Starting phenix.real_space_refine on Mon Apr 8 01:50:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuc_37853/04_2024/8wuc_37853_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuc_37853/04_2024/8wuc_37853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuc_37853/04_2024/8wuc_37853.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuc_37853/04_2024/8wuc_37853.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuc_37853/04_2024/8wuc_37853_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuc_37853/04_2024/8wuc_37853_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 28 5.49 5 Mg 14 5.21 5 S 252 5.16 5 C 40712 2.51 5 N 11424 2.21 5 O 12908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "a GLU 16": "OE1" <-> "OE2" Residue "a GLU 18": "OE1" <-> "OE2" Residue "a GLU 33": "OE1" <-> "OE2" Residue "a ASP 63": "OD1" <-> "OD2" Residue "a GLU 78": "OE1" <-> "OE2" Residue "a GLU 95": "OE1" <-> "OE2" Residue "B GLU 14": "OE1" <-> "OE2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 391": "OE1" <-> "OE2" Residue "b GLU 16": "OE1" <-> "OE2" Residue "b GLU 33": "OE1" <-> "OE2" Residue "b ASP 45": "OD1" <-> "OD2" Residue "b ASP 50": "OD1" <-> "OD2" Residue "b ASP 51": "OD1" <-> "OD2" Residue "b TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 78": "OE1" <-> "OE2" Residue "b GLU 80": "OE1" <-> "OE2" Residue "b GLU 81": "OE1" <-> "OE2" Residue "b GLU 95": "OE1" <-> "OE2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 391": "OE1" <-> "OE2" Residue "c GLU 33": "OE1" <-> "OE2" Residue "c ASP 45": "OD1" <-> "OD2" Residue "c ASP 50": "OD1" <-> "OD2" Residue "c PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 78": "OE1" <-> "OE2" Residue "c ASP 88": "OD1" <-> "OD2" Residue "c GLU 95": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D ASP 83": "OD1" <-> "OD2" Residue "D GLU 178": "OE1" <-> "OE2" Residue "D ASP 179": "OD1" <-> "OD2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "d GLU 33": "OE1" <-> "OE2" Residue "d ASP 50": "OD1" <-> "OD2" Residue "d TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 88": "OD1" <-> "OD2" Residue "d ASP 89": "OD1" <-> "OD2" Residue "d GLU 95": "OE1" <-> "OE2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "E ASP 83": "OD1" <-> "OD2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "E GLU 191": "OE1" <-> "OE2" Residue "E TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 255": "OE1" <-> "OE2" Residue "E PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 525": "OE1" <-> "OE2" Residue "e GLU 16": "OE1" <-> "OE2" Residue "e GLU 18": "OE1" <-> "OE2" Residue "e GLU 33": "OE1" <-> "OE2" Residue "e ASP 63": "OD1" <-> "OD2" Residue "e ASP 88": "OD1" <-> "OD2" Residue "e GLU 95": "OE1" <-> "OE2" Residue "F GLU 14": "OE1" <-> "OE2" Residue "F GLU 191": "OE1" <-> "OE2" Residue "F PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 18": "OE1" <-> "OE2" Residue "f ASP 45": "OD1" <-> "OD2" Residue "f ASP 50": "OD1" <-> "OD2" Residue "f ASP 51": "OD1" <-> "OD2" Residue "f GLU 78": "OE1" <-> "OE2" Residue "f ASP 88": "OD1" <-> "OD2" Residue "f GLU 95": "OE1" <-> "OE2" Residue "G GLU 14": "OE1" <-> "OE2" Residue "G ASP 83": "OD1" <-> "OD2" Residue "G GLU 178": "OE1" <-> "OE2" Residue "G GLU 191": "OE1" <-> "OE2" Residue "G PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 367": "OE1" <-> "OE2" Residue "G GLU 391": "OE1" <-> "OE2" Residue "G GLU 397": "OE1" <-> "OE2" Residue "G GLU 520": "OE1" <-> "OE2" Residue "g GLU 16": "OE1" <-> "OE2" Residue "g ASP 29": "OD1" <-> "OD2" Residue "g GLU 33": "OE1" <-> "OE2" Residue "g ASP 45": "OD1" <-> "OD2" Residue "g TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 78": "OE1" <-> "OE2" Residue "g GLU 80": "OE1" <-> "OE2" Residue "g GLU 81": "OE1" <-> "OE2" Residue "g GLU 95": "OE1" <-> "OE2" Residue "H GLU 14": "OE1" <-> "OE2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H GLU 178": "OE1" <-> "OE2" Residue "H GLU 191": "OE1" <-> "OE2" Residue "H TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 255": "OE1" <-> "OE2" Residue "H PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 386": "OE1" <-> "OE2" Residue "h GLU 16": "OE1" <-> "OE2" Residue "h GLU 18": "OE1" <-> "OE2" Residue "h ASP 29": "OD1" <-> "OD2" Residue "h GLU 39": "OE1" <-> "OE2" Residue "h ASP 45": "OD1" <-> "OD2" Residue "h ASP 50": "OD1" <-> "OD2" Residue "h ASP 51": "OD1" <-> "OD2" Residue "h ASP 63": "OD1" <-> "OD2" Residue "h TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 78": "OE1" <-> "OE2" Residue "h GLU 81": "OE1" <-> "OE2" Residue "h ASP 88": "OD1" <-> "OD2" Residue "h ASP 89": "OD1" <-> "OD2" Residue "h GLU 95": "OE1" <-> "OE2" Residue "I ASP 83": "OD1" <-> "OD2" Residue "I GLU 191": "OE1" <-> "OE2" Residue "I ASP 216": "OD1" <-> "OD2" Residue "I PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 386": "OE1" <-> "OE2" Residue "I GLU 424": "OE1" <-> "OE2" Residue "I GLU 463": "OE1" <-> "OE2" Residue "i ASP 29": "OD1" <-> "OD2" Residue "i ASP 45": "OD1" <-> "OD2" Residue "i ASP 50": "OD1" <-> "OD2" Residue "i GLU 81": "OE1" <-> "OE2" Residue "i ASP 88": "OD1" <-> "OD2" Residue "J ASP 179": "OD1" <-> "OD2" Residue "J GLU 191": "OE1" <-> "OE2" Residue "J PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 386": "OE1" <-> "OE2" Residue "j GLU 16": "OE1" <-> "OE2" Residue "j ASP 29": "OD1" <-> "OD2" Residue "j ASP 45": "OD1" <-> "OD2" Residue "j PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 78": "OE1" <-> "OE2" Residue "j ASP 88": "OD1" <-> "OD2" Residue "j ASP 89": "OD1" <-> "OD2" Residue "j GLU 95": "OE1" <-> "OE2" Residue "K ASP 83": "OD1" <-> "OD2" Residue "K GLU 191": "OE1" <-> "OE2" Residue "K TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 359": "OD1" <-> "OD2" Residue "K GLU 424": "OE1" <-> "OE2" Residue "k GLU 33": "OE1" <-> "OE2" Residue "k GLU 39": "OE1" <-> "OE2" Residue "k ASP 45": "OD1" <-> "OD2" Residue "k GLU 80": "OE1" <-> "OE2" Residue "k GLU 81": "OE1" <-> "OE2" Residue "k ASP 88": "OD1" <-> "OD2" Residue "k GLU 95": "OE1" <-> "OE2" Residue "L GLU 14": "OE1" <-> "OE2" Residue "L PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 178": "OE1" <-> "OE2" Residue "L ASP 179": "OD1" <-> "OD2" Residue "L GLU 191": "OE1" <-> "OE2" Residue "L ASP 196": "OD1" <-> "OD2" Residue "L ASP 216": "OD1" <-> "OD2" Residue "L PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 334": "OD1" <-> "OD2" Residue "L TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 16": "OE1" <-> "OE2" Residue "l GLU 18": "OE1" <-> "OE2" Residue "l GLU 33": "OE1" <-> "OE2" Residue "l ASP 45": "OD1" <-> "OD2" Residue "l ASP 50": "OD1" <-> "OD2" Residue "l ASP 51": "OD1" <-> "OD2" Residue "l GLU 78": "OE1" <-> "OE2" Residue "l GLU 80": "OE1" <-> "OE2" Residue "l GLU 81": "OE1" <-> "OE2" Residue "l GLU 95": "OE1" <-> "OE2" Residue "M GLU 191": "OE1" <-> "OE2" Residue "M ASP 216": "OD1" <-> "OD2" Residue "M TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 424": "OE1" <-> "OE2" Residue "m GLU 16": "OE1" <-> "OE2" Residue "m GLU 18": "OE1" <-> "OE2" Residue "m GLU 33": "OE1" <-> "OE2" Residue "m ASP 45": "OD1" <-> "OD2" Residue "m ASP 88": "OD1" <-> "OD2" Residue "m ASP 89": "OD1" <-> "OD2" Residue "m GLU 95": "OE1" <-> "OE2" Residue "N GLU 14": "OE1" <-> "OE2" Residue "N ASP 83": "OD1" <-> "OD2" Residue "N PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 391": "OE1" <-> "OE2" Residue "N GLU 492": "OE1" <-> "OE2" Residue "N GLU 525": "OE1" <-> "OE2" Residue "n GLU 16": "OE1" <-> "OE2" Residue "n GLU 18": "OE1" <-> "OE2" Residue "n GLU 33": "OE1" <-> "OE2" Residue "n ASP 45": "OD1" <-> "OD2" Residue "n GLU 78": "OE1" <-> "OE2" Residue "n GLU 80": "OE1" <-> "OE2" Residue "n GLU 81": "OE1" <-> "OE2" Residue "n ASP 89": "OD1" <-> "OD2" Residue "n GLU 95": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 65338 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "a" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "B" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "b" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "C" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "c" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "D" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "d" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "E" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "e" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "F" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "f" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "G" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "g" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "H" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "h" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "I" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "i" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "J" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "j" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "K" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "k" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "L" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "l" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "M" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "m" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "N" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "n" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 24.99, per 1000 atoms: 0.38 Number of scatterers: 65338 At special positions: 0 Unit cell: (152.04, 151.2, 256.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 252 16.00 P 28 15.00 Mg 14 11.99 O 12908 8.00 N 11424 7.00 C 40712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 20.71 Conformation dependent library (CDL) restraints added in 8.8 seconds 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15820 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 278 helices and 112 sheets defined 46.3% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.94 Creating SS restraints... Processing helix chain 'A' and resid 9 through 30 removed outlier: 3.713A pdb=" N ARG A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 removed outlier: 3.674A pdb=" N GLU A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 84 removed outlier: 3.574A pdb=" N GLY A 70 " --> pdb=" O PHE A 66 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 108 removed outlier: 3.747A pdb=" N LYS A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 134 Processing helix chain 'A' and resid 141 through 151 Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 230 through 243 Proline residue: A 235 - end of helix removed outlier: 3.542A pdb=" N LYS A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 282 through 296 removed outlier: 3.621A pdb=" N MET A 288 " --> pdb=" O ARG A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 355 removed outlier: 3.741A pdb=" N GLU A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU A 355 " --> pdb=" O VAL A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 373 Processing helix chain 'A' and resid 386 through 409 Processing helix chain 'A' and resid 417 through 428 Processing helix chain 'A' and resid 436 through 460 removed outlier: 4.247A pdb=" N GLU A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) Proline residue: A 452 - end of helix Processing helix chain 'A' and resid 464 through 473 Processing helix chain 'A' and resid 490 through 493 No H-bonds generated for 'chain 'A' and resid 490 through 493' Processing helix chain 'A' and resid 499 through 518 removed outlier: 3.517A pdb=" N LEU A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR A 518 " --> pdb=" O GLY A 514 " (cutoff:3.500A) Processing helix chain 'a' and resid 77 through 79 No H-bonds generated for 'chain 'a' and resid 77 through 79' Processing helix chain 'B' and resid 9 through 30 removed outlier: 3.597A pdb=" N THR B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 59 removed outlier: 3.696A pdb=" N GLU B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 84 removed outlier: 3.553A pdb=" N GLY B 70 " --> pdb=" O PHE B 66 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 77 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 108 removed outlier: 3.769A pdb=" N LYS B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 134 Processing helix chain 'B' and resid 141 through 151 Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 231 through 243 Proline residue: B 235 - end of helix removed outlier: 3.570A pdb=" N LYS B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA B 243 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 268 Processing helix chain 'B' and resid 282 through 296 removed outlier: 3.572A pdb=" N MET B 288 " --> pdb=" O ARG B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 355 removed outlier: 3.627A pdb=" N GLU B 354 " --> pdb=" O ARG B 350 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU B 355 " --> pdb=" O VAL B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 373 Processing helix chain 'B' and resid 386 through 409 Processing helix chain 'B' and resid 417 through 428 Processing helix chain 'B' and resid 436 through 460 removed outlier: 4.292A pdb=" N GLU B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) Proline residue: B 452 - end of helix Processing helix chain 'B' and resid 464 through 473 Processing helix chain 'B' and resid 499 through 518 removed outlier: 3.537A pdb=" N LEU B 515 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR B 518 " --> pdb=" O GLY B 514 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 79 No H-bonds generated for 'chain 'b' and resid 77 through 79' Processing helix chain 'b' and resid 87 through 89 No H-bonds generated for 'chain 'b' and resid 87 through 89' Processing helix chain 'C' and resid 9 through 30 removed outlier: 3.580A pdb=" N THR C 29 " --> pdb=" O ASN C 25 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 59 removed outlier: 3.682A pdb=" N GLU C 59 " --> pdb=" O THR C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 84 removed outlier: 3.670A pdb=" N GLY C 70 " --> pdb=" O PHE C 66 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 108 removed outlier: 3.766A pdb=" N LYS C 105 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 134 Processing helix chain 'C' and resid 141 through 151 Processing helix chain 'C' and resid 156 through 169 Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 230 through 243 Proline residue: C 235 - end of helix removed outlier: 3.504A pdb=" N GLN C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 267 Processing helix chain 'C' and resid 282 through 296 removed outlier: 3.869A pdb=" N MET C 288 " --> pdb=" O ARG C 285 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR C 296 " --> pdb=" O ALA C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 355 removed outlier: 3.614A pdb=" N GLU C 354 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU C 355 " --> pdb=" O VAL C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 373 removed outlier: 4.002A pdb=" N