Starting phenix.real_space_refine on Thu Mar 21 15:13:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kif_9994/03_2024/6kif_9994_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kif_9994/03_2024/6kif_9994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kif_9994/03_2024/6kif_9994.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kif_9994/03_2024/6kif_9994.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kif_9994/03_2024/6kif_9994_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kif_9994/03_2024/6kif_9994_updated.pdb" } resolution = 3.3 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= 0.003 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: 7 Type Number sf(0) Gaussians Fe 36 7.16 5 P 48 5.49 5 Mg 594 5.21 5 S 348 5.16 5 C 101640 2.51 5 N 19569 2.21 5 O 22077 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 36": "NH1" <-> "NH2" Residue "A ASP 59": "OD1" <-> "OD2" Residue "A PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 445": "NH1" <-> "NH2" Residue "A ARG 474": "NH1" <-> "NH2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "A PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 702": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 162": "NH1" <-> "NH2" Residue "B ARG 410": "NH1" <-> "NH2" Residue "B PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 61": "OD1" <-> "OD2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 61": "NH1" <-> "NH2" Residue "D ARG 73": "NH1" <-> "NH2" Residue "D ARG 120": "NH1" <-> "NH2" Residue "E ASP 7": "OD1" <-> "OD2" Residue "L ARG 39": "NH1" <-> "NH2" Residue "L ARG 45": "NH1" <-> "NH2" Residue "P GLU 145": "OE1" <-> "OE2" Residue "1 PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 113": "NH1" <-> "NH2" Residue "1 PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 175": "NH1" <-> "NH2" Residue "1 PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 324": "NH1" <-> "NH2" Residue "1 ARG 332": "NH1" <-> "NH2" Residue "2 PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 113": "NH1" <-> "NH2" Residue "2 ARG 175": "NH1" <-> "NH2" Residue "2 PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 324": "NH1" <-> "NH2" Residue "2 ARG 332": "NH1" <-> "NH2" Residue "3 PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 113": "NH1" <-> "NH2" Residue "3 ARG 127": "NH1" <-> "NH2" Residue "3 PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 175": "NH1" <-> "NH2" Residue "3 PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 324": "NH1" <-> "NH2" Residue "3 ARG 332": "NH1" <-> "NH2" Residue "4 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 113": "NH1" <-> "NH2" Residue "4 PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 175": "NH1" <-> "NH2" Residue "4 TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 324": "NH1" <-> "NH2" Residue "4 ARG 332": "NH1" <-> "NH2" Residue "5 PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 113": "NH1" <-> "NH2" Residue "5 PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 175": "NH1" <-> "NH2" Residue "5 TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 324": "NH1" <-> "NH2" Residue "5 ARG 332": "NH1" <-> "NH2" Residue "6 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 113": "NH1" <-> "NH2" Residue "6 ARG 175": "NH1" <-> "NH2" Residue "6 TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 324": "NH1" <-> "NH2" Residue "6 ARG 332": "NH1" <-> "NH2" Residue "G ARG 36": "NH1" <-> "NH2" Residue "G ASP 59": "OD1" <-> "OD2" Residue "G PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 445": "NH1" <-> "NH2" Residue "G ARG 474": "NH1" <-> "NH2" Residue "G ARG 591": "NH1" <-> "NH2" Residue "G PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 702": "NH1" <-> "NH2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 162": "NH1" <-> "NH2" Residue "H ARG 410": "NH1" <-> "NH2" Residue "H PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 61": "OD1" <-> "OD2" Residue "N ARG 66": "NH1" <-> "NH2" Residue "N TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 61": "NH1" <-> "NH2" Residue "O ARG 73": "NH1" <-> "NH2" Residue "O ARG 120": "NH1" <-> "NH2" Residue "Q ASP 7": "OD1" <-> "OD2" Residue "V ARG 39": "NH1" <-> "NH2" Residue "V ARG 45": "NH1" <-> "NH2" Residue "X GLU 145": "OE1" <-> "OE2" Residue "Y PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 113": "NH1" <-> "NH2" Residue "Y PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 175": "NH1" <-> "NH2" Residue "Y PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 324": "NH1" <-> "NH2" Residue "Y ARG 332": "NH1" <-> "NH2" Residue "Z PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 113": "NH1" <-> "NH2" Residue "Z ARG 175": "NH1" <-> "NH2" Residue "Z PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 324": "NH1" <-> "NH2" Residue "Z ARG 332": "NH1" <-> "NH2" Residue "a PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 113": "NH1" <-> "NH2" Residue "a ARG 127": "NH1" <-> "NH2" Residue "a PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 175": "NH1" <-> "NH2" Residue "a PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 324": "NH1" <-> "NH2" Residue "a ARG 332": "NH1" <-> "NH2" Residue "b TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 113": "NH1" <-> "NH2" Residue "b PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 175": "NH1" <-> "NH2" Residue "b TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 324": "NH1" <-> "NH2" Residue "b ARG 332": "NH1" <-> "NH2" Residue "c PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 113": "NH1" <-> "NH2" Residue "c PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 175": "NH1" <-> "NH2" Residue "c TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 324": "NH1" <-> "NH2" Residue "c ARG 332": "NH1" <-> "NH2" Residue "d PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 113": "NH1" <-> "NH2" Residue "d ARG 175": "NH1" <-> "NH2" Residue "d TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 324": "NH1" <-> "NH2" Residue "d ARG 332": "NH1" <-> "NH2" Residue "e ARG 36": "NH1" <-> "NH2" Residue "e ASP 59": "OD1" <-> "OD2" Residue "e PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 445": "NH1" <-> "NH2" Residue "e ARG 474": "NH1" <-> "NH2" Residue "e ARG 591": "NH1" <-> "NH2" Residue "e PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 702": "NH1" <-> "NH2" Residue "f ARG 19": "NH1" <-> "NH2" Residue "f ARG 130": "NH1" <-> "NH2" Residue "f PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 410": "NH1" <-> "NH2" Residue "f PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 61": "OD1" <-> "OD2" Residue "g ARG 66": "NH1" <-> "NH2" Residue "g TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 61": "NH1" <-> "NH2" Residue "h ARG 73": "NH1" <-> "NH2" Residue "h ARG 120": "NH1" <-> "NH2" Residue "i ASP 7": "OD1" <-> "OD2" Residue "n ARG 39": "NH1" <-> "NH2" Residue "n ARG 45": "NH1" <-> "NH2" Residue "p GLU 145": "OE1" <-> "OE2" Residue "q PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 113": "NH1" <-> "NH2" Residue "q PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 175": "NH1" <-> "NH2" Residue "q PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 324": "NH1" <-> "NH2" Residue "q ARG 332": "NH1" <-> "NH2" Residue "r PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 113": "NH1" <-> "NH2" Residue "r ARG 175": "NH1" <-> "NH2" Residue "r PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 324": "NH1" <-> "NH2" Residue "r ARG 332": "NH1" <-> "NH2" Residue "s PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 113": "NH1" <-> "NH2" Residue "s ARG 127": "NH1" <-> "NH2" Residue "s PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 175": "NH1" <-> "NH2" Residue "s PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 324": "NH1" <-> "NH2" Residue "s ARG 332": "NH1" <-> "NH2" Residue "t TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 113": "NH1" <-> "NH2" Residue "t PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 175": "NH1" <-> "NH2" Residue "t TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 324": "NH1" <-> "NH2" Residue "t ARG 332": "NH1" <-> "NH2" Residue "u PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 113": "NH1" <-> "NH2" Residue "u PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 175": "NH1" <-> "NH2" Residue "u TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 324": "NH1" <-> "NH2" Residue "u ARG 332": "NH1" <-> "NH2" Residue "v PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 113": "NH1" <-> "NH2" Residue "v ARG 175": "NH1" <-> "NH2" Residue "v TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 324": "NH1" <-> "NH2" Residue "v ARG 332": "NH1" <-> "NH2" Time to flip residues: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 144312 Number of models: 1 Model: "" Number of chains: 114 Chain: "A" Number of atoms: 5865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5865 Classifications: {'peptide': 751} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 719} Chain: "B" Number of atoms: 5789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5789 Classifications: {'peptide': 733} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 702} Chain: "C" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 598 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 74} Chain: "D" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 131} Chain: "E" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 543 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "F" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1036 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 127} Chain: "I" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 282 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "J" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 335 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "K" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 549 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 71} Chain: "L" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1210 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 151} Chain: "M" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "P" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1318 Classifications: {'peptide': 169} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 165} Chain: "1" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2605 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain: "2" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2605 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain: "3" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2605 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain: "4" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2605 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain: "5" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2605 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain: "6" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2605 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain: "G" Number of atoms: 5865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5865 Classifications: {'peptide': 751} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 719} Chain: "H" Number of atoms: 5789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5789 Classifications: {'peptide': 733} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 702} Chain: "N" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 598 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 74} Chain: "O" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 131} Chain: "Q" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 543 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "R" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1036 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 127} Chain: "S" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 282 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "T" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 335 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "U" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 549 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 71} Chain: "V" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1210 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 151} Chain: "W" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "X" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1318 Classifications: {'peptide': 169} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 165} Chain: "Y" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2605 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain: "Z" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2605 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain: "a" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2605 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain: "b" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2605 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain: "c" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2605 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain: "d" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2605 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain: "e" Number of atoms: 5865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5865 Classifications: {'peptide': 751} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 719} Chain: "f" Number of atoms: 5789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5789 Classifications: {'peptide': 733} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 702} Chain: "g" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 598 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 74} Chain: "h" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 131} Chain: "i" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 543 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "j" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1036 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 127} Chain: "k" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 282 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "l" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 335 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "m" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 549 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 71} Chain: "n" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1210 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 151} Chain: "o" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "p" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1318 Classifications: {'peptide': 169} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 165} Chain: "q" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2605 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain: "r" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2605 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain: "s" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2605 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain: "t" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2605 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain: "u" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2605 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain: "v" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2605 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain: "A" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 3425 Unusual residues: {'BCR': 6, 'CLA': 45, 'LHG': 9, 'LMU': 2, 'PQN': 1, 'SF4': 1} Classifications: {'undetermined': 64} Link IDs: {None: 63} Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'CLA:plan-5': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 3034 Unusual residues: {'BCR': 7, 'CLA': 41, 'LHG': 2, 'LMG': 1, 'LMU': 1, 'PQN': 1, 'SQD': 1} Classifications: {'undetermined': 54} Link IDs: {None: 53} Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 130 Unusual residues: {'BCR': 1, 'CLA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'BCR': 1, 'LHG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 274 Unusual residues: {'BCR': 3, 'CLA': 2, 'LMG': 1, 'LMU': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 188 Unusual residues: {'BCR': 1, 'CLA': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 518 Unusual residues: {'BCR': 4, 'CLA': 3, 'LHG': 3, 'SQD': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 34 Chain: "M" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 957 Unusual residues: {'BCR': 4, 'CLA': 17, 'SQD': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 430 Unresolved non-hydrogen dihedrals: 209 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'CLA:plan-5': 17} Unresolved non-hydrogen planarities: 85 Chain: "2" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 1038 Unusual residues: {'BCR': 4, 'CLA': 17, 'SQD': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 332 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'CLA:plan-5': 12} Unresolved non-hydrogen planarities: 60 Chain: "3" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 973 Unusual residues: {'BCR': 4, 'CLA': 17, 'SQD': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 346 Unresolved non-hydrogen angles: 410 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'CLA:plan-5': 15} Unresolved non-hydrogen planarities: 75 Chain: "4" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 951 Unusual residues: {'BCR': 4, 'CLA': 17, 'SQD': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 368 Unresolved non-hydrogen angles: 436 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'CLA:plan-5': 17} Unresolved non-hydrogen planarities: 85 Chain: "5" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 971 Unusual residues: {'BCR': 4, 'CLA': 17, 'SQD': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 412 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'CLA:plan-5': 16} Unresolved non-hydrogen planarities: 80 Chain: "6" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 971 Unusual residues: {'BCR': 4, 'CLA': 17, 'SQD': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 412 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'CLA:plan-5': 16} Unresolved non-hydrogen planarities: 80 Chain: "G" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 3425 Unusual residues: {'BCR': 6, 'CLA': 45, 'LHG': 9, 'LMU': 2, 'PQN': 1, 'SF4': 1} Classifications: {'undetermined': 64} Link IDs: {None: 63} Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'CLA:plan-5': 3} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 3034 Unusual residues: {'BCR': 7, 'CLA': 41, 'LHG': 2, 'LMG': 1, 'LMU': 1, 'PQN': 1, 'SQD': 1} Classifications: {'undetermined': 54} Link IDs: {None: 53} Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 13 Chain: "N" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 130 Unusual residues: {'BCR': 1, 'CLA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 10 Chain: "S" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'BCR': 1, 'LHG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "T" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 274 Unusual residues: {'BCR': 3, 'CLA': 2, 'LMG': 1, 'LMU': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "U" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 188 Unusual residues: {'BCR': 1, 'CLA': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 7 Chain: "V" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 518 Unusual residues: {'BCR': 4, 'CLA': 3, 'LHG': 3, 'SQD': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 34 Chain: "W" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 957 Unusual residues: {'BCR': 4, 'CLA': 17, 'SQD': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 430 Unresolved non-hydrogen dihedrals: 209 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'CLA:plan-5': 17} Unresolved non-hydrogen planarities: 85 Chain: "Z" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 1038 Unusual residues: {'BCR': 4, 'CLA': 17, 'SQD': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 332 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'CLA:plan-5': 12} Unresolved non-hydrogen planarities: 60 Chain: "a" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 973 Unusual residues: {'BCR': 4, 'CLA': 17, 'SQD': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 346 Unresolved non-hydrogen angles: 410 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'CLA:plan-5': 15} Unresolved non-hydrogen planarities: 75 Chain: "b" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 951 Unusual residues: {'BCR': 4, 'CLA': 17, 'SQD': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 368 Unresolved non-hydrogen angles: 436 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'CLA:plan-5': 17} Unresolved non-hydrogen planarities: 85 Chain: "c" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 971 Unusual residues: {'BCR': 4, 'CLA': 17, 'SQD': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 412 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'CLA:plan-5': 16} Unresolved non-hydrogen planarities: 80 Chain: "d" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 971 Unusual residues: {'BCR': 4, 'CLA': 17, 'SQD': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 412 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'CLA:plan-5': 16} Unresolved non-hydrogen planarities: 80 Chain: "e" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 3425 Unusual residues: {'BCR': 6, 'CLA': 45, 'LHG': 9, 'LMU': 2, 'PQN': 1, 'SF4': 1} Classifications: {'undetermined': 64} Link IDs: {None: 63} Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'CLA:plan-5': 3} Unresolved non-hydrogen planarities: 15 Chain: "f" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 3034 Unusual residues: {'BCR': 7, 'CLA': 41, 'LHG': 2, 'LMG': 1, 'LMU': 1, 'PQN': 1, 'SQD': 1} Classifications: {'undetermined': 54} Link IDs: {None: 53} Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 13 Chain: "g" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 130 Unusual residues: {'BCR': 1, 'CLA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 10 Chain: "k" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'BCR': 1, 'LHG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "l" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 274 Unusual residues: {'BCR': 3, 'CLA': 2, 'LMG': 1, 'LMU': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "m" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 188 Unusual residues: {'BCR': 1, 'CLA': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 7 Chain: "n" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 518 Unusual residues: {'BCR': 4, 'CLA': 3, 'LHG': 3, 'SQD': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 34 Chain: "o" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 957 Unusual residues: {'BCR': 4, 'CLA': 17, 'SQD': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 430 Unresolved non-hydrogen dihedrals: 209 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'CLA:plan-5': 17} Unresolved non-hydrogen planarities: 85 Chain: "r" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 1038 Unusual residues: {'BCR': 4, 'CLA': 17, 'SQD': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 332 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'CLA:plan-5': 12} Unresolved non-hydrogen planarities: 60 Chain: "s" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 973 Unusual residues: {'BCR': 4, 'CLA': 17, 'SQD': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 346 Unresolved non-hydrogen angles: 410 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'CLA:plan-5': 15} Unresolved non-hydrogen planarities: 75 Chain: "t" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 951 Unusual residues: {'BCR': 4, 'CLA': 17, 'SQD': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 368 Unresolved non-hydrogen angles: 436 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'CLA:plan-5': 17} Unresolved non-hydrogen planarities: 85 Chain: "u" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 971 Unusual residues: {'BCR': 4, 'CLA': 17, 'SQD': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 412 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'CLA:plan-5': 16} Unresolved non-hydrogen planarities: 80 Chain: "v" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 971 Unusual residues: {'BCR': 4, 'CLA': 17, 'SQD': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 412 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'CLA:plan-5': 16} Unresolved non-hydrogen planarities: 80 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "H" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "f" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10275 SG CYS B 568 173.150 200.382 66.292 1.00 28.35 S ATOM 4533 SG CYS A 595 169.779 194.527 66.402 1.00 21.53 S ATOM 4478 SG CYS A 586 168.664 198.575 70.309 1.00 20.24 S ATOM 10220 SG CYS B 559 174.152 195.971 70.332 1.00 24.53 S ATOM 12019 SG CYS C 51 167.378 194.683 79.050 1.00 24.27 S ATOM 11802 SG CYS C 21 166.805 193.618 85.086 1.00 25.96 S ATOM 12045 SG CYS C 54 172.179 196.326 82.791 1.00 24.58 S ATOM 12002 SG CYS C 48 171.191 189.985 81.535 1.00 26.53 S ATOM 12072 SG CYS C 58 176.468 202.960 85.976 1.00 32.66 S ATOM 11773 SG CYS C 17 171.843 199.132 88.679 1.00 31.85 S ATOM 11751 SG CYS C 14 172.570 205.178 89.619 1.00 35.38 S ATOM 11733 SG CYS C 11 176.373 201.039 92.532 1.00 37.08 S ATOM 44756 SG CYS H 568 189.161 102.921 66.287 1.00 28.35 S ATOM 39014 SG CYS G 595 185.770 108.764 66.397 1.00 21.53 S ATOM 38959 SG CYS G 586 189.836 107.711 70.303 1.00 20.24 S ATOM 44701 SG CYS H 559 184.840 104.255 70.329 1.00 24.53 S ATOM 46500 SG CYS N 51 187.109 110.770 79.044 1.00 24.27 S ATOM 46283 SG CYS N 21 186.474 111.799 85.080 1.00 25.96 S ATOM 46526 SG CYS N 54 186.137 105.790 82.787 1.00 24.58 S ATOM 46483 SG CYS N 48 181.135 109.811 81.532 1.00 26.53 S ATOM 46553 SG CYS N 58 189.746 98.763 85.972 1.00 32.66 S ATOM 46254 SG CYS N 17 188.739 104.682 88.674 1.00 31.85 S ATOM 46232 SG CYS N 14 193.615 101.034 89.613 1.00 35.38 S ATOM 46214 SG CYS N 11 188.131 99.806 92.528 1.00 37.08 S ATOM 79237 SG CYS f 568 96.681 137.773 66.279 1.00 28.35 S ATOM 73495 SG CYS e 595 103.438 137.781 66.384 1.00 21.53 S ATOM 73440 SG CYS e 586 100.492 134.790 70.292 1.00 20.24 S ATOM 79182 SG CYS f 559 100.003 140.845 70.317 1.00 24.53 S ATOM 80981 SG CYS g 51 104.511 135.620 79.031 1.00 24.27 S ATOM 80764 SG CYS g 21 105.724 135.655 85.066 1.00 25.96 S ATOM 81007 SG CYS g 54 100.691 138.956 82.775 1.00 24.58 S ATOM 80964 SG CYS g 48 106.675 141.271 81.516 1.00 26.53 S ATOM 81034 SG CYS g 58 92.803 139.352 85.966 1.00 32.66 S ATOM 80735 SG CYS g 17 98.433 137.260 88.664 1.00 31.85 S ATOM 80713 SG CYS g 14 92.834 134.867 89.608 1.00 35.38 S ATOM 80695 SG CYS g 11 94.519 140.229 92.521 1.00 37.08 S Time building chain proxies: 53.90, per 1000 atoms: 0.37 Number of scatterers: 144312 At special positions: 0 Unit cell: (300, 298, 117, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 36 26.01 S 348 16.00 P 48 15.00 Mg 594 11.99 O 22077 8.00 N 19569 7.00 C 101640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS F 31 " - pdb=" SG CYS F 61 " distance=2.03 Simple disulfide: pdb=" SG CYS R 31 " - pdb=" SG CYS R 61 " distance=2.03 Simple disulfide: pdb=" SG CYS j 31 " - pdb=" SG CYS j 61 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=510, symmetry=0 Number of additional bonds: simple=510, symmetry=0 Coordination: Other bonds: Time building additional restraints: 48.33 Conformation dependent library (CDL) restraints added in 14.