q 411 ASN R 543 ASN R 577 GLN R 590 GLN S 97 HIS V 101 GLN ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 33309 Z= 0.208 Angle : 0.645 8.858 45288 Z= 0.338 Chirality : 0.046 0.348 5589 Planarity : 0.005 0.060 5508 Dihedral : 9.844 111.210 5613 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.45 % Favored : 94.45 % Rotamer Outliers : 2.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.13), residues: 3801 helix: -0.04 (0.27), residues: 363 sheet: -0.58 (0.14), residues: 1230 loop : -1.59 (0.13), residues: 2208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 234 time to evaluate : 4.077 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 outliers start: 94 outliers final: 26 residues processed: 318 average time/residue: 0.4487 time to fit residues: 229.8903 Evaluate side-chains 222 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 196 time to evaluate : 3.812 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2867 time to fit residues: 19.7327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 4.9990 chunk 258 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 38 optimal weight: 0.3980 chunk 164 optimal weight: 0.9990 chunk 230 optimal weight: 8.9990 chunk 345 optimal weight: 0.9980 chunk 365 optimal weight: 20.0000 chunk 180 optimal weight: 4.9990 chunk 327 optimal weight: 4.9990 chunk 98 optimal weight: 0.0980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN B 543 ASN D 36 GLN I 543 ASN L 27 GLN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 36 GLN ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 411 ASN R 543 ASN ** T 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 33309 Z= 0.258 Angle : 0.640 9.155 45288 Z= 0.337 Chirality : 0.045 0.330 5589 Planarity : 0.005 0.054 5508 Dihedral : 9.779 111.655 5613 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.66 % Favored : 94.26 % Rotamer Outliers : 2.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.13), residues: 3801 helix: 0.41 (0.28), residues: 363 sheet: -0.49 (0.14), residues: 1233 loop : -1.48 (0.13), residues: 2205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 205 time to evaluate : 3.540 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 outliers start: 69 outliers final: 23 residues processed: 260 average time/residue: 0.4680 time to fit residues: 194.8272 Evaluate side-chains 205 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 182 time to evaluate : 3.902 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 3 residues processed: 23 average time/residue: 0.2848 time to fit residues: 18.1118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 272 optimal weight: 2.9990 chunk 150 optimal weight: 20.0000 chunk 311 optimal weight: 7.9990 chunk 252 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 186 optimal weight: 0.0770 chunk 327 optimal weight: 0.7980 chunk 92 optimal weight: 9.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN D 36 GLN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 101 GLN ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 411 ASN R 543 ASN U 36 GLN ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 53 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 33309 Z= 0.208 Angle : 0.616 12.983 45288 Z= 0.323 Chirality : 0.044 0.324 5589 Planarity : 0.004 0.055 5508 Dihedral : 9.652 111.677 5613 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.52 % Favored : 94.42 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.13), residues: 3801 helix: 0.55 (0.28), residues: 363 sheet: -0.43 (0.14), residues: 1266 loop : -1.33 (0.13), residues: 2172 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 204 time to evaluate : 4.065 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 outliers start: 52 outliers final: 13 residues processed: 251 average time/residue: 0.4994 time to fit residues: 197.0366 Evaluate side-chains 195 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 182 time to evaluate : 3.424 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 13 average time/residue: 0.3548 time to fit residues: 14.8325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 7.9990 chunk 329 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 214 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 365 optimal weight: 7.9990 chunk 303 optimal weight: 0.3980 chunk 169 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN B 543 ASN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 36 GLN O 76 ASN ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN Q 411 ASN R 543 ASN ** T 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 33309 Z= 0.320 Angle : 0.646 12.343 45288 Z= 0.340 Chirality : 0.045 0.306 5589 Planarity : 0.004 0.052 5508 Dihedral : 9.676 111.737 5613 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.13), residues: 3801 helix: 0.64 (0.28), residues: 363 sheet: -0.44 (0.14), residues: 1266 loop : -1.30 (0.13), residues: 2172 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 188 time to evaluate : 3.859 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 outliers start: 51 outliers final: 21 residues processed: 230 average time/residue: 0.4946 time to fit residues: 180.8003 Evaluate side-chains 194 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 173 time to evaluate : 3.818 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 3 residues processed: 21 average time/residue: 0.3303 time to fit residues: 17.5233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 267 optimal weight: 3.9990 chunk 206 optimal weight: 7.9990 chunk 307 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 chunk 364 optimal weight: 40.0000 chunk 228 optimal weight: 0.1980 chunk 222 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 411 ASN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 293 GLN ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 411 ASN ** T 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 33309 Z= 0.312 Angle : 0.650 12.306 45288 Z= 