GLU C 363 " --> pdb=" O ASP C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 409 Processing helix chain 'C' and resid 417 through 428 Processing helix chain 'C' and resid 436 through 460 removed outlier: 3.523A pdb=" N VAL C 445 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU C 450 " --> pdb=" O LEU C 446 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN C 451 " --> pdb=" O ARG C 447 " (cutoff:3.500A) Proline residue: C 452 - end of helix Processing helix chain 'C' and resid 464 through 473 Processing helix chain 'C' and resid 490 through 493 No H-bonds generated for 'chain 'C' and resid 490 through 493' Processing helix chain 'C' and resid 499 through 518 removed outlier: 3.525A pdb=" N LEU C 515 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR C 518 " --> pdb=" O GLY C 514 " (cutoff:3.500A) Processing helix chain 'c' and resid 77 through 79 No H-bonds generated for 'chain 'c' and resid 77 through 79' Processing helix chain 'D' and resid 9 through 30 removed outlier: 3.584A pdb=" N THR D 29 " --> pdb=" O ASN D 25 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 59 removed outlier: 3.677A pdb=" N GLU D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 84 removed outlier: 3.548A pdb=" N GLY D 70 " --> pdb=" O PHE D 66 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU D 76 " --> pdb=" O GLN D 72 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL D 77 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 108 removed outlier: 3.737A pdb=" N LYS D 105 " --> pdb=" O ARG D 101 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 134 Processing helix chain 'D' and resid 141 through 151 Processing helix chain 'D' and resid 156 through 169 Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 234 through 243 Processing helix chain 'D' and resid 256 through 268 Processing helix chain 'D' and resid 282 through 296 removed outlier: 3.835A pdb=" N MET D 288 " --> pdb=" O ARG D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 355 removed outlier: 3.758A pdb=" N GLU D 355 " --> pdb=" O VAL D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 373 removed outlier: 3.884A pdb=" N GLU D 363 " --> pdb=" O ASP D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 409 Processing helix chain 'D' and resid 417 through 428 Processing helix chain 'D' and resid 436 through 460 removed outlier: 4.256A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN D 451 " --> pdb=" O ARG D 447 " (cutoff:3.500A) Proline residue: D 452 - end of helix Processing helix chain 'D' and resid 464 through 473 Processing helix chain 'D' and resid 499 through 518 removed outlier: 3.541A pdb=" N LEU D 515 " --> pdb=" O SER D 511 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR D 518 " --> pdb=" O GLY D 514 " (cutoff:3.500A) Processing helix chain 'd' and resid 77 through 79 No H-bonds generated for 'chain 'd' and resid 77 through 79' Processing helix chain 'd' and resid 87 through 89 No H-bonds generated for 'chain 'd' and resid 87 through 89' Processing helix chain 'E' and resid 9 through 30 removed outlier: 3.676A pdb=" N ARG E 15 " --> pdb=" O SER E 11 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR E 29 " --> pdb=" O ASN E 25 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THR E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 59 removed outlier: 3.707A pdb=" N GLU E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 84 removed outlier: 3.520A pdb=" N GLY E 70 " --> pdb=" O PHE E 66 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 108 removed outlier: 3.729A pdb=" N LYS E 105 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 134 Processing helix chain 'E' and resid 141 through 151 Processing helix chain 'E' and resid 156 through 169 Processing helix chain 'E' and resid 202 through 204 No H-bonds generated for 'chain 'E' and resid 202 through 204' Processing helix chain 'E' and resid 234 through 243 removed outlier: 3.617A pdb=" N GLN E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA E 243 " --> pdb=" O GLN E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 268 Processing helix chain 'E' and resid 282 through 296 removed outlier: 3.576A pdb=" N MET E 288 " --> pdb=" O ARG E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 355 removed outlier: 3.626A pdb=" N GLU E 354 " --> pdb=" O ARG E 350 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU E 355 " --> pdb=" O VAL E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 373 removed outlier: 4.192A pdb=" N GLU E 363 " --> pdb=" O ASP E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 409 Processing helix chain 'E' and resid 417 through 428 Processing helix chain 'E' and resid 436 through 460 removed outlier: 4.239A pdb=" N GLU E 450 " --> pdb=" O LEU E 446 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN E 451 " --> pdb=" O ARG E 447 " (cutoff:3.500A) Proline residue: E 452 - end of helix Processing helix chain 'E' and resid 464 through 473 Processing helix chain 'E' and resid 490 through 493 No H-bonds generated for 'chain 'E' and resid 490 through 493' Processing helix chain 'E' and resid 499 through 518 removed outlier: 3.567A pdb=" N LEU E 515 " --> pdb=" O SER E 511 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR E 518 " --> pdb=" O GLY E 514 " (cutoff:3.500A) Processing helix chain 'e' and resid 77 through 79 No H-bonds generated for 'chain 'e' and resid 77 through 79' Processing helix chain 'e' and resid 87 through 89 No H-bonds generated for 'chain 'e' and resid 87 through 89' Processing helix chain 'F' and resid 9 through 30 removed outlier: 3.679A pdb=" N ARG F 15 " --> pdb=" O SER F 11 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR F 29 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 59 removed outlier: 3.743A pdb=" N GLU F 59 " --> pdb=" O THR F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 84 removed outlier: 3.764A pdb=" N GLY F 70 " --> pdb=" O PHE F 66 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL F 77 " --> pdb=" O MET F 73 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 78 " --> pdb=" O VAL F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 108 removed outlier: 3.757A pdb=" N LYS F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR F 106 " --> pdb=" O GLU F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 134 Processing helix chain 'F' and resid 141 through 151 Processing helix chain 'F' and resid 156 through 169 Processing helix chain 'F' and resid 202 through 204 No H-bonds generated for 'chain 'F' and resid 202 through 204' Processing helix chain 'F' and resid 233 through 243 removed outlier: 3.888A pdb=" N ALA F 243 " --> pdb=" O GLN F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 268 Processing helix chain 'F' and resid 282 through 296 removed outlier: 3.700A pdb=" N MET F 288 " --> pdb=" O ARG F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 355 removed outlier: 3.543A pdb=" N GLU F 355 " --> pdb=" O VAL F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 373 removed outlier: 3.539A pdb=" N GLU F 363 " --> pdb=" O ASP F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 409 Processing helix chain 'F' and resid 417 through 428 Processing helix chain 'F' and resid 436 through 460 removed outlier: 4.283A pdb=" N GLU F 450 " --> pdb=" O LEU F 446 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN F 451 " --> pdb=" O ARG F 447 " (cutoff:3.500A) Proline residue: F 452 - end of helix Processing helix chain 'F' and resid 464 through 473 Processing helix chain 'F' and resid 490 through 493 No H-bonds generated for 'chain 'F' and resid 490 through 493' Processing helix chain 'F' and resid 499 through 518 removed outlier: 3.559A pdb=" N LEU F 515 " --> pdb=" O SER F 511 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR F 518 " --> pdb=" O GLY F 514 " (cutoff:3.500A) Processing helix chain 'f' and resid 77 through 79 No H-bonds generated for 'chain 'f' and resid 77 through 79' Processing helix chain 'f' and resid 87 through 89 No H-bonds generated for 'chain 'f' and resid 87 through 89' Processing helix chain 'G' and resid 9 through 30 removed outlier: 3.640A pdb=" N ARG G 15 " --> pdb=" O SER G 11 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR G 29 " --> pdb=" O ASN G 25 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 59 removed outlier: 3.640A pdb=" N GLU G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 84 removed outlier: 3.613A pdb=" N GLY G 70 " --> pdb=" O PHE G 66 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 108 removed outlier: 3.745A pdb=" N LYS G 105 " --> pdb=" O ARG G 101 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 134 Processing helix chain 'G' and resid 141 through 151 Processing helix chain 'G' and resid 156 through 169 Processing helix chain 'G' and resid 202 through 204 No H-bonds generated for 'chain 'G' and resid 202 through 204' Processing helix chain 'G' and resid 231 through 243 Proline residue: G 235 - end of helix removed outlier: 3.624A pdb=" N GLN G 239 " --> pdb=" O PRO G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 267 Processing helix chain 'G' and resid 282 through 296 removed outlier: 3.664A pdb=" N MET G 288 " --> pdb=" O ARG G 285 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 355 removed outlier: 3.730A pdb=" N GLU G 354 " --> pdb=" O ARG G 350 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU G 355 " --> pdb=" O VAL G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 373 removed outlier: 3.788A pdb=" N GLU G 363 " --> pdb=" O ASP G 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 409 Processing helix chain 'G' and resid 417 through 429 Processing helix chain 'G' and resid 436 through 460 removed outlier: 4.218A pdb=" N GLU G 450 " --> pdb=" O LEU G 446 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN G 451 " --> pdb=" O ARG G 447 " (cutoff:3.500A) Proline residue: G 452 - end of helix Processing helix chain 'G' and resid 464 through 473 Processing helix chain 'G' and resid 499 through 518 removed outlier: 3.531A pdb=" N LEU G 515 " --> pdb=" O SER G 511 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR G 518 " --> pdb=" O GLY G 514 " (cutoff:3.500A) Processing helix chain 'g' and resid 77 through 79 No H-bonds generated for 'chain 'g' and resid 77 through 79' Processing helix chain 'H' and resid 9 through 30 removed outlier: 3.553A pdb=" N THR H 29 " --> pdb=" O ASN H 25 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 59 removed outlier: 3.757A pdb=" N GLU H 59 " --> pdb=" O THR H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 84 removed outlier: 3.921A pdb=" N GLY H 70 " --> pdb=" O PHE H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 108 removed outlier: 3.749A pdb=" N LYS H 105 " --> pdb=" O ARG H 101 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 134 Processing helix chain 'H' and resid 141 through 151 Processing helix chain 'H' and resid 156 through 169 Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'H' and resid 230 through 242 Proline residue: H 235 - end of helix Processing helix chain 'H' and resid 256 through 267 Processing helix chain 'H' and resid 282 through 296 removed outlier: 3.718A pdb=" N MET H 288 " --> pdb=" O ARG H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 355 removed outlier: 3.588A pdb=" N GLU H 354 " --> pdb=" O ARG H 350 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU H 355 " --> pdb=" O VAL H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 373 Processing helix chain 'H' and resid 386 through 409 Processing helix chain 'H' and resid 417 through 429 Processing helix chain 'H' and resid 436 through 460 removed outlier: 4.263A pdb=" N GLU H 450 " --> pdb=" O LEU H 446 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN H 451 " --> pdb=" O ARG H 447 " (cutoff:3.500A) Proline residue: H 452 - end of helix Processing helix chain 'H' and resid 464 through 473 Processing helix chain 'H' and resid 490 through 493 No H-bonds generated for 'chain 'H' and resid 490 through 493' Processing helix chain 'H' and resid 499 through 517 removed outlier: 3.543A pdb=" N LEU H 515 " --> pdb=" O SER H 511 " (cutoff:3.500A) Processing helix chain 'h' and resid 87 through 89 No H-bonds generated for 'chain 'h' and resid 87 through 89' Processing helix chain 'I' and resid 9 through 30 removed outlier: 3.582A pdb=" N THR I 29 " --> pdb=" O ASN I 25 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 59 removed outlier: 3.711A pdb=" N GLU I 59 " --> pdb=" O THR I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 84 removed outlier: 3.547A pdb=" N GLY I 70 " --> pdb=" O PHE I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 108 removed outlier: 3.737A pdb=" N LYS I 105 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 134 Processing helix chain 'I' and resid 141 through 151 Processing helix chain 'I' and resid 156 through 169 Processing helix chain 'I' and resid 202 through 204 No H-bonds generated for 'chain 'I' and resid 202 through 204' Processing helix chain 'I' and resid 233 through 243 removed outlier: 3.515A pdb=" N LYS I 242 " --> pdb=" O GLU I 238 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA I 243 " --> pdb=" O GLN I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 256 through 268 Processing helix chain 'I' and resid 282 through 296 removed outlier: 3.562A pdb=" N MET I 288 " --> pdb=" O ARG I 285 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 355 removed outlier: 3.604A pdb=" N GLU I 354 " --> pdb=" O ARG I 350 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU I 355 " --> pdb=" O VAL I 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 359 through 373 removed outlier: 4.110A pdb=" N GLU I 363 " --> pdb=" O ASP I 359 " (cutoff:3.500A) Processing helix chain 'I' and resid 386 through 409 Processing helix chain 'I' and resid 417 through 429 Processing helix chain 'I' and resid 436 through 460 removed outlier: 3.504A pdb=" N VAL I 445 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU I 450 " --> pdb=" O LEU I 446 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN I 451 " --> pdb=" O ARG I 447 " (cutoff:3.500A) Proline residue: I 452 - end of helix Processing helix chain 'I' and resid 464 through 473 Processing helix chain 'I' and resid 490 through 493 No H-bonds generated for 'chain 'I' and resid 490 through 493' Processing helix chain 'I' and resid 499 through 517 removed outlier: 3.557A pdb=" N LEU I 515 " --> pdb=" O SER I 511 " (cutoff:3.500A) Processing helix chain 'i' and resid 87 through 89 No H-bonds generated for 'chain 'i' and resid 87 through 89' Processing helix chain 'J' and resid 9 through 30 removed outlier: 3.595A pdb=" N THR J 29 " --> pdb=" O ASN J 25 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR J 30 " --> pdb=" O ALA J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 59 removed outlier: 3.665A pdb=" N GLU J 59 " --> pdb=" O THR J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 84 removed outlier: 3.609A pdb=" N