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A3001 " pdb="FE3 SF4 A3001 " - pdb=" SG CYS A 586 " pdb="FE2 SF4 A3001 " - pdb=" SG CYS A 595 " pdb="FE1 SF4 A3001 " - pdb=" SG CYS B 568 " pdb="FE4 SF4 A3001 " - pdb=" SG CYS B 559 " pdb=" SF4 C3002 " pdb="FE3 SF4 C3002 " - pdb=" SG CYS C 54 " pdb="FE2 SF4 C3002 " - pdb=" SG CYS C 21 " pdb="FE4 SF4 C3002 " - pdb=" SG CYS C 48 " pdb="FE1 SF4 C3002 " - pdb=" SG CYS C 51 " pdb=" SF4 C3003 " pdb="FE3 SF4 C3003 " - pdb=" SG CYS C 14 " pdb="FE4 SF4 C3003 " - pdb=" SG CYS C 11 " pdb="FE2 SF4 C3003 " - pdb=" SG CYS C 17 " pdb="FE1 SF4 C3003 " - pdb=" SG CYS C 58 " pdb=" SF4 G3001 " pdb="FE3 SF4 G3001 " - pdb=" SG CYS G 586 " pdb="FE2 SF4 G3001 " - pdb=" SG CYS G 595 " pdb="FE1 SF4 G3001 " - pdb=" SG CYS H 568 " pdb="FE4 SF4 G3001 " - pdb=" SG CYS H 559 " pdb=" SF4 N3002 " pdb="FE3 SF4 N3002 " - pdb=" SG CYS N 54 " pdb="FE2 SF4 N3002 " - pdb=" SG CYS N 21 " pdb="FE4 SF4 N3002 " - pdb=" SG CYS N 48 " pdb="FE1 SF4 N3002 " - pdb=" SG CYS N 51 " pdb=" SF4 N3003 " pdb="FE3 SF4 N3003 " - pdb=" SG CYS N 14 " pdb="FE4 SF4 N3003 " - pdb=" SG CYS N 11 " pdb="FE2 SF4 N3003 " - pdb=" SG CYS N 17 " pdb="FE1 SF4 N3003 " - pdb=" SG CYS N 58 " pdb=" SF4 e3001 " pdb="FE3 SF4 e3001 " - pdb=" SG CYS e 586 " pdb="FE2 SF4 e3001 " - pdb=" SG CYS e 595 " pdb="FE1 SF4 e3001 " - pdb=" SG CYS f 568 " pdb="FE4 SF4 e3001 " - pdb=" SG CYS f 559 " pdb=" SF4 g3002 " pdb="FE3 SF4 g3002 " - pdb=" SG CYS g 54 " pdb="FE2 SF4 g3002 " - pdb=" SG CYS g 21 " pdb="FE4 SF4 g3002 " - pdb=" SG CYS g 48 " pdb="FE1 SF4 g3002 " - pdb=" SG CYS g 51 " pdb=" SF4 g3003 " pdb="FE3 SF4 g3003 " - pdb=" SG CYS g 14 " pdb="FE4 SF4 g3003 " - pdb=" SG CYS g 11 " pdb="FE2 SF4 g3003 " - pdb=" SG CYS g 17 " pdb="FE1 SF4 g3003 " - pdb=" SG CYS g 58 " Number of angles added : 108 26574 Ramachandran restraints generated. 13287 Oldfield, 0 Emsley, 13287 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 24120 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 591 helices and 54 sheets defined 67.5% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 30.05 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.689A pdb=" N GLY A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Proline residue: A 31 - end of helix No H-bonds generated for 'chain 'A' and resid 25 through 31' Processing helix chain 'A' and resid 35 through 40 removed outlier: 3.808A pdb=" N LYS A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 removed outlier: 4.559A pdb=" N ILE A 48 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.507A pdb=" N HIS A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A 62 " --> pdb=" O PHE A 58 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER A 63 " --> pdb=" O ASP A 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 57 through 63' Processing helix chain 'A' and resid 64 through 97 Processing helix chain 'A' and resid 99 through 107 Proline residue: A 107 - end of helix Processing helix chain 'A' and resid 123 through 128 removed outlier: 4.470A pdb=" N ASN A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLY A 128 " --> pdb=" O GLU A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 128' Processing helix chain 'A' and resid 142 through 151 Processing helix chain 'A' and resid 154 through 181 removed outlier: 4.031A pdb=" N LEU A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 193 removed outlier: 3.560A pdb=" N ASN A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL A 193 " --> pdb=" O TRP A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 202 Processing helix chain 'A' and resid 204 through 219 Processing helix chain 'A' and resid 220 through 233 removed outlier: 3.585A pdb=" N GLY A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 257 removed outlier: 3.730A pdb=" N PHE A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 256 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP A 257 " --> pdb=" O HIS A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 257' Processing helix chain 'A' and resid 258 through 265 removed outlier: 4.081A pdb=" N LEU A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 4.127A pdb=" N ALA A 270 " --> pdb=" O PRO A 266 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 271' Processing helix chain 'A' and resid 272 through 278 removed outlier: 3.662A pdb=" N LEU A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 removed outlier: 4.395A pdb=" N TYR A 283 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA A 284 " --> pdb=" O TRP A 280 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ASP A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 285' Processing helix chain 'A' and resid 301 through 322 removed outlier: 3.878A pdb=" N HIS A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N MET A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 341 removed outlier: 3.518A pdb=" N HIS A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LYS A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 359 Processing helix chain 'A' and resid 360 through 385 Processing helix chain 'A' and resid 390 through 395 removed outlier: 3.969A pdb=" N ASP A 394 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N TYR A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 390 through 395' Processing helix chain 'A' and resid 396 through 426 Processing helix chain 'A' and resid 429 through 434 removed outlier: 3.580A pdb=" N ASN A 433 " --> pdb=" O ASP A 429 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 429 through 434' Processing helix chain 'A' and resid 436 through 445 Processing helix chain 'A' and resid 446 through 477 removed outlier: 5.080A pdb=" N LEU A 466 " --> pdb=" O HIS A 462 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.868A pdb=" N MET A 482 " --> pdb=" O ARG A 478 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N PHE A 483 " --> pdb=" O PRO A 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 478 through 483' Processing helix chain 'A' and resid 492 through 506 Proline residue: A 506 - end of helix Processing helix chain 'A' and resid 518 through 523 removed outlier: 4.586A pdb=" N GLY A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY A 523 " --> pdb=" O GLN A 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 518 through 523' Processing helix chain 'A' and resid 540 through 567 Processing helix chain 'A' and resid 576 through 581 removed outlier: 3.833A pdb=" N LEU A 580 " --> pdb=" O ASP A 576 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 576 through 581' Processing helix chain 'A' and resid 598 through 628 removed outlier: 3.767A pdb=" N PHE A 608 " --> pdb=" O PHE A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 660 Processing helix chain 'A' and resid 662 through 672 removed outlier: 4.014A pdb=" N SER A 667 " --> pdb=" O TRP A 663 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLN A 668 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL A 669 " --> pdb=" O GLN A 665 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER A 672 " --> pdb=" O GLN A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 699 removed outlier: 3.879A pdb=" N LEU A 695 " --> pdb=" O TRP A 691 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N MET A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE A 697 " --> pdb=" O PHE A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 720 removed outlier: 3.920A pdb=" N TRP A 705 " --> pdb=" O GLY A 701 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 763 removed outlier: 3.702A pdb=" N ALA A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 651 removed outlier: 4.172A pdb=" N ALA A 651 " --> pdb=" O ASN A 646 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 646 through 651' Processing helix chain 'G' and resid 25 through 31 removed outlier: 3.690A pdb=" N GLY G 29 " --> pdb=" O PHE G 25 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS G 30 " --> pdb=" O GLU G 26 " (cutoff:3.500A) Proline residue: G 31 - end of helix No H-bonds generated for 'chain 'G' and resid 25 through 31' Processing helix chain 'G' and resid 35 through 40 removed outlier: 3.807A pdb=" N LYS G 40 " --> pdb=" O ARG G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 55 removed outlier: 4.559A pdb=" N ILE G 48 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP G 49 " --> pdb=" O THR G 45 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA G 55 " --> pdb=" O LEU G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 63 removed outlier: 3.508A pdb=" N HIS G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR G 62 " --> pdb=" O PHE G 58 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER G 63 " --> pdb=" O ASP G 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 57 through 63' Processing helix chain 'G' and resid 64 through 97 Processing helix chain 'G' and resid 99 through 107 Proline residue: G 107 - end of helix Processing helix chain 'G' and resid 123 through 128 removed outlier: 4.469A pdb=" N ASN G 127 " --> pdb=" O GLN G 123 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLY G 128 " --> pdb=" O GLU G 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 123 through 128' Processing helix chain 'G' and resid 142 through 151 Processing helix chain 'G' and resid 154 through 181 removed outlier: 4.031A pdb=" N LEU G 158 " --> pdb=" O ASN G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 193 removed outlier: 3.560A pdb=" N ASN G 192 " --> pdb=" O GLU G 188 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL G 193 " --> pdb=" O TRP G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 202 Processing helix chain 'G' and resid 204 through 219 Processing helix chain 'G' and resid 220 through 233 removed outlier: 3.585A pdb=" N GLY G 233 " --> pdb=" O ALA G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 257 removed outlier: 3.729A pdb=" N PHE G 255 " --> pdb=" O LEU G 251 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU G 256 " --> pdb=" O PRO G 252 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP G 257 " --> pdb=" O HIS G 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 251 through 257' Processing helix chain 'G' and resid 258 through 265 removed outlier: 4.081A pdb=" N LEU G 264 " --> pdb=" O LEU G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 271 removed outlier: 4.127A pdb=" N ALA G 270 " --> pdb=" O PRO G 266 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY G 271 " --> pdb=" O GLY G 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 266 through 271' Processing helix chain 'G' and resid 272 through 278 removed outlier: 3.662A pdb=" N LEU G 278 " --> pdb=" O ALA G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 285 removed outlier: 4.394A pdb=" N TYR G 283 " --> pdb=" O ASN G 279 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA G 284 " --> pdb=" O TRP G 280 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ASP G 285 " --> pdb=" O SER G 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 279 through 285' Processing helix chain 'G' and resid 301 through 322 removed outlier: 3.878A pdb=" N HIS G 321 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N MET G 322 " --> pdb=" O VAL G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 341 removed outlier: 3.517A pdb=" N HIS G 340 " --> pdb=" O ILE G 336 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LYS G 341 " --> pdb=" O LEU G 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 359 Processing helix chain 'G' and resid 360 through 385 Processing helix chain 'G' and resid 390 through 395 removed outlier: 3.968A pdb=" N ASP G 394 " --> pdb=" O TYR G 390 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N TYR G 395 " --> pdb=" O LEU G 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 390 through 395' Processing helix chain 'G' and resid 396 through 426 Processing helix chain 'G' and resid 429 through 434 removed outlier: 3.580A pdb=" N ASN G 433 " --> pdb=" O ASP G 429 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL G 434 " --> pdb=" O PRO G 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 429 through 434' Processing helix chain 'G' and resid 436 through 445 Processing helix chain 'G' and resid 446 through 477 removed outlier: 5.080A pdb=" N LEU G 466 " --> pdb=" O HIS G 462 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR G 467 " --> pdb=" O SER G 463 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 483 removed outlier: 3.868A pdb=" N MET G 482 " --> pdb=" O ARG G 478 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N PHE G 483 " --> pdb=" O PRO G 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 478 through 483' Processing helix chain 'G' and resid 492 through 506 Proline residue: G 506 - end of helix Processing helix chain 'G' and resid 518 through 523 removed outlier: 4.586A pdb=" N GLY G 522 " --> pdb=" O SER G 518 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY G 523 " --> pdb=" O GLN G 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 518 through 523' Processing helix chain 'G' and resid 540 through 567 Processing helix chain 'G' and resid 576 through 581 removed outlier: 3.833A pdb=" N LEU G 580 " --> pdb=" O ASP G 576 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY G 581 " --> pdb=" O LYS G 577 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 576 through 581' Processing helix chain 'G' and resid 598 through 628 removed outlier: 3.767A pdb=" N PHE G 608 " --> pdb=" O PHE G 604 " (cutoff:3.500A) Processing helix chain 'G' and resid 653 through 660 Processing helix chain 'G' and resid 662 through 672 removed outlier: 4.015A pdb=" N SER G 667 " --> pdb=" O TRP G 663 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLN G 668 " --> pdb=" O ALA G 664 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL G 669 " --> pdb=" O GLN G 665 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER G 672 " --> pdb=" O GLN G 668 " (cutoff:3.500A) Processing helix chain 'G' and resid 677 through 699 removed outlier: 3.879A pdb=" N LEU G 695 " --> pdb=" O TRP G 691 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET G 696 " --> pdb=" O ALA G 692 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE G 697 " --> pdb=" O PHE G 693 " (cutoff:3.500A) Processing helix chain 'G' and resid 701 through 720 removed outlier: 3.920A pdb=" N TRP G 705 " --> pdb=" O GLY G 701 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU G 719 " --> pdb=" O ALA G 715 " (cutoff:3.500A) Processing helix chain 'G' and resid 731 through 763 removed outlier: 3.702A pdb=" N ALA G 761 " --> pdb=" O ALA G 757 " (cutoff:3.500A) Processing helix chain 'G' and resid 646 through 651 removed outlier: 4.171A pdb=" N ALA G 651 " --> pdb=" O ASN G 646 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 646 through 651' Processing helix chain 'e' and resid 25 through 31 removed outlier: 3.689A pdb=" N GLY e 29 " --> pdb=" O PHE e 25 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS e 30 " --> pdb=" O GLU e 26 " (cutoff:3.500A) Proline residue: e 31 - end of helix No H-bonds generated for 'chain 'e' and resid 25 through 31' Processing helix chain 'e' and resid 35 through 40 removed outlier: 3.808A pdb=" N LYS e 40 " --> pdb=" O ARG e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 55 removed outlier: 4.558A pdb=" N ILE e 48 " --> pdb=" O THR e 44 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP e 49 " --> pdb=" O THR e 45 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA e 55 " --> pdb=" O LEU e 51 " (cutoff:3.500A) Processing helix chain 'e' and resid 57 through 63 removed outlier: 3.507A pdb=" N HIS e 61 " --> pdb=" O ASP e 57 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR e 62 " --> pdb=" O PHE e 58 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER e 63 " --> pdb=" O ASP e 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 57 through 63' Processing helix chain 'e' and resid 64 through 97 Processing helix chain 'e' and resid 99 through 107 Proline residue: e 107 - end of helix Processing helix chain 'e' and resid 123 through 128 removed outlier: 4.469A pdb=" N ASN e 127 " --> pdb=" O GLN e 123 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLY e 128 " --> pdb=" O GLU e 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 123 through 128' Processing helix chain 'e' and resid 142 through 151 Processing helix chain 'e' and resid 154 through 181 removed outlier: 4.031A pdb=" N LEU e 158 " --> pdb=" O ASN e 154 " (cutoff:3.500A) Processing helix chain 'e' and resid 186 through 193 removed outlier: 3.560A pdb=" N ASN e 192 " --> pdb=" O GLU e 188 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL e 193 " --> pdb=" O TRP e 189 " (cutoff:3.500A) Processing helix chain 'e' and resid 194 through 202 Processing helix chain 'e' and resid 204 through 219 Processing helix chain 'e' and resid 220 through 233 removed outlier: 3.585A pdb=" N GLY e 233 " --> pdb=" O ALA e 229 " (cutoff:3.500A) Processing helix chain 'e' and resid 251 through 257 removed outlier: 3.730A pdb=" N PHE e 255 " --> pdb=" O LEU e 251 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU e 256 " --> pdb=" O PRO e 252 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP e 257 " --> pdb=" O HIS e 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 251 through 257' Processing helix chain 'e' and resid 258 through 265 removed outlier: 4.082A pdb=" N LEU e 264 " --> pdb=" O LEU e 260 " (cutoff:3.500A) Processing helix chain 'e' and resid 266 through 271 removed outlier: 4.127A pdb=" N ALA e 270 " --> pdb=" O PRO e 266 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY e 271 " --> pdb=" O GLY e 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 266 through 271' Processing helix chain 'e' and resid 272 through 278 removed outlier: 3.662A pdb=" N LEU e 278 " --> pdb=" O ALA e 274 " (cutoff:3.500A) Processing helix chain 'e' and resid 279 through 285 removed outlier: 4.395A pdb=" N TYR e 283 " --> pdb=" O ASN e 279 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA e 284 " --> pdb=" O TRP e 280 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ASP e 285 " --> pdb=" O SER e 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 279 through 285' Processing helix chain 'e' and resid 301 through 322 removed outlier: 3.878A pdb=" N HIS e 321 " --> pdb=" O ILE e 317 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N MET e 322 " --> pdb=" O VAL e 318 " (cutoff:3.500A) Processing helix chain 'e' and resid 332 through 341 removed outlier: 3.517A pdb=" N HIS e 340 " --> pdb=" O ILE e 336 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LYS e 341 " --> pdb=" O LEU e 337 " (cutoff:3.500A) Processing helix chain 'e' and resid 351 through 359 Processing helix chain 'e' and resid 360 through 385 Processing helix chain 'e' and resid 390 through 395 removed outlier: 3.969A pdb=" N ASP e 394 " --> pdb=" O TYR e 390 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N TYR e 395 " --> pdb=" O LEU e 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 390 through 395' Processing helix chain 'e' and resid 396 through 426 Processing helix chain 'e' and resid 429 through 434 removed outlier: 3.580A pdb=" N ASN e 433 " --> pdb=" O ASP e 429 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL e 434 " --> pdb=" O PRO e 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 429 through 434' Processing helix chain 'e' and resid 436 through 445 Processing helix chain 'e' and resid 446 through 477 removed outlier: 5.080A pdb=" N LEU e 466 " --> pdb=" O HIS e 462 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR e 467 " --> pdb=" O SER e 463 " (cutoff:3.500A) Processing helix chain 'e' and resid 478 through 483 removed outlier: 3.868A pdb=" N MET e 482 " --> pdb=" O ARG e 478 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N PHE e 483 " --> pdb=" O PRO e 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 478 through 483' Processing helix chain 'e' and resid 492 through 506 Proline residue: e 506 - end of helix Processing helix chain 'e' and resid 518 through 523 removed outlier: 4.586A pdb=" N GLY e 522 " --> pdb=" O SER e 518 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY e 523 " --> pdb=" O GLN e 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 518 through 523' Processing helix chain 'e' and resid 540 through 567 Processing helix chain 'e' and resid 576 through 581 removed outlier: 3.832A pdb=" N LEU e 580 " --> pdb=" O ASP e 576 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY e 581 " --> pdb=" O LYS e 577 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 576 through 581' Processing helix chain 'e' and resid 598 through 628 removed outlier: 3.767A pdb=" N PHE e 608 " --> pdb=" O PHE e 604 " (cutoff:3.500A) Processing helix chain 'e' and resid 653 through 660 Processing helix chain 'e' and resid 662 through 672 removed outlier: 4.014A pdb=" N SER e 667 " --> pdb=" O TRP e 663 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLN e 668 " --> pdb=" O ALA e 664 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL e 669 " --> pdb=" O GLN e 665 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER e 672 " --> pdb=" O GLN e 668 " (cutoff:3.500A) Processing helix chain 'e' and resid 677 through 699 removed outlier: 3.878A pdb=" N LEU e 695 " --> pdb=" O TRP e 691 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET e 696 " --> pdb=" O ALA e 692 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE e 697 " --> pdb=" O PHE e 693 " (cutoff:3.500A) Processing helix chain 'e' and resid 701 through 720 removed outlier: 3.920A pdb=" N TRP e 705 " --> pdb=" O GLY e 701 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU e 719 " --> pdb=" O ALA e 715 " (cutoff:3.500A) Processing helix chain 'e' and resid 731 through 763 removed outlier: 3.702A pdb=" N ALA e 761 " --> pdb=" O ALA e 757 " (cutoff:3.500A) Processing helix chain 'e' and resid 646 through 651 removed outlier: 4.171A pdb=" N ALA e 651 " --> pdb=" O ASN e 646 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 646 through 651' Processing helix chain 'B' and resid 9 through 16 removed outlier: 4.024A pdb=" N ASP B 15 " --> pdb=" O ASP B 11 " (cutoff:3.500A) Proline residue: B 16 - end of helix Processing helix chain 'B' and resid 17 through 28 removed outlier: 4.801A pdb=" N ILE B 21 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.904A pdb=" N HIS B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ASP B 35 " --> pdb=" O PHE B 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 35' Processing helix chain 'B' and resid 38 through 71 Processing helix chain 'B' and resid 73 through 81 removed outlier: 3.542A pdb=" N ASP B 80 " --> pdb=" O GLN B 76 " (cutoff:3.500A) Proline residue: B 81 - end of helix Processing helix chain 'B' and resid 97 through 106 removed outlier: 5.840A pdb=" N GLN B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 128 Processing helix chain 'B' and resid 131 through 159 removed outlier: 3.763A pdb=" N LEU B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN B 158 " --> pdb=" O TRP B 154 " (cutoff:3.500A) Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 164 through 170 Processing helix chain 'B' and resid 171 through 181 Processing helix chain 'B' and resid 183 through 204 removed outlier: 4.883A pdb=" N ILE B 199 " --> pdb=" O VAL B 195 " (cutoff:3.500A) Proline residue: B 200 - end of helix Processing helix chain 'B' and resid 222 through 228 removed outlier: 3.910A pdb=" N GLY B 228 " --> pdb=" O PRO B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 removed outlier: 4.181A pdb=" N ALA B 234 " --> pdb=" O TRP B 230 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 230 through 235' Processing helix chain 'B' and resid 269 through 290 removed outlier: 3.952A pdb=" N HIS B 289 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N MET B 290 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 removed outlier: 4.861A pdb=" N LYS B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 329 removed outlier: 3.584A pdb=" N SER B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 355 removed outlier: 3.610A pdb=" N TYR B 353 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER B 354 " --> pdb=" O GLN B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 365 removed outlier: 3.657A pdb=" N ASP B 364 " --> pdb=" O PHE B 360 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TYR B 365 " --> pdb=" O ILE B 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 360 through 365' Processing helix chain 'B' and resid 366 through 396 Processing helix chain 'B' and resid 399 through 404 removed outlier: 4.058A pdb=" N LYS B 404 " --> pdb=" O PRO B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 447 removed outlier: 5.758A pdb=" N GLU