0.340 Chirality : 0.045 0.307 5589 Planarity : 0.004 0.052 5508 Dihedral : 9.655 111.559 5613 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.14), residues: 3801 helix: 0.72 (0.28), residues: 363 sheet: -0.44 (0.14), residues: 1263 loop : -1.21 (0.13), residues: 2175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 190 time to evaluate : 3.975 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 outliers start: 39 outliers final: 23 residues processed: 219 average time/residue: 0.5267 time to fit residues: 183.3310 Evaluate side-chains 201 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 178 time to evaluate : 4.085 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 3 residues processed: 23 average time/residue: 0.2744 time to fit residues: 17.1961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 71 optimal weight: 0.0370 chunk 70 optimal weight: 0.9980 chunk 231 optimal weight: 4.9990 chunk 248 optimal weight: 20.0000 chunk 180 optimal weight: 9.9990 chunk 33 optimal weight: 0.0770 chunk 286 optimal weight: 4.9990 overall best weight: 1.1818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN A 411 ASN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 27 GLN P 42 GLN ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN Q 411 ASN R 543 ASN ** T 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 33309 Z= 0.226 Angle : 0.633 16.405 45288 Z= 0.328 Chirality : 0.044 0.308 5589 Planarity : 0.004 0.052 5508 Dihedral : 9.554 111.468 5613 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 3801 helix: 1.04 (0.29), residues: 345 sheet: -0.33 (0.14), residues: 1263 loop : -1.13 (0.14), residues: 2193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 190 time to evaluate : 3.898 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 outliers start: 30 outliers final: 11 residues processed: 215 average time/residue: 0.4872 time to fit residues: 167.1487 Evaluate side-chains 189 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 178 time to evaluate : 3.815 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 11 average time/residue: 0.3129 time to fit residues: 11.4788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 6.9990 chunk 349 optimal weight: 4.9990 chunk 318 optimal weight: 10.0000 chunk 339 optimal weight: 10.0000 chunk 348 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 266 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 306 optimal weight: 4.9990 chunk 321 optimal weight: 0.8980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 33309 Z= 0.367 Angle : 0.689 18.074 45288 Z= 0.357 Chirality : 0.045 0.294 5589 Planarity : 0.005 0.059 5508 Dihedral : 9.644 111.783 5613 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.14), residues: 3801 helix: 0.84 (0.28), residues: 363 sheet: -0.30 (0.14), residues: 1242 loop : -1.21 (0.13), residues: 2196 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 186 time to evaluate : 3.708 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 outliers start: 28 outliers final: 17 residues processed: 205 average time/residue: 0.4758 time to fit residues: 155.9279 Evaluate side-chains 192 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 175 time to evaluate : 4.124 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 3 residues processed: 17 average time/residue: 0.2948 time to fit residues: 15.0680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 0.9980 chunk 222 optimal weight: 0.3980 chunk 359 optimal weight: 8.9990 chunk 219 optimal weight: 0.9990 chunk 170 optimal weight: 8.9990 chunk 249 optimal weight: 0.4980 chunk 376 optimal weight: 10.0000 chunk 346 optimal weight: 1.9990 chunk 299 optimal weight: 0.0980 chunk 31 optimal weight: 2.9990 chunk 231 optimal weight: 0.0470 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 411 ASN D 36 GLN ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 82 GLN Q 94 ASN T 17 GLN ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 33309 Z= 0.194 Angle : 0.657 17.327 45288 Z= 0.334 Chirality : 0.044 0.303 5589 Planarity : 0.005 0.087 5508 Dihedral : 9.454 111.640 5613 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3801 helix: 1.19 (0.29), residues: 345 sheet: -0.15 (0.14), residues: 1248 loop : -1.06 (0.14), residues: 2208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 198 time to evaluate : 4.872 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 outliers start: 16 outliers final: 10 residues processed: 211 average time/residue: 0.5196 time to fit residues: 176.8952 Evaluate side-chains 194 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 184 time to evaluate : 3.490 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 10 average time/residue: 0.2961 time to fit residues: 10.1599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 0.4980 chunk 238 optimal weight: 30.0000 chunk 319 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 276 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 300 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 308 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN B 543 ASN ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.085282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.057338 restraints weight = 112774.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.059238 restraints weight = 61644.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.060462 restraints weight = 44192.756| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 33309 Z= 0.264 Angle : 0.669 22.070 45288 Z= 0.341 Chirality : 0.044 0.284 5589 Planarity : 0.005 0.080 5508 Dihedral : 9.473 111.644 5613 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3801 helix: 1.26 (0.29), residues: 345 sheet: -0.10 (0.15), residues: 1224 loop : -1.11 (0.13), residues: 2232 =============================================================================== Job complete usr+sys time: 5335.76 seconds wall clock time: 100 minutes 21.13 seconds (6021.13 seconds total)