GLY J 70 " --> pdb=" O PHE J 66 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL J 77 " --> pdb=" O MET J 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 108 removed outlier: 3.728A pdb=" N LYS J 105 " --> pdb=" O ARG J 101 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 134 Processing helix chain 'J' and resid 141 through 151 Processing helix chain 'J' and resid 156 through 169 Processing helix chain 'J' and resid 202 through 204 No H-bonds generated for 'chain 'J' and resid 202 through 204' Processing helix chain 'J' and resid 233 through 243 removed outlier: 3.583A pdb=" N GLN J 239 " --> pdb=" O PRO J 235 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS J 242 " --> pdb=" O GLU J 238 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA J 243 " --> pdb=" O GLN J 239 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 268 Processing helix chain 'J' and resid 282 through 296 removed outlier: 3.624A pdb=" N LYS J 286 " --> pdb=" O GLY J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 339 through 355 removed outlier: 3.710A pdb=" N GLU J 355 " --> pdb=" O VAL J 351 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 373 removed outlier: 4.442A pdb=" N GLU J 363 " --> pdb=" O ASP J 359 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU J 367 " --> pdb=" O GLU J 363 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG J 368 " --> pdb=" O LYS J 364 " (cutoff:3.500A) Processing helix chain 'J' and resid 386 through 409 Processing helix chain 'J' and resid 417 through 428 Processing helix chain 'J' and resid 436 through 460 removed outlier: 4.252A pdb=" N GLU J 450 " --> pdb=" O LEU J 446 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN J 451 " --> pdb=" O ARG J 447 " (cutoff:3.500A) Proline residue: J 452 - end of helix Processing helix chain 'J' and resid 464 through 473 Processing helix chain 'J' and resid 499 through 518 removed outlier: 3.515A pdb=" N LEU J 515 " --> pdb=" O SER J 511 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR J 518 " --> pdb=" O GLY J 514 " (cutoff:3.500A) Processing helix chain 'j' and resid 77 through 79 No H-bonds generated for 'chain 'j' and resid 77 through 79' Processing helix chain 'j' and resid 87 through 89 No H-bonds generated for 'chain 'j' and resid 87 through 89' Processing helix chain 'K' and resid 9 through 30 removed outlier: 3.580A pdb=" N THR K 29 " --> pdb=" O ASN K 25 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR K 30 " --> pdb=" O ALA K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 59 removed outlier: 3.607A pdb=" N GLU K 59 " --> pdb=" O THR K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 84 removed outlier: 3.684A pdb=" N GLY K 70 " --> pdb=" O PHE K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 108 removed outlier: 3.771A pdb=" N LYS K 105 " --> pdb=" O ARG K 101 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR K 106 " --> pdb=" O GLU K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 134 Processing helix chain 'K' and resid 141 through 151 Processing helix chain 'K' and resid 156 through 169 Processing helix chain 'K' and resid 202 through 204 No H-bonds generated for 'chain 'K' and resid 202 through 204' Processing helix chain 'K' and resid 230 through 243 Proline residue: K 235 - end of helix removed outlier: 3.531A pdb=" N GLN K 239 " --> pdb=" O PRO K 235 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 268 Processing helix chain 'K' and resid 282 through 296 removed outlier: 3.642A pdb=" N LYS K 286 " --> pdb=" O GLY K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 339 through 355 Processing helix chain 'K' and resid 359 through 373 Processing helix chain 'K' and resid 386 through 409 Processing helix chain 'K' and resid 417 through 429 Processing helix chain 'K' and resid 436 through 460 removed outlier: 3.527A pdb=" N VAL K 445 " --> pdb=" O GLY K 441 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU K 450 " --> pdb=" O LEU K 446 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN K 451 " --> pdb=" O ARG K 447 " (cutoff:3.500A) Proline residue: K 452 - end of helix Processing helix chain 'K' and resid 464 through 473 Processing helix chain 'K' and resid 490 through 493 No H-bonds generated for 'chain 'K' and resid 490 through 493' Processing helix chain 'K' and resid 499 through 518 removed outlier: 3.514A pdb=" N LEU K 515 " --> pdb=" O SER K 511 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR K 518 " --> pdb=" O GLY K 514 " (cutoff:3.500A) Processing helix chain 'k' and resid 87 through 89 No H-bonds generated for 'chain 'k' and resid 87 through 89' Processing helix chain 'L' and resid 9 through 30 removed outlier: 3.589A pdb=" N THR L 29 " --> pdb=" O ASN L 25 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR L 30 " --> pdb=" O ALA L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 59 removed outlier: 3.651A pdb=" N GLU L 59 " --> pdb=" O THR L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 84 removed outlier: 3.510A pdb=" N GLY L 70 " --> pdb=" O PHE L 66 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL L 77 " --> pdb=" O MET L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 108 removed outlier: 3.752A pdb=" N LYS L 105 " --> pdb=" O ARG L 101 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 134 Processing helix chain 'L' and resid 141 through 151 Processing helix chain 'L' and resid 156 through 169 Processing helix chain 'L' and resid 202 through 204 No H-bonds generated for 'chain 'L' and resid 202 through 204' Processing helix chain 'L' and resid 234 through 243 removed outlier: 3.682A pdb=" N ALA L 243 " --> pdb=" O GLN L 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 256 through 268 Processing helix chain 'L' and resid 282 through 296 removed outlier: 3.598A pdb=" N MET L 288 " --> pdb=" O ARG L 285 " (cutoff:3.500A) Processing helix chain 'L' and resid 339 through 355 removed outlier: 3.587A pdb=" N GLU L 354 " --> pdb=" O ARG L 350 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU L 355 " --> pdb=" O VAL L 351 " (cutoff:3.500A) Processing helix chain 'L' and resid 359 through 373 removed outlier: 4.046A pdb=" N GLU L 363 " --> pdb=" O ASP L 359 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS L 364 " --> pdb=" O TYR L 360 " (cutoff:3.500A) Processing helix chain 'L' and resid 386 through 409 Processing helix chain 'L' and resid 417 through 429 Processing helix chain 'L' and resid 436 through 460 removed outlier: 4.283A pdb=" N GLU L 450 " --> pdb=" O LEU L 446 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN L 451 " --> pdb=" O ARG L 447 " (cutoff:3.500A) Proline residue: L 452 - end of helix Processing helix chain 'L' and resid 464 through 473 Processing helix chain 'L' and resid 499 through 518 removed outlier: 3.519A pdb=" N LEU L 515 " --> pdb=" O SER L 511 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR L 518 " --> pdb=" O GLY L 514 " (cutoff:3.500A) Processing helix chain 'l' and resid 77 through 79 No H-bonds generated for 'chain 'l' and resid 77 through 79' Processing helix chain 'M' and resid 9 through 30 removed outlier: 3.521A pdb=" N ARG M 15 " --> pdb=" O SER M 11 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR M 29 " --> pdb=" O ASN M 25 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 59 removed outlier: 3.658A pdb=" N GLU M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 84 removed outlier: 3.548A pdb=" N GLY M 70 " --> pdb=" O PHE M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 108 removed outlier: 3.739A pdb=" N LYS M 105 " --> pdb=" O ARG M 101 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR M 106 " --> pdb=" O GLU M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 134 Processing helix chain 'M' and resid 141 through 151 Processing helix chain 'M' and resid 156 through 169 Processing helix chain 'M' and resid 202 through 204 No H-bonds generated for 'chain 'M' and resid 202 through 204' Processing helix chain 'M' and resid 230 through 243 Proline residue: M 235 - end of helix removed outlier: 3.622A pdb=" N LYS M 242 " --> pdb=" O GLU M 238 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA M 243 " --> pdb=" O GLN M 239 " (cutoff:3.500A) Processing helix chain 'M' and resid 257 through 268 Processing helix chain 'M' and resid 282 through 296 removed outlier: 3.586A pdb=" N MET M 288 " --> pdb=" O ARG M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 339 through 355 removed outlier: 3.695A pdb=" N GLU M 354 " --> pdb=" O ARG M 350 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU M 355 " --> pdb=" O VAL M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 359 through 373 Processing helix chain 'M' and resid 386 through 409 Processing helix chain 'M' and resid 417 through 428 Processing helix chain 'M' and resid 436 through 460 removed outlier: 4.241A pdb=" N GLU M 450 " --> pdb=" O LEU M 446 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN M 451 " --> pdb=" O ARG M 447 " (cutoff:3.500A) Proline residue: M 452 - end of helix Processing helix chain 'M' and resid 464 through 473 Processing helix chain 'M' and resid 499 through 518 removed outlier: 3.540A pdb=" N LEU M 515 " --> pdb=" O SER M 511 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR M 518 " --> pdb=" O GLY M 514 " (cutoff:3.500A) Processing helix chain 'm' and resid 77 through 79 No H-bonds generated for 'chain 'm' and resid 77 through 79' Processing helix chain 'N' and resid 9 through 30 removed outlier: 3.563A pdb=" N ARG N 15 " --> pdb=" O SER N 11 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR N 29 " --> pdb=" O ASN N 25 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR N 30 " --> pdb=" O ALA N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 59 removed outlier: 3.631A pdb=" N GLU N 59 " --> pdb=" O THR N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 84 removed outlier: 3.618A pdb=" N GLY N 70 " --> pdb=" O PHE N 66 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL N 77 " --> pdb=" O MET N 73 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA N 78 " --> pdb=" O VAL N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 108 removed outlier: 3.729A pdb=" N LYS N 105 " --> pdb=" O ARG N 101 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR N 106 " --> pdb=" O GLU N 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 113 through 134 Processing helix chain 'N' and resid 141 through 151 Processing helix chain 'N' and resid 156 through 169 Processing helix chain 'N' and resid 202 through 204 No H-bonds generated for 'chain 'N' and resid 202 through 204' Processing helix chain 'N' and resid 230 through 243 Proline residue: N 235 - end of helix removed outlier: 3.608A pdb=" N LYS N 242 " --> pdb=" O GLU N 238 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA N 243 " --> pdb=" O GLN N 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 256 through 267 Processing helix chain 'N' and resid 282 through 296 removed outlier: 3.628A pdb=" N MET N 288 " --> pdb=" O ARG N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 339 through 355 removed outlier: 3.575A pdb=" N GLU N 354 " --> pdb=" O ARG N 350 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU N 355 " --> pdb=" O VAL N 351 " (cutoff:3.500A) Processing helix chain 'N' and resid 359 through 373 removed outlier: 3.780A pdb=" N GLU N 363 " --> pdb=" O ASP N 359 " (cutoff:3.500A) Processing helix chain 'N' and resid 386 through 409 Processing helix chain 'N' and resid 417 through 429 Processing helix chain 'N' and resid 436 through 460 removed outlier: 4.238A pdb=" N GLU N 450 " --> pdb=" O LEU N 446 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN N 451 " --> pdb=" O ARG N 447 " (cutoff:3.500A) Proline residue: N 452 - end of helix Processing helix chain 'N' and resid 464 through 473 Processing helix chain 'N' and resid 499 through 518 removed outlier: 3.568A pdb=" N LEU N 515 " --> pdb=" O SER N 511 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR N 518 " --> pdb=" O GLY N 514 " (cutoff:3.500A) Processing helix chain 'n' and resid 77 through 79 No H-bonds generated for 'chain 'n' and resid 77 through 79' Processing sheet with id= A, first strand: chain 'A' and resid 4 through 8 Processing sheet with id= B, first strand: chain 'A' and resid 38 through 40 Processing sheet with id= C, first strand: chain 'A' and resid 174 through 179 Processing sheet with id= D, first strand: chain 'A' and resid 213 through 216 Processing sheet with id= E, first strand: chain 'A' and resid 219 through 222 Processing sheet with id= F, first strand: chain 'A' and resid 411 through 413 Processing sheet with id= G, first strand: chain 'A' and resid 478 through 481 Processing sheet with id= H, first strand: chain 'a' and resid 73 through 75 removed outlier: 4.100A pdb=" N LEU a 82 " --> pdb=" O VAL a 75 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA a 42 " --> pdb=" O VAL a 11 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS a 13 " --> pdb=" O VAL a 40 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL a 40 " --> pdb=" O LYS a 13 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS a 64 " --> pdb=" O ILE a 94 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 4 through 8 Processing sheet with id= J, first strand: chain 'B' and resid 38 through 40 Processing sheet with id= K, first strand: chain 'B' and resid 174 through 179 Processing sheet with id= L, first strand: chain 'B' and resid 213 through 216 Processing sheet with id= M, first strand: chain 'B' and resid 219 through 222 Processing sheet with id= N, first strand: chain 'B' and resid 411 through 413 Processing sheet with id= O, first strand: chain 'B' and resid 478 through 481 Processing sheet with id= P, first strand: chain 'b' and resid 83 through 86 removed outlier: 3.857A pdb=" N ALA b 42 " --> pdb=" O VAL b 11 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS b 13 " --> pdb=" O VAL b 40 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL b 40 " --> pdb=" O LYS b 13 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS b 64 " --> pdb=" O ILE b 94 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 4 through 8 Processing sheet with id= R, first strand: chain 'C' and resid 38 through 40 Processing sheet with id= S, first strand: chain 'C' and resid 174 through 179 Processing sheet with id= T, first strand: chain 'C' and resid 213 through 216 Processing sheet with id= U, first strand: chain 'C' and resid 219 through 222 Processing sheet with id= V, first strand: chain 'C' and resid 411 through 413 Processing sheet with id= W, first strand: chain 'C' and resid 478 through 481 Processing sheet with id= X, first strand: chain 'c' and resid 73 through 75 removed outlier: 3.767A pdb=" N LEU c 82 " --> pdb=" O VAL c 75 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA c 42 " --> pdb=" O VAL c 11 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS c 13 " --> pdb=" O VAL c 40 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL c 40 " --> pdb=" O LYS c 13 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS c 64 " --> pdb=" O ILE c 94 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA c 92 " --> pdb=" O LEU c 66 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 4 through 8 Processing sheet with id= Z, first strand: chain 'D' and resid 38 through 40 Processing sheet with id= AA, first strand: chain 'D' and resid 174 through 179 Processing sheet with id= AB, first strand: chain 'D' and resid 213 through 216 Processing sheet with id= AC, first strand: chain 'D' and resid 219 through 222 Processing sheet with id= AD, first strand: chain 'D' and resid 411 through 413 Processing sheet with id= AE, first strand: chain 'D' and resid 478 through 481 Processing sheet with id= AF, first strand: chain 'd' and resid 73 through 75 removed outlier: 4.485A pdb=" N LEU d 82 " --> pdb=" O VAL d 75 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA d 42 " --> pdb=" O VAL d 11 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS d 13 " --> pdb=" O VAL d 40 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL d 40 " --> pdb=" O LYS d 13 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LYS d 64 " --> pdb=" O ILE d 94 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 4 through 8 Processing sheet with id= AH, first strand: chain 'E' and resid 38 through 40 Processing sheet with id= AI, first strand: chain 'E' and resid 174 through 179 Processing sheet with id= AJ, first strand: chain 'E' and resid 213 through 216 Processing sheet with id= AK, first strand: chain 'E' and resid 219 through 222 Processing sheet with id= AL, first strand: chain 'E' and resid 411 through 413 Processing sheet with id= AM, first strand: chain 'E' and resid 478 through 481 Processing sheet with id= AN, first strand: chain 'e' and resid 73 through 75 removed outlier: 4.134A pdb=" N LEU e 82 " --> pdb=" O VAL e 75 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA e 42 " --> pdb=" O VAL e 11 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LYS e 13 " --> pdb=" O VAL e 40 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL e 40 " --> pdb=" O LYS e 13 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS e 64 " --> pdb=" O ILE e 94 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA e 92 " --> pdb=" O LEU e 66 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'F' and resid 4 through 8 Processing sheet with id= AP, first strand: chain 'F' and resid 38 through 40 Processing sheet with id= AQ, first strand: chain 'F' and resid 174 through 179 Processing sheet with id= AR, first strand: chain 'F' and resid 213 through 216 Processing sheet with id= AS, first strand: chain 'F' and resid 219 through 222 Processing sheet with id= AT, first strand: chain 'F' and resid 411 through 413 Processing sheet with id= AU, first strand: chain 'F' and resid 478 through 481 Processing sheet with id= AV, first strand: chain 'f' and resid 82 through 86 removed outlier: 3.872A pdb=" N ALA f 42 " --> pdb=" O VAL f 11 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LYS f 13 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N VAL f 40 " --> pdb=" O LYS f 13 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS f 64 " --> pdb=" O ILE f 94 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'G' and resid 4 through 8 Processing sheet with id= AX, first strand: chain 'G' and resid 38 through 40 Processing sheet with id= AY, first strand: chain 'G' and resid 174 through 179 Processing sheet with id= AZ, first strand: chain 'G' and resid 213 through 216 Processing sheet with id= BA, first strand: chain 'G' and resid 219 through 222 Processing sheet with id= BB, first strand: chain 'G' and resid 411 through 413 Processing sheet with id= BC, first strand: chain 'G' and resid 478 through 481 Processing sheet with id= BD, first strand: chain 'g' and resid 73 through 75 removed outlier: 4.147A pdb=" N LEU g 82 " --> pdb=" O VAL g 75 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA g 42 " --> pdb=" O VAL g 11 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LYS g 13 " --> pdb=" O VAL g 40 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N VAL g 40 " --> pdb=" O LYS g 13 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS g 64 " --> pdb=" O ILE g 94 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA g 92 " --> pdb=" O LEU g 66 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'H' and resid 4 through 8 Processing sheet with id= BF, first strand: chain 'H' and resid 38 through 40 Processing sheet with id= BG, first strand: chain 'H' and resid 174 through 179 Processing sheet with id= BH, first strand: chain 'H' and resid 213 through 216 Processing sheet with id= BI, first strand: chain 'H' and resid 219 through 222 Processing sheet with id= BJ, first strand: chain 'H' and resid 411 through 413 Processing sheet with id= BK, first strand: chain 'H' and resid 478 through 481 Processing sheet with id= BL, first strand: chain 'h' and resid 73 through 75 removed outlier: 3.708A pdb=" N LEU h 82 " --> pdb=" O VAL h 75 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA h 42 " --> pdb=" O VAL h 11 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS h 13 " --> pdb=" O VAL h 40 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL h 40 " --> pdb=" O LYS h 13 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS h 64 " --> pdb=" O ILE h 94 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'I' and resid 4 through 8 Processing sheet with id= BN, first strand: chain 'I' and resid 38 through 40 Processing sheet with id= BO, first strand: chain 'I' and resid 174 through 179 Processing sheet with id= BP, first strand: chain 'I' and resid 213 through 216 Processing sheet with id= BQ, first strand: chain 'I' and resid 219 through 222 Processing sheet with id= BR, first strand: chain 'I' and resid 411 through 413 Processing sheet with id= BS, first strand: chain 'I' and resid 478 through 481 Processing sheet with id= BT, first strand: chain 'i' and resid 73 through 75 removed outlier: 3.988A pdb=" N LEU i 82 " --> pdb=" O VAL i 75 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA i 42 " --> pdb=" O VAL i 11 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS i 13 " --> pdb=" O VAL i 40 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL i 40 " --> pdb=" O LYS i 13 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS i 64 " --> pdb=" O ILE i 94 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'J' and resid 4 through 8 Processing sheet with id= BV, first strand: chain 'J' and resid 38 through 40 Processing sheet with id= BW, first strand: chain 'J' and resid 174 through 179 Processing sheet with id= BX, first strand: chain 'J' and resid 213 through 216 Processing sheet with id= BY, first strand: chain 'J' and resid 219 through 222 Processing sheet with id= BZ, first strand: chain 'J' and resid 411 through 413 Processing sheet with id= CA, first strand: chain 'J' and resid 478 through 481 Processing sheet with id= CB, first strand: chain 'j' and resid 82 through 86 removed outlier: 3.764A pdb=" N ALA j 42 " --> pdb=" O VAL j 11 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LYS j 13 " --> pdb=" O VAL j 40 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL j 40 " --> pdb=" O LYS j 13 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS j 64 " --> pdb=" O ILE j 94 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'K' and resid 4 through 8 Processing sheet with id= CD, first strand: chain 'K' and resid 38 through 40 Processing sheet with id= CE, first strand: chain 'K' and resid 174 through 179 Processing sheet with id= CF, first strand: chain 'K' and resid 213 through 216 Processing sheet with id= CG, first strand: chain 'K' and resid 219 through 222 Processing sheet with id= CH, first strand: chain 'K' and resid 411 through 413 Processing sheet with id= CI, first strand: chain 'K' and resid 478 through 481 Processing sheet with id= CJ, first strand: chain 'k' and resid 83 through 86 removed outlier: 3.758A pdb=" N ALA k 42 " --> pdb=" O VAL k 11 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS k 13 " --> pdb=" O VAL k 40 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL k 40 " --> pdb=" O LYS k 13 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS k 64 " --> pdb=" O ILE k 94 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'L' and resid 4 through 8 Processing sheet with id= CL, first strand: chain 'L' and resid 38 through 40 Processing sheet with id= CM, first strand: chain 'L' and resid 174 through 179 Processing sheet with id= CN, first strand: chain 'L' and resid 213 through 216 Processing sheet with id= CO, first strand: chain 'L' and resid 219 through 222 Processing sheet with id= CP, first strand: chain 'L' and resid 411 through 413 Processing sheet with id= CQ, first strand: chain 'L' and resid 478 through 481 Processing sheet with id= CR, first strand: chain 'l' and resid 73 through 75 removed outlier: 4.090A pdb=" N LEU l 82 " --> pdb=" O VAL l 75 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA l 42 " --> pdb=" O VAL l 11 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LYS l 13 " --> pdb=" O VAL l 40 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N VAL l 40 " --> pdb=" O LYS l 13 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS l 64 " --> pdb=" O ILE l 94 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA l 92 " --> pdb=" O LEU l 66 " (cutoff:3.500A) Processing sheet with id= CS, first strand: chain 'M' and resid 4 through 8 Processing sheet with id= CT, first strand: chain 'M' and resid 38 through 40 Processing sheet with id= CU, first strand: chain 'M' and resid 174 through 179 Processing sheet with id= CV, first strand: chain 'M' and resid 213 through 216 Processing sheet with id= CW, first strand: chain 'M' and resid 219 through 222 Processing sheet with id= CX, first strand: chain 'M' and resid 411 through 413 Processing sheet with id= CY, first strand: chain 'M' and resid 478 through 481 Processing sheet with id= CZ, first strand: chain 'm' and resid 73 through 75 removed outlier: 4.344A pdb=" N LEU m 82 " --> pdb=" O VAL m 75 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA m 42 " --> pdb=" O VAL m 11 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LYS m 13 " --> pdb=" O VAL m 40 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL m 40 " --> pdb=" O LYS m 13 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS m 64 " --> pdb=" O ILE m 94 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA m 92 " --> pdb=" O LEU m 66 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'N' and resid 4 through 8 Processing sheet with id= DB, first strand: chain 'N' and resid 38 through 40 Processing sheet with id= DC, first strand: chain 'N' and resid 174 through 179 Processing sheet with id= DD, first strand: chain 'N' and resid 213 through 216 Processing sheet with id= DE, first strand: chain 'N' and resid 219 through 222 Processing sheet with id= DF, first strand: chain 'N' and resid 411 through 413 Processing sheet with id= DG, first strand: chain 'N' and resid 478 through 481 Processing sheet with id= DH, first strand: chain 'n' and resid 73 through 75 removed outlier: 4.273A pdb=" N LEU n 82 " --> pdb=" O VAL n 75 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA n 42 " --> pdb=" O VAL n 11 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS n 13 " --> pdb=" O VAL n 40 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL n 40 " --> pdb=" O LYS n 13 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS n 64 " --> pdb=" O ILE n 94 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA n 92 " --> pdb=" O LEU n 66 " (cutoff:3.500A) 3377 hydrogen bonds defined for protein. 9429 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: 27.06 Time building geometry restraints manager: 22.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 22524 1.34 - 1.46: 10365 1.46 - 1.58: 32519 1.58 - 1.70: 42 1.70 - 1.82: 462 Bond restraints: 65912 Sorted by residual: bond pdb=" N GLU i 78 " pdb=" CA GLU i 78 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.40e+00 bond pdb=" CB GLU e 16 " pdb=" CG GLU e 16 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.16e+00 bond pdb=" CB LYS b 69 " pdb=" CG LYS b 69 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.09e+00 bond pdb=" CB GLU n 16 " pdb=" CG GLU n 16 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.06e+00 bond pdb=" CB GLU l 16 " pdb=" CG GLU l 16 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.04e+00 ... (remaining 65907 not shown) Histogram of bond angle deviations from ideal: 96.83 - 104.74: 975 104.74 - 112.65: 36619 112.65 - 120.56: 28452 120.56 - 128.47: 22764 128.47 - 136.37: 174 Bond angle restraints: 88984 Sorted by residual: angle pdb=" CA LYS E 210 " pdb=" CB LYS E 210 " pdb=" CG LYS E 210 " ideal model delta sigma weight residual 114.10 125.86 -11.76 2.00e+00 2.50e-01 3.46e+01 angle pdb=" CA GLU f 81 " pdb=" CB GLU f 81 " pdb=" CG GLU f 81 " ideal model delta sigma weight residual 114.10 123.95 -9.85 2.00e+00 2.50e-01 2.43e+01 angle pdb=" CA GLU i 78 " pdb=" CB GLU i 78 " pdb=" CG GLU i 78 " ideal model delta sigma weight residual 114.10 123.91 -9.81 2.00e+00 2.50e-01 2.40e+01 angle pdb=" N VAL M 305 " pdb=" CA VAL M 305 " pdb=" C VAL M 305 " ideal model delta sigma weight residual 113.42 108.31 5.11 1.17e+00 7.31e-01 1.91e+01 angle pdb=" C VAL l 77 " pdb=" N GLU l 78 " pdb=" CA GLU l 78 " ideal model delta sigma weight residual 121.54 129.77 -8.23 1.91e+00 2.74e-01 1.86e+01 ... (remaining 88979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.77: 39808 35.77 - 71.53: 1176 71.53 - 107.30: 76 107.30 - 143.07: 3 143.07 - 178.84: 13 Dihedral angle restraints: 41076 sinusoidal: 16464 harmonic: 24612 Sorted by residual: dihedral pdb=" O2A ADP I 601 " pdb=" O3A ADP I 601 " pdb=" PA ADP I 601 " pdb=" PB ADP I 601 " ideal model delta sinusoidal sigma weight residual -60.00 118.84 -178.84 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP H 601 " pdb=" O3A ADP H 601 " pdb=" PA ADP H 601 " pdb=" PB ADP H 601 " ideal model delta sinusoidal sigma weight residual -60.00 115.42 -175.42 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP J 601 " pdb=" O3A ADP J 601 " pdb=" PA ADP J 601 " pdb=" PB ADP J 601 " ideal model delta sinusoidal sigma weight residual -60.00 114.77 -174.77 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 41073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 8699 0.053 - 0.106: 1654 0.106 - 0.159: 308 0.159 - 0.211: 6 0.211 - 0.264: 1 Chirality restraints: 10668 Sorted by residual: chirality pdb=" CA GLU i 78 " pdb=" N GLU i 78 " pdb=" C GLU i 78 " pdb=" CB GLU i 78 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA GLU b 78 " pdb=" N GLU b 78 " pdb=" C GLU b 78 " pdb=" CB GLU b 78 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.21e-01 chirality pdb=" CB ILE i 94 " pdb=" CA ILE i 94 " pdb=" CG1 ILE i 94 " pdb=" CG2 ILE i 94 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.94e-01 ... (remaining 10665 not shown) Planarity restraints: 11578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 210 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C LYS E 210 " 0.045 2.00e-02 2.50e+03 pdb=" O LYS E 210 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN E 211 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE f 48 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" C ILE f 48 " 0.042 2.00e-02 2.50e+03 pdb=" O ILE f 48 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU f 49 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU l 78 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.50e+00 pdb=" C GLU l 78 " -0.041 2.00e-02 2.50e+03 pdb=" O GLU l 78 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY l 79 " 0.014 2.00e-02 2.50e+03 ... (remaining 11575 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 490 2.53 - 3.12: 50145 3.12 - 3.72: 108320 3.72 - 4.31: 149625 4.31 - 4.90: 250048 Nonbonded interactions: 558628 Sorted by model distance: nonbonded pdb=" O3B ADP F 601 " pdb="MG MG F 602 " model vdw 1.940 2.170 nonbonded pdb=" O2A ADP E 601 " pdb="MG MG E 602 " model vdw 2.023 2.170 nonbonded pdb=" O2A ADP G 601 " pdb="MG MG G 602 " model vdw 2.042 2.170 nonbonded pdb=" O1A ADP N 601 " pdb="MG MG N 602 " model vdw 2.043 2.170 nonbonded pdb=" O1A ADP L 601 " pdb="MG MG L 602 " model vdw 2.054 2.170 ... (remaining 558623 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.270 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: 0.060 Extract box with map and model: 24.800 Check model and map are aligned: 0.720 Set scattering table: 0.450 Process input model: 138.720 Find NCS groups from input model: 4.050 Set up NCS constraints: 0.740 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 187.