B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 417 " --> pdb=" O GLU B 413 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY B 447 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 468 Processing helix chain 'B' and resid 483 through 491 removed outlier: 4.796A pdb=" N GLY B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 503 Processing helix chain 'B' and resid 513 through 541 Processing helix chain 'B' and resid 549 through 554 removed outlier: 3.988A pdb=" N PHE B 553 " --> pdb=" O ASP B 549 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 554 " --> pdb=" O LYS B 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 549 through 554' Processing helix chain 'B' and resid 571 through 604 removed outlier: 4.071A pdb=" N PHE B 581 " --> pdb=" O TYR B 577 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TRP B 582 " --> pdb=" O LEU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 612 removed outlier: 4.185A pdb=" N PHE B 609 " --> pdb=" O ASN B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 622 removed outlier: 3.564A pdb=" N TRP B 619 " --> pdb=" O TYR B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 634 removed outlier: 3.653A pdb=" N SER B 628 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER B 629 " --> pdb=" O TRP B 625 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLN B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU B 631 " --> pdb=" O ASN B 627 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 666 removed outlier: 3.682A pdb=" N PHE B 663 " --> pdb=" O THR B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 685 removed outlier: 4.039A pdb=" N TRP B 671 " --> pdb=" O TRP B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 692 removed outlier: 6.942A pdb=" N ILE B 690 " --> pdb=" O PRO B 686 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLY B 692 " --> pdb=" O ALA B 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 686 through 692' Processing helix chain 'B' and resid 701 through 733 Processing helix chain 'H' and resid 9 through 16 removed outlier: 4.024A pdb=" N ASP H 15 " --> pdb=" O ASP H 11 " (cutoff:3.500A) Proline residue: H 16 - end of helix Processing helix chain 'H' and resid 17 through 28 removed outlier: 4.800A pdb=" N ILE H 21 " --> pdb=" O THR H 17 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP H 22 " --> pdb=" O THR H 18 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA H 28 " --> pdb=" O GLY H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 35 removed outlier: 3.904A pdb=" N HIS H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASP H 35 " --> pdb=" O PHE H 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 30 through 35' Processing helix chain 'H' and resid 38 through 71 Processing helix chain 'H' and resid 73 through 81 removed outlier: 3.542A pdb=" N ASP H 80 " --> pdb=" O GLN H 76 " (cutoff:3.500A) Proline residue: H 81 - end of helix Processing helix chain 'H' and resid 97 through 106 removed outlier: 5.840A pdb=" N GLN H 106 " --> pdb=" O ASP H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 128 Processing helix chain 'H' and resid 131 through 159 removed outlier: 3.763A pdb=" N LEU H 135 " --> pdb=" O THR H 131 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU H 157 " --> pdb=" O GLY H 153 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN H 158 " --> pdb=" O TRP H 154 " (cutoff:3.500A) Proline residue: H 159 - end of helix Processing helix chain 'H' and resid 164 through 170 Processing helix chain 'H' and resid 171 through 181 Processing helix chain 'H' and resid 183 through 204 removed outlier: 4.883A pdb=" N ILE H 199 " --> pdb=" O VAL H 195 " (cutoff:3.500A) Proline residue: H 200 - end of helix Processing helix chain 'H' and resid 222 through 228 removed outlier: 3.910A pdb=" N GLY H 228 " --> pdb=" O PRO H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 235 removed outlier: 4.181A pdb=" N ALA H 234 " --> pdb=" O TRP H 230 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU H 235 " --> pdb=" O SER H 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 230 through 235' Processing helix chain 'H' and resid 269 through 290 removed outlier: 3.951A pdb=" N HIS H 289 " --> pdb=" O ILE H 285 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N MET H 290 " --> pdb=" O ILE H 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 309 removed outlier: 4.861A pdb=" N LYS H 309 " --> pdb=" O LEU H 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 321 through 329 removed outlier: 3.584A pdb=" N SER H 329 " --> pdb=" O THR H 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 330 through 355 removed outlier: 3.610A pdb=" N TYR H 353 " --> pdb=" O ALA H 349 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER H 354 " --> pdb=" O GLN H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 360 through 365 removed outlier: 3.656A pdb=" N ASP H 364 " --> pdb=" O PHE H 360 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR H 365 " --> pdb=" O ILE H 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 360 through 365' Processing helix chain 'H' and resid 366 through 396 Processing helix chain 'H' and resid 399 through 404 removed outlier: 4.057A pdb=" N LYS H 404 " --> pdb=" O PRO H 400 " (cutoff:3.500A) Processing helix chain 'H' and resid 406 through 447 removed outlier: 5.759A pdb=" N GLU H 416 " --> pdb=" O LEU H 412 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA H 417 " --> pdb=" O GLU H 413 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY H 447 " --> pdb=" O VAL H 443 " (cutoff:3.500A) Processing helix chain 'H' and resid 457 through 468 Processing helix chain 'H' and resid 483 through 491 removed outlier: 4.796A pdb=" N GLY H 491 " --> pdb=" O ALA H 487 " (cutoff:3.500A) Processing helix chain 'H' and resid 493 through 503 Processing helix chain 'H' and resid 513 through 541 Processing helix chain 'H' and resid 549 through 554 removed outlier: 3.988A pdb=" N PHE H 553 " --> pdb=" O ASP H 549 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY H 554 " --> pdb=" O LYS H 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 549 through 554' Processing helix chain 'H' and resid 571 through 604 removed outlier: 4.072A pdb=" N PHE H 581 " --> pdb=" O TYR H 577 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TRP H 582 " --> pdb=" O LEU H 578 " (cutoff:3.500A) Processing helix chain 'H' and resid 605 through 612 removed outlier: 4.185A pdb=" N PHE H 609 " --> pdb=" O ASN H 605 " (cutoff:3.500A) Processing helix chain 'H' and resid 615 through 622 removed outlier: 3.564A pdb=" N TRP H 619 " --> pdb=" O TYR H 615 " (cutoff:3.500A) Processing helix chain 'H' and resid 624 through 634 removed outlier: 3.654A pdb=" N SER H 628 " --> pdb=" O LEU H 624 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER H 629 " --> pdb=" O TRP H 625 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLN H 630 " --> pdb=" O LEU H 626 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU H 631 " --> pdb=" O ASN H 627 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY H 634 " --> pdb=" O GLN H 630 " (cutoff:3.500A) Processing helix chain 'H' and resid 643 through 666 removed outlier: 3.682A pdb=" N PHE H 663 " --> pdb=" O THR H 659 " (cutoff:3.500A) Processing helix chain 'H' and resid 667 through 685 removed outlier: 4.040A pdb=" N TRP H 671 " --> pdb=" O TRP H 667 " (cutoff:3.500A) Processing helix chain 'H' and resid 686 through 692 removed outlier: 6.941A pdb=" N ILE H 690 " --> pdb=" O PRO H 686 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL H 691 " --> pdb=" O LEU H 687 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLY H 692 " --> pdb=" O ALA H 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 686 through 692' Processing helix chain 'H' and resid 701 through 733 Processing helix chain 'f' and resid 9 through 16 removed outlier: 4.023A pdb=" N ASP f 15 " --> pdb=" O ASP f 11 " (cutoff:3.500A) Proline residue: f 16 - end of helix Processing helix chain 'f' and resid 17 through 28 removed outlier: 4.801A pdb=" N ILE f 21 " --> pdb=" O THR f 17 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP f 22 " --> pdb=" O THR f 18 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA f 28 " --> pdb=" O GLY f 24 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 35 removed outlier: 3.904A pdb=" N HIS f 34 " --> pdb=" O ASP f 30 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ASP f 35 " --> pdb=" O PHE f 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 30 through 35' Processing helix chain 'f' and resid 38 through 71 Processing helix chain 'f' and resid 73 through 81 removed outlier: 3.542A pdb=" N ASP f 80 " --> pdb=" O GLN f 76 " (cutoff:3.500A) Proline residue: f 81 - end of helix Processing helix chain 'f' and resid 97 through 106 removed outlier: 5.841A pdb=" N GLN f 106 " --> pdb=" O ASP f 102 " (cutoff:3.500A) Processing helix chain 'f' and resid 119 through 128 Processing helix chain 'f' and resid 131 through 159 removed outlier: 3.763A pdb=" N LEU f 135 " --> pdb=" O THR f 131 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU f 157 " --> pdb=" O GLY f 153 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN f 158 " --> pdb=" O TRP f 154 " (cutoff:3.500A) Proline residue: f 159 - end of helix Processing helix chain 'f' and resid 164 through 170 Processing helix chain 'f' and resid 171 through 181 Processing helix chain 'f' and resid 183 through 204 removed outlier: 4.883A pdb=" N ILE f 199 " --> pdb=" O VAL f 195 " (cutoff:3.500A) Proline residue: f 200 - end of helix Processing helix chain 'f' and resid 222 through 228 removed outlier: 3.910A pdb=" N GLY f 228 " --> pdb=" O PRO f 224 " (cutoff:3.500A) Processing helix chain 'f' and resid 230 through 235 removed outlier: 4.181A pdb=" N ALA f 234 " --> pdb=" O TRP f 230 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU f 235 " --> pdb=" O SER f 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 230 through 235' Processing helix chain 'f' and resid 269 through 290 removed outlier: 3.953A pdb=" N HIS f 289 " --> pdb=" O ILE f 285 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N MET f 290 " --> pdb=" O ILE f 286 " (cutoff:3.500A) Processing helix chain 'f' and resid 300 through 309 removed outlier: 4.861A pdb=" N LYS f 309 " --> pdb=" O LEU f 305 " (cutoff:3.500A) Processing helix chain 'f' and resid 321 through 329 removed outlier: 3.585A pdb=" N SER f 329 " --> pdb=" O THR f 325 " (cutoff:3.500A) Processing helix chain 'f' and resid 330 through 355 removed outlier: 3.611A pdb=" N TYR f 353 " --> pdb=" O ALA f 349 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER f 354 " --> pdb=" O GLN f 350 " (cutoff:3.500A) Processing helix chain 'f' and resid 360 through 365 removed outlier: 3.656A pdb=" N ASP f 364 " --> pdb=" O PHE f 360 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TYR f 365 " --> pdb=" O ILE f 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 360 through 365' Processing helix chain 'f' and resid 366 through 396 Processing helix chain 'f' and resid 399 through 404 removed outlier: 4.058A pdb=" N LYS f 404 " --> pdb=" O PRO f 400 " (cutoff:3.500A) Processing helix chain 'f' and resid 406 through 447 removed outlier: 5.758A pdb=" N GLU f 416 " --> pdb=" O LEU f 412 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA f 417 " --> pdb=" O GLU f 413 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY f 447 " --> pdb=" O VAL f 443 " (cutoff:3.500A) Processing helix chain 'f' and resid 457 through 468 Processing helix chain 'f' and resid 483 through 491 removed outlier: 4.795A pdb=" N GLY f 491 " --> pdb=" O ALA f 487 " (cutoff:3.500A) Processing helix chain 'f' and resid 493 through 503 Processing helix chain 'f' and resid 513 through 541 Processing helix chain 'f' and resid 549 through 554 removed outlier: 3.988A pdb=" N PHE f 553 " --> pdb=" O ASP f 549 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY f 554 " --> pdb=" O LYS f 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 549 through 554' Processing helix chain 'f' and resid 571 through 604 removed outlier: 4.072A pdb=" N PHE f 581 " --> pdb=" O TYR f 577 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP f 582 " --> pdb=" O LEU f 578 " (cutoff:3.500A) Processing helix chain 'f' and resid 605 through 612 removed outlier: 4.185A pdb=" N PHE f 609 " --> pdb=" O ASN f 605 " (cutoff:3.500A) Processing helix chain 'f' and resid 615 through 622 removed outlier: 3.564A pdb=" N TRP f 619 " --> pdb=" O TYR f 615 " (cutoff:3.500A) Processing helix chain 'f' and resid 624 through 634 removed outlier: 3.653A pdb=" N SER f 628 " --> pdb=" O LEU f 624 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER f 629 " --> pdb=" O TRP f 625 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLN f 630 " --> pdb=" O LEU f 626 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU f 631 " --> pdb=" O ASN f 627 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY f 634 " --> pdb=" O GLN f 630 " (cutoff:3.500A) Processing helix chain 'f' and resid 643 through 666 removed outlier: 3.681A pdb=" N PHE f 663 " --> pdb=" O THR f 659 " (cutoff:3.500A) Processing helix chain 'f' and resid 667 through 685 removed outlier: 4.039A pdb=" N TRP f 671 " --> pdb=" O TRP f 667 " (cutoff:3.500A) Processing helix chain 'f' and resid 686 through 692 removed outlier: 6.941A pdb=" N ILE f 690 " --> pdb=" O PRO f 686 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL f 691 " --> pdb=" O LEU f 687 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLY f 692 " --> pdb=" O ALA f 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 686 through 692' Processing helix chain 'f' and resid 701 through 733 Processing helix chain 'C' and resid 15 through 21 Processing helix chain 'C' and resid 44 through 49 removed outlier: 3.764A pdb=" N CYS C 48 " --> pdb=" O ARG C 44 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N VAL C 49 " --> pdb=" O THR C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 44 through 49' Processing helix chain 'C' and resid 52 through 59 Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 73 through 78 Processing helix chain 'N' and resid 15 through 21 Processing helix chain 'N' and resid 44 through 49 removed outlier: 3.765A pdb=" N CYS N 48 " --> pdb=" O ARG N 44 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N VAL N 49 " --> pdb=" O THR N 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 44 through 49' Processing helix chain 'N' and resid 52 through 59 Proline residue: N 59 - end of helix Processing helix chain 'N' and resid 73 through 78 Processing helix chain 'g' and resid 15 through 21 Processing helix chain 'g' and resid 44 through 49 removed outlier: 3.764A pdb=" N CYS g 48 " --> pdb=" O ARG g 44 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N VAL g 49 " --> pdb=" O THR g 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 44 through 49' Processing helix chain 'g' and resid 52 through 59 Proline residue: g 59 - end of helix Processing helix chain 'g' and resid 73 through 78 Processing helix chain 'D' and resid 19 through 25 removed outlier: 4.317A pdb=" N GLU D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 75 removed outlier: 3.577A pdb=" N ALA D 65 " --> pdb=" O ARG D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 removed outlier: 3.604A pdb=" N ILE D 131 " --> pdb=" O ASN D 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 25 removed outlier: 4.317A pdb=" N GLU O 23 " --> pdb=" O LEU O 19 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 75 removed outlier: 3.578A pdb=" N ALA O 65 " --> pdb=" O ARG O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 132 removed outlier: 3.603A pdb=" N ILE O 131 " --> pdb=" O ASN O 127 " (cutoff:3.500A) Processing helix chain 'h' and resid 19 through 25 removed outlier: 4.318A pdb=" N GLU h 23 " --> pdb=" O LEU h 19 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 75 removed outlier: 3.577A pdb=" N ALA h 65 " --> pdb=" O ARG h 61 " (cutoff:3.500A) Processing helix chain 'h' and resid 127 through 132 removed outlier: 3.604A pdb=" N ILE h 131 " --> pdb=" O ASN h 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 67 removed outlier: 3.966A pdb=" N LEU E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLN E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 67' Processing helix chain 'Q' and resid 62 through 67 removed outlier: 3.966A pdb=" N LEU Q 66 " --> pdb=" O ALA Q 62 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLN Q 67 " --> pdb=" O GLU Q 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 62 through 67' Processing helix chain 'i' and resid 62 through 67 removed outlier: 3.966A pdb=" N LEU i 66 " --> pdb=" O ALA i 62 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLN i 67 " --> pdb=" O GLU i 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 62 through 67' Processing helix chain 'F' and resid 34 through 44 removed outlier: 3.502A pdb=" N ALA F 43 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA F 44 " --> pdb=" O ARG F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 60 removed outlier: 4.439A pdb=" N GLN F 58 " --> pdb=" O GLU F 54 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ALA F 59 " --> pdb=" O ASN F 55 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LEU F 60 " --> pdb=" O TYR F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 110 removed outlier: 3.596A pdb=" N PHE F 81 " --> pdb=" O HIS F 77 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ILE F 83 " --> pdb=" O GLY F 79 " (cutoff:3.500A) Proline residue: F 84 - end of helix removed outlier: 3.798A pdb=" N LYS F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER F 108 " --> pdb=" O GLN F 104 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASP F 109 " --> pdb=" O ALA F 105 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LYS F 110 " --> pdb=" O ILE F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 119 removed outlier: 3.551A pdb=" N LYS F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 135 removed outlier: 4.746A pdb=" N PHE F 132 " --> pdb=" O SER F 128 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ALA F 133 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N TRP F 134 " --> pdb=" O THR F 130 " (cutoff:3.500A) Proline residue: F 135 - end of helix Processing helix chain 'F' and resid 136 through 145 removed outlier: 3.562A pdb=" N GLY F 145 " --> pdb=" O GLU F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 155 removed outlier: 3.749A pdb=" N ILE F 154 " --> pdb=" O LYS F 150 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N THR F 155 " --> pdb=" O ALA F 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 150 through 155' Processing helix chain 'R' and resid 34 through 44 removed outlier: 3.502A pdb=" N ALA R 43 " --> pdb=" O GLN R 39 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA R 44 " --> pdb=" O ARG R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 60 removed outlier: 4.439A pdb=" N GLN R 58 " --> pdb=" O GLU R 54 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ALA R 59 " --> pdb=" O ASN R 55 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU R 60 " --> pdb=" O TYR R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 110 removed outlier: 3.597A pdb=" N PHE R 81 " --> pdb=" O HIS R 77 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ILE R 83 " --> pdb=" O GLY R 79 " (cutoff:3.500A) Proline residue: R 84 - end of helix removed outlier: 3.798A pdb=" N LYS R 107 " --> pdb=" O LEU R 103 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER R 108 " --> pdb=" O GLN R 104 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASP R 109 " --> pdb=" O ALA R 105 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LYS R 110 " --> pdb=" O ILE R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 119 removed outlier: 3.551A pdb=" N LYS R 115 " --> pdb=" O ASP R 111 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE R 119 " --> pdb=" O LYS R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 135 removed outlier: 4.746A pdb=" N PHE R 132 " --> pdb=" O SER R 128 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ALA R 133 " --> pdb=" O LEU R 129 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N TRP R 134 " --> pdb=" O THR R 130 " (cutoff:3.500A) Proline residue: R 135 - end of helix Processing helix chain 'R' and resid 136 through 145 removed outlier: 3.563A pdb=" N GLY R 145 " --> pdb=" O GLU R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 155 removed outlier: 3.749A pdb=" N ILE R 154 " --> pdb=" O LYS R 150 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N THR R 155 " --> pdb=" O ALA R 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 150 through 155' Processing helix chain 'j' and resid 34 through 44 removed outlier: 3.501A pdb=" N ALA j 43 " --> pdb=" O GLN j 39 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA j 44 " --> pdb=" O ARG j 40 " (cutoff:3.500A) Processing helix chain 'j' and resid 46 through 60 removed outlier: 4.439A pdb=" N GLN j 58 " --> pdb=" O GLU j 54 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ALA j 59 " --> pdb=" O ASN j 55 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LEU j 60 " --> pdb=" O TYR j 56 " (cutoff:3.500A) Processing helix chain 'j' and resid 77 through 110 removed outlier: 3.597A pdb=" N PHE j 81 " --> pdb=" O HIS j 77 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ILE j 83 " --> pdb=" O GLY j 79 " (cutoff:3.500A) Proline residue: j 84 - end of helix removed outlier: 3.798A pdb=" N LYS j 107 " --> pdb=" O LEU j 103 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER j 108 " --> pdb=" O GLN j 104 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASP j 109 " --> pdb=" O ALA j 105 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LYS j 110 " --> pdb=" O ILE j 106 " (cutoff:3.500A) Processing helix chain 'j' and resid 111 through 119 removed outlier: 3.552A pdb=" N LYS j 115 " --> pdb=" O ASP j 111 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE j 119 " --> pdb=" O LYS j 115 " (cutoff:3.500A) Processing helix chain 'j' and resid 120 through 135 removed outlier: 4.746A pdb=" N PHE j 132 " --> pdb=" O SER j 128 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ALA j 133 " --> pdb=" O LEU j 129 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N TRP j 134 " --> pdb=" O THR j 130 " (cutoff:3.500A) Proline residue: j 135 - end of helix Processing helix chain 'j' and resid 136 through 145 removed outlier: 3.562A pdb=" N GLY j 145 " --> pdb=" O GLU j 141 " (cutoff:3.500A) Processing helix chain 'j' and resid 150 through 155 removed outlier: 3.749A pdb=" N ILE j 154 " --> pdb=" O LYS j 150 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N THR j 155 " --> pdb=" O ALA j 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 150 through 155' Processing helix chain 'I' and resid 7 through 36 Proline residue: I 11 - end of helix Proline residue: I 16 - end of helix removed outlier: 4.702A pdb=" N LEU I 22 " --> pdb=" O VAL I 18 " (cutoff:3.500A) Proline residue: I 23 - end of helix removed outlier: 3.571A pdb=" N SER I 36 " --> pdb=" O THR I 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 7 through 36 Proline residue: S 11 - end of helix Proline residue: S 16 - end of helix removed outlier: 4.702A pdb=" N LEU S 22 " --> pdb=" O VAL S 18 " (cutoff:3.500A) Proline residue: S 23 - end of helix removed outlier: 3.571A pdb=" N SER S 36 " --> pdb=" O THR S 32 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 36 Proline residue: k 11 - end of helix Proline residue: k 16 - end of helix removed outlier: 4.702A pdb=" N LEU k 22 " --> pdb=" O VAL k 18 " (cutoff:3.500A) Proline residue: k 23 - end of helix removed outlier: 3.571A pdb=" N SER k 36 " --> pdb=" O THR k 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 1 through 10 Processing helix chain 'J' and resid 11 through 34 Proline residue: J 34 - end of helix Processing helix chain 'T' and resid 1 through 10 Processing helix chain 'T' and resid 11 through 34 Proline residue: T 34 - end of helix Processing helix chain 'l' and resid 1 through 10 Processing helix chain 'l' and resid 11 through 34 Proline residue: l 34 - end of helix Processing helix chain 'K' and resid 15 through 36 Processing helix chain 'K' and resid 48 through 53 removed outlier: 4.311A pdb=" N PHE K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 82 Processing helix chain 'U' and resid 15 through 36 Processing helix chain 'U' and resid 48 through 53 removed outlier: 4.311A pdb=" N PHE U 52 " --> pdb=" O SER U 48 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 82 Processing helix chain 'm' and resid 15 through 36 Processing helix chain 'm' and resid 48 through 53 removed outlier: 4.310A pdb=" N PHE m 52 " --> pdb=" O SER m 48 " (cutoff:3.500A) Processing helix chain 'm' and resid 56 through 82 Processing helix chain 'L' and resid 24 through 35 Proline residue: L 35 - end of helix Processing helix chain 'L' and resid 42 through 63 removed outlier: 3.731A pdb=" N TYR L 59 " --> pdb=" O GLY L 55 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY L 60 " --> pdb=" O PHE L 56 " (cutoff:3.500A) Proline residue: L 61 - end of helix Processing helix chain 'L' and resid 73 through 99 Processing helix chain 'L' and resid 116 through 121 removed outlier: 6.750A pdb=" N PHE L 120 " --> pdb=" O PRO L 116 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N THR L 121 " --> pdb=" O GLN L 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 116 through 121' Processing helix chain 'L' and resid 122 through 150 removed outlier: 3.598A pdb=" N THR L 149 " --> pdb=" O TYR L 145 " (cutoff:3.500A) Proline residue: L 150 - end of helix Processing helix chain 'L' and resid 151 through 164 removed outlier: 4.860A pdb=" N LEU L 155 " --> pdb=" O TYR L 151 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL L 162 " --> pdb=" O ILE L 158 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TRP L 163 " --> pdb=" O ALA L 159 " (cutoff:3.500A) Processing helix chain 'V' and resid 24 through 35 Proline residue: V 35 - end of helix Processing helix chain 'V' and resid 42 through 63 removed outlier: 3.731A pdb=" N TYR V 59 " --> pdb=" O GLY V 55 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLY V 60 " --> pdb=" O PHE V 56 " (cutoff:3.500A) Proline residue: V 61 - end of helix Processing helix chain 'V' and resid 73 through 99 Processing helix chain 'V' and resid 116 through 121 removed outlier: 6.751A pdb=" N PHE V 120 " --> pdb=" O PRO V 116 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N THR V 121 " --> pdb=" O GLN V 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 116 through 121' Processing helix chain 'V' and resid 122 through 150 removed outlier: 3.598A pdb=" N THR V 149 " --> pdb=" O TYR V 145 " (cutoff:3.500A) Proline residue: V 150 - end of helix Processing helix chain 'V' and resid 151 through 164 removed outlier: 4.861A pdb=" N LEU V 155 " --> pdb=" O TYR V 151 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL V 162 " --> pdb=" O ILE V 158 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TRP V 163 " --> pdb=" O ALA V 159 " (cutoff:3.500A) Processing helix chain 'n' and resid 24 through 35 Proline residue: n 35 - end of helix Processing helix chain 'n' and resid 42 through 63 removed outlier: 3.732A pdb=" N TYR n 59 " --> pdb=" O GLY n 55 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLY n 60 " --> pdb=" O PHE n 56 " (cutoff:3.500A) Proline residue: n 61 - end of helix Processing helix chain 'n' and resid 73 through 99 Processing helix chain 'n' and resid 116 through 121 removed outlier: 6.751A pdb=" N PHE n 120 " --> pdb=" O PRO n 116 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N THR n 121 " --> pdb=" O GLN n 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 116 through 121' Processing helix chain 'n' and resid 122 through 150 removed outlier: 3.598A pdb=" N THR n 149 " --> pdb=" O TYR n 145 " (cutoff:3.500A) Proline residue: n 150 - end of helix Processing helix chain 'n' and resid 151 through 164 removed outlier: 4.861A pdb=" N LEU n 155 " --> pdb=" O TYR n 151 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL n 162 " --> pdb=" O ILE n 158 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TRP n 163 " --> pdb=" O ALA n 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 29 removed outlier: 4.291A pdb=" N VAL M 15 " --> pdb=" O LEU M 11 " (cutoff:3.500A) Proline residue: M 16 - end of helix Processing helix chain 'W' and resid 2 through 29 removed outlier: 4.292A pdb=" N VAL W 15 " --> pdb=" O LEU W 11 " (cutoff:3.500A) Proline residue: W 16 - end of helix Processing helix chain 'o' and resid 2 through 29 removed outlier: 4.291A pdb=" N VAL o 15 " --> pdb=" O LEU o 11 " (cutoff:3.500A) Proline residue: o 16 - end of helix Processing helix chain 'P' and resid 12 through 26 Processing helix chain 'P' and resid 27 through 32 removed outlier: 3.757A pdb=" N VAL P 31 " --> pdb=" O GLY P 27 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASP P 32 " --> pdb=" O GLU P 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 27 through 32' Processing helix chain 'P' and resid 40 through 45 removed outlier: 4.265A pdb=" N LEU P 44 " --> pdb=" O ASP P 40 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASN P 45 " --> pdb=" O ALA P 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 40 through 45' Processing helix chain 'P' and resid 63 through 70 Processing helix chain 'P' and resid 99 through 113 removed outlier: 4.022A pdb=" N LEU P 112 " --> pdb=" O LYS P 108 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY P 113 " --> pdb=" O ILE P 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 167 removed outlier: 5.262A pdb=" N LYS P 153 " --> pdb=" O PRO P 149 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN P 154 " --> pdb=" O ASP P 150 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER P 161 " --> pdb=" O LYS P 157 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N SER P 165 " --> pdb=" O SER P 161 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLU P 166 " --> pdb=" O GLN P 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 95 removed outlier: 4.184A pdb=" N SER P 95 " --> pdb=" O ASP P 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 90 through 95' Processing helix chain 'X' and resid 12 through 26 Processing helix chain 'X' and resid 27 through 32 removed outlier: 3.757A pdb=" N VAL X 31 " --> pdb=" O GLY X 27 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASP X 32 " --> pdb=" O GLU X 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 27 through 32' Processing helix chain 'X' and resid 40 through 45 removed outlier: 4.265A pdb=" N LEU X 44 " --> pdb=" O ASP X 40 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASN X 45 " --> pdb=" O ALA X 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 40 through 45' Processing helix chain 'X' and resid 63 through 70 Processing helix chain 'X' and resid 99 through 113 removed outlier: 4.022A pdb=" N LEU X 112 " --> pdb=" O LYS X 108 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY X 113 " --> pdb=" O ILE X 109 " (cutoff:3.500A) Processing helix chain 'X' and resid 149 through 167 removed outlier: 5.262A pdb=" N LYS X 153 " --> pdb=" O PRO X 149 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN X 154 " --> pdb=" O ASP X 150 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER X 161 " --> pdb=" O LYS X 157 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N SER X 165 " --> pdb=" O SER X 161 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLU X 166 " --> pdb=" O GLN X 162 " (cutoff:3.500A) Processing helix chain 'X' and resid 90 through 95 removed outlier: 4.184A pdb=" N SER X 95 " --> pdb=" O ASP X 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 90 through 95' Processing helix chain 'p' and resid 12 through 26 Processing helix chain 'p' and resid 27 through 32 removed outlier: 3.757A pdb=" N VAL p 31 " --> pdb=" O GLY p 27 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASP p 32 " --> pdb=" O GLU p 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 27 through 32' Processing helix chain 'p' and resid 40 through 45 removed outlier: 4.265A pdb=" N LEU p 44 " --> pdb=" O ASP p 40 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASN p 45 " --> pdb=" O ALA p 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 40 through 45' Processing helix chain 'p' and resid 63 through 70 Processing helix chain 'p' and resid 99 through 113 removed outlier: 4.021A pdb=" N LEU p 112 " --> pdb=" O LYS p 108 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY p 113 " --> pdb=" O ILE p 109 " (cutoff:3.500A) Processing helix chain 'p' and resid 149 through 167 removed outlier: 5.262A pdb=" N LYS p 153 " --> pdb=" O PRO p 149 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN p 154 " --> pdb=" O ASP p 150 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER p 161 " --> pdb=" O LYS p 157 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N SER p 165 " --> pdb=" O SER p 161 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLU p 166 " --> pdb=" O GLN p 162 " (cutoff:3.500A) Processing helix chain 'p' and resid 90 through 95 removed outlier: 4.184A pdb=" N SER p 95 " --> pdb=" O ASP p 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 90 through 95' Processing helix chain '1' and resid 15 through 20 removed outlier: 4.560A pdb=" N ARG 1 19 " --> pdb=" O ALA 1 15 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N PHE 1 20 " --> pdb=" O GLY 1 16 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 15 through 20' Processing helix chain '1' and resid 23 through 53 Processing helix chain '1' and resid 58 through 63 removed outlier: 4.008A pdb=" N GLN 1 62 " --> pdb=" O SER 1 58 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLY 1 63 " --> pdb=" O MET 1 59 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 58 through 63' Processing helix chain '1' and resid 64 through 74 Proline residue: 1 68 - end of helix Processing helix chain '1' and resid 86 through 112 Processing helix chain '1' and resid 117 through 122 removed outlier: 3.820A pdb=" N ALA 1 121 " --> pdb=" O ASP 1 117 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N SER 1 122 " --> pdb=" O LEU 1 118 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 117 through 122' Processing helix chain '1' and resid 124 through 130 removed outlier: 5.476A pdb=" N PHE 1 128 " --> pdb=" O ALA 1 124 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS 1 129 " --> pdb=" O ALA 1 125 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N PHE 1 130 " --> pdb=" O LYS 1 126 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 124 through 130' Processing helix chain '1' and resid 134 through 162 removed outlier: 3.840A pdb=" N LEU 1 138 " --> pdb=" O ASP 1 134 " (cutoff:3.500A) Processing helix chain '1' and resid 183 through 194 removed outlier: 4.250A pdb=" N GLN 1 191 " --> pdb=" O ILE 1 187 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N THR 1 192 " --> pdb=" O TYR 1 188 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS 1 193 " --> pdb=" O GLY 1 189 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE 1 194 " --> pdb=" O TYR 1 190 " (cutoff:3.500A) Processing helix chain '1' and resid 199 through 224 removed outlier: 3.725A pdb=" N LEU 1 203 " --> pdb=" O ASN 1 199 " (cutoff:3.500A) Processing helix chain '1' and resid 227 through 234 removed outlier: 3.534A pdb=" N LYS 1 231 " --> pdb=" O PHE 1 227 " (cutoff:3.500A) Processing helix chain '1' and resid 237 through 262 Processing helix chain '1' and resid 263 through 268 removed outlier: 4.221A pdb=" N TYR 1 267 " --> pdb=" O ASN 1 263 " (cutoff:3.500A) Proline residue: 1 268 - end of helix No H-bonds generated for 'chain '1' and resid 263 through 268' Processing helix chain '1' and resid 298 through 327 removed outlier: 5.190A pdb=" N GLY 1 327 " --> pdb=" O LEU 1 323 " (cutoff:3.500A) Processing helix chain '1' and resid 329 through 338 removed outlier: 4.288A pdb=" N VAL 1 333 " --> pdb=" O ASP 1 329 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU 1 334 " --> pdb=" O PHE 1 330 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU 1 337 " --> pdb=" O VAL 1 333 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER 1 338 " --> pdb=" O GLU 1 334 " (cutoff:3.500A) Processing helix chain '2' and resid 15 through 20 removed outlier: 4.286A pdb=" N ARG 2 19 " --> pdb=" O ALA 2 15 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N PHE 2 20 " --> pdb=" O GLY 2 16 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 15 through 20' Processing helix chain '2' and resid 23 through 53 Processing helix chain '2' and resid 58 through 63 removed outlier: 4.086A pdb=" N GLN 2 62 " --> pdb=" O SER 2 58 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLY 2 63 " --> pdb=" O MET 2 59 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 58 through 63' Processing helix chain '2' and resid 64 through 74 Proline residue: 2 68 - end of helix Processing helix chain '2' and resid 86 through 112 Processing helix chain '2' and resid 117 through 122 removed outlier: 4.102A pdb=" N ALA 2 121 " --> pdb=" O ASP 2 117 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N SER 2 122 " --> pdb=" O LEU 2 118 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 117 through 122' Processing helix chain '2' and resid 124 through 130 removed outlier: 5.070A pdb=" N PHE 2 128 " --> pdb=" O ALA 2 124 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS 2 129 " --> pdb=" O ALA 2 125 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N PHE 2 130 " --> pdb=" O LYS 2 126 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 124 through 130' Processing helix chain '2' and resid 134 through 162 removed outlier: 3.798A pdb=" N LEU 2 138 " --> pdb=" O ASP 2 134 " (cutoff:3.500A) Processing helix chain '2' and resid 183 through 194 removed outlier: 3.552A pdb=" N ILE 2 187 " --> pdb=" O ASN 2 183 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLN 2 191 " --> pdb=" O ILE 2 187 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N THR 2 192 " --> pdb=" O TYR 2 188 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N HIS 2 193 " --> pdb=" O GLY 2 189 " (cutoff:3.500A) Processing helix chain '2' and resid 199 through 224 removed outlier: 3.570A pdb=" N LEU 2 203 " --> pdb=" O ASN 2 199 " (cutoff:3.500A) Processing helix chain '2' and resid 227 through 234 removed outlier: 3.643A pdb=" N LYS 2 231 " --> pdb=" O PHE 2 227 " (cutoff:3.500A) Processing helix chain '2' and resid 237 through 262 removed outlier: 3.652A pdb=" N ILE 2 241 " --> pdb=" O SER 2 237 " (cutoff:3.500A) Processing helix chain '2' and resid 263 through 268 removed outlier: 4.108A pdb=" N TYR 2 267 " --> pdb=" O ASN 2 263 " (cutoff:3.500A) Proline residue: 2 268 - end of helix No H-bonds generated for 'chain '2' and resid 263 through 268' Processing helix chain '2' and resid 298 through 327 removed outlier: 4.893A pdb=" N GLY 2 327 " --> pdb=" O LEU 2 323 " (cutoff:3.500A) Processing helix chain '2' and resid 329 through 338 removed outlier: 4.458A pdb=" N VAL 2 333 " --> pdb=" O ASP 2 329 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU 2 334 " --> pdb=" O PHE 2 330 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER 2 338 " --> pdb=" O GLU 2 334 " (cutoff:3.500A) Processing helix chain '3' and resid 15 through 20 removed outlier: 4.063A pdb=" N ARG 3 19 " --> pdb=" O ALA 3 15 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N PHE 3 20 " --> pdb=" O GLY 3 16 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 15 through 20' Processing helix chain '3' and resid 23 through 53 Processing helix chain '3' and resid 58 through 63 removed outlier: 4.108A pdb=" N GLN 3 62 " --> pdb=" O SER 3 58 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLY 3 63 " --> pdb=" O MET 3 59 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 58 through 63' Processing helix chain '3' and resid 64 through 74 Proline residue: 3 68 - end of helix Processing helix chain '3' and resid 86 through 112 Processing helix chain '3' and resid 117 through 122 removed outlier: 3.740A pdb=" N ALA 3 121 " --> pdb=" O ASP 3 117 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N SER 3 122 " --> pdb=" O LEU 3 118 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 117 through 122' Processing helix chain '3' and resid 124 through 130 removed outlier: 5.022A pdb=" N PHE 3 128 " --> pdb=" O ALA 3 124 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N PHE 3 130 " --> pdb=" O LYS 3 126 " (cutoff:3.500A) Processing helix chain '3' and resid 134 through 162 removed outlier: 3.911A pdb=" N LEU 3 138 " --> pdb=" O ASP 3 134 " (cutoff:3.500A) Processing helix chain '3' and resid 183 through 194 removed outlier: 3.668A pdb=" N ILE 3 187 " --> pdb=" O ASN 3 183 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLN 3 191 " --> pdb=" O ILE 3 187 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N THR 3 192 " --> pdb=" O TYR 3 188 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N HIS 3 193 " --> pdb=" O GLY 3 189 " (cutoff:3.500A) Processing helix chain '3' and resid 199 through 224 Processing helix chain '3' and resid 227 through 234 removed outlier: 3.701A pdb=" N LYS 3 231 " --> pdb=" O PHE 3 227 " (cutoff:3.500A) Processing helix chain '3' and resid 237 through 262 Processing helix chain '3' and resid 263 through 268 removed outlier: 4.173A pdb=" N TYR 3 267 " --> pdb=" O ASN 3 263 " (cutoff:3.500A) Proline residue: 3 268 - end of helix No H-bonds generated for 'chain '3' and resid 263 through 268' Processing helix chain '3' and resid 298 through 327 removed outlier: 5.088A pdb=" N GLY 3 327 " --> pdb=" O LEU 3 323 " (cutoff:3.500A) Processing helix chain '3' and resid 329 through 338 removed outlier: 4.363A pdb=" N VAL 3 333 " --> pdb=" O ASP 3 329 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU 3 334 " --> pdb=" O PHE 3 330 " (cutoff:3.500A) Processing helix chain '5' and resid 15 through 20 removed outlier: 4.576A pdb=" N ARG 5 19 " --> pdb=" O ALA 5 15 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE 5 20 " --> pdb=" O GLY 5 16 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 15 through 20' Processing helix chain '5' and resid 23 through 53 Processing helix chain '5' and resid 58 through 63 removed outlier: 4.245A pdb=" N GLN 5 62 " --> pdb=" O SER 5 58 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLY 5 63 " --> pdb=" O MET 5 59 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 58 through 63' Processing helix chain '5' and resid 64 through 74 Proline residue: 5 68 - end of helix Processing helix chain '5' and resid 86 through 112 Processing helix chain '5' and resid 117 through 122 removed outlier: 4.174A pdb=" N ALA 5 121 " --> pdb=" O ASP 5 117 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N SER 5 122 " --> pdb=" O LEU 5 118 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 117 through 122' Processing helix chain '5' and resid 124 through 130 removed outlier: 3.920A pdb=" N PHE 5 128 " --> pdb=" O ALA 5 124 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N PHE 5 130 " --> pdb=" O LYS 5 126 " (cutoff:3.500A) Processing helix chain '5' and resid 134 through 162 removed outlier: 3.630A pdb=" N LEU 5 138 " --> pdb=" O ASP 5 134 " (cutoff:3.500A) Processing helix chain '5' and resid 183 through 194 removed outlier: 4.258A pdb=" N GLN 5 191 " --> pdb=" O ILE 5 187 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N THR 5 192 " --> pdb=" O TYR 5 188 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N HIS 5 193 " --> pdb=" O GLY 5 189 " (cutoff:3.500A) Processing helix chain '5' and resid 199 through 224 Processing helix chain '5' and resid 227 through 234 removed outlier: 3.689A pdb=" N LYS 5 231 " --> pdb=" O PHE 5 227 " (cutoff:3.500A) Processing helix chain '5' and resid 237 through 262 Processing helix chain '5' and resid 263 through 268 removed outlier: 4.208A pdb=" N TYR 5 267 " --> pdb=" O ASN 5 263 " (cutoff:3.500A) Proline residue: 5 268 - end of helix No H-bonds generated for 'chain '5' and resid 263 through 268' Processing helix chain '5' and resid 298 through 327 removed outlier: 4.960A pdb=" N GLY 5 327 " --> pdb=" O LEU 5 323 " (cutoff:3.500A) Processing helix chain '5' and resid 329 through 338 removed outlier: 4.065A pdb=" N VAL 5 333 " --> pdb=" O ASP 5 329 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU 5 334 " --> pdb=" O PHE 5 330 " (cutoff:3.500A) Processing helix chain '6' and resid 15 through 20 removed outlier: 4.590A pdb=" N ARG 6 19 " --> pdb=" O ALA 6 15 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE 6 20 " --> pdb=" O GLY 6 16 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 15 through 20' Processing helix chain '6' and resid 23 through 53 Processing helix chain '6' and resid 58 through 63 removed outlier: 3.789A pdb=" N GLN 6 62 " --> pdb=" O SER 6 58 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLY 6 63 " --> pdb=" O MET 6 59 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 58 through 63' Processing helix chain '6' and resid 64 through 74 Proline residue: 6 68 - end of helix Processing helix chain '6' and resid 86 through 112 Processing helix chain '6' and resid 117 through 122 removed outlier: 3.980A pdb=" N ALA 6 121 " --> pdb=" O ASP 6 117 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N SER 6 122 " --> pdb=" O LEU 6 118 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 117 through 122' Processing helix chain '6' and resid 124 through 130 removed outlier: 4.459A pdb=" N PHE 6 128 " --> pdb=" O ALA 6 124 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE 6 130 " --> pdb=" O LYS 6 126 " (cutoff:3.500A) Processing helix chain '6' and resid 134 through 162 removed outlier: 3.764A pdb=" N LEU 6 138 " --> pdb=" O ASP 6 134 " (cutoff:3.500A) Processing helix chain '6' and resid 183 through 194 removed outlier: 4.311A pdb=" N GLN 6 191 " --> pdb=" O ILE 6 187 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N THR 6 192 " --> pdb=" O TYR 6 188 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N HIS 6 193 " --> pdb=" O GLY 6 189 " (cutoff:3.500A) Processing helix chain '6' and resid 199 through 224 Processing helix chain '6' and resid 227 through 234 Processing helix chain '6' and resid 237 through 262 Processing helix chain '6' and resid 263 through 268 removed outlier: 4.457A pdb=" N TYR 6 267 " --> pdb=" O ASN 6 263 " (cutoff:3.500A) Proline residue: 6 268 - end of helix No H-bonds generated for 'chain '6' and resid 263 through 268' Processing helix chain '6' and resid 298 through 327 removed outlier: 4.859A pdb=" N GLY 6 327 " --> pdb=" O LEU 6 323 " (cutoff:3.500A) Processing helix chain '6' and resid 329 through 338 removed outlier: 3.670A pdb=" N VAL 6 333 " --> pdb=" O ASP 6 329 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER 6 338 " --> pdb=" O GLU 6 334 " (cutoff:3.500A) Processing helix chain 'Y' and resid 15 through 20 removed outlier: 4.560A pdb=" N ARG Y 19 " --> pdb=" O ALA Y 15 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N PHE Y 20 " --> pdb=" O GLY Y 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 15 through 20' Processing helix chain 'Y' and resid 23 through 53 Processing helix chain 'Y' and resid 58 through 63 removed outlier: 4.007A pdb=" N GLN Y 62 " --> pdb=" O SER Y 58 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLY Y 63 " --> pdb=" O MET Y 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 58 through 63' Processing helix chain 'Y' and resid 64 through 74 Proline residue: Y 68 - end of helix Processing helix chain 'Y' and resid 86 through 112 Processing helix chain 'Y' and resid 117 through 122 removed outlier: 3.820A pdb=" N ALA Y 121 " --> pdb=" O ASP Y 117 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N SER Y 122 " --> pdb=" O LEU Y 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 117 through 122' Processing helix chain 'Y' and resid 124 through 130 removed outlier: 5.475A pdb=" N PHE Y 128 " --> pdb=" O ALA Y 124 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS Y 129 " --> pdb=" O ALA Y 125 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N PHE Y 130 " --> pdb=" O LYS Y 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 124 through 130' Processing helix chain 'Y' and resid 134 through 162 removed outlier: 3.840A pdb=" N LEU Y 138 " --> pdb=" O ASP Y 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 183 through 194 removed outlier: 4.251A pdb=" N GLN Y 191 " --> pdb=" O ILE Y 187 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N THR Y 192 " --> pdb=" O TYR Y 188 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS Y 193 " --> pdb=" O GLY Y 189 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE Y 194 " --> pdb=" O TYR Y 190 " (cutoff:3.500A) Processing helix chain 'Y' and resid 199 through 224 removed outlier: 3.726A pdb=" N LEU Y 203 " --> pdb=" O ASN Y 199 " (cutoff:3.500A) Processing helix chain 'Y' and resid 227 through 234 removed outlier: 3.534A pdb=" N LYS Y 231 " --> pdb=" O PHE Y 227 " (cutoff:3.500A) Processing helix chain 'Y' and resid 237 through 262 Processing helix chain 'Y' and resid 263 through 268 removed outlier: 4.221A pdb=" N TYR Y 267 " --> pdb=" O ASN Y 263 " (cutoff:3.500A) Proline residue: Y 268 - end of helix No H-bonds generated for 'chain 'Y' and resid 263 through 268' Processing helix chain 'Y' and resid 298 through 327 removed outlier: 5.189A pdb=" N GLY Y 327 " --> pdb=" O LEU Y 323 " (cutoff:3.500A) Processing helix chain 'Y' and resid 329 through 338 removed outlier: 4.288A pdb=" N VAL Y 333 " --> pdb=" O ASP Y 329 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU Y 334 " --> pdb=" O PHE Y 330 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU Y 337 " --> pdb=" O VAL Y 333 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER Y 338 " --> pdb=" O GLU Y 334 " (cutoff:3.500A) Processing helix chain 'Z' and resid 15 through 20 removed outlier: 4.285A pdb=" N ARG Z 19 " --> pdb=" O ALA Z 15 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N PHE Z 20 " --> pdb=" O GLY Z 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 15 through 20' Processing helix chain 'Z' and resid 23 through 53 Processing helix chain 'Z' and resid 58 through 63 removed outlier: 4.086A pdb=" N GLN Z 62 " --> pdb=" O SER Z 58 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLY Z 63 " --> pdb=" O MET Z 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 58 through 63' Processing helix chain 'Z' and resid 64 through 74 Proline residue: Z 68 - end of helix Processing helix chain 'Z' and resid 86 through 112 Processing helix chain 'Z' and resid 117 through 122 removed outlier: 4.102A pdb=" N ALA Z 121 " --> pdb=" O ASP Z 117 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N SER Z 122 " --> pdb=" O LEU Z 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 117 through 122' Processing helix chain 'Z' and resid 124 through 130 removed outlier: 5.070A pdb=" N PHE Z 128 " --> pdb=" O ALA Z 124 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS Z 129 " --> pdb=" O ALA Z 125 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N PHE Z 130 " --> pdb=" O LYS Z 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 124 through 130' Processing helix chain 'Z' and resid 134 through 162 removed outlier: 3.798A pdb=" N LEU Z 138 " --> pdb=" O ASP Z 134 " (cutoff:3.500A) Processing helix chain 'Z' and resid 183 through 194 removed outlier: 3.553A pdb=" N ILE Z 187 " --> pdb=" O ASN Z 183 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLN Z 191 " --> pdb=" O ILE Z 187 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N THR Z 192 " --> pdb=" O TYR Z 188 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS Z 193 " --> pdb=" O GLY Z 189 " (cutoff:3.500A) Processing helix chain 'Z' and resid 199 through 224 removed outlier: 3.569A pdb=" N LEU Z 203 " --> pdb=" O ASN Z 199 " (cutoff:3.500A) Processing helix chain 'Z' and resid 227 through 234 removed outlier: 3.643A pdb=" N LYS Z 231 " --> pdb=" O PHE Z 227 " (cutoff:3.500A) Processing helix chain 'Z' and resid 237 through 262 removed outlier: 3.653A pdb=" N ILE Z 241 " --> pdb=" O SER Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 263 through 268 removed outlier: 4.108A pdb=" N TYR Z 267 " --> pdb=" O ASN Z 263 " (cutoff:3.500A) Proline residue: Z 268 - end of helix No H-bonds generated for 'chain 'Z' and resid 263 through 268' Processing helix chain 'Z' and resid 298 through 327 removed outlier: 4.893A pdb=" N GLY Z 327 " --> pdb=" O LEU Z 323 " (cutoff:3.500A) Processing helix chain 'Z' and resid 329 through 338 removed outlier: 4.458A pdb=" N VAL Z 333 " --> pdb=" O ASP Z 329 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU Z 334 " --> pdb=" O PHE Z 330 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER Z 338 " --> pdb=" O GLU Z 334 " (cutoff:3.500A) Processing helix chain 'a' and resid 15 through 20 removed outlier: 4.063A pdb=" N ARG a 19 " --> pdb=" O ALA a 15 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE a 20 " --> pdb=" O GLY a 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 15 through 20' Processing helix chain 'a' and resid 23 through 53 Processing helix chain 'a' and resid 58 through 63 removed outlier: 4.107A pdb=" N GLN a 62 " --> pdb=" O SER a 58 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLY a 63 " --> pdb=" O MET a 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 58 through 63' Processing helix chain 'a' and resid 64 through 74 Proline residue: a 68 - end of helix Processing helix chain 'a' and resid 86 through 112 Processing helix chain 'a' and resid 117 through 122 removed outlier: 3.740A pdb=" N ALA a 121 " --> pdb=" O ASP a 117 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N SER a 122 " --> pdb=" O LEU a 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 117 through 122' Processing helix chain 'a' and resid 124 through 130 removed outlier: 5.022A pdb=" N PHE a 128 " --> pdb=" O ALA a 124 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N PHE a 130 " --> pdb=" O LYS a 126 " (cutoff:3.500A) Processing helix chain 'a' and resid 134 through 162 removed outlier: 3.910A pdb=" N LEU a 138 " --> pdb=" O ASP a 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 183 through 194 removed outlier: 3.667A pdb=" N ILE a 187 " --> pdb=" O ASN a 183 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLN a 191 " --> pdb=" O ILE a 187 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N THR a 192 " --> pdb=" O TYR a 188 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N HIS a 193 " --> pdb=" O GLY a 189 " (cutoff:3.500A) Processing helix chain 'a' and resid 199 through 224 Processing helix chain 'a' and resid 227 through 234 removed outlier: 3.701A pdb=" N LYS a 231 " --> pdb=" O PHE a 227 " (cutoff:3.500A) Processing helix chain 'a' and resid 237 through 262 Processing helix chain 'a' and resid 263 through 268 removed outlier: 4.172A pdb=" N TYR a 267 " --> pdb=" O ASN a 263 " (cutoff:3.500A) Proline residue: a 268 - end of helix No H-bonds generated for 'chain 'a' and resid 263 through 268' Processing helix chain 'a' and resid 298 through 327 removed outlier: 5.088A pdb=" N GLY a 327 " --> pdb=" O LEU a 323 " (cutoff:3.500A) Processing helix chain 'a' and resid 329 through 338 removed outlier: 4.363A pdb=" N VAL a 333 " --> pdb=" O ASP a 329 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU a 334 " --> pdb=" O PHE a 330 " (cutoff:3.500A) Processing helix chain 'c' and resid 15 through 20 removed outlier: 4.575A pdb=" N ARG c 19 " --> pdb=" O ALA c 15 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE c 20 " --> pdb=" O GLY c 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 15 through 20' Processing helix chain 'c' and resid 23 through 53 Processing helix chain 'c' and resid 58 through 63 removed outlier: 4.245A pdb=" N GLN c 62 " --> pdb=" O SER c 58 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLY c 63 " --> pdb=" O MET c 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 58 through 63' Processing helix chain 'c' and resid 64 through 74 Proline residue: c 68 - end of helix Processing helix chain 'c' and resid 86 through 112 Processing helix chain 'c' and resid 117 through 122 removed outlier: 4.174A pdb=" N ALA c 121 " --> pdb=" O ASP c 117 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N SER c 122 " --> pdb=" O LEU c 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 117 through 122' Processing helix chain 'c' and resid 124 through 130 removed outlier: 3.920A pdb=" N PHE c 128 " --> pdb=" O ALA c 124 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N PHE c 130 " --> pdb=" O LYS c 126 " (cutoff:3.500A) Processing helix chain 'c' and resid 134 through 162 removed outlier: 3.630A pdb=" N LEU c 138 " --> pdb=" O ASP c 134 " (cutoff:3.500A) Processing helix chain 'c' and resid 183 through 194 removed outlier: 4.259A pdb=" N GLN c 191 " --> pdb=" O ILE c 187 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N THR c 192 " --> pdb=" O TYR c 188 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N HIS c 193 " --> pdb=" O GLY c 189 " (cutoff:3.500A) Processing helix chain 'c' and resid 199 through 224 Processing helix chain 'c' and resid 227 through 234 removed outlier: 3.689A pdb=" N LYS c 231 " --> pdb=" O PHE c 227 " (cutoff:3.500A) Processing helix chain 'c' and resid 237 through 262 Processing helix chain 'c' and resid 263 through 268 removed outlier: 4.207A pdb=" N TYR c 267 " --> pdb=" O ASN c 263 " (cutoff:3.500A) Proline residue: c 268 - end of helix No H-bonds generated for 'chain 'c' and resid 263 through 268' Processing helix chain 'c' and resid 298 through 327 removed outlier: 4.960A pdb=" N GLY c 327 " --> pdb=" O LEU c 323 " (cutoff:3.500A) Processing helix chain 'c' and resid 329 through 338 removed outlier: 4.064A pdb=" N VAL c 333 " --> pdb=" O ASP c 329 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU c 334 " --> pdb=" O PHE c 330 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 20 removed outlier: 4.591A pdb=" N ARG d 19 " --> pdb=" O ALA d 15 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE d 20 " --> pdb=" O GLY d 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 15 through 20' Processing helix chain 'd' and resid 23 through 53 Processing helix chain 'd' and resid 58 through 63 removed outlier: 3.789A pdb=" N GLN d 62 " --> pdb=" O SER d 58 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLY d 63 " --> pdb=" O MET d 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 58 through 63' Processing helix chain 'd' and resid 64 through 74 Proline residue: d 68 - end of helix Processing helix chain 'd' and resid 86 through 112 Processing helix chain 'd' and resid 117 through 122 removed outlier: 3.980A pdb=" N ALA d 121 " --> pdb=" O ASP d 117 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N SER d 122 " --> pdb=" O LEU d 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 117 through 122' Processing helix chain 'd' and resid 124 through 130 removed outlier: 4.459A pdb=" N PHE d 128 " --> pdb=" O ALA d 124 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE d 130 " --> pdb=" O LYS d 126 " (cutoff:3.500A) Processing helix chain 'd' and resid 134 through 162 removed outlier: 3.764A pdb=" N LEU d 138 " --> pdb=" O ASP d 134 " (cutoff:3.500A) Processing helix chain 'd' and resid 183 through 194 removed outlier: 4.311A pdb=" N GLN d 191 " --> pdb=" O ILE d 187 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N THR d 192 " --> pdb=" O TYR d 188 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N HIS d 193 " --> pdb=" O GLY d 189 " (cutoff:3.500A) Processing helix chain 'd' and resid 199 through 224 Processing helix chain 'd' and resid 227 through 234 Processing helix chain 'd' and resid 237 through 262 Processing helix chain 'd' and resid 263 through 268 removed outlier: 4.457A pdb=" N TYR d 267 " --> pdb=" O ASN d 263 " (cutoff:3.500A) Proline residue: d 268 - end of helix No H-bonds generated for 'chain 'd' and resid 263 through 268' Processing helix chain 'd' and resid 298 through 327 removed outlier: 4.860A pdb=" N GLY d 327 " --> pdb=" O LEU d 323 " (cutoff:3.500A) Processing helix chain 'd' and resid 329 through 338 removed outlier: 3.670A pdb=" N VAL d 333 " --> pdb=" O ASP d 329 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER d 338 " --> pdb=" O GLU d 334 " (cutoff:3.500A) Processing helix chain 'q' and resid 15 through 20 removed outlier: 4.560A pdb=" N ARG q 19 " --> pdb=" O ALA q 15 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N PHE q 20 " --> pdb=" O GLY q 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 15 through 20' Processing helix chain 'q' and resid 23 through 53 Processing helix chain 'q' and resid 58 through 63 removed outlier: 4.008A pdb=" N GLN q 62 " --> pdb=" O SER q 58 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLY q 63 " --> pdb=" O MET q 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 58 through 63' Processing helix chain 'q' and resid 64 through 74 Proline residue: q 68 - end of helix Processing helix chain 'q' and resid 86 through 112 Processing helix chain 'q' and resid 117 through 122 removed outlier: 3.821A pdb=" N ALA q 121 " --> pdb=" O ASP q 117 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N SER q 122 " --> pdb=" O LEU q 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 117 through 122' Processing helix chain 'q' and resid 124 through 130 removed outlier: 5.476A pdb=" N PHE q 128 " --> pdb=" O ALA q 124 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS q 129 " --> pdb=" O ALA q 125 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N PHE q 130 " --> pdb=" O LYS q 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 124 through 130' Processing helix chain 'q' and resid 134 through 162 removed outlier: 3.840A pdb=" N LEU q 138 " --> pdb=" O ASP q 134 " (cutoff:3.500A) Processing helix chain 'q' and resid 183 through 194 removed outlier: 4.251A pdb=" N GLN q 191 " --> pdb=" O ILE q 187 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N THR q 192 " --> pdb=" O TYR q 188 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS q 193 " --> pdb=" O GLY q 189 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE q 194 " --> pdb=" O TYR q 190 " (cutoff:3.500A) Processing helix chain 'q' and resid 199 through 224 removed outlier: 3.726A pdb=" N LEU q 203 " --> pdb=" O ASN q 199 " (cutoff:3.500A) Processing helix chain 'q' and resid 227 through 234 removed outlier: 3.534A pdb=" N LYS q 231 " --> pdb=" O PHE q 227 " (cutoff:3.500A) Processing helix chain 'q' and resid 237 through 262 Processing helix chain 'q' and resid 263 through 268 removed outlier: 4.221A pdb=" N TYR q 267 " --> pdb=" O ASN q 263 " (cutoff:3.500A) Proline residue: q 268 - end of helix No H-bonds generated for 'chain 'q' and resid 263 through 268' Processing helix chain 'q' and resid 298 through 327 removed outlier: 5.190A pdb=" N GLY q 327 " --> pdb=" O LEU q 323 " (cutoff:3.500A) Processing helix chain 'q' and resid 329 through 338 removed outlier: 4.288A pdb=" N VAL q 333 " --> pdb=" O ASP q 329 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU q 334 " --> pdb=" O PHE q 330 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU q 337 " --> pdb=" O VAL q 333 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER q 338 " --> pdb=" O GLU q 334 " (cutoff:3.500A) Processing helix chain 'r' and resid 15 through 20 removed outlier: 4.286A pdb=" N ARG r 19 " --> pdb=" O ALA r 15 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N PHE r 20 " --> pdb=" O GLY r 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 15 through 20' Processing helix chain 'r' and resid 23 through 53 Processing helix chain 'r' and resid 58 through 63 removed outlier: 4.086A pdb=" N GLN r 62 " --> pdb=" O SER r 58 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLY r 63 " --> pdb=" O MET r 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 58 through 63' Processing helix chain 'r' and resid 64 through 74 Proline residue: r 68 - end of helix Processing helix chain 'r' and resid 86 through 112 Processing helix chain 'r' and resid 117 through 122 removed outlier: 4.102A pdb=" N ALA r 121 " --> pdb=" O ASP r 117 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N SER r 122 " --> pdb=" O LEU r 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 117 through 122' Processing helix chain 'r' and resid 124 through 130 removed outlier: 5.070A pdb=" N PHE r 128 " --> pdb=" O ALA r 124 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS r 129 " --> pdb=" O ALA r 125 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N PHE r 130 " --> pdb=" O LYS r 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 124 through 130' Processing helix chain 'r' and resid 134 through 162 removed outlier: 3.798A pdb=" N LEU r 138 " --> pdb=" O ASP r 134 " (cutoff:3.500A) Processing helix chain 'r' and resid 183 through 194 removed outlier: 3.552A pdb=" N ILE r 187 " --> pdb=" O ASN r 183 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN r 191 " --> pdb=" O ILE r 187 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N THR r 192 " --> pdb=" O TYR r 188 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N HIS r 193 " --> pdb=" O GLY r 189 " (cutoff:3.500A) Processing helix chain 'r' and resid 199 through 224 removed outlier: 3.570A pdb=" N LEU r 203 " --> pdb=" O ASN r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 227 through 234 removed outlier: 3.643A pdb=" N LYS r 231 " --> pdb=" O PHE r 227 " (cutoff:3.500A) Processing helix chain 'r' and resid 237 through 262 removed outlier: 3.652A pdb=" N ILE r 241 " --> pdb=" O SER r 237 " (cutoff:3.500A) Processing helix chain 'r' and resid 263 through 268 removed outlier: 4.108A pdb=" N TYR r 267 " --> pdb=" O ASN r 263 " (cutoff:3.500A) Proline residue: r 268 - end of helix No H-bonds generated for 'chain 'r' and resid 263 through 268' Processing helix chain 'r' and resid 298 through 327 removed outlier: 4.893A pdb=" N GLY r 327 " --> pdb=" O LEU r 323 " (cutoff:3.500A) Processing helix chain 'r' and resid 329 through 338 removed outlier: 4.458A pdb=" N VAL r 333 " --> pdb=" O ASP r 329 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU r 334 " --> pdb=" O PHE r 330 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER r 338 " --> pdb=" O GLU r 334 " (cutoff:3.500A) Processing helix chain 's' and resid 15 through 20 removed outlier: 4.063A pdb=" N ARG s 19 " --> pdb=" O ALA s 15 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N PHE s 20 " --> pdb=" O GLY s 16 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 15 through 20' Processing helix chain 's' and resid 23 through 53 Processing helix chain 's' and resid 58 through 63 removed outlier: 4.108A pdb=" N GLN s 62 " --> pdb=" O SER s 58 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLY s 63 " --> pdb=" O MET s 59 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 58 through 63' Processing helix chain 's' and resid 64 through 74 Proline residue: s 68 - end of helix Processing helix chain 's' and resid 86 through 112 Processing helix chain 's' and resid 117 through 122 removed outlier: 3.741A pdb=" N ALA s 121 " --> pdb=" O ASP s 117 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N SER s 122 " --> pdb=" O LEU s 118 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 117 through 122' Processing helix chain 's' and resid 124 through 130 removed outlier: 5.022A pdb=" N PHE s 128 " --> pdb=" O ALA s 124 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N PHE s 130 " --> pdb=" O LYS s 126 " (cutoff:3.500A) Processing helix chain 's' and resid 134 through 162 removed outlier: 3.911A pdb=" N LEU s 138 " --> pdb=" O ASP s 134 " (cutoff:3.500A) Processing helix chain 's' and resid 183 through 194 removed outlier: 3.667A pdb=" N ILE s 187 " --> pdb=" O ASN s 183 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLN s 191 " --> pdb=" O ILE s 187 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N THR s 192 " --> pdb=" O TYR s 188 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N HIS s 193 " --> pdb=" O GLY s 189 " (cutoff:3.500A) Processing helix chain 's' and resid 199 through 224 Processing helix chain 's' and resid 227 through 234 removed outlier: 3.701A pdb=" N LYS s 231 " --> pdb=" O PHE s 227 " (cutoff:3.500A) Processing helix chain 's' and resid 237 through 262 Processing helix chain 's' and resid 263 through 268 removed outlier: 4.172A pdb=" N TYR s 267 " --> pdb=" O ASN s 263 " (cutoff:3.500A) Proline residue: s 268 - end of helix No H-bonds generated for 'chain 's' and resid 263 through 268' Processing helix chain 's' and resid 298 through 327 removed outlier: 5.088A pdb=" N GLY s 327 " --> pdb=" O LEU s 323 " (cutoff:3.500A) Processing helix chain 's' and resid 329 through 338 removed outlier: 4.362A pdb=" N VAL s 333 " --> pdb=" O ASP s 329 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU s 334 " --> pdb=" O PHE s 330 " (cutoff:3.500A) Processing helix chain 'u' and resid 15 through 20 removed outlier: 4.576A pdb=" N ARG u 19 " --> pdb=" O ALA u 15 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE u 20 " --> pdb=" O GLY u 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 15 through 20' Processing helix chain 'u' and resid 23 through 53 Processing helix chain 'u' and resid 58 through 63 removed outlier: 4.244A pdb=" N GLN u 62 " --> pdb=" O SER u 58 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLY u 63 " --> pdb=" O MET u 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 58 through 63' Processing helix chain 'u' and resid 64 through 74 Proline residue: u 68 - end of helix Processing helix chain 'u' and resid 86 through 112 Processing helix chain 'u' and resid 117 through 122 removed outlier: 4.174A pdb=" N ALA u 121 " --> pdb=" O ASP u 117 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N SER u 122 " --> pdb=" O LEU u 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 117 through 122' Processing helix chain 'u' and resid 124 through 130 removed outlier: 3.921A pdb=" N PHE u 128 " --> pdb=" O ALA u 124 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N PHE u 130 " --> pdb=" O LYS u 126 " (cutoff:3.500A) Processing helix chain 'u' and resid 134 through 162 removed outlier: 3.629A pdb=" N LEU u 138 " --> pdb=" O ASP u 134 " (cutoff:3.500A) Processing helix chain 'u' and resid 183 through 194 removed outlier: 4.258A pdb=" N GLN u 191 " --> pdb=" O ILE u 187 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N THR u 192 " --> pdb=" O TYR u 188 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N HIS u 193 " --> pdb=" O GLY u 189 " (cutoff:3.500A) Processing helix chain 'u' and resid 199 through 224 Processing helix chain 'u' and resid 227 through 234 removed outlier: 3.689A pdb=" N LYS u 231 " --> pdb=" O PHE u 227 " (cutoff:3.500A) Processing helix chain 'u' and resid 237 through 262 Processing helix chain 'u' and resid 263 through 268 removed outlier: 4.208A pdb=" N TYR u 267 " --> pdb=" O ASN u 263 " (cutoff:3.500A) Proline residue: u 268 - end of helix No H-bonds generated for 'chain 'u' and resid 263 through 268' Processing helix chain 'u' and resid 298 through 327 removed outlier: 4.960A pdb=" N GLY u 327 " --> pdb=" O LEU u 323 " (cutoff:3.500A) Processing helix chain 'u' and resid 329 through 338 removed outlier: 4.065A pdb=" N VAL u 333 " --> pdb=" O ASP u 329 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU u 334 " --> pdb=" O PHE u 330 " (cutoff:3.500A) Processing helix chain 'v' and resid 15 through 20 removed outlier: 4.590A pdb=" N ARG v 19 " --> pdb=" O ALA v 15 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE v 20 " --> pdb=" O GLY v 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 15 through 20' Processing helix chain 'v' and resid 23 through 53 Processing helix chain 'v' and resid 58 through 63 removed outlier: 3.789A pdb=" N GLN v 62 " --> pdb=" O SER v 58 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLY v 63 " --> pdb=" O MET v 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 58 through 63' Processing helix chain 'v' and resid 64 through 74 Proline residue: v 68 - end of helix Processing helix chain 'v' and resid 86 through 112 Processing helix chain 'v' and resid 117 through 122 removed outlier: 3.980A pdb=" N ALA v 121 " --> pdb=" O ASP v 117 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N SER v 122 " --> pdb=" O LEU v 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 117 through 122' Processing helix chain 'v' and resid 124 through 130 removed outlier: 4.459A pdb=" N PHE v 128 " --> pdb=" O ALA v 124 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE v 130 " --> pdb=" O LYS v 126 " (cutoff:3.500A) Processing helix chain 'v' and resid 134 through 162 removed outlier: 3.764A pdb=" N LEU v 138 " --> pdb=" O ASP v 134 " (cutoff:3.500A) Processing helix chain 'v' and resid 183 through 194 removed outlier: 4.312A pdb=" N GLN v 191 " --> pdb=" O ILE v 187 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N THR v 192 " --> pdb=" O TYR v 188 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N HIS v 193 " --> pdb=" O GLY v 189 " (cutoff:3.500A) Processing helix chain 'v' and resid 199 through 224 Processing helix chain 'v' and resid 227 through 234 Processing helix chain 'v' and resid 237 through 262 Processing helix chain 'v' and resid 263 through 268 removed outlier: 4.457A pdb=" N TYR v 267 " --> pdb=" O ASN v 263 " (cutoff:3.500A) Proline residue: v 268 - end of helix No H-bonds generated for 'chain 'v' and resid 263 through 268' Processing helix chain 'v' and resid 298 through 327 removed outlier: 4.860A pdb=" N GLY v 327 " --> pdb=" O LEU v 323 " (cutoff:3.500A) Processing helix chain 'v' and resid 329 through 338 removed outlier: 3.670A pdb=" N VAL v 333 " --> pdb=" O ASP v 329 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER v 338 " --> pdb=" O GLU v 334 " (cutoff:3.500A) Processing helix chain '4' and resid 15 through 21 removed outlier: 4.769A pdb=" N ARG 4 19 " --> pdb=" O ALA 4 15 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N PHE 4 20 " --> pdb=" O GLY 4 16 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ALA 4 21 " --> pdb=" O ASN 4 17 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 15 through 21' Processing helix chain '4' and resid 23 through 53 Processing helix chain '4' and resid 58 through 63 removed outlier: 3.603A pdb=" N GLN 4 62 " --> pdb=" O SER 4 58 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLY 4 63 " --> pdb=" O MET 4 59 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 58 through 63' Processing helix chain '4' and resid 64 through 74 Proline residue: 4 68 - end of helix Processing helix chain '4' and resid 86 through 112 Processing helix chain '4' and resid 117 through 122 removed outlier: 4.089A pdb=" N ALA 4 121 " --> pdb=" O ASP 4 117 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N SER 4 122 " --> pdb=" O LEU 4 118 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 117 through 122' Processing helix chain '4' and resid 124 through 130 removed outlier: 4.879A pdb=" N PHE 4 128 " --> pdb=" O ALA 4 124 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N PHE 4 130 " --> pdb=" O LYS 4 126 " (cutoff:3.500A) Processing helix chain '4' and resid 134 through 162 removed outlier: 3.941A pdb=" N LEU 4 138 " --> pdb=" O ASP 4 134 " (cutoff:3.500A) Processing helix chain '4' and resid 183 through 191 removed outlier: 3.735A pdb=" N ILE 4 187 " --> pdb=" O ASN 4 183 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN 4 191 " --> pdb=" O ILE 4 187 " (cutoff:3.500A) Processing helix chain '4' and resid 199 through 224 Processing helix chain '4' and resid 227 through 234 Processing helix chain '4' and resid 237 through 263 Processing helix chain '4' and resid 298 through 327 removed outlier: 4.944A pdb=" N GLY 4 327 " --> pdb=" O LEU 4 323 " (cutoff:3.500A) Processing helix chain '4' and resid 329 through 339 removed outlier: 4.469A pdb=" N VAL 4 333 " --> pdb=" O ASP 4 329 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU 4 334 " --> pdb=" O PHE 4 330 " (cutoff:3.500A) Processing helix chain 'b' and resid 15 through 21 removed outlier: 4.769A pdb=" N ARG b 19 " --> pdb=" O ALA b 15 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N PHE b 20 " --> pdb=" O GLY b 16 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ALA b 21 " --> pdb=" O ASN b 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 15 through 21' Processing helix chain 'b' and resid 23 through 53 Processing helix chain 'b' and resid 58 through 63 removed outlier: 3.603A pdb=" N GLN b 62 " --> pdb=" O SER b 58 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLY b 63 " --> pdb=" O MET b 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 58 through 63' Processing helix chain 'b' and resid 64 through 74 Proline residue: b 68 - end of helix Processing helix chain 'b' and resid 86 through 112 Processing helix chain 'b' and resid 117 through 122 removed outlier: 4.088A pdb=" N ALA b 121 " --> pdb=" O ASP b 117 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N SER b 122 " --> pdb=" O LEU b 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 117 through 122' Processing helix chain 'b' and resid 124 through 130 removed outlier: 4.879A pdb=" N PHE b 128 " --> pdb=" O ALA b 124 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N PHE b 130 " --> pdb=" O LYS b 126 " (cutoff:3.500A) Processing helix chain 'b' and resid 134 through 162 removed outlier: 3.941A pdb=" N LEU b 138 " --> pdb=" O ASP b 134 " (cutoff:3.500A) Processing helix chain 'b' and resid 183 through 191 removed outlier: 3.736A pdb=" N ILE b 187 " --> pdb=" O ASN b 183 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN b 191 " --> pdb=" O ILE b 187 " (cutoff:3.500A) Processing helix chain 'b' and resid 199 through 224 Processing helix chain 'b' and resid 227 through 234 Processing helix chain 'b' and resid 237 through 263 Processing helix chain 'b' and resid 298 through 327 removed outlier: 4.944A pdb=" N GLY b 327 " --> pdb=" O LEU b 323 " (cutoff:3.500A) Processing helix chain 'b' and resid 329 through 339 removed outlier: 4.469A pdb=" N VAL b 333 " --> pdb=" O ASP b 329 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU b 334 " --> pdb=" O PHE b 330 " (cutoff:3.500A) Processing helix chain 't' and resid 15 through 21 removed outlier: 4.769A pdb=" N ARG t 19 " --> pdb=" O ALA t 15 