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 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 : 0.004 0.044 65912 Z= 0.238 Angle : 0.667 13.322 88984 Z= 0.327 Chirality : 0.043 0.264 10668 Planarity : 0.003 0.051 11578 Dihedral : 16.600 178.837 25256 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.49 % Favored : 98.50 % Rotamer: Outliers : 1.01 % Allowed : 21.44 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.08), residues: 8652 helix: 1.25 (0.08), residues: 4214 sheet: 0.79 (0.17), residues: 896 loop : -0.33 (0.09), residues: 3542 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.000 HIS M 329 PHE 0.010 0.001 PHE M 195 TYR 0.025 0.001 TYR g 70 ARG 0.010 0.000 ARG L 268 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 998 time to evaluate : 5.624 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: a 15 ILE cc_start: 0.8673 (pt) cc_final: 0.8308 (pp) REVERT: a 63 ASP cc_start: 0.7674 (m-30) cc_final: 0.6781 (m-30) REVERT: C 226 LYS cc_start: 0.9090 (mppt) cc_final: 0.8836 (ttmm) REVERT: c 15 ILE cc_start: 0.8781 (pt) cc_final: 0.8481 (pp) REVERT: D 268 ARG cc_start: 0.8843 (mtt-85) cc_final: 0.8631 (mtt90) REVERT: e 15 ILE cc_start: 0.8645 (pt) cc_final: 0.8235 (pp) REVERT: F 178 GLU cc_start: 0.8796 (pt0) cc_final: 0.8500 (pt0) REVERT: f 60 LYS cc_start: 0.8075 (pptt) cc_final: 0.7836 (pmtt) REVERT: g 15 ILE cc_start: 0.8872 (pt) cc_final: 0.8600 (pp) REVERT: g 82 LEU cc_start: 0.8557 (mt) cc_final: 0.8262 (mp) REVERT: H 362 ARG cc_start: 0.7633 (ptp90) cc_final: 0.7253 (ptp90) REVERT: I 321 LYS cc_start: 0.8173 (mppt) cc_final: 0.7904 (mppt) REVERT: i 57 MET cc_start: 0.7787 (mmm) cc_final: 0.7520 (mmm) REVERT: i 89 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7894 (m-30) REVERT: j 15 ILE cc_start: 0.8618 (pt) cc_final: 0.8263 (pp) REVERT: j 63 ASP cc_start: 0.7616 (p0) cc_final: 0.7257 (p0) REVERT: k 15 ILE cc_start: 0.8536 (pt) cc_final: 0.8221 (pp) REVERT: k 89 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7474 (m-30) REVERT: l 15 ILE cc_start: 0.8571 (pt) cc_final: 0.8255 (pp) REVERT: l 60 LYS cc_start: 0.8173 (mppt) cc_final: 0.7877 (mmpt) REVERT: m 15 ILE cc_start: 0.8565 (pt) cc_final: 0.8289 (pp) REVERT: n 15 ILE cc_start: 0.8773 (pt) cc_final: 0.8508 (pp) outliers start: 69 outliers final: 54 residues processed: 1051 average time/residue: 1.7035 time to fit residues: 2249.1350 Evaluate side-chains 991 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 935 time to evaluate : 5.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 91 MET Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain d residue 13 LYS Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain e residue 23 SER Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain h residue 51 ASP Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain i residue 51 ASP Chi-restraints excluded: chain i residue 88 ASP Chi-restraints excluded: chain i residue 89 ASP Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain j residue 13 LYS Chi-restraints excluded: chain K residue 216 ASP Chi-restraints excluded: chain K residue 334 ASP Chi-restraints excluded: chain k residue 89 ASP Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 330 THR Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 216 ASP Chi-restraints excluded: chain m residue 89 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 176 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 721 optimal weight: 2.9990 chunk 647 optimal weight: 6.9990 chunk 359 optimal weight: 5.9990 chunk 221 optimal weight: 2.9990 chunk 436 optimal weight: 0.9980 chunk 345 optimal weight: 3.9990 chunk 669 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 chunk 407 optimal weight: 0.9980 chunk 498 optimal weight: 1.9990 chunk 775 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 37 GLN C 37 ASN c 37 GLN h 37 GLN I 37 ASN i 37 GLN j 37 GLN K 37 ASN L 37 ASN M 37 ASN m 7 HIS m 37 GLN ** n 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 65912 Z= 0.300 Angle : 0.658 10.892 88984 Z= 0.324 Chirality : 0.045 0.173 10668 Planarity : 0.004 0.043 11578 Dihedral : 9.094 176.016 9481 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.65 % Allowed : 20.90 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.08), residues: 8652 helix: 1.47 (0.08), residues: 4270 sheet: 0.36 (0.16), residues: 924 loop : -0.41 (0.09), residues: 3458 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 9 PHE 0.011 0.001 PHE A 195 TYR 0.007 0.001 TYR F 199 ARG 0.012 0.001 ARG e 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1179 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 998 time to evaluate : 6.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 80 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7453 (mm-30) REVERT: C 226 LYS cc_start: 0.9099 (mppt) cc_final: 0.8816 (ttmm) REVERT: C 397 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8261 (mm-30) REVERT: c 82 LEU cc_start: 0.8492 (mm) cc_final: 0.8266 (mp) REVERT: c 87 GLU cc_start: 0.7977 (tt0) cc_final: 0.7552 (tt0) REVERT: D 268 ARG cc_start: 0.8889 (mtt-85) cc_final: 0.8658 (mtt90) REVERT: d 80 GLU cc_start: 0.6205 (mp0) cc_final: 0.5881 (mp0) REVERT: d 87 GLU cc_start: 0.7987 (tt0) cc_final: 0.7723 (tt0) REVERT: d 91 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7624 (mtm) REVERT: E 341 LYS cc_start: 0.9464 (mtpp) cc_final: 0.9231 (mtpm) REVERT: e 57 MET cc_start: 0.8000 (mmm) cc_final: 0.7702 (mmt) REVERT: F 178 GLU cc_start: 0.8746 (pt0) cc_final: 0.8470 (pt0) REVERT: h 55 ARG cc_start: 0.7796 (ptm160) cc_final: 0.7444 (ttp80) REVERT: I 268 ARG cc_start: 0.8790 (mtt90) cc_final: 0.8556 (mtt90) REVERT: I 288 MET cc_start: 0.8803 (mtm) cc_final: 0.8561 (mtm) REVERT: I 321 LYS cc_start: 0.8220 (mppt) cc_final: 0.8013 (mppt) REVERT: I 363 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8521 (pp20) REVERT: i 91 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7804 (mpp) REVERT: J 76 GLU cc_start: 0.8340 (tt0) cc_final: 0.7984 (tm-30) REVERT: J 268 ARG cc_start: 0.8904 (mtt-85) cc_final: 0.8655 (mtt90) REVERT: J 362 ARG cc_start: 0.7557 (mpp80) cc_final: 0.7189 (mtm-85) REVERT: j 15 ILE cc_start: 0.8606 (pt) cc_final: 0.8322 (pp) REVERT: j 55 ARG cc_start: 0.7791 (ptm160) cc_final: 0.7273 (ttp80) REVERT: j 86 ARG cc_start: 0.8456 (mtp85) cc_final: 0.8022 (mtp85) REVERT: j 87 GLU cc_start: 0.7877 (tt0) cc_final: 0.7415 (tt0) REVERT: j 88 ASP cc_start: 0.7722 (p0) cc_final: 0.7339 (p0) REVERT: j 89 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: K 321 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7259 (ptpp) REVERT: k 55 ARG cc_start: 0.7654 (ptm160) cc_final: 0.7327 (ttp80) REVERT: k 57 MET cc_start: 0.7881 (mmt) cc_final: 0.7519 (tpt) REVERT: L 277 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.8008 (mmmm) REVERT: M 486 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7893 (pp20) REVERT: m 55 ARG cc_start: 0.7874 (ptm160) cc_final: 0.7598 (ttp80) REVERT: N 171 LYS cc_start: 0.7837 (mmtm) cc_final: 0.7536 (mmpt) REVERT: n 87 GLU cc_start: 0.7808 (tt0) cc_final: 0.7599 (tt0) outliers start: 181 outliers final: 61 residues processed: 1128 average time/residue: 1.6621 time to fit residues: 2351.2347 Evaluate side-chains 1003 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 935 time to evaluate : 5.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 51 ASP Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain d residue 91 MET Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain e residue 23 SER Chi-restraints excluded: chain e residue 89 ASP Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 334 ASP Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 363 GLU Chi-restraints excluded: chain i residue 81 GLU Chi-restraints excluded: chain i residue 88 ASP Chi-restraints excluded: chain i residue 91 MET Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain j residue 51 ASP Chi-restraints excluded: chain j residue 89 ASP Chi-restraints excluded: chain K residue 216 ASP Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 321 LYS Chi-restraints excluded: chain k residue 23 SER Chi-restraints excluded: chain k residue 51 ASP Chi-restraints excluded: chain k residue 66 LEU Chi-restraints excluded: chain k residue 81 GLU Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 277 LYS Chi-restraints excluded: chain L residue 330 THR Chi-restraints excluded: chain l residue 51 ASP Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 486 GLU Chi-restraints excluded: chain m residue 51 ASP Chi-restraints excluded: chain N residue 331 THR Chi-restraints excluded: chain N residue 352 GLN Chi-restraints excluded: chain n residue 51 ASP Chi-restraints excluded: chain n residue 94 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 431 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 chunk 645 optimal weight: 10.0000 chunk 528 optimal weight: 0.8980 chunk 213 optimal weight: 4.9990 chunk 776 optimal weight: 2.9990 chunk 839 optimal weight: 1.9990 chunk 691 optimal weight: 0.0870 chunk 770 optimal weight: 0.9990 chunk 264 optimal weight: 10.0000 chunk 623 optimal weight: 0.7980 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 7 HIS I 37 ASN i 7 HIS K 37 ASN L 37 ASN M 37 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 65912 Z= 0.214 Angle : 0.622 10.103 88984 Z= 0.304 Chirality : 0.044 0.162 10668 Planarity : 0.004 0.058 11578 Dihedral : 8.733 168.620 9428 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.71 % Allowed : 20.87 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.08), residues: 8652 helix: 1.53 (0.08), residues: 4242 sheet: 0.24 (0.16), residues: 924 loop : -0.43 (0.09), residues: 3486 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS K 9 PHE 0.012 0.001 PHE A 195 TYR 0.010 0.001 TYR b 70 ARG 0.009 0.001 ARG n 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1178 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 993 time to evaluate : 5.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 VAL cc_start: 0.8698 (t) cc_final: 0.8491 (m) REVERT: a 80 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7426 (mm-30) REVERT: b 55 ARG cc_start: 0.7507 (ttp80) cc_final: 0.7287 (ttp80) REVERT: b 63 ASP cc_start: 0.7741 (p0) cc_final: 0.7534 (p0) REVERT: C 226 LYS cc_start: 0.9090 (mppt) cc_final: 0.8761 (ttmm) REVERT: C 285 ARG cc_start: 0.8728 (ttp-170) cc_final: 0.8513 (ttm-80) REVERT: C 397 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8248 (mm-30) REVERT: c 55 ARG cc_start: 0.7686 (ttp80) cc_final: 0.6531 (ttp80) REVERT: c 87 GLU cc_start: 0.7865 (tt0) cc_final: 0.7644 (tt0) REVERT: D 210 LYS cc_start: 0.8798 (ptpp) cc_final: 0.8485 (tptt) REVERT: d 55 ARG cc_start: 0.7416 (ttp80) cc_final: 0.6417 (ttp80) REVERT: d 91 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7703 (mtm) REVERT: E 272 LYS cc_start: 0.9109 (ptpp) cc_final: 0.8877 (pttm) REVERT: E 288 MET cc_start: 0.8579 (mtm) cc_final: 0.8293 (mtm) REVERT: E 341 LYS cc_start: 0.9467 (mtpp) cc_final: 0.9208 (mtpm) REVERT: F 178 GLU cc_start: 0.8681 (pt0) cc_final: 0.8422 (pt0) REVERT: G 385 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8470 (p) REVERT: I 321 LYS cc_start: 0.8226 (mppt) cc_final: 0.7982 (mppt) REVERT: J 76 GLU cc_start: 0.8242 (tt0) cc_final: 0.7967 (tm-30) REVERT: J 362 ARG cc_start: 0.7694 (mpp80) cc_final: 0.7165 (ptp90) REVERT: j 63 ASP cc_start: 0.7598 (p0) cc_final: 0.7333 (p0) REVERT: j 88 ASP cc_start: 0.7758 (p0) cc_final: 0.7318 (p0) REVERT: j 89 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: K 73 MET cc_start: 0.8544 (mtp) cc_final: 0.8339 (mtm) REVERT: K 397 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8215 (mm-30) REVERT: k 63 ASP cc_start: 0.7767 (p0) cc_final: 0.7427 (p0) REVERT: k 89 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7456 (m-30) REVERT: L 362 ARG cc_start: 0.7283 (pmm-80) cc_final: 0.6955 (ptp90) REVERT: l 87 GLU cc_start: 0.7869 (tt0) cc_final: 0.7554 (tt0) REVERT: M 486 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7851 (pp20) REVERT: m 47 LYS cc_start: 0.8763 (ptpp) cc_final: 0.8114 (ptpp) REVERT: N 171 LYS cc_start: 0.7820 (mmtm) cc_final: 0.7531 (mmpt) REVERT: N 386 GLU cc_start: 0.7887 (pm20) cc_final: 0.7643 (pm20) outliers start: 185 outliers final: 68 residues processed: 1126 average time/residue: 1.6729 time to fit residues: 2360.1280 Evaluate side-chains 1028 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 955 time to evaluate : 5.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 91 MET Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain c residue 14 ARG Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 51 ASP Chi-restraints excluded: chain c residue 63 ASP Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain d residue 37 GLN Chi-restraints excluded: chain d residue 91 MET Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain e residue 23 SER Chi-restraints excluded: chain e residue 37 GLN Chi-restraints excluded: chain e residue 89 ASP Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain h residue 51 ASP Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 331 THR Chi-restraints excluded: chain i residue 51 ASP Chi-restraints excluded: chain i residue 88 ASP Chi-restraints excluded: chain J residue 186 GLU Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain j residue 51 ASP Chi-restraints excluded: chain j residue 89 ASP Chi-restraints excluded: chain K residue 216 ASP Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 321 LYS Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 23 SER Chi-restraints excluded: chain k residue 51 ASP Chi-restraints excluded: chain k residue 89 ASP Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 330 THR Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain l residue 37 GLN Chi-restraints excluded: chain l residue 51 ASP Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 486 GLU Chi-restraints excluded: chain m residue 51 ASP Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 331 THR Chi-restraints excluded: chain N residue 403 THR Chi-restraints excluded: chain n residue 51 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 767 optimal weight: 10.0000 chunk 584 optimal weight: 0.0570 chunk 403 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 370 optimal weight: 2.9990 chunk 521 optimal weight: 10.0000 chunk 779 optimal weight: 0.8980 chunk 825 optimal weight: 7.9990 chunk 407 optimal weight: 0.6980 chunk 738 optimal weight: 4.9990 chunk 222 optimal weight: 4.9990 overall best weight: 1.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN I 37 ASN K 37 ASN L 37 ASN M 37 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 65912 Z= 0.310 Angle : 0.646 8.909 88984 Z= 0.316 Chirality : 0.045 0.172 10668 Planarity : 0.004 0.050 11578 Dihedral : 8.660 173.720 9421 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.94 % Allowed : 20.96 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.08), residues: 8652 helix: 1.43 (0.08), residues: 4256 sheet: 0.10 (0.16), residues: 924 loop : -0.42 (0.09), residues: 3472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 9 PHE 0.013 0.001 PHE e 67 TYR 0.013 0.001 TYR k 70 ARG 0.011 0.001 ARG c 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1188 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 987 time to evaluate : 5.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 63 ASP cc_start: 0.8035 (m-30) cc_final: 0.7676 (m-30) REVERT: a 80 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7563 (mm-30) REVERT: B 277 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8052 (mmmm) REVERT: B 321 LYS cc_start: 0.8012 (mppt) cc_final: 0.7737 (mppt) REVERT: b 47 LYS cc_start: 0.8684 (ptmm) cc_final: 0.8062 (ptmm) REVERT: C 226 LYS cc_start: 0.9091 (mppt) cc_final: 0.8818 (ttmm) REVERT: C 397 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8290 (mm-30) REVERT: D 210 LYS cc_start: 0.8806 (ptpp) cc_final: 0.8488 (tptt) REVERT: D 277 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8083 (mmmm) REVERT: d 89 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7824 (m-30) REVERT: E 272 LYS cc_start: 0.9131 (ptpp) cc_final: 0.8892 (pttm) REVERT: E 341 LYS cc_start: 0.9460 (mtpp) cc_final: 0.9193 (mtpm) REVERT: F 178 GLU cc_start: 0.8698 (pt0) cc_final: 0.8435 (pt0) REVERT: f 88 ASP cc_start: 0.8522 (p0) cc_final: 0.8306 (p0) REVERT: f 91 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7587 (mtt) REVERT: G 385 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8513 (p) REVERT: H 69 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.7271 (mmt) REVERT: H 76 GLU cc_start: 0.8313 (tt0) cc_final: 0.7990 (tm-30) REVERT: I 321 LYS cc_start: 0.8212 (mppt) cc_final: 0.7942 (mppt) REVERT: i 91 MET cc_start: 0.8045 (mpp) cc_final: 0.7595 (mpp) REVERT: J 321 LYS cc_start: 0.7705 (mppt) cc_final: 0.7363 (mppt) REVERT: J 362 ARG cc_start: 0.7752 (mpp80) cc_final: 0.7304 (ptp90) REVERT: k 89 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7527 (m-30) REVERT: L 277 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8025 (mmmm) REVERT: l 55 ARG cc_start: 0.7695 (ttp80) cc_final: 0.6495 (ttp80) REVERT: M 486 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7860 (pp20) REVERT: m 47 LYS cc_start: 0.8421 (ptpp) cc_final: 0.8158 (ptpp) REVERT: m 55 ARG cc_start: 0.7725 (ttp80) cc_final: 0.7522 (ttp80) REVERT: N 171 LYS cc_start: 0.7855 (mmtm) cc_final: 0.7574 (mmpt) REVERT: N 386 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7686 (pm20) REVERT: n 13 LYS cc_start: 0.8635 (tppt) cc_final: 0.8427 (tppt) REVERT: n 55 ARG cc_start: 0.7455 (ttp80) cc_final: 0.6942 (ttp80) outliers start: 201 outliers final: 85 residues processed: 1137 average time/residue: 1.6485 time to fit residues: 2350.7251 Evaluate side-chains 1038 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 943 time to evaluate : 5.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain a residue 37 GLN Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain b residue 37 GLN Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 91 MET Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain c residue 14 ARG Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 51 ASP Chi-restraints excluded: chain c residue 63 ASP Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 277 LYS Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain d residue 89 ASP Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain e residue 23 SER Chi-restraints excluded: chain e residue 37 GLN Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain f residue 91 MET Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 334 ASP Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 334 ASP Chi-restraints excluded: chain H residue 473 GLU Chi-restraints excluded: chain h residue 51 ASP Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 331 THR Chi-restraints excluded: chain i residue 51 ASP Chi-restraints excluded: chain i residue 88 ASP Chi-restraints excluded: chain J residue 186 GLU Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain j residue 51 ASP Chi-restraints excluded: chain K residue 186 GLU Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain k residue 23 SER Chi-restraints excluded: chain k residue 51 ASP Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain k residue 89 ASP Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 277 LYS Chi-restraints excluded: chain L residue 330 THR Chi-restraints excluded: chain l residue 37 GLN Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 51 ASP Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 486 GLU Chi-restraints excluded: chain m residue 51 ASP Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 331 THR Chi-restraints excluded: chain N residue 352 GLN Chi-restraints excluded: chain N residue 386 GLU Chi-restraints excluded: chain n residue 51 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 687 optimal weight: 0.4980 chunk 468 optimal weight: 0.0980 chunk 11 optimal weight: 0.7980 chunk 614 optimal weight: 5.9990 chunk 340 optimal weight: 9.9990 chunk 704 optimal weight: 6.9990 chunk 570 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 421 optimal weight: 6.9990 chunk 740 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN M 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 65912 Z= 0.229 Angle : 0.637 11.833 88984 Z= 0.309 Chirality : 0.044 0.210 10668 Planarity : 0.004 0.055 11578 Dihedral : 8.397 169.570 9417 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.46 % Favored : 98.53 % Rotamer: Outliers : 2.69 % Allowed : 21.78 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.08), residues: 8652 helix: 1.47 (0.08), residues: 4270 sheet: 0.08 (0.16), residues: 924 loop : -0.46 (0.09), residues: 3458 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 9 PHE 0.019 0.001 PHE c 67 TYR 0.006 0.001 TYR h 70 ARG 0.011 0.001 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1181 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 997 time to evaluate : 5.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 80 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7569 (mm-30) REVERT: B 321 LYS cc_start: 0.8054 (mppt) cc_final: 0.7755 (mppt) REVERT: B 362 ARG cc_start: 0.7703 (ttm110) cc_final: 0.7140 (ptp-110) REVERT: C 226 LYS cc_start: 0.9049 (mppt) cc_final: 0.8814 (ttmm) REVERT: C 397 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8283 (mm-30) REVERT: c 55 ARG cc_start: 0.7521 (ptm160) cc_final: 0.6849 (ptm160) REVERT: D 111 MET cc_start: 0.9153 (mtp) cc_final: 0.8913 (mtt) REVERT: D 210 LYS cc_start: 0.8820 (ptpp) cc_final: 0.8491 (tptt) REVERT: D 277 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8088 (mmmm) REVERT: d 89 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7884 (m-30) REVERT: d 91 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7810 (mpp) REVERT: E 272 LYS cc_start: 0.9125 (ptpp) cc_final: 0.8889 (pttm) REVERT: E 341 LYS cc_start: 0.9453 (mtpp) cc_final: 0.9178 (mtpm) REVERT: F 178 GLU cc_start: 0.8659 (pt0) cc_final: 0.8395 (pt0) REVERT: f 91 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7580 (mtt) REVERT: G 385 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8531 (p) REVERT: H 69 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.7248 (mmt) REVERT: H 76 GLU cc_start: 0.8188 (tt0) cc_final: 0.7938 (tm-30) REVERT: h 91 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7730 (mpp) REVERT: I 288 MET cc_start: 0.8683 (mtm) cc_final: 0.8418 (mtm) REVERT: I 321 LYS cc_start: 0.8229 (mppt) cc_final: 0.7990 (mppt) REVERT: J 76 GLU cc_start: 0.8390 (tt0) cc_final: 0.7933 (tm-30) REVERT: J 362 ARG cc_start: 0.7834 (mpp80) cc_final: 0.7433 (ptp90) REVERT: j 86 ARG cc_start: 0.8620 (mmm-85) cc_final: 0.8409 (mtp85) REVERT: K 397 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8237 (mm-30) REVERT: k 63 ASP cc_start: 0.7435 (p0) cc_final: 0.7208 (p0) REVERT: k 85 LEU cc_start: 0.8900 (pt) cc_final: 0.8186 (pt) REVERT: L 321 LYS cc_start: 0.7881 (mppt) cc_final: 0.7676 (mppt) REVERT: L 362 ARG cc_start: 0.7395 (pmm-80) cc_final: 0.7051 (ptp90) REVERT: l 47 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8240 (ptpp) REVERT: l 60 LYS cc_start: 0.8173 (tmmt) cc_final: 0.7940 (tmmt) REVERT: M 52 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8450 (m-30) REVERT: M 486 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7821 (pp20) REVERT: N 171 LYS cc_start: 0.7887 (mmtm) cc_final: 0.7571 (mmpt) REVERT: N 385 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8555 (p) REVERT: n 47 LYS cc_start: 0.8304 (ptpp) cc_final: 0.8076 (ptpp) outliers start: 184 outliers final: 90 residues processed: 1123 average time/residue: 1.6436 time to fit residues: 2313.8126 Evaluate side-chains 1050 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 949 time to evaluate : 5.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain a residue 37 GLN Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 37 GLN Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 91 MET Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain c residue 14 ARG Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 37 GLN Chi-restraints excluded: chain c residue 51 ASP Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 277 LYS Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain d residue 89 ASP Chi-restraints excluded: chain d residue 91 MET Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain e residue 23 SER Chi-restraints excluded: chain e residue 37 GLN Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain f residue 37 GLN Chi-restraints excluded: chain f residue 91 MET Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 299 THR Chi-restraints excluded: chain G residue 334 ASP Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain g residue 37 GLN Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 334 ASP Chi-restraints excluded: chain H residue 473 GLU Chi-restraints excluded: chain h residue 37 GLN Chi-restraints excluded: chain h residue 51 ASP Chi-restraints excluded: chain h residue 91 MET Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 331 THR Chi-restraints excluded: chain i residue 37 GLN Chi-restraints excluded: chain i residue 51 ASP Chi-restraints excluded: chain J residue 186 GLU Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain j residue 37 GLN Chi-restraints excluded: chain j residue 51 ASP Chi-restraints excluded: chain K residue 216 ASP Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 23 SER Chi-restraints excluded: chain k residue 37 GLN Chi-restraints excluded: chain k residue 51 ASP Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 330 THR Chi-restraints excluded: chain l residue 37 GLN Chi-restraints excluded: chain l residue 47 LYS Chi-restraints excluded: chain l residue 51 ASP Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 486 GLU Chi-restraints excluded: chain m residue 37 GLN Chi-restraints excluded: chain m residue 51 ASP Chi-restraints excluded: chain N residue 331 THR Chi-restraints excluded: chain N residue 352 GLN Chi-restraints excluded: chain N residue 385 THR Chi-restraints excluded: chain N residue 403 THR Chi-restraints excluded: chain n residue 37 GLN Chi-restraints excluded: chain n residue 51 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 277 optimal weight: 3.9990 chunk 743 optimal weight: 0.9990 chunk 163 optimal weight: 0.8980 chunk 484 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 826 optimal weight: 9.9990 chunk 685 optimal weight: 6.9990 chunk 382 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 273 optimal weight: 10.0000 chunk 433 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN L 37 ASN M 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 65912 Z= 0.245 Angle : 0.652 14.339 88984 Z= 0.315 Chirality : 0.044 0.181 10668 Planarity : 0.004 0.062 11578 Dihedral : 8.085 168.078 9415 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.72 % Allowed : 22.56 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.08), residues: 8652 helix: 1.48 (0.08), residues: 4270 sheet: 0.04 (0.16), residues: 924 loop : -0.49 (0.09), residues: 3458 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 9 PHE 0.013 0.001 PHE e 67 TYR 0.006 0.001 TYR L 199 ARG 0.014 0.001 ARG i 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 979 time to evaluate : 5.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 80 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7393 (mm-30) REVERT: B 321 LYS cc_start: 0.8070 (mppt) cc_final: 0.7748 (mppt) REVERT: B 362 ARG cc_start: 0.7737 (ttm110) cc_final: 0.7196 (ptp-110) REVERT: b 19 ARG cc_start: 0.7846 (mmp80) cc_final: 0.7451 (mmp80) REVERT: b 55 ARG cc_start: 0.7433 (ptm160) cc_final: 0.6519 (ptm160) REVERT: C 226 LYS cc_start: 0.9052 (mppt) cc_final: 0.8750 (ttmm) REVERT: C 397 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8308 (mm-30) REVERT: D 210 LYS cc_start: 0.8831 (ptpp) cc_final: 0.8505 (tptt) REVERT: D 277 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7904 (ttmm) REVERT: d 13 LYS cc_start: 0.9016 (tppp) cc_final: 0.8792 (tppt) REVERT: d 89 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7862 (m-30) REVERT: d 91 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7734 (mpp) REVERT: E 272 LYS cc_start: 0.9101 (ptpp) cc_final: 0.8873 (pttm) REVERT: E 341 LYS cc_start: 0.9448 (mtpp) cc_final: 0.9165 (mtpm) REVERT: F 178 GLU cc_start: 0.8653 (pt0) cc_final: 0.8390 (pt0) REVERT: f 82 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8151 (mm) REVERT: f 91 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7618 (mtt) REVERT: G 385 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8541 (p) REVERT: g 69 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7881 (pptt) REVERT: H 69 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.7231 (mmt) REVERT: H 76 GLU cc_start: 0.8208 (tt0) cc_final: 0.7968 (tm-30) REVERT: I 321 LYS cc_start: 0.8209 (mppt) cc_final: 0.7934 (mppt) REVERT: J 76 GLU cc_start: 0.8405 (tt0) cc_final: 0.7903 (tm-30) REVERT: j 21 THR cc_start: 0.8016 (p) cc_final: 0.7796 (p) REVERT: j 86 ARG cc_start: 0.8662 (mmm-85) cc_final: 0.8448 (mmm-85) REVERT: K 362 ARG cc_start: 0.7793 (ptp90) cc_final: 0.7555 (ptp90) REVERT: K 397 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8238 (mm-30) REVERT: L 210 LYS cc_start: 0.8899 (ptpp) cc_final: 0.8312 (tptt) REVERT: l 47 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8197 (ptpp) REVERT: M 52 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8453 (m-30) REVERT: M 486 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7816 (pp20) REVERT: M 516 MET cc_start: 0.9217 (mtm) cc_final: 0.8954 (mtp) REVERT: N 171 LYS cc_start: 0.7893 (mmtm) cc_final: 0.7584 (mmpt) REVERT: n 80 GLU cc_start: 0.7291 (mp0) cc_final: 0.7047 (mp0) outliers start: 186 outliers final: 102 residues processed: 1107 average time/residue: 1.6545 time to fit residues: 2297.3857 Evaluate side-chains 1056 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 943 time to evaluate : 5.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain a residue 37 GLN Chi-restraints excluded: chain a residue 57 MET Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 37 GLN Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 91 MET Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain c residue 14 ARG Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 37 GLN Chi-restraints excluded: chain c residue 51 ASP Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 277 LYS Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain d residue 37 GLN Chi-restraints excluded: chain d residue 89 ASP Chi-restraints excluded: chain d residue 91 MET Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain e residue 37 GLN Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain f residue 37 GLN Chi-restraints excluded: chain f residue 81 GLU Chi-restraints excluded: chain f residue 82 LEU Chi-restraints excluded: chain f residue 91 MET Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 334 ASP Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain g residue 69 LYS Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 473 GLU Chi-restraints excluded: chain h residue 37 GLN Chi-restraints excluded: chain h residue 51 ASP Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 331 THR Chi-restraints excluded: chain i residue 37 GLN Chi-restraints excluded: chain i residue 51 ASP Chi-restraints excluded: chain J residue 186 GLU Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 268 ARG Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain j residue 37 GLN Chi-restraints excluded: chain j residue 51 ASP Chi-restraints excluded: chain j residue 88 ASP Chi-restraints excluded: chain K residue 186 GLU Chi-restraints excluded: chain K residue 216 ASP Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain k residue 23 SER Chi-restraints excluded: chain k residue 51 ASP Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 330 THR Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain l residue 37 GLN Chi-restraints excluded: chain l residue 47 LYS Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 51 ASP Chi-restraints excluded: chain l residue 69 LYS Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 486 GLU Chi-restraints excluded: chain m residue 51 ASP Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain N residue 331 THR Chi-restraints excluded: chain N residue 352 GLN Chi-restraints excluded: chain N residue 403 THR Chi-restraints excluded: chain n residue 37 GLN Chi-restraints excluded: chain n residue 51 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 796 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 470 optimal weight: 5.9990 chunk 603 optimal weight: 3.9990 chunk 467 optimal weight: 0.9990 chunk 695 optimal weight: 4.9990 chunk 461 optimal weight: 0.9990 chunk 823 optimal weight: 8.9990 chunk 515 optimal weight: 7.9990 chunk 501 optimal weight: 0.6980 chunk 380 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 65912 Z= 0.273 Angle : 0.671 12.205 88984 Z= 0.324 Chirality : 0.045 0.255 10668 Planarity : 0.004 0.070 11578 Dihedral : 7.742 163.771 9410 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.50 % Allowed : 23.04 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.08), residues: 8652 helix: 1.45 (0.08), residues: 4270 sheet: -0.01 (0.16), residues: 924 loop : -0.52 (0.09), residues: 3458 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 9 PHE 0.012 0.001 PHE e 67 TYR 0.009 0.001 TYR l 70 ARG 0.018 0.001 ARG h 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1148 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 977 time to evaluate : 5.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 80 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7503 (mm-30) REVERT: B 231 ARG cc_start: 0.9358 (ttp-110) cc_final: 0.9120 (ptp90) REVERT: B 321 LYS cc_start: 0.8087 (mppt) cc_final: 0.7833 (mppt) REVERT: B 362 ARG cc_start: 0.7771 (ttm110) cc_final: 0.7227 (ptp-110) REVERT: b 19 ARG cc_start: 0.7867 (mmp80) cc_final: 0.7540 (mmp-170) REVERT: C 226 LYS cc_start: 0.9051 (mppt) cc_final: 0.8730 (ttmm) REVERT: c 45 ASP cc_start: 0.8026 (p0) cc_final: 0.7700 (p0) REVERT: D 111 MET cc_start: 0.9141 (mtp) cc_final: 0.8923 (mtt) REVERT: D 210 LYS cc_start: 0.8837 (ptpp) cc_final: 0.8513 (tptt) REVERT: D 277 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.8113 (mmmm) REVERT: d 89 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7864 (m-30) REVERT: d 91 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7803 (mpp) REVERT: E 272 LYS cc_start: 0.9096 (ptpp) cc_final: 0.8742 (pmtt) REVERT: E 321 LYS cc_start: 0.7940 (mppt) cc_final: 0.7487 (mmtm) REVERT: E 341 LYS cc_start: 0.9446 (mtpp) cc_final: 0.9157 (mtpm) REVERT: F 321 LYS cc_start: 0.7831 (mppt) cc_final: 0.7604 (mppt) REVERT: f 91 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7585 (mtt) REVERT: G 362 ARG cc_start: 0.7435 (pmm-80) cc_final: 0.7226 (pmm-80) REVERT: G 385 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8604 (p) REVERT: g 69 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7786 (pptt) REVERT: H 69 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.7244 (mmt) REVERT: H 76 GLU cc_start: 0.8244 (tt0) cc_final: 0.7941 (tm-30) REVERT: I 321 LYS cc_start: 0.8183 (mppt) cc_final: 0.7892 (mppt) REVERT: J 76 GLU cc_start: 0.8377 (tt0) cc_final: 0.7906 (tm-30) REVERT: J 111 MET cc_start: 0.9132 (mtp) cc_final: 0.8922 (mtt) REVERT: j 21 THR cc_start: 0.8047 (p) cc_final: 0.7846 (p) REVERT: j 86 ARG cc_start: 0.8614 (mmm-85) cc_final: 0.8374 (mmm-85) REVERT: K 397 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8266 (mm-30) REVERT: L 210 LYS cc_start: 0.8886 (ptpp) cc_final: 0.8316 (tptt) REVERT: L 362 ARG cc_start: 0.7457 (pmm-80) cc_final: 0.7158 (ptp90) REVERT: M 52 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8449 (m-30) REVERT: M 321 LYS cc_start: 0.7811 (mppt) cc_final: 0.7295 (mppt) REVERT: M 486 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7834 (pp20) REVERT: M 516 MET cc_start: 0.9205 (mtm) cc_final: 0.8921 (mtp) REVERT: N 171 LYS cc_start: 0.7959 (mmtm) cc_final: 0.7613 (mmpt) outliers start: 171 outliers final: 106 residues processed: 1099 average time/residue: 1.6653 time to fit residues: 2295.2862 Evaluate side-chains 1070 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 955 time to evaluate : 5.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain a residue 37 GLN Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain c residue 14 ARG Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 37 GLN Chi-restraints excluded: chain c residue 51 ASP Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 277 LYS Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain d residue 37 GLN Chi-restraints excluded: chain d residue 89 ASP Chi-restraints excluded: chain d residue 91 MET Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain e residue 37 GLN Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain f residue 37 GLN Chi-restraints excluded: chain f residue 91 MET Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 299 THR Chi-restraints excluded: chain G residue 334 ASP Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain g residue 69 LYS Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 473 GLU Chi-restraints excluded: chain h residue 37 GLN Chi-restraints excluded: chain h residue 51 ASP Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 331 THR Chi-restraints excluded: chain i residue 37 GLN Chi-restraints excluded: chain i residue 51 ASP Chi-restraints excluded: chain J residue 186 GLU Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 268 ARG Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain j residue 37 GLN Chi-restraints excluded: chain j residue 51 ASP Chi-restraints excluded: chain K residue 186 GLU Chi-restraints excluded: chain K residue 216 ASP Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 37 GLN Chi-restraints excluded: chain k residue 51 ASP Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 330 THR Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain l residue 51 ASP Chi-restraints excluded: chain l residue 69 LYS Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 486 GLU Chi-restraints excluded: chain m residue 37 GLN Chi-restraints excluded: chain m residue 51 ASP Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 331 THR Chi-restraints excluded: chain N residue 352 GLN Chi-restraints excluded: chain N residue 403 THR Chi-restraints excluded: chain n residue 37 GLN Chi-restraints excluded: chain n residue 51 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 509 optimal weight: 5.9990 chunk 328 optimal weight: 5.9990 chunk 491 optimal weight: 0.9980 chunk 247 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 159 optimal weight: 0.5980 chunk 523 optimal weight: 20.0000 chunk 560 optimal weight: 1.9990 chunk 406 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 646 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 37 ASN L 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 65912 Z= 0.217 Angle : 0.669 11.217 88984 Z= 0.324 Chirality : 0.044 0.251 10668 Planarity : 0.004 0.072 11578 Dihedral : 7.413 145.285 9410 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.08 % Allowed : 23.80 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.08), residues: 8652 helix: 1.54 (0.08), residues: 4256 sheet: 0.04 (0.16), residues: 924 loop : -0.56 (0.09), residues: 3472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 9 PHE 0.022 0.001 PHE g 67 TYR 0.008 0.001 TYR l 70 ARG 0.015 0.001 ARG m 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 996 time to evaluate : 5.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 80 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7472 (mm-30) REVERT: B 231 ARG cc_start: 0.9343 (ttp-110) cc_final: 0.9095 (ptp90) REVERT: B 321 LYS cc_start: 0.8126 (mppt) cc_final: 0.7883 (mppt) REVERT: B 362 ARG cc_start: 0.7827 (ttm110) cc_final: 0.7271 (ptp-110) REVERT: b 19 ARG cc_start: 0.7845 (mmp80) cc_final: 0.7524 (mmp80) REVERT: C 226 LYS cc_start: 0.9042 (mppt) cc_final: 0.8712 (ttmm) REVERT: C 397 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8271 (mm-30) REVERT: c 45 ASP cc_start: 0.7948 (p0) cc_final: 0.7638 (p0) REVERT: c 55 ARG cc_start: 0.7073 (ptp-110) cc_final: 0.6687 (ptm160) REVERT: D 111 MET cc_start: 0.9123 (mtp) cc_final: 0.8910 (mtt) REVERT: D 210 LYS cc_start: 0.8842 (ptpp) cc_final: 0.8510 (tptt) REVERT: D 268 ARG cc_start: 0.8990 (ttm170) cc_final: 0.8635 (mtt90) REVERT: d 89 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7849 (m-30) REVERT: d 91 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7548 (mpp) REVERT: E 272 LYS cc_start: 0.9071 (ptpp) cc_final: 0.8724 (pmtt) REVERT: E 321 LYS cc_start: 0.7945 (mppt) cc_final: 0.7443 (mmtm) REVERT: E 341 LYS cc_start: 0.9442 (mtpp) cc_final: 0.9149 (mtpm) REVERT: F 321 LYS cc_start: 0.7811 (mppt) cc_final: 0.7611 (mppt) REVERT: f 82 LEU cc_start: 0.8204 (mm) cc_final: 0.7841 (mm) REVERT: f 91 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7558 (mtt) REVERT: G 362 ARG cc_start: 0.7464 (pmm-80) cc_final: 0.7242 (pmm-80) REVERT: G 385 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8613 (p) REVERT: H 69 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.7230 (mmt) REVERT: H 76 GLU cc_start: 0.8158 (tt0) cc_final: 0.7921 (tm-30) REVERT: H 321 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7611 (pttm) REVERT: I 321 LYS cc_start: 0.8191 (mppt) cc_final: 0.7889 (mppt) REVERT: J 111 MET cc_start: 0.9137 (mtp) cc_final: 0.8926 (mtt) REVERT: J 309 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8466 (tt) REVERT: J 362 ARG cc_start: 0.7341 (mtm-85) cc_final: 0.6876 (ptp90) REVERT: j 21 THR cc_start: 0.8030 (p) cc_final: 0.7823 (p) REVERT: K 390 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8221 (mtpm) REVERT: K 397 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8260 (mm-30) REVERT: k 19 ARG cc_start: 0.7767 (mmp80) cc_final: 0.7392 (mmp-170) REVERT: k 47 LYS cc_start: 0.7896 (ptpp) cc_final: 0.7584 (ptpp) REVERT: k 90 ILE cc_start: 0.8701 (mp) cc_final: 0.8488 (mp) REVERT: L 210 LYS cc_start: 0.8891 (ptpp) cc_final: 0.8316 (tptt) REVERT: L 321 LYS cc_start: 0.8000 (mppt) cc_final: 0.7695 (mppt) REVERT: L 362 ARG cc_start: 0.7435 (pmm-80) cc_final: 0.7132 (ptp90) REVERT: M 52 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8414 (m-30) REVERT: M 210 LYS cc_start: 0.8832 (ptpp) cc_final: 0.8323 (tptt) REVERT: M 486 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7800 (pp20) REVERT: M 516 MET cc_start: 0.9213 (mtm) cc_final: 0.8944 (mtp) REVERT: N 171 LYS cc_start: 0.8008 (mmtm) cc_final: 0.7669 (mmpt) REVERT: N 321 LYS cc_start: 0.8076 (mppt) cc_final: 0.7868 (mppt) outliers start: 142 outliers final: 90 residues processed: 1094 average time/residue: 1.6751 time to fit residues: 2291.7919 Evaluate side-chains 1054 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 954 time to evaluate : 5.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 37 GLN Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 91 MET Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain c residue 37 GLN Chi-restraints excluded: chain c residue 51 ASP Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain d residue 37 GLN Chi-restraints excluded: chain d residue 89 ASP Chi-restraints excluded: chain d residue 91 MET Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain e residue 37 GLN Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain f residue 37 GLN Chi-restraints excluded: chain f residue 81 GLU Chi-restraints excluded: chain f residue 91 MET Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 299 THR Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain g residue 69 LYS Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 321 LYS Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 473 GLU Chi-restraints excluded: chain h residue 37 GLN Chi-restraints excluded: chain h residue 51 ASP Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 331 THR Chi-restraints excluded: chain i residue 51 ASP Chi-restraints excluded: chain J residue 186 GLU Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 268 ARG Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain j residue 37 GLN Chi-restraints excluded: chain j residue 51 ASP Chi-restraints excluded: chain K residue 186 GLU Chi-restraints excluded: chain K residue 216 ASP Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 390 LYS Chi-restraints excluded: chain k residue 37 GLN Chi-restraints excluded: chain k residue 51 ASP Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 330 THR Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 51 ASP Chi-restraints excluded: chain l residue 69 LYS Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 486 GLU Chi-restraints excluded: chain m residue 37 GLN Chi-restraints excluded: chain m residue 51 ASP Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain N residue 331 THR Chi-restraints excluded: chain N residue 403 THR Chi-restraints excluded: chain n residue 51 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 748 optimal weight: 0.6980 chunk 788 optimal weight: 20.0000 chunk 719 optimal weight: 0.0270 chunk 767 optimal weight: 6.9990 chunk 461 optimal weight: 0.7980 chunk 334 optimal weight: 8.9990 chunk 602 optimal weight: 7.9990 chunk 235 optimal weight: 10.0000 chunk 693 optimal weight: 8.9990 chunk 725 optimal weight: 0.3980 chunk 764 optimal weight: 5.9990 overall best weight: 1.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 266 ASN K 37 ASN L 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 65912 Z= 0.281 Angle : 0.701 11.581 88984 Z= 0.339 Chirality : 0.045 0.178 10668 Planarity : 0.004 0.072 11578 Dihedral : 7.401 141.621 9409 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.80 % Allowed : 24.47 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.08), residues: 8652 helix: 1.46 (0.08), residues: 4270 sheet: -0.01 (0.16), residues: 924 loop : -0.57 (0.09), residues: 3458 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS h 7 PHE 0.022 0.001 PHE c 67 TYR 0.012 0.001 TYR j 70 ARG 0.015 0.001 ARG l 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 973 time to evaluate : 5.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.8661 (mtm) cc_final: 0.8452 (mtm) REVERT: a 80 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7510 (mm-30) REVERT: B 321 LYS cc_start: 0.8095 (mppt) cc_final: 0.7770 (mppt) REVERT: b 19 ARG cc_start: 0.7862 (mmp80) cc_final: 0.7491 (mmp80) REVERT: C 226 LYS cc_start: 0.9057 (mppt) cc_final: 0.8728 (ttmm) REVERT: C 397 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8277 (mm-30) REVERT: c 19 ARG cc_start: 0.7940 (mmp80) cc_final: 0.7627 (mmp-170) REVERT: c 45 ASP cc_start: 0.7993 (p0) cc_final: 0.7661 (p0) REVERT: D 111 MET cc_start: 0.9148 (mtp) cc_final: 0.8908 (mtt) REVERT: D 210 LYS cc_start: 0.8845 (ptpp) cc_final: 0.8514 (tptt) REVERT: D 268 ARG cc_start: 0.9002 (ttm170) cc_final: 0.8740 (mtt90) REVERT: D 321 LYS cc_start: 0.7868 (mppt) cc_final: 0.7366 (mppt) REVERT: D 334 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8160 (p0) REVERT: E 272 LYS cc_start: 0.9093 (ptpp) cc_final: 0.8736 (pmtt) REVERT: E 321 LYS cc_start: 0.7962 (mppt) cc_final: 0.7487 (mmtm) REVERT: E 341 LYS cc_start: 0.9439 (mtpp) cc_final: 0.9142 (mtpm) REVERT: F 231 ARG cc_start: 0.9345 (ttp-110) cc_final: 0.9022 (ptp90) REVERT: f 19 ARG cc_start: 0.7957 (mmp80) cc_final: 0.7690 (mmp-170) REVERT: f 91 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7573 (mtt) REVERT: G 362 ARG cc_start: 0.7480 (pmm-80) cc_final: 0.7250 (pmm-80) REVERT: G 385 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8631 (p) REVERT: H 69 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.7228 (mmt) REVERT: I 321 LYS cc_start: 0.8154 (mppt) cc_final: 0.7872 (mppt) REVERT: J 309 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8404 (tt) REVERT: j 13 LYS cc_start: 0.8558 (tppp) cc_final: 0.8304 (tppt) REVERT: j 19 ARG cc_start: 0.7805 (mmp80) cc_final: 0.7346 (mmm160) REVERT: K 397 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8273 (mm-30) REVERT: k 47 LYS cc_start: 0.7879 (ptpp) cc_final: 0.7576 (ptpp) REVERT: k 82 LEU cc_start: 0.8349 (mm) cc_final: 0.8125 (mm) REVERT: k 94 ILE cc_start: 0.8605 (pt) cc_final: 0.8385 (mp) REVERT: L 210 LYS cc_start: 0.8910 (ptpp) cc_final: 0.8330 (tptt) REVERT: L 277 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7990 (mmmm) REVERT: L 321 LYS cc_start: 0.7981 (mppt) cc_final: 0.7599 (mppt) REVERT: M 52 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8452 (m-30) REVERT: M 486 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7814 (pp20) REVERT: M 516 MET cc_start: 0.9207 (mtm) cc_final: 0.8959 (mtp) REVERT: N 171 LYS cc_start: 0.8029 (mmtm) cc_final: 0.7627 (mmpt) REVERT: N 321 LYS cc_start: 0.8083 (mppt) cc_final: 0.7856 (mppt) outliers start: 123 outliers final: 89 residues processed: 1067 average time/residue: 1.6902 time to fit residues: 2265.2644 Evaluate side-chains 1046 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 949 time to evaluate : 5.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 37 GLN Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain c residue 3 LEU Chi-restraints excluded: chain c residue 51 ASP Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain e residue 37 GLN Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain f residue 37 GLN Chi-restraints excluded: chain f residue 91 MET Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain g residue 69 LYS Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 473 GLU Chi-restraints excluded: chain h residue 51 ASP Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 331 THR Chi-restraints excluded: chain i residue 51 ASP Chi-restraints excluded: chain J residue 186 GLU Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 268 ARG Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain j residue 51 ASP Chi-restraints excluded: chain K residue 186 GLU Chi-restraints excluded: chain K residue 216 ASP Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain k residue 37 GLN Chi-restraints excluded: chain k residue 51 ASP Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 277 LYS Chi-restraints excluded: chain L residue 330 THR Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain l residue 51 ASP Chi-restraints excluded: chain l residue 69 LYS Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 216 ASP Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 486 GLU Chi-restraints excluded: chain m residue 37 GLN Chi-restraints excluded: chain m residue 51 ASP Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 331 THR Chi-restraints excluded: chain N residue 403 THR Chi-restraints excluded: chain n residue 51 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 503 optimal weight: 0.8980 chunk 811 optimal weight: 1.9990 chunk 495 optimal weight: 0.7980 chunk 384 optimal weight: 4.9990 chunk 563 optimal weight: 5.9990 chunk 850 optimal weight: 20.0000 chunk 783 optimal weight: 0.0070 chunk 677 optimal weight: 1.9990 chunk 70 optimal weight: 0.0030 chunk 523 optimal weight: 10.0000 chunk 415 optimal weight: 1.9990 overall best weight: 0.7410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 37 ASN l 7 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 65912 Z= 0.209 Angle : 0.691 11.284 88984 Z= 0.333 Chirality : 0.044 0.171 10668 Planarity : 0.004 0.059 11578 Dihedral : 7.255 133.181 9408 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.45 % Allowed : 25.07 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.08), residues: 8652 helix: 1.59 (0.08), residues: 4242 sheet: 0.04 (0.16), residues: 924 loop : -0.55 (0.09), residues: 3486 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS l 7 PHE 0.010 0.001 PHE e 67 TYR 0.010 0.001 TYR j 70 ARG 0.018 0.001 ARG l 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 976 time to evaluate : 5.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 80 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7516 (mm-30) REVERT: B 321 LYS cc_start: 0.8111 (mppt) cc_final: 0.7785 (mppt) REVERT: b 19 ARG cc_start: 0.7851 (mmp80) cc_final: 0.7541 (mmp-170) REVERT: C 226 LYS cc_start: 0.9080 (mppt) cc_final: 0.8746 (ttmm) REVERT: C 231 ARG cc_start: 0.9280 (ttp80) cc_final: 0.8966 (ptp90) REVERT: C 397 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8261 (mm-30) REVERT: c 19 ARG cc_start: 0.7908 (mmp80) cc_final: 0.7636 (mmp-170) REVERT: c 45 ASP cc_start: 0.8023 (p0) cc_final: 0.7767 (p0) REVERT: D 111 MET cc_start: 0.9120 (mtp) cc_final: 0.8864 (mtt) REVERT: D 210 LYS cc_start: 0.8853 (ptpp) cc_final: 0.8507 (tptt) REVERT: D 268 ARG cc_start: 0.8993 (ttm170) cc_final: 0.8716 (mtt90) REVERT: D 334 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8147 (p0) REVERT: d 47 LYS cc_start: 0.7472 (pmmt) cc_final: 0.7191 (pptt) REVERT: d 91 MET cc_start: 0.8171 (mpp) cc_final: 0.7811 (mtt) REVERT: E 272 LYS cc_start: 0.9090 (ptpp) cc_final: 0.8734 (pmtt) REVERT: E 321 LYS cc_start: 0.7943 (mppt) cc_final: 0.7408 (mmtm) REVERT: E 341 LYS cc_start: 0.9437 (mtpp) cc_final: 0.9140 (mtpm) REVERT: F 231 ARG cc_start: 0.9345 (ttp-110) cc_final: 0.9011 (ptp90) REVERT: F 268 ARG cc_start: 0.9015 (ttm170) cc_final: 0.8801 (mtt-85) REVERT: f 91 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7527 (mtt) REVERT: H 69 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7201 (mmt) REVERT: H 76 GLU cc_start: 0.8180 (tt0) cc_final: 0.7864 (tm-30) REVERT: h 45 ASP cc_start: 0.7571 (p0) cc_final: 0.7336 (p0) REVERT: I 321 LYS cc_start: 0.8172 (mppt) cc_final: 0.7857 (mppt) REVERT: i 19 ARG cc_start: 0.7834 (mmp80) cc_final: 0.7396 (mmp-170) REVERT: J 111 MET cc_start: 0.9014 (mtp) cc_final: 0.8762 (mtt) REVERT: j 13 LYS cc_start: 0.8561 (tppp) cc_final: 0.8318 (tppt) REVERT: j 91 MET cc_start: 0.8046 (mpp) cc_final: 0.7766 (mtm) REVERT: K 390 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8221 (mtpm) REVERT: K 397 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8256 (mm-30) REVERT: k 47 LYS cc_start: 0.7822 (ptpp) cc_final: 0.7578 (ptpp) REVERT: L 210 LYS cc_start: 0.8920 (ptpp) cc_final: 0.8329 (tptt) REVERT: L 321 LYS cc_start: 0.7997 (mppt) cc_final: 0.7697 (mppt) REVERT: M 52 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8414 (m-30) REVERT: M 210 LYS cc_start: 0.8867 (ptpp) cc_final: 0.8354 (tptt) REVERT: M 274 CYS cc_start: 0.8483 (t) cc_final: 0.7940 (m) REVERT: M 486 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7819 (pp20) REVERT: M 516 MET cc_start: 0.9205 (mtm) cc_final: 0.8911 (mtp) REVERT: N 171 LYS cc_start: 0.8009 (mmtm) cc_final: 0.7610 (mmpt) REVERT: n 47 LYS cc_start: 0.7641 (pptt) cc_final: 0.7266 (pptt) outliers start: 99 outliers final: 71 residues processed: 1044 average time/residue: 1.6803 time to fit residues: 2192.7828 Evaluate side-chains 1033 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 956 time to evaluate : 5.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 37 GLN Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 91 MET Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain c residue 51 ASP Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain e residue 37 GLN Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain f residue 37 GLN Chi-restraints excluded: chain f residue 91 MET Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain g residue 69 LYS Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 473 GLU Chi-restraints excluded: chain h residue 37 GLN Chi-restraints excluded: chain h residue 51 ASP Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 331 THR Chi-restraints excluded: chain i residue 51 ASP Chi-restraints excluded: chain J residue 186 GLU Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 268 ARG Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain j residue 51 ASP Chi-restraints excluded: chain K residue 216 ASP Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 390 LYS Chi-restraints excluded: chain k residue 37 GLN Chi-restraints excluded: chain k residue 51 ASP Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 330 THR Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain l residue 51 ASP Chi-restraints excluded: chain l residue 69 LYS Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 486 GLU Chi-restraints excluded: chain m residue 37 GLN Chi-restraints excluded: chain m residue 51 ASP Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain N residue 331 THR Chi-restraints excluded: chain n residue 49 LEU Chi-restraints excluded: chain n residue 51 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 538 optimal weight: 0.8980 chunk 721 optimal weight: 0.6980 chunk 207 optimal weight: 6.9990 chunk 624 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 188 optimal weight: 0.9980 chunk 678 optimal weight: 0.7980 chunk 283 optimal weight: 0.9980 chunk 696 optimal weight: 10.0000 chunk 85 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 37 ASN L 37 ASN l 7 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.122480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.076882 restraints weight = 104192.813| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.17 r_work: 0.2873 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 65912 Z= 0.213 Angle : 0.696 12.446 88984 Z= 0.335 Chirality : 0.044 0.202 10668 Planarity : 0.004 0.066 11578 Dihedral : 7.188 131.954 9406 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.30 % Allowed : 25.42 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.08), residues: 8652 helix: 1.61 (0.08), residues: 4242 sheet: 0.16 (0.17), residues: 854 loop : -0.46 (0.09), residues: 3556 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS l 7 PHE 0.010 0.001 PHE A 195 TYR 0.007 0.001 TYR j 70 ARG 0.016 0.001 ARG l 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31150.60 seconds wall clock time: 536 minutes 0.03 seconds (32160.03 seconds total)