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N PHE t 20 " --> pdb=" O GLY t 16 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ALA t 21 " --> pdb=" O ASN t 17 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 15 through 21' Processing helix chain 't' and resid 23 through 53 Processing helix chain 't' and resid 58 through 63 removed outlier: 3.603A pdb=" N GLN t 62 " --> pdb=" O SER t 58 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLY t 63 " --> pdb=" O MET t 59 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 58 through 63' Processing helix chain 't' and resid 64 through 74 Proline residue: t 68 - end of helix Processing helix chain 't' and resid 86 through 112 Processing helix chain 't' and resid 117 through 122 removed outlier: 4.089A pdb=" N ALA t 121 " --> pdb=" O ASP t 117 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N SER t 122 " --> pdb=" O LEU t 118 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 117 through 122' Processing helix chain 't' and resid 124 through 130 removed outlier: 4.879A pdb=" N PHE t 128 " --> pdb=" O ALA t 124 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N PHE t 130 " --> pdb=" O LYS t 126 " (cutoff:3.500A) Processing helix chain 't' and resid 134 through 162 removed outlier: 3.941A pdb=" N LEU t 138 " --> pdb=" O ASP t 134 " (cutoff:3.500A) Processing helix chain 't' and resid 183 through 191 removed outlier: 3.735A pdb=" N ILE t 187 " --> pdb=" O ASN t 183 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN t 191 " --> pdb=" O ILE t 187 " (cutoff:3.500A) Processing helix chain 't' and resid 199 through 224 Processing helix chain 't' and resid 227 through 234 Processing helix chain 't' and resid 237 through 263 Processing helix chain 't' and resid 298 through 327 removed outlier: 4.944A pdb=" N GLY t 327 " --> pdb=" O LEU t 323 " (cutoff:3.500A) Processing helix chain 't' and resid 329 through 339 removed outlier: 4.469A pdb=" N VAL t 333 " --> pdb=" O ASP t 329 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU t 334 " --> pdb=" O PHE t 330 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'C' and resid 2 through 8 removed outlier: 5.620A pdb=" N SER C 2 " --> pdb=" O GLY C 70 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY C 70 " --> pdb=" O SER C 2 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N SER C 64 " --> pdb=" O TYR C 8 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C' and resid 26 through 31 No H-bonds generated for sheet with id= 2 Processing sheet with id= 3, first strand: chain 'N' and resid 2 through 8 removed outlier: 5.620A pdb=" N SER N 2 " --> pdb=" O GLY N 70 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY N 70 " --> pdb=" O SER N 2 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N SER N 64 " --> pdb=" O TYR N 8 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'N' and resid 26 through 31 No H-bonds generated for sheet with id= 4 Processing sheet with id= 5, first strand: chain 'g' and resid 2 through 8 removed outlier: 5.620A pdb=" N SER g 2 " --> pdb=" O GLY g 70 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY g 70 " --> pdb=" O SER g 2 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N SER g 64 " --> pdb=" O TYR g 8 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'g' and resid 26 through 31 No H-bonds generated for sheet with id= 6 Processing sheet with id= 7, first strand: chain 'D' and resid 37 through 42 removed outlier: 4.283A pdb=" N GLY D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 54 through 60 removed outlier: 6.437A pdb=" N ILE D 85 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'O' and resid 37 through 42 removed outlier: 4.283A pdb=" N GLY O 46 " --> pdb=" O LEU O 42 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'O' and resid 54 through 60 removed outlier: 6.437A pdb=" N ILE O 85 " --> pdb=" O LEU O 97 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'h' and resid 37 through 42 removed outlier: 4.283A pdb=" N GLY h 46 " --> pdb=" O LEU h 42 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'h' and resid 54 through 60 removed outlier: 6.437A pdb=" N ILE h 85 " --> pdb=" O LEU h 97 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 7 through 10 removed outlier: 4.231A pdb=" N ASP E 7 " --> pdb=" O VAL E 25 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ASN E 57 " --> pdb=" O PHE E 41 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'Q' and resid 7 through 10 removed outlier: 4.231A pdb=" N ASP Q 7 " --> pdb=" O VAL Q 25 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ASN Q 57 " --> pdb=" O PHE Q 41 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'i' and resid 7 through 10 removed outlier: 4.231A pdb=" N ASP i 7 " --> pdb=" O VAL i 25 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ASN i 57 " --> pdb=" O PHE i 41 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'P' and resid 33 through 36 removed outlier: 3.774A pdb=" N GLY P 8 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA P 88 " --> pdb=" O CYS P 54 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN P 115 " --> pdb=" O LYS P 81 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR P 85 " --> pdb=" O VAL P 117 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'P' and resid 85 through 89 Processing sheet with id= 18, first strand: chain 'X' and resid 33 through 36 removed outlier: 3.774A pdb=" N GLY X 8 " --> pdb=" O GLY X 53 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA X 88 " --> pdb=" O CYS X 54 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN X 115 " --> pdb=" O LYS X 81 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR X 85 " --> pdb=" O VAL X 117 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'X' and resid 85 through 89 Processing sheet with id= 20, first strand: chain 'p' and resid 33 through 36 removed outlier: 3.774A pdb=" N GLY p 8 " --> pdb=" O GLY p 53 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA p 88 " --> pdb=" O CYS p 54 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN p 115 " --> pdb=" O LYS p 81 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR p 85 " --> pdb=" O VAL p 117 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'p' and resid 85 through 89 Processing sheet with id= 22, first strand: chain '1' and resid 165 through 169 removed outlier: 3.647A pdb=" N THR 1 173 " --> pdb=" O ASP 1 168 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain '1' and resid 276 through 280 Processing sheet with id= 24, first strand: chain '2' and resid 165 through 169 removed outlier: 3.840A pdb=" N THR 2 173 " --> pdb=" O ASP 2 168 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain '2' and resid 276 through 280 Processing sheet with id= 26, first strand: chain '3' and resid 165 through 169 Processing sheet with id= 27, first strand: chain '3' and resid 276 through 280 Processing sheet with id= 28, first strand: chain '5' and resid 165 through 169 removed outlier: 3.541A pdb=" N ASP 5 168 " --> pdb=" O THR 5 173 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR 5 173 " --> pdb=" O ASP 5 168 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain '5' and resid 276 through 280 Processing sheet with id= 30, first strand: chain '6' and resid 165 through 169 removed outlier: 3.609A pdb=" N LEU 6 166 " --> pdb=" O ARG 6 175 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR 6 173 " --> pdb=" O ASP 6 168 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain '6' and resid 276 through 280 Processing sheet with id= 32, first strand: chain 'Y' and resid 165 through 169 removed outlier: 3.646A pdb=" N THR Y 173 " --> pdb=" O ASP Y 168 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Y' and resid 276 through 280 Processing sheet with id= 34, first strand: chain 'Z' and resid 165 through 169 removed outlier: 3.840A pdb=" N THR Z 173 " --> pdb=" O ASP Z 168 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'Z' and resid 276 through 280 Processing sheet with id= 36, first strand: chain 'a' and resid 165 through 169 Processing sheet with id= 37, first strand: chain 'a' and resid 276 through 280 Processing sheet with id= 38, first strand: chain 'c' and resid 165 through 169 removed outlier: 3.542A pdb=" N ASP c 168 " --> pdb=" O THR c 173 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR c 173 " --> pdb=" O ASP c 168 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'c' and resid 276 through 280 Processing sheet with id= 40, first strand: chain 'd' and resid 165 through 169 removed outlier: 3.609A pdb=" N LEU d 166 " --> pdb=" O ARG d 175 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR d 173 " --> pdb=" O ASP d 168 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'd' and resid 276 through 280 Processing sheet with id= 42, first strand: chain 'q' and resid 165 through 169 removed outlier: 3.647A pdb=" N THR q 173 " --> pdb=" O ASP q 168 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'q' and resid 276 through 280 Processing sheet with id= 44, first strand: chain 'r' and resid 165 through 169 removed outlier: 3.840A pdb=" N THR r 173 " --> pdb=" O ASP r 168 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'r' and resid 276 through 280 Processing sheet with id= 46, first strand: chain 's' and resid 165 through 169 Processing sheet with id= 47, first strand: chain 's' and resid 276 through 280 Processing sheet with id= 48, first strand: chain 'u' and resid 165 through 169 removed outlier: 3.541A pdb=" N ASP u 168 " --> pdb=" O THR u 173 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR u 173 " --> pdb=" O ASP u 168 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'u' and resid 276 through 280 Processing sheet with id= 50, first strand: chain 'v' and resid 165 through 169 removed outlier: 3.608A pdb=" N LEU v 166 " --> pdb=" O ARG v 175 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR v 173 " --> pdb=" O ASP v 168 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'v' and resid 276 through 280 Processing sheet with id= 52, first strand: chain '4' and resid 276 through 280 Processing sheet with id= 53, first strand: chain 'b' and resid 276 through 280 Processing sheet with id= 54, first strand: chain 't' and resid 276 through 280 6006 hydrogen bonds defined for protein. 18000 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: 56.96 Time building geometry restraints manager: 53.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.41: 62915 1.41 - 1.63: 86440 1.63 - 1.84: 549 1.84 - 2.06: 1188 2.06 - 2.27: 1296 Bond restraints: 152388 Sorted by residual: bond pdb=" C12 PQN G2001 " pdb=" C13 PQN G2001 " ideal model delta sigma weight residual 1.334 1.528 -0.194 2.00e-02 2.50e+03 9.43e+01 bond pdb=" C12 PQN A2001 " pdb=" C13 PQN A2001 " ideal model delta sigma weight residual 1.334 1.528 -0.194 2.00e-02 2.50e+03 9.38e+01 bond pdb=" C12 PQN e2001 " pdb=" C13 PQN e2001 " ideal model delta sigma weight residual 1.334 1.528 -0.194 2.00e-02 2.50e+03 9.38e+01 bond pdb=" C12 PQN B2002 " pdb=" C13 PQN B2002 " ideal model delta sigma weight residual 1.334 1.526 -0.192 2.00e-02 2.50e+03 9.25e+01 bond pdb=" C12 PQN H2002 " pdb=" C13 PQN H2002 " ideal model delta sigma weight residual 1.334 1.526 -0.192 2.00e-02 2.50e+03 9.25e+01 ... (remaining 152383 not shown) Histogram of bond angle deviations from ideal: 73.07 - 94.16: 2487 94.16 - 115.25: 97712 115.25 - 136.34: 114751 136.34 - 157.43: 618 157.43 - 178.52: 1188 Bond angle restraints: 216756 Sorted by residual: angle pdb=" N VAL L 5 " pdb=" CA VAL L 5 " pdb=" C VAL L 5 " ideal model delta sigma weight residual 110.72 117.84 -7.12 1.01e+00 9.80e-01 4.97e+01 angle pdb=" N VAL n 5 " pdb=" CA VAL n 5 " pdb=" C VAL n 5 " ideal model delta sigma weight residual 110.72 117.84 -7.12 1.01e+00 9.80e-01 4.97e+01 angle pdb=" N VAL V 5 " pdb=" CA VAL V 5 " pdb=" C VAL V 5 " ideal model delta sigma weight residual 110.72 117.84 -7.12 1.01e+00 9.80e-01 4.97e+01 angle pdb=" N VAL 1 282 " pdb=" CA VAL 1 282 " pdb=" C VAL 1 282 " ideal model delta sigma weight residual 112.12 107.37 4.75 8.40e-01 1.42e+00 3.19e+01 angle pdb=" N VAL Y 282 " pdb=" CA VAL Y 282 " pdb=" C VAL Y 282 " ideal model delta sigma weight residual 112.12 107.39 4.73 8.40e-01 1.42e+00 3.18e+01 ... (remaining 216751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.45: 63526 25.45 - 50.90: 5472 50.90 - 76.35: 1424 76.35 - 101.80: 156 101.80 - 127.26: 78 Dihedral angle restraints: 70656 sinusoidal: 32706 harmonic: 37950 Sorted by residual: dihedral pdb=" CA ASP s 288 " pdb=" C ASP s 288 " pdb=" N THR s 289 " pdb=" CA THR s 289 " ideal model delta harmonic sigma weight residual -180.00 -158.32 -21.68 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ASP 3 288 " pdb=" C ASP 3 288 " pdb=" N THR 3 289 " pdb=" CA THR 3 289 " ideal model delta harmonic sigma weight residual -180.00 -158.34 -21.66 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ASP a 288 " pdb=" C ASP a 288 " pdb=" N THR a 289 " pdb=" CA THR a 289 " ideal model delta harmonic sigma weight residual 180.00 -158.34 -21.66 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 70653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.306: 18717 0.306 - 0.613: 30 0.613 - 0.919: 0 0.919 - 1.226: 0 1.226 - 1.532: 3 Chirality restraints: 18750 Sorted by residual: chirality pdb=" CBD CLA A1011 " pdb=" CAD CLA A1011 " pdb=" CGD CLA A1011 " pdb=" CHA CLA A1011 " both_signs ideal model delta sigma weight residual False 2.67 1.14 1.53 2.00e-01 2.50e+01 5.87e+01 chirality pdb=" CBD CLA e1011 " pdb=" CAD CLA e1011 " pdb=" CGD CLA e1011 " pdb=" CHA CLA e1011 " both_signs ideal model delta sigma weight residual False 2.67 1.14 1.53 2.00e-01 2.50e+01 5.87e+01 chirality pdb=" CBD CLA G1011 " pdb=" CAD CLA G1011 " pdb=" CGD CLA G1011 " pdb=" CHA CLA G1011 " both_signs ideal model delta sigma weight residual False 2.67 1.14 1.53 2.00e-01 2.50e+01 5.85e+01 ... (remaining 18747 not shown) Planarity restraints: 28482 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 PQN B2002 " -0.105 2.00e-02 2.50e+03 2.23e-01 6.23e+02 pdb=" C12 PQN B2002 " 0.276 2.00e-02 2.50e+03 pdb=" C13 PQN B2002 " -0.368 2.00e-02 2.50e+03 pdb=" C14 PQN B2002 " 0.158 2.00e-02 2.50e+03 pdb=" C15 PQN B2002 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 PQN H2002 " 0.104 2.00e-02 2.50e+03 2.23e-01 6.23e+02 pdb=" C12 PQN H2002 " -0.276 2.00e-02 2.50e+03 pdb=" C13 PQN H2002 " 0.368 2.00e-02 2.50e+03 pdb=" C14 PQN H2002 " -0.158 2.00e-02 2.50e+03 pdb=" C15 PQN H2002 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 PQN f2002 " 0.105 2.00e-02 2.50e+03 2.23e-01 6.22e+02 pdb=" C12 PQN f2002 " -0.276 2.00e-02 2.50e+03 pdb=" C13 PQN f2002 " 0.368 2.00e-02 2.50e+03 pdb=" C14 PQN f2002 " -0.158 2.00e-02 2.50e+03 pdb=" C15 PQN f2002 " -0.039 2.00e-02 2.50e+03 ... (remaining 28479 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 13358 2.74 - 3.28: 124049 3.28 - 3.82: 281542 3.82 - 4.36: 333937 4.36 - 4.90: 555061 Nonbonded interactions: 1307947 Sorted by model distance: nonbonded pdb=" OH TYR S 33 " pdb=" OH TYR W 28 " model vdw 2.205 2.440 nonbonded pdb=" OH TYR I 33 " pdb=" OH TYR M 28 " model vdw 2.205 2.440 nonbonded pdb=" OH TYR k 33 " pdb=" OH TYR o 28 " model vdw 2.205 2.440 nonbonded pdb=" OH TYR f 670 " pdb=" OBD CLA f1023 " model vdw 2.256 2.440 nonbonded pdb=" OH TYR H 670 " pdb=" OBD CLA H1023 " model vdw 2.257 2.440 ... (remaining 1307942 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 '1' and (resid 1 through 339 or resid 501 through 524 or (resid 822 and ( \ name C1 or name C2 or name C23 or name C24 or name C3 or name C4 or name C44 or \ name C45 or name C46 or name C5 or name C6 or name C7 or name C8 or name O10 or \ name O2 or name O3 or name O4 or name O47 or name O48 or name O49 or name O5 or \ name O6 or name O7 or name O8 or name O9 or name S )))) selection = (chain '2' and (resid 1 through 339 or (resid 501 through 519 and (name NB or na \ me ND or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or \ name C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C4 \ A or name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or nam \ e CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or \ name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CM \ B or name CMC or name CMD or name NA or name NC or name O1A or name O1D or name \ O2A or name O2D or name OBD or name MG )) or resid 521 through 524 or (resid 822 \ and (name C1 or name C2 or name C23 or name C24 or name C3 or name C4 or name C \ 44 or name C45 or name C46 or name C5 or name C6 or name C7 or name C8 or name O \ 10 or name O2 or name O3 or name O4 or name O47 or name O48 or name O49 or name \ O5 or name O6 or name O7 or name O8 or name O9 or name S )))) selection = (chain '3' and (resid 1 through 339 or (resid 501 through 519 and (name NB or na \ me ND or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or \ name C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C4 \ A or name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or nam \ e CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or \ name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CM \ B or name CMC or name CMD or name NA or name NC or name O1A or name O1D or name \ O2A or name O2D or name OBD or name MG )) or resid 521 through 524 or (resid 822 \ and (name C1 or name C2 or name C23 or name C24 or name C3 or name C4 or name C \ 44 or name C45 or name C46 or name C5 or name C6 or name C7 or name C8 or name O \ 10 or name O2 or name O3 or name O4 or name O47 or name O48 or name O49 or name \ O5 or name O6 or name O7 or name O8 or name O9 or name S )))) selection = chain '4' selection = (chain '5' and (resid 1 through 339 or (resid 501 through 519 and (name NB or na \ me ND or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or \ name C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C4 \ A or name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or nam \ e CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or \ name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CM \ B or name CMC or name CMD or name NA or name NC or name O1A or name O1D or name \ O2A or name O2D or name OBD or name MG )) or resid 521 through 822)) selection = (chain '6' and (resid 1 through 339 or (resid 501 through 519 and (name NB or na \ me ND or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or \ name C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C4 \ A or name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or nam \ e CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or \ name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CM \ B or name CMC or name CMD or name NA or name NC or name O1A or name O1D or name \ O2A or name O2D or name OBD or name MG )) or resid 521 through 822)) selection = (chain 'Y' and (resid 1 through 339 or resid 501 through 524 or (resid 822 and ( \ name C1 or name C2 or name C23 or name C24 or name C3 or name C4 or name C44 or \ name C45 or name C46 or name C5 or name C6 or name C7 or name C8 or name O10 or \ name O2 or name O3 or name O4 or name O47 or name O48 or name O49 or name O5 or \ name O6 or name O7 or name O8 or name O9 or name S )))) selection = (chain 'Z' and (resid 1 through 339 or (resid 501 through 519 and (name NB or na \ me ND or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or \ name C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C4 \ A or name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or nam \ e CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or \ name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CM \ B or name CMC or name CMD or name NA or name NC or name O1A or name O1D or name \ O2A or name O2D or name OBD or name MG )) or resid 521 through 524 or (resid 822 \ and (name C1 or name C2 or name C23 or name C24 or name C3 or name C4 or name C \ 44 or name C45 or name C46 or name C5 or name C6 or name C7 or name C8 or name O \ 10 or name O2 or name O3 or name O4 or name O47 or name O48 or name O49 or name \ O5 or name O6 or name O7 or name O8 or name O9 or name S )))) selection = (chain 'a' and (resid 1 through 339 or (resid 501 through 519 and (name NB or na \ me ND or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or \ name C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C4 \ A or name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or nam \ e CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or \ name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CM \ B or name CMC or name CMD or name NA or name NC or name O1A or name O1D or name \ O2A or name O2D or name OBD or name MG )) or resid 521 through 524 or (resid 822 \ and (name C1 or name C2 or name C23 or name C24 or name C3 or name C4 or name C \ 44 or name C45 or name C46 or name C5 or name C6 or name C7 or name C8 or name O \ 10 or name O2 or name O3 or name O4 or name O47 or name O48 or name O49 or name \ O5 or name O6 or name O7 or name O8 or name O9 or name S )))) selection = chain 'b' selection = (chain 'c' and (resid 1 through 339 or (resid 501 through 519 and (name NB or na \ me ND or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or \ name C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C4 \ A or name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or nam \ e CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or \ name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CM \ B or name CMC or name CMD or name NA or name NC or name O1A or name O1D or name \ O2A or name O2D or name OBD or name MG )) or resid 521 through 822)) selection = (chain 'd' and (resid 1 through 339 or (resid 501 through 519 and (name NB or na \ me ND or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or \ name C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C4 \ A or name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or nam \ e CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or \ name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CM \ B or name CMC or name CMD or name NA or name NC or name O1A or name O1D or name \ O2A or name O2D or name OBD or name MG )) or resid 521 through 822)) selection = (chain 'q' and (resid 1 through 339 or resid 501 through 524 or (resid 822 and ( \ name C1 or name C2 or name C23 or name C24 or name C3 or name C4 or name C44 or \ name C45 or name C46 or name C5 or name C6 or name C7 or name C8 or name O10 or \ name O2 or name O3 or name O4 or name O47 or name O48 or name O49 or name O5 or \ name O6 or name O7 or name O8 or name O9 or name S )))) selection = (chain 'r' and (resid 1 through 339 or (resid 501 through 519 and (name NB or na \ me ND or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or \ name C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C4 \ A or name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or nam \ e CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or \ name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CM \ B or name CMC or name CMD or name NA or name NC or name O1A or name O1D or name \ O2A or name O2D or name OBD or name MG )) or resid 521 through 524 or (resid 822 \ and (name C1 or name C2 or name C23 or name C24 or name C3 or name C4 or name C \ 44 or name C45 or name C46 or name C5 or name C6 or name C7 or name C8 or name O \ 10 or name O2 or name O3 or name O4 or name O47 or name O48 or name O49 or name \ O5 or name O6 or name O7 or name O8 or name O9 or name S )))) selection = (chain 's' and (resid 1 through 339 or (resid 501 through 519 and (name NB or na \ me ND or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or \ name C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C4 \ A or name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or nam \ e CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or \ name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CM \ B or name CMC or name CMD or name NA or name NC or name O1A or name O1D or name \ O2A or name O2D or name OBD or name MG )) or resid 521 through 524 or (resid 822 \ and (name C1 or name C2 or name C23 or name C24 or name C3 or name C4 or name C \ 44 or name C45 or name C46 or name C5 or name C6 or name C7 or name C8 or name O \ 10 or name O2 or name O3 or name O4 or name O47 or name O48 or name O49 or name \ O5 or name O6 or name O7 or name O8 or name O9 or name S )))) selection = chain 't' selection = (chain 'u' and (resid 1 through 339 or (resid 501 through 519 and (name NB or na \ me ND or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or \ name C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C4 \ A or name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or nam \ e CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or \ name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CM \ B or name CMC or name CMD or name NA or name NC or name O1A or name O1D or name \ O2A or name O2D or name OBD or name MG )) or resid 521 through 822)) selection = (chain 'v' and (resid 1 through 339 or (resid 501 through 519 and (name NB or na \ me ND or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or \ name C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C4 \ A or name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or nam \ e CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or \ name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CM \ B or name CMC or name CMD or name NA or name NC or name O1A or name O1D or name \ O2A or name O2D or name OBD or name MG )) or resid 521 through 822)) } ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'e' } ncs_group { reference = chain 'B' selection = chain 'H' selection = chain 'f' } ncs_group { reference = chain 'C' selection = chain 'N' selection = chain 'g' } ncs_group { reference = chain 'D' selection = chain 'O' selection = chain 'h' } ncs_group { reference = chain 'E' selection = chain 'Q' selection = chain 'i' } ncs_group { reference = chain 'F' selection = chain 'R' selection = chain 'j' } ncs_group { reference = chain 'I' selection = chain 'S' selection = chain 'k' } ncs_group { reference = chain 'J' selection = chain 'T' selection = chain 'l' } ncs_group { reference = chain 'K' selection = chain 'U' selection = chain 'm' } ncs_group { reference = chain 'L' selection = chain 'V' selection = chain 'n' } ncs_group { reference = chain 'M' selection = chain 'W' selection = chain 'o' } ncs_group { reference = chain 'P' selection = chain 'X' selection = chain 'p' } 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: 5.520 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: 0.120 Extract box with map and model: 28.070 Check model and map are aligned: 1.620 Set scattering table: 1.030 Process input model: 332.670 Find NCS groups from input model: 8.290 Set up NCS constraints: 2.550 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 382.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 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 : 0.010 0.194 152388 Z= 0.577 Angle : 1.305 15.596 216756 Z= 0.533 Chirality : 0.064 1.532 18750 Planarity : 0.009 0.223 28482 Dihedral : 19.920 127.255 46527 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.03 % Allowed : 4.52 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.02 % 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: -2.65 (0.06), residues: 13287 helix: -1.47 (0.05), residues: 7602 sheet: -2.77 (0.17), residues: 681 loop : -1.82 (0.08), residues: 5004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP b 163 HIS 0.011 0.002 HIS e 405 PHE 0.045 0.003 PHE f 718 TYR 0.027 0.002 TYR G 704 ARG 0.008 0.001 ARG R 159 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26574 Ramachandran restraints generated. 13287 Oldfield, 0 Emsley, 13287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26574 Ramachandran restraints generated. 13287 Oldfield, 0 Emsley, 13287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2501 residues out of total 10437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2498 time to evaluate : 9.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 HIS cc_start: 0.7417 (m90) cc_final: 0.7014 (m170) REVERT: B 277 HIS cc_start: 0.7490 (m90) cc_final: 0.7180 (m-70) REVERT: B 534 LEU cc_start: 0.9041 (mt) cc_final: 0.8821 (mt) REVERT: B 617 MET cc_start: 0.8756 (tpp) cc_final: 0.8528 (tpp) REVERT: L 96 TYR cc_start: 0.9142 (t80) cc_final: 0.8682 (t80) REVERT: P 66 TRP cc_start: 0.6696 (m100) cc_final: 0.6431 (m100) REVERT: 2 259 PHE cc_start: 0.6355 (m-80) cc_final: 0.5208 (m-80) REVERT: 3 67 LEU cc_start: 0.5861 (mt) cc_final: 0.5344 (mp) REVERT: 3 210 VAL cc_start: 0.7933 (t) cc_final: 0.7728 (t) REVERT: 4 11 TYR cc_start: 0.4757 (m-80) cc_final: 0.4217 (m-80) REVERT: 5 46 THR cc_start: 0.6556 (m) cc_final: 0.6126 (m) REVERT: G 610 MET cc_start: 0.9160 (tmm) cc_final: 0.8857 (tmm) REVERT: H 277 HIS cc_start: 0.7279 (m90) cc_final: 0.6925 (m-70) REVERT: H 441 ASP cc_start: 0.8164 (m-30) cc_final: 0.7868 (m-30) REVERT: X 66 TRP cc_start: 0.6964 (m100) cc_final: 0.6700 (m100) REVERT: Z 151 VAL cc_start: 0.7779 (t) cc_final: 0.7449 (p) REVERT: Z 279 LYS cc_start: 0.7995 (mttm) cc_final: 0.7782 (mtpt) REVERT: a 67 LEU cc_start: 0.5240 (mt) cc_final: 0.4721 (mp) REVERT: b 47 LEU cc_start: 0.7005 (mt) cc_final: 0.6770 (mp) REVERT: b 202 ASP cc_start: 0.1268 (m-30) cc_final: 0.0965 (m-30) REVERT: c 4 TYR cc_start: 0.0839 (m-80) cc_final: 0.0601 (m-80) REVERT: c 224 VAL cc_start: 0.2180 (t) cc_final: 0.1909 (t) REVERT: c 297 HIS cc_start: 0.1373 (m-70) cc_final: 0.1165 (m-70) REVERT: f 277 HIS cc_start: 0.7433 (m90) cc_final: 0.7212 (m-70) REVERT: f 278 LEU cc_start: 0.8666 (tp) cc_final: 0.8431 (tp) REVERT: f 534 LEU cc_start: 0.8888 (mt) cc_final: 0.8640 (mt) REVERT: j 116 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7258 (mt-10) REVERT: n 96 TYR cc_start: 0.9171 (t80) cc_final: 0.8938 (t80) REVERT: p 66 TRP cc_start: 0.6895 (m100) cc_final: 0.6622 (m100) REVERT: u 46 THR cc_start: 0.6432 (m) cc_final: 0.5978 (m) REVERT: u 320 TRP cc_start: 0.5843 (t-100) cc_final: 0.5409 (t-100) outliers start: 3 outliers final: 3 residues processed: 2501 average time/residue: 1.3109 time to fit residues: 5685.2757 Evaluate side-chains 1150 residues out of total 10437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1147 time to evaluate : 8.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain f residue 443 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1308 random chunks: chunk 1104 optimal weight: 5.9990 chunk 991 optimal weight: 0.9990 chunk 550 optimal weight: 2.9990 chunk 338 optimal weight: 8.9990 chunk 668 optimal weight: 5.9990 chunk 529 optimal weight: 0.9990 chunk 1025 optimal weight: 0.7980 chunk 396 optimal weight: 20.0000 chunk 623 optimal weight: 6.9990 chunk 763 optimal weight: 20.0000 chunk 1187 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 216 GLN A 224 ASN A 239 ASN A 612 ASN B 34 HIS B 218 HIS B 452 GLN B 603 GLN B 610 ASN B 636 ASN D 71 GLN F 48 GLN ** P 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 57 GLN ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 263 ASN ** 6 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 69 HIS ** 6 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 ASN G 216 GLN G 239 ASN G 612 ASN H 34 HIS H 218 HIS H 452 GLN H 603 GLN H 610 ASN O 71 GLN R 48 GLN U 80 ASN Y 57 GLN ** Z 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 57 GLN ** b 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 263 ASN ** d 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 19 ASN e 216 GLN e 612 ASN f 34 HIS f 218 HIS f 452 GLN f 603 GLN f 610 ASN h 71 GLN m 26 ASN q 57 GLN ** r 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 199 ASN s 263 ASN t 57 GLN ** t 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 191 GLN t 263 ASN ** t 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 69 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 152388 Z= 0.258 Angle : 0.664 10.265 216756 Z= 0.296 Chirality : 0.044 0.909 18750 Planarity : 0.005 0.059 28482 Dihedral : 19.523 117.753 25014 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.56 % Favored : 97.42 % Rotamer: Outliers : 2.64 % Allowed : 11.49 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.02 % 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 (0.07), residues: 13287 helix: 0.12 (0.05), residues: 7767 sheet: -2.43 (0.19), residues: 654 loop : -1.33 (0.08), residues: 4866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP Z 14 HIS 0.028 0.002 HIS t 144 PHE 0.040 0.002 PHE 2 294 TYR 0.019 0.001 TYR b 258 ARG 0.007 0.001 ARG L 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26574 Ramachandran restraints generated. 13287 Oldfield, 0 Emsley, 13287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26574 Ramachandran restraints generated. 13287 Oldfield, 0 Emsley, 13287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1564 residues out of total 10437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 1288 time to evaluate : 9.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 111 ASP cc_start: 0.7708 (p0) cc_final: 0.7446 (p0) REVERT: L 96 TYR cc_start: 0.9274 (t80) cc_final: 0.8981 (t80) REVERT: P 66 TRP cc_start: 0.7112 (m100) cc_final: 0.6783 (m100) REVERT: 3 136 LYS cc_start: 0.7102 (ttpp) cc_final: 0.6890 (tttm) REVERT: 3 263 ASN cc_start: 0.6367 (t0) cc_final: 0.6069 (t0) REVERT: 3 332 ARG cc_start: 0.5207 (tmt170) cc_final: 0.4107 (tpt170) REVERT: 5 174 VAL cc_start: 0.4396 (OUTLIER) cc_final: 0.4161 (p) REVERT: 5 263 ASN cc_start: 0.4008 (t0) cc_final: 0.3755 (t0) REVERT: G 310 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8532 (mt) REVERT: G 610 MET cc_start: 0.9254 (tmm) cc_final: 0.8916 (tmm) REVERT: H 574 ASP cc_start: 0.8052 (m-30) cc_final: 0.7841 (m-30) REVERT: Q 15 GLU cc_start: 0.7956 (pm20) cc_final: 0.7565 (pm20) REVERT: V 28 ARG cc_start: 0.7895 (mtm-85) cc_final: 0.7579 (mtm-85) REVERT: V 153 GLN cc_start: 0.7946 (mt0) cc_final: 0.7743 (mt0) REVERT: X 66 TRP cc_start: 0.7240 (m100) cc_final: 0.6855 (m100) REVERT: Y 320 TRP cc_start: 0.5847 (OUTLIER) cc_final: 0.5443 (t-100) REVERT: Z 279 LYS cc_start: 0.7967 (mttm) cc_final: 0.7602 (mtpt) REVERT: Z 320 TRP cc_start: 0.6939 (OUTLIER) cc_final: 0.6581 (t-100) REVERT: a 103 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6356 (mm) REVERT: b 202 ASP cc_start: 0.1423 (m-30) cc_final: 0.1202 (m-30) REVERT: c 4 TYR cc_start: 0.0843 (m-80) cc_final: 0.0363 (m-80) REVERT: c 297 HIS cc_start: 0.1213 (m-70) cc_final: 0.0987 (m-70) REVERT: d 13 TRP cc_start: 0.3634 (p90) cc_final: 0.3096 (p90) REVERT: f 355 MET cc_start: 0.8349 (mtm) cc_final: 0.8028 (ptp) REVERT: f 574 ASP cc_start: 0.8025 (m-30) cc_final: 0.7718 (m-30) REVERT: h 73 ARG cc_start: 0.7521 (ttm-80) cc_final: 0.7229 (ttm-80) REVERT: j 111 ASP cc_start: 0.7814 (p0) cc_final: 0.7503 (p0) REVERT: n 96 TYR cc_start: 0.9307 (t80) cc_final: 0.9068 (t80) REVERT: p 66 TRP cc_start: 0.7065 (m100) cc_final: 0.6611 (m100) REVERT: p 139 VAL cc_start: 0.7831 (m) cc_final: 0.7235 (m) REVERT: q 334 GLU cc_start: 0.4572 (tt0) cc_final: 0.4117 (tm-30) REVERT: s 163 TRP cc_start: 0.4476 (m100) cc_final: 0.4222 (m100) REVERT: v 215 ILE cc_start: 0.4765 (pt) cc_final: 0.4429 (mt) outliers start: 276 outliers final: 158 residues processed: 1480 average time/residue: 1.2878 time to fit residues: 3320.4754 Evaluate side-chains 1141 residues out of total 10437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 978 time to evaluate : 9.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain M residue 3 ASP Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 150 ASP Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain 1 residue 67 LEU Chi-restraints excluded: chain 1 residue 84 THR Chi-restraints excluded: chain 1 residue 103 LEU Chi-restraints excluded: chain 1 residue 148 PHE Chi-restraints excluded: chain 1 residue 183 ASN Chi-restraints excluded: chain 1 residue 196 SER Chi-restraints excluded: chain 1 residue 270 GLU Chi-restraints excluded: chain 2 residue 3 THR Chi-restraints excluded: chain 2 residue 73 LEU Chi-restraints excluded: chain 2 residue 79 ASP Chi-restraints excluded: chain 2 residue 212 VAL Chi-restraints excluded: chain 2 residue 251 LEU Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 315 LEU Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 174 VAL Chi-restraints excluded: chain 3 residue 239 GLU Chi-restraints excluded: chain 3 residue 289 THR Chi-restraints excluded: chain 4 residue 3 THR Chi-restraints excluded: chain 4 residue 9 VAL Chi-restraints excluded: chain 4 residue 85 ASP Chi-restraints excluded: chain 4 residue 178 THR Chi-restraints excluded: chain 4 residue 202 ASP Chi-restraints excluded: chain 4 residue 290 VAL Chi-restraints excluded: chain 5 residue 40 PHE Chi-restraints excluded: chain 5 residue 155 LEU Chi-restraints excluded: chain 5 residue 174 VAL Chi-restraints excluded: chain 6 residue 14 TRP Chi-restraints excluded: chain 6 residue 85 ASP Chi-restraints excluded: chain 6 residue 130 PHE Chi-restraints excluded: chain 6 residue 147 LEU Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain G residue 310 LEU Chi-restraints excluded: chain G residue 383 TYR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 297 ILE Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain H residue 478 LEU Chi-restraints excluded: chain N residue 9 ASP Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain V residue 114 ASN Chi-restraints excluded: chain V residue 158 ILE Chi-restraints excluded: chain W residue 3 ASP Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 158 THR Chi-restraints excluded: chain Y residue 14 TRP Chi-restraints excluded: chain Y residue 183 ASN Chi-restraints excluded: chain Y residue 196 SER Chi-restraints excluded: chain Y residue 320 TRP Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 73 LEU Chi-restraints excluded: chain Z residue 79 ASP Chi-restraints excluded: chain Z residue 133 ASN Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 314 CYS Chi-restraints excluded: chain Z residue 320 TRP Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 103 LEU Chi-restraints excluded: chain a residue 235 ILE Chi-restraints excluded: chain b residue 3 THR Chi-restraints excluded: chain b residue 9 VAL Chi-restraints excluded: chain b residue 85 ASP Chi-restraints excluded: chain b residue 178 THR Chi-restraints excluded: chain b residue 290 VAL Chi-restraints excluded: chain c residue 3 THR Chi-restraints excluded: chain c residue 89 LEU Chi-restraints excluded: chain c residue 155 LEU Chi-restraints excluded: chain c residue 173 THR Chi-restraints excluded: chain d residue 14 TRP Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 130 PHE Chi-restraints excluded: chain d residue 147 LEU Chi-restraints excluded: chain e residue 207 LEU Chi-restraints excluded: chain e residue 383 TYR Chi-restraints excluded: chain f residue 144 ILE Chi-restraints excluded: chain f residue 166 SER Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain f residue 246 THR Chi-restraints excluded: chain f residue 408 LEU Chi-restraints excluded: chain f residue 478 LEU Chi-restraints excluded: chain g residue 9 ASP Chi-restraints excluded: chain h residue 108 VAL Chi-restraints excluded: chain h residue 113 SER Chi-restraints excluded: chain i residue 69 VAL Chi-restraints excluded: chain j residue 46 THR Chi-restraints excluded: chain j residue 128 SER Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain n residue 114 ASN Chi-restraints excluded: chain o residue 3 ASP Chi-restraints excluded: chain p residue 14 THR Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 107 GLU Chi-restraints excluded: chain p residue 158 THR Chi-restraints excluded: chain q residue 14 TRP Chi-restraints excluded: chain q residue 84 THR Chi-restraints excluded: chain q residue 148 PHE Chi-restraints excluded: chain q residue 183 ASN Chi-restraints excluded: chain q residue 196 SER Chi-restraints excluded: chain r residue 3 THR Chi-restraints excluded: chain r residue 79 ASP Chi-restraints excluded: chain r residue 212 VAL Chi-restraints excluded: chain r residue 251 LEU Chi-restraints excluded: chain r residue 314 CYS Chi-restraints excluded: chain s residue 239 GLU Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 178 THR Chi-restraints excluded: chain t residue 191 GLN Chi-restraints excluded: chain t residue 290 VAL Chi-restraints excluded: chain u residue 40 PHE Chi-restraints excluded: chain u residue 155 LEU Chi-restraints excluded: chain u residue 174 VAL Chi-restraints excluded: chain u residue 282 VAL Chi-restraints excluded: chain u residue 289 THR Chi-restraints excluded: chain v residue 14 TRP Chi-restraints excluded: chain v residue 130 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1308 random chunks: chunk 660 optimal weight: 9.9990 chunk 368 optimal weight: 20.0000 chunk 988 optimal weight: 0.9980 chunk 808 optimal weight: 30.0000 chunk 327 optimal weight: 20.0000 chunk 1189 optimal weight: 20.0000 chunk 1285 optimal weight: 10.0000 chunk 1059 optimal weight: 1.9990 chunk 1180 optimal weight: 9.9990 chunk 405 optimal weight: 30.0000 chunk 954 optimal weight: 6.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 192 ASN A 294 ASN A 579 ASN B 636 ASN L 153 GLN P 91 GLN P 115 GLN 3 183 ASN 3 191 GLN ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 297 HIS ** 4 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 22 ASN 6 57 GLN ** 6 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 ASN G 294 ASN G 579 ASN H 114 ASN H 137 GLN H 636 ASN X 91 GLN ** Y 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 57 GLN ** Z 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 263 ASN a 183 ASN b 57 GLN ** b 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 137 GLN b 191 GLN ** b 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 297 HIS ** b 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 57 GLN e 19 ASN e 192 ASN ** e 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 294 ASN f 137 GLN g 16 GLN n 153 GLN p 58 ASN p 91 GLN q 57 GLN ** q 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 228 GLN s 183 ASN s 191 GLN ** s 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 137 GLN t 297 HIS ** t 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 69 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 152388 Z= 0.515 Angle : 0.834 11.248 216756 Z= 0.367 Chirality : 0.051 1.104 18750 Planarity : 0.006 0.068 28482 Dihedral : 19.772 119.324 25011 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.74 % Favored : 96.24 % Rotamer: Outliers : 3.97 % Allowed : 13.16 % Favored : 82.87 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.02 % 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: -0.57 (0.07), residues: 13287 helix: 0.30 (0.06), residues: 7794 sheet: -2.38 (0.18), residues: 690 loop : -1.03 (0.09), residues: 4803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP Z 14 HIS 0.048 0.002 HIS 4 144 PHE 0.033 0.003 PHE H 718 TYR 0.026 0.002 TYR d 48 ARG 0.015 0.001 ARG b 324 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26574 Ramachandran restraints generated. 13287 Oldfield, 0 Emsley, 13287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26574 Ramachandran restraints generated. 13287 Oldfield, 0 Emsley, 13287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1491 residues out of total 10437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 414 poor density : 1077 time to evaluate : 8.705 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 25 PHE cc_start: 0.8658 (m-80) cc_final: 0.8306 (m-10) REVERT: A 152 TYR cc_start: 0.8422 (m-80) cc_final: 0.8136 (m-80) REVERT: A 315 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8626 (mp) REVERT: A 547 HIS cc_start: 0.8736 (OUTLIER) cc_final: 0.8532 (m90) REVERT: A 680 TYR cc_start: 0.8898 (m-80) cc_final: 0.8572 (m-80) REVERT: B 520 HIS cc_start: 0.8768 (OUTLIER) cc_final: 0.8211 (m90) REVERT: F 111 ASP cc_start: 0.8209 (p0) cc_final: 0.7721 (p0) REVERT: L 28 ARG cc_start: 0.8178 (mtm-85) cc_final: 0.7728 (mtm-85) REVERT: 1 200 LEU cc_start: 0.6101 (OUTLIER) cc_final: 0.5695 (mp) REVERT: 1 307 HIS cc_start: 0.6868 (OUTLIER) cc_final: 0.4814 (m90) REVERT: 3 136 LYS cc_start: 0.7345 (ttpp) cc_final: 0.7102 (tttm) REVERT: 3 332 ARG cc_start: 0.5522 (tmt170) cc_final: 0.4618 (tpt170) REVERT: 4 175 ARG cc_start: 0.4860 (mtm180) cc_final: 0.4647 (ptt180) REVERT: 5 312 PHE cc_start: 0.6194 (t80) cc_final: 0.5690 (t80) REVERT: G 680 TYR cc_start: 0.8907 (m-80) cc_final: 0.8620 (m-80) REVERT: H 520 HIS cc_start: 0.8645 (OUTLIER) cc_final: 0.8085 (m90) REVERT: H 574 ASP cc_start: 0.8252 (m-30) cc_final: 0.7982 (m-30) REVERT: R 116 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7211 (mt-10) REVERT: V 88 ILE cc_start: 0.9371 (mt) cc_final: 0.9149 (mt) REVERT: Y 17 ASN cc_start: 0.5363 (m-40) cc_final: 0.4916 (m-40) REVERT: Y 200 LEU cc_start: 0.5943 (OUTLIER) cc_final: 0.5699 (mp) REVERT: Y 307 HIS cc_start: 0.6913 (OUTLIER) cc_final: 0.4907 (m90) REVERT: Z 320 TRP cc_start: 0.7251 (OUTLIER) cc_final: 0.6956 (t-100) REVERT: c 4 TYR cc_start: 0.0719 (m-80) cc_final: -0.0000 (m-10) REVERT: e 595 CYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8160 (m) REVERT: f 51 PHE cc_start: 0.8741 (m-80) cc_final: 0.8511 (m-10) REVERT: f 520 HIS cc_start: 0.8816 (OUTLIER) cc_final: 0.8286 (m90) REVERT: f 574 ASP cc_start: 0.8187 (m-30) cc_final: 0.7913 (m-30) REVERT: q 334 GLU cc_start: 0.4527 (tt0) cc_final: 0.4311 (tm-30) REVERT: r 90 PHE cc_start: 0.7444 (t80) cc_final: 0.7192 (t80) REVERT: v 215 ILE cc_start: 0.5096 (pt) cc_final: 0.4755 (mt) outliers start: 414 outliers final: 264 residues processed: 1391 average time/residue: 1.2443 time to fit residues: 3029.7045 Evaluate side-chains 1158 residues out of total 10437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 883 time to evaluate : 9.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain A residue 595 CYS Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 520 HIS Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 115 GLN Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain P residue 150 ASP Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain 1 residue 14 TRP Chi-restraints excluded: chain 1 residue 67 LEU Chi-restraints excluded: chain 1 residue 84 THR Chi-restraints excluded: chain 1 residue 103 LEU Chi-restraints excluded: chain 1 residue 148 PHE Chi-restraints excluded: chain 1 residue 183 ASN Chi-restraints excluded: chain 1 residue 190 TYR Chi-restraints excluded: chain 1 residue 196 SER Chi-restraints excluded: chain 1 residue 198 ASP Chi-restraints excluded: chain 1 residue 200 LEU Chi-restraints excluded: chain 1 residue 213 MET Chi-restraints excluded: chain 1 residue 307 HIS Chi-restraints excluded: chain 2 residue 3 THR Chi-restraints excluded: chain 2 residue 14 TRP Chi-restraints excluded: chain 2 residue 52 TRP Chi-restraints excluded: chain 2 residue 103 LEU Chi-restraints excluded: chain 2 residue 133 ASN Chi-restraints excluded: chain 2 residue 212 VAL Chi-restraints excluded: chain 2 residue 251 LEU Chi-restraints excluded: chain 2 residue 262 VAL Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 315 LEU Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 3 residue 174 VAL Chi-restraints excluded: chain 3 residue 289 THR Chi-restraints excluded: chain 3 residue 323 LEU Chi-restraints excluded: chain 4 residue 3 THR Chi-restraints excluded: chain 4 residue 9 VAL Chi-restraints excluded: chain 4 residue 64 LEU Chi-restraints excluded: chain 4 residue 85 ASP Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 178 THR Chi-restraints excluded: chain 4 residue 259 PHE Chi-restraints excluded: chain 4 residue 290 VAL Chi-restraints excluded: chain 5 residue 3 THR Chi-restraints excluded: chain 5 residue 40 PHE Chi-restraints excluded: chain 5 residue 155 LEU Chi-restraints excluded: chain 5 residue 269 VAL Chi-restraints excluded: chain 5 residue 290 VAL Chi-restraints excluded: chain 5 residue 294 PHE Chi-restraints excluded: chain 5 residue 320 TRP Chi-restraints excluded: chain 6 residue 14 TRP Chi-restraints excluded: chain 6 residue 130 PHE Chi-restraints excluded: chain 6 residue 147 LEU Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 209 SER Chi-restraints excluded: chain G residue 228 ASP Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 325 THR Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 383 TYR Chi-restraints excluded: chain G residue 547 HIS Chi-restraints excluded: chain G residue 595 CYS Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 478 LEU Chi-restraints excluded: chain H residue 482 ASP Chi-restraints excluded: chain H residue 512 ILE Chi-restraints excluded: chain H residue 520 HIS Chi-restraints excluded: chain H residue 535 VAL Chi-restraints excluded: chain N residue 9 ASP Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain O residue 134 THR Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 76 ASP Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain U residue 30 ILE Chi-restraints excluded: chain U residue 46 LEU Chi-restraints excluded: chain V residue 5 VAL Chi-restraints excluded: chain V residue 114 ASN Chi-restraints excluded: chain V residue 158 ILE Chi-restraints excluded: chain W residue 3 ASP Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 158 THR Chi-restraints excluded: chain Y residue 14 TRP Chi-restraints excluded: chain Y residue 148 PHE Chi-restraints excluded: chain Y residue 183 ASN Chi-restraints excluded: chain Y residue 196 SER Chi-restraints excluded: chain Y residue 200 LEU Chi-restraints excluded: chain Y residue 213 MET Chi-restraints excluded: chain Y residue 307 HIS Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain Z residue 103 LEU Chi-restraints excluded: chain Z residue 133 ASN Chi-restraints excluded: chain Z residue 190 TYR Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 251 LEU Chi-restraints excluded: chain Z residue 314 CYS Chi-restraints excluded: chain Z residue 315 LEU Chi-restraints excluded: chain Z residue 320 TRP Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 174 VAL Chi-restraints excluded: chain a residue 229 TRP Chi-restraints excluded: chain a residue 235 ILE Chi-restraints excluded: chain b residue 3 THR Chi-restraints excluded: chain b residue 9 VAL Chi-restraints excluded: chain b residue 64 LEU Chi-restraints excluded: chain b residue 85 ASP Chi-restraints excluded: chain b residue 131 ASP Chi-restraints excluded: chain b residue 178 THR Chi-restraints excluded: chain b residue 191 GLN Chi-restraints excluded: chain b residue 290 VAL Chi-restraints excluded: chain c residue 40 PHE Chi-restraints excluded: chain c residue 155 LEU Chi-restraints excluded: chain c residue 173 THR Chi-restraints excluded: chain c residue 210 VAL Chi-restraints excluded: chain d residue 14 TRP Chi-restraints excluded: chain d residue 38 ILE Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 130 PHE Chi-restraints excluded: chain d residue 147 LEU Chi-restraints excluded: chain e residue 62 THR Chi-restraints excluded: chain e residue 129 ASP Chi-restraints excluded: chain e residue 207 LEU Chi-restraints excluded: chain e residue 228 ASP Chi-restraints excluded: chain e residue 288 THR Chi-restraints excluded: chain e residue 358 THR Chi-restraints excluded: chain e residue 383 TYR Chi-restraints excluded: chain e residue 406 ILE Chi-restraints excluded: chain e residue 471 ASP Chi-restraints excluded: chain e residue 595 CYS Chi-restraints excluded: chain f residue 96 PHE Chi-restraints excluded: chain f residue 127 ILE Chi-restraints excluded: chain f residue 144 ILE Chi-restraints excluded: chain f residue 160 LYS Chi-restraints excluded: chain f residue 166 SER Chi-restraints excluded: chain f residue 199 ILE Chi-restraints excluded: chain f residue 222 LEU Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain f residue 246 THR Chi-restraints excluded: chain f residue 408 LEU Chi-restraints excluded: chain f residue 467 SER Chi-restraints excluded: chain f residue 478 LEU Chi-restraints excluded: chain f residue 482 ASP Chi-restraints excluded: chain f residue 512 ILE Chi-restraints excluded: chain f residue 520 HIS Chi-restraints excluded: chain f residue 535 VAL Chi-restraints excluded: chain f residue 540 ASP Chi-restraints excluded: chain g residue 9 ASP Chi-restraints excluded: chain g residue 29 VAL Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 108 VAL Chi-restraints excluded: chain h residue 113 SER Chi-restraints excluded: chain i residue 69 VAL Chi-restraints excluded: chain j residue 46 THR Chi-restraints excluded: chain j residue 76 ASP Chi-restraints excluded: chain j residue 128 SER Chi-restraints excluded: chain j residue 130 THR Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain l residue 14 LEU Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain n residue 114 ASN Chi-restraints excluded: chain o residue 3 ASP Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 116 THR Chi-restraints excluded: chain p residue 117 VAL Chi-restraints excluded: chain p residue 150 ASP Chi-restraints excluded: chain p residue 158 THR Chi-restraints excluded: chain q residue 14 TRP Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 84 THR Chi-restraints excluded: chain q residue 89 LEU Chi-restraints excluded: chain q residue 103 LEU Chi-restraints excluded: chain q residue 148 PHE Chi-restraints excluded: chain q residue 183 ASN Chi-restraints excluded: chain q residue 196 SER Chi-restraints excluded: chain q residue 199 ASN Chi-restraints excluded: chain r residue 3 THR Chi-restraints excluded: chain r residue 14 TRP Chi-restraints excluded: chain r residue 52 TRP Chi-restraints excluded: chain r residue 133 ASN Chi-restraints excluded: chain r residue 212 VAL Chi-restraints excluded: chain r residue 251 LEU Chi-restraints excluded: chain r residue 314 CYS Chi-restraints excluded: chain r residue 315 LEU Chi-restraints excluded: chain s residue 9 VAL Chi-restraints excluded: chain s residue 174 VAL Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 85 ASP Chi-restraints excluded: chain t residue 144 HIS Chi-restraints excluded: chain t residue 178 THR Chi-restraints excluded: chain t residue 259 PHE Chi-restraints excluded: chain t residue 290 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 40 PHE Chi-restraints excluded: chain u residue 155 LEU Chi-restraints excluded: chain u residue 210 VAL Chi-restraints excluded: chain u residue 269 VAL Chi-restraints excluded: chain u residue 282 VAL Chi-restraints excluded: chain u residue 320 TRP Chi-restraints excluded: chain v residue 14 TRP Chi-restraints excluded: chain v residue 61 GLU Chi-restraints excluded: chain v residue 126 LYS Chi-restraints excluded: chain v residue 130 PHE Chi-restraints excluded: chain v residue 147 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1308 random chunks: chunk 1175 optimal weight: 20.0000 chunk 894 optimal weight: 0.2980 chunk 617 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 567 optimal weight: 3.9990 chunk 799 optimal weight: 9.9990 chunk 1194 optimal weight: 0.5980 chunk 1264 optimal weight: 9.9990 chunk 623 optimal weight: 3.9990 chunk 1131 optimal weight: 5.9990 chunk 340 optimal weight: 40.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN F 104 GLN ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 263 ASN ** 6 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 137 GLN G 294 ASN V 153 GLN ** Y 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 34 GLN ** Z 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 62 GLN ** c 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 263 ASN ** d 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 361 HIS e 579 ASN f 636 ASN n 153 GLN n 166 HIS q 199 ASN s 199 ASN ** t 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 228 GLN ** v 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 69 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 152388 Z= 0.215 Angle : 0.604 10.472 216756 Z= 0.271 Chirality : 0.042 0.728 18750 Planarity : 0.005 0.047 28482 Dihedral : 18.636 114.315 25011 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.00 % Favored : 96.97 % Rotamer: Outliers : 2.86 % Allowed : 15.43 % Favored : 81.72 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.02 % 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: 0.04 (0.07), residues: 13287 helix: 0.87 (0.06), residues: 7806 sheet: -2.37 (0.19), residues: 654 loop : -0.91 (0.09), residues: 4827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP Z 14 HIS 0.032 0.001 HIS 4 144 PHE 0.031 0.002 PHE 2 294 TYR 0.031 0.001 TYR R 56 ARG 0.010 0.000 ARG q 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26574 Ramachandran restraints generated. 13287 Oldfield, 0 Emsley, 13287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26574 Ramachandran restraints generated. 13287 Oldfield, 0 Emsley, 13287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1414 residues out of total 10437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 1116 time to evaluate : 9.834 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 104 LEU cc_start: 0.8219 (tp) cc_final: 0.8016 (tp) REVERT: A 363 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8038 (mm-40) REVERT: B 51 PHE cc_start: 0.8570 (m-10) cc_final: 0.8331 (m-80) REVERT: B 361 ILE cc_start: 0.9050 (tt) cc_final: 0.8764 (tt) REVERT: F 111 ASP cc_start: 0.8080 (p0) cc_final: 0.7581 (p0) REVERT: K 50 GLN cc_start: 0.7092 (mm110) cc_final: 0.6690 (mp10) REVERT: 1 203 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.6409 (tp) REVERT: 3 136 LYS cc_start: 0.7225 (ttpp) cc_final: 0.6989 (tttm) REVERT: 3 332 ARG cc_start: 0.5392 (tmt170) cc_final: 0.4412 (tpt170) REVERT: 5 312 PHE cc_start: 0.6326 (t80) cc_final: 0.5747 (t80) REVERT: H 258 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7849 (mp) REVERT: H 574 ASP cc_start: 0.8139 (m-30) cc_final: 0.7888 (m-30) REVERT: R 116 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7217 (mt-10) REVERT: X 66 TRP cc_start: 0.7339 (m100) cc_final: 0.6913 (m100) REVERT: Y 203 LEU cc_start: 0.6303 (OUTLIER) cc_final: 0.6095 (tp) REVERT: Z 90 PHE cc_start: 0.7179 (t80) cc_final: 0.6817 (t80) REVERT: Z 207 HIS cc_start: 0.7274 (OUTLIER) cc_final: 0.6287 (m170) REVERT: a 67 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.5987 (tp) REVERT: c 4 TYR cc_start: 0.0895 (m-80) cc_final: 0.0467 (m-10) REVERT: c 312 PHE cc_start: 0.6406 (t80) cc_final: 0.5905 (t80) REVERT: d 61 GLU cc_start: 0.4746 (OUTLIER) cc_final: 0.4544 (mt-10) REVERT: e 310 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8741 (mt) REVERT: f 574 ASP cc_start: 0.7969 (m-30) cc_final: 0.7666 (m-30) REVERT: i 15 GLU cc_start: 0.8043 (pm20) cc_final: 0.7704 (pm20) REVERT: q 201 GLU cc_start: 0.6042 (mp0) cc_final: 0.5831 (mp0) REVERT: r 90 PHE cc_start: 0.7304 (t80) cc_final: 0.7047 (t80) REVERT: r 220 TRP cc_start: 0.6427 (OUTLIER) cc_final: 0.6050 (t-100) REVERT: s 67 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6338 (tp) REVERT: u 320 TRP cc_start: 0.6139 (t-100) cc_final: 0.5597 (t-100) REVERT: v 215 ILE cc_start: 0.4935 (pt) cc_final: 0.4561 (mt) outliers start: 298 outliers final: 199 residues processed: 1334 average time/residue: 1.2596 time to fit residues: 2948.1260 Evaluate side-chains 1123 residues out of total 10437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 915 time to evaluate : 9.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain M residue 3 ASP Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 150 ASP Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain 1 residue 103 LEU Chi-restraints excluded: chain 1 residue 148 PHE Chi-restraints excluded: chain 1 residue 155 LEU Chi-restraints excluded: chain 1 residue 183 ASN Chi-restraints excluded: chain 1 residue 196 SER Chi-restraints excluded: chain 1 residue 198 ASP Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain 1 residue 213 MET Chi-restraints excluded: chain 1 residue 270 GLU Chi-restraints excluded: chain 2 residue 22 ASN Chi-restraints excluded: chain 2 residue 52 TRP Chi-restraints excluded: chain 2 residue 212 VAL Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 315 LEU Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 3 residue 79 ASP Chi-restraints excluded: chain 3 residue 208 VAL Chi-restraints excluded: chain 3 residue 289 THR Chi-restraints excluded: chain 4 residue 64 LEU Chi-restraints excluded: chain 4 residue 85 ASP Chi-restraints excluded: chain 4 residue 131 ASP Chi-restraints excluded: chain 4 residue 144 HIS Chi-restraints excluded: chain 4 residue 178 THR Chi-restraints excluded: chain 4 residue 202 ASP Chi-restraints excluded: chain 4 residue 259 PHE Chi-restraints excluded: chain 4 residue 290 VAL Chi-restraints excluded: chain 5 residue 40 PHE Chi-restraints excluded: chain 5 residue 155 LEU Chi-restraints excluded: chain 6 residue 14 TRP Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 6 residue 126 LYS Chi-restraints excluded: chain 6 residue 130 PHE Chi-restraints excluded: chain 6 residue 147 LEU Chi-restraints excluded: chain 6 residue 282 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 209 SER Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 383 TYR Chi-restraints excluded: chain G residue 406 ILE Chi-restraints excluded: chain G residue 595 CYS Chi-restraints excluded: chain G residue 713 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain N residue 9 ASP Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 76 ASP Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain U residue 30 ILE Chi-restraints excluded: chain V residue 5 VAL Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain V residue 114 ASN Chi-restraints excluded: chain W residue 3 ASP Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 158 THR Chi-restraints excluded: chain Y residue 14 TRP Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 148 PHE Chi-restraints excluded: chain Y residue 183 ASN Chi-restraints excluded: chain Y residue 190 TYR Chi-restraints excluded: chain Y residue 196 SER Chi-restraints excluded: chain Y residue 198 ASP Chi-restraints excluded: chain Y residue 203 LEU Chi-restraints excluded: chain Y residue 213 MET Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain Z residue 79 ASP Chi-restraints excluded: chain Z residue 103 LEU Chi-restraints excluded: chain Z residue 207 HIS Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 251 LEU Chi-restraints excluded: chain Z residue 314 CYS Chi-restraints excluded: chain Z residue 315 LEU Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 174 VAL Chi-restraints excluded: chain a residue 229 TRP Chi-restraints excluded: chain a residue 235 ILE Chi-restraints excluded: chain b residue 64 LEU Chi-restraints excluded: chain b residue 85 ASP Chi-restraints excluded: chain b residue 131 ASP Chi-restraints excluded: chain b residue 178 THR Chi-restraints excluded: chain b residue 259 PHE Chi-restraints excluded: chain b residue 290 VAL Chi-restraints excluded: chain c residue 155 LEU Chi-restraints excluded: chain c residue 173 THR Chi-restraints excluded: chain d residue 14 TRP Chi-restraints excluded: chain d residue 38 ILE Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 56 ASP Chi-restraints excluded: chain d residue 61 GLU Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 130 PHE Chi-restraints excluded: chain d residue 147 LEU Chi-restraints excluded: chain e residue 129 ASP Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain e residue 310 LEU Chi-restraints excluded: chain e residue 383 TYR Chi-restraints excluded: chain e residue 471 ASP Chi-restraints excluded: chain f residue 96 PHE Chi-restraints excluded: chain f residue 144 ILE Chi-restraints excluded: chain f residue 246 THR Chi-restraints excluded: chain f residue 467 SER Chi-restraints excluded: chain f residue 478 LEU Chi-restraints excluded: chain f residue 512 ILE Chi-restraints excluded: chain g residue 9 ASP Chi-restraints excluded: chain g residue 29 VAL Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 108 VAL Chi-restraints excluded: chain h residue 113 SER Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain i residue 69 VAL Chi-restraints excluded: chain j residue 46 THR Chi-restraints excluded: chain j residue 128 SER Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain l residue 14 LEU Chi-restraints excluded: chain m residue 80 ASN Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain n residue 114 ASN Chi-restraints excluded: chain n residue 166 HIS Chi-restraints excluded: chain o residue 3 ASP Chi-restraints excluded: chain p residue 14 THR Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 150 ASP Chi-restraints excluded: chain p residue 158 THR Chi-restraints excluded: chain q residue 14 TRP Chi-restraints excluded: chain q residue 103 LEU Chi-restraints excluded: chain q residue 148 PHE Chi-restraints excluded: chain q residue 183 ASN Chi-restraints excluded: chain q residue 190 TYR Chi-restraints excluded: chain q residue 196 SER Chi-restraints excluded: chain q residue 198 ASP Chi-restraints excluded: chain q residue 213 MET Chi-restraints excluded: chain q residue 270 GLU Chi-restraints excluded: chain r residue 22 ASN Chi-restraints excluded: chain r residue 79 ASP Chi-restraints excluded: chain r residue 212 VAL Chi-restraints excluded: chain r residue 220 TRP Chi-restraints excluded: chain r residue 251 LEU Chi-restraints excluded: chain r residue 314 CYS Chi-restraints excluded: chain r residue 315 LEU Chi-restraints excluded: chain s residue 9 VAL Chi-restraints excluded: chain s residue 67 LEU Chi-restraints excluded: chain s residue 108 LEU Chi-restraints excluded: chain s residue 174 VAL Chi-restraints excluded: chain t residue 144 HIS Chi-restraints excluded: chain t residue 290 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 40 PHE Chi-restraints excluded: chain u residue 111 THR Chi-restraints excluded: chain u residue 155 LEU Chi-restraints excluded: chain u residue 174 VAL Chi-restraints excluded: chain u residue 282 VAL Chi-restraints excluded: chain u residue 289 THR Chi-restraints excluded: chain v residue 14 TRP Chi-restraints excluded: chain v residue 47 LEU Chi-restraints excluded: chain v residue 126 LYS Chi-restraints excluded: chain v residue 130 PHE Chi-restraints excluded: chain v residue 147 LEU Chi-restraints excluded: chain v residue 282 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1308 random chunks: chunk 1052 optimal weight: 9.9990 chunk 717 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 941 optimal weight: 3.9990 chunk 521 optimal weight: 8.9990 chunk 1078 optimal weight: 0.0570 chunk 873 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 645 optimal weight: 0.8980 chunk 1134 optimal weight: 10.0000 chunk 319 optimal weight: 40.0000 overall best weight: 4.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 114 ASN C 16 GLN L 153 GLN P 115 GLN ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 62 GLN H 137 GLN ** U 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 361 HIS f 114 ASN n 153 GLN ** t 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 69 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 152388 Z= 0.375 Angle : 0.709 12.534 216756 Z= 0.314 Chirality : 0.045 0.568 18750 Planarity : 0.005 0.053 28482 Dihedral : 18.708 117.083 25011 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.01 % Favored : 95.97 % Rotamer: Outliers : 3.77 % Allowed : 15.73 % Favored : 80.50 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.07), residues: 13287 helix: 0.78 (0.06), residues: 7857 sheet: -2.37 (0.18), residues: 660 loop : -0.82 (0.10), residues: 4770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP Z 14 HIS 0.033 0.002 HIS 4 144 PHE 0.030 0.002 PHE H 718 TYR 0.020 0.002 TYR 6 48 ARG 0.007 0.001 ARG 3 324 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26574 Ramachandran restraints generated. 13287 Oldfield, 0 Emsley, 13287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26574 Ramachandran restraints generated. 13287 Oldfield, 0 Emsley, 13287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1367 residues out of total 10437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 393 poor density : 974 time to evaluate : 9.825 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 51 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8970 (tp) REVERT: A 104 LEU cc_start: 0.8381 (tp) cc_final: 0.8140 (tp) REVERT: A 315 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8670 (mp) REVERT: A 680 TYR cc_start: 0.8826 (m-80) cc_final: 0.8479 (m-80) REVERT: B 520 HIS cc_start: 0.8677 (OUTLIER) cc_final: 0.8130 (m90) REVERT: B 568 CYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8522 (m) REVERT: K 50 GLN cc_start: 0.7388 (mm110) cc_final: 0.6873 (mp10) REVERT: M 26 GLU cc_start: 0.8128 (tp30) cc_final: 0.7828 (tp30) REVERT: 1 200 LEU cc_start: 0.6149 (OUTLIER) cc_final: 0.5777 (mp) REVERT: 1 203 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6565 (tp) REVERT: 1 307 HIS cc_start: 0.6886 (OUTLIER) cc_final: 0.6192 (m90) REVERT: 2 207 HIS cc_start: 0.7246 (OUTLIER) cc_final: 0.6436 (m170) REVERT: 2 326 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6626 (mpt) REVERT: 3 69 HIS cc_start: 0.5949 (OUTLIER) cc_final: 0.5159 (m-70) REVERT: 3 136 LYS cc_start: 0.7389 (ttpp) cc_final: 0.7146 (tttm) REVERT: 3 332 ARG cc_start: 0.5402 (tmt170) cc_final: 0.4457 (tpt170) REVERT: 4 14 TRP cc_start: 0.6716 (p-90) cc_final: 0.6460 (p-90) REVERT: 4 45 PHE cc_start: 0.0670 (OUTLIER) cc_final: -0.0234 (m-80) REVERT: 5 312 PHE cc_start: 0.6286 (t80) cc_final: 0.5803 (t80) REVERT: 6 67 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.6327 (mp) REVERT: G 13 LYS cc_start: 0.6705 (OUTLIER) cc_final: 0.6386 (tptt) REVERT: G 172 MET cc_start: 0.8245 (mmt) cc_final: 0.7870 (mmt) REVERT: G 310 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8870 (mt) REVERT: G 680 TYR cc_start: 0.8858 (m-80) cc_final: 0.8512 (m-80) REVERT: H 520 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.8090 (m90) REVERT: H 574 ASP cc_start: 0.8217 (m-30) cc_final: 0.7992 (m-30) REVERT: R 116 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7263 (mt-10) REVERT: V 28 ARG cc_start: 0.7857 (mtm-85) cc_final: 0.7497 (mtm-85) REVERT: Y 22 ASN cc_start: 0.4418 (m-40) cc_final: 0.4153 (m-40) REVERT: Y 307 HIS cc_start: 0.6862 (OUTLIER) cc_final: 0.4730 (m90) REVERT: Z 90 PHE cc_start: 0.7185 (t80) cc_final: 0.6877 (t80) REVERT: Z 207 HIS cc_start: 0.7367 (OUTLIER) cc_final: 0.6411 (m170) REVERT: c 4 TYR cc_start: 0.1018 (m-80) cc_final: 0.0638 (m-80) REVERT: c 312 PHE cc_start: 0.6348 (t80) cc_final: 0.5872 (t80) REVERT: e 25 PHE cc_start: 0.8681 (m-80) cc_final: 0.8416 (m-80) REVERT: e 51 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8921 (tp) REVERT: f 216 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7902 (pt) REVERT: f 226 PHE cc_start: 0.7452 (m-10) cc_final: 0.7162 (m-10) REVERT: f 520 HIS cc_start: 0.8799 (OUTLIER) cc_final: 0.8286 (m90) REVERT: f 568 CYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8578 (m) REVERT: f 574 ASP cc_start: 0.8113 (m-30) cc_final: 0.7823 (m-30) REVERT: i 15 GLU cc_start: 0.7998 (pm20) cc_final: 0.7688 (pm20) REVERT: m 23 ILE cc_start: 0.7134 (OUTLIER) cc_final: 0.6267 (tp) REVERT: q 22 ASN cc_start: 0.5065 (m-40) cc_final: 0.4648 (m-40) REVERT: r 207 HIS cc_start: 0.6850 (OUTLIER) cc_final: 0.6053 (m170) REVERT: r 220 TRP cc_start: 0.6572 (OUTLIER) cc_final: 0.6136 (t-100) REVERT: u 59 MET cc_start: 0.6054 (mmm) cc_final: 0.5837 (tpp) REVERT: v 215 ILE cc_start: 0.5087 (pt) cc_final: 0.4652 (mt) outliers start: 393 outliers final: 276 residues processed: 1271 average time/residue: 1.2577 time to fit residues: 2809.0678 Evaluate side-chains 1166 residues out of total 10437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 866 time to evaluate : 9.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 595 CYS Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 520 HIS Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 114 ASN Chi-restraints excluded: chain M residue 3 ASP Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 150 ASP Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain 1 residue 103 LEU Chi-restraints excluded: chain 1 residue 148 PHE Chi-restraints excluded: chain 1 residue 155 LEU Chi-restraints excluded: chain 1 residue 183 ASN Chi-restraints excluded: chain 1 residue 190 TYR Chi-restraints excluded: chain 1 residue 196 SER Chi-restraints excluded: chain 1 residue 198 ASP Chi-restraints excluded: chain 1 residue 200 LEU Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain 1 residue 213 MET Chi-restraints excluded: chain 1 residue 270 GLU Chi-restraints excluded: chain 1 residue 307 HIS Chi-restraints excluded: chain 2 residue 3 THR Chi-restraints excluded: chain 2 residue 22 ASN Chi-restraints excluded: chain 2 residue 52 TRP Chi-restraints excluded: chain 2 residue 207 HIS Chi-restraints excluded: chain 2 residue 212 VAL Chi-restraints excluded: chain 2 residue 251 LEU Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 315 LEU Chi-restraints excluded: chain 2 residue 326 MET Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 3 residue 69 HIS Chi-restraints excluded: chain 3 residue 79 ASP Chi-restraints excluded: chain 3 residue 174 VAL Chi-restraints excluded: chain 3 residue 208 VAL Chi-restraints excluded: chain 3 residue 289 THR Chi-restraints excluded: chain 4 residue 3 THR Chi-restraints excluded: chain 4 residue 45 PHE Chi-restraints excluded: chain 4 residue 64 LEU Chi-restraints excluded: chain 4 residue 85 ASP Chi-restraints excluded: chain 4 residue 131 ASP Chi-restraints excluded: chain 4 residue 144 HIS Chi-restraints excluded: chain 4 residue 178 THR Chi-restraints excluded: chain 4 residue 202 ASP Chi-restraints excluded: chain 4 residue 259 PHE Chi-restraints excluded: chain 4 residue 290 VAL Chi-restraints excluded: chain 4 residue 323 LEU Chi-restraints excluded: chain 5 residue 3 THR Chi-restraints excluded: chain 5 residue 40 PHE Chi-restraints excluded: chain 5 residue 111 THR Chi-restraints excluded: chain 5 residue 155 LEU Chi-restraints excluded: chain 5 residue 187 ILE Chi-restraints excluded: chain 5 residue 198 ASP Chi-restraints excluded: chain 5 residue 320 TRP Chi-restraints excluded: chain 6 residue 14 TRP Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 6 residue 67 LEU Chi-restraints excluded: chain 6 residue 130 PHE Chi-restraints excluded: chain 6 residue 282 VAL Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 209 SER Chi-restraints excluded: chain G residue 228 ASP Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 310 LEU Chi-restraints excluded: chain G residue 383 TYR Chi-restraints excluded: chain G residue 406 ILE Chi-restraints excluded: chain G residue 547 HIS Chi-restraints excluded: chain G residue 595 CYS Chi-restraints excluded: chain G residue 713 VAL Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain H residue 458 VAL Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain H residue 478 LEU Chi-restraints excluded: chain H residue 512 ILE Chi-restraints excluded: chain H residue 520 HIS Chi-restraints excluded: chain H residue 606 VAL Chi-restraints excluded: chain N residue 9 ASP Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain R residue 25 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 76 ASP Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 153 GLU Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 30 ILE Chi-restraints excluded: chain V residue 5 VAL Chi-restraints excluded: chain V residue 114 ASN Chi-restraints excluded: chain W residue 3 ASP Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 117 VAL Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 158 THR Chi-restraints excluded: chain Y residue 14 TRP Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 148 PHE Chi-restraints excluded: chain Y residue 183 ASN Chi-restraints excluded: chain Y residue 190 TYR Chi-restraints excluded: chain Y residue 196 SER Chi-restraints excluded: chain Y residue 198 ASP Chi-restraints excluded: chain Y residue 307 HIS Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 52 TRP Chi-restraints excluded: chain Z residue 79 ASP Chi-restraints excluded: chain Z residue 103 LEU Chi-restraints excluded: chain Z residue 190 TYR Chi-restraints excluded: chain Z residue 207 HIS Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 251 LEU Chi-restraints excluded: chain Z residue 314 CYS Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 174 VAL Chi-restraints excluded: chain a residue 229 TRP Chi-restraints excluded: chain a residue 235 ILE Chi-restraints excluded: chain b residue 3 THR Chi-restraints excluded: chain b residue 64 LEU Chi-restraints excluded: chain b residue 85 ASP Chi-restraints excluded: chain b residue 178 THR Chi-restraints excluded: chain b residue 259 PHE Chi-restraints excluded: chain b residue 290 VAL Chi-restraints excluded: chain c residue 40 PHE Chi-restraints excluded: chain c residue 111 THR Chi-restraints excluded: chain c residue 155 LEU Chi-restraints excluded: chain c residue 198 ASP Chi-restraints excluded: chain d residue 14 TRP Chi-restraints excluded: chain d residue 38 ILE Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 56 ASP Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 130 PHE Chi-restraints excluded: chain d residue 147 LEU Chi-restraints excluded: chain e residue 51 LEU Chi-restraints excluded: chain e residue 129 ASP Chi-restraints excluded: chain e residue 141 SER Chi-restraints excluded: chain e residue 228 ASP Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain e residue 288 THR Chi-restraints excluded: chain e residue 383 TYR Chi-restraints excluded: chain e residue 471 ASP Chi-restraints excluded: chain e residue 595 CYS Chi-restraints excluded: chain f residue 96 PHE Chi-restraints excluded: chain f residue 144 ILE Chi-restraints excluded: chain f residue 166 SER Chi-restraints excluded: chain f residue 199 ILE Chi-restraints excluded: chain f residue 216 LEU Chi-restraints excluded: chain f residue 246 THR Chi-restraints excluded: chain f residue 301 ILE Chi-restraints excluded: chain f residue 467 SER Chi-restraints excluded: chain f residue 482 ASP Chi-restraints excluded: chain f residue 489 SER Chi-restraints excluded: chain f residue 512 ILE Chi-restraints excluded: chain f residue 520 HIS Chi-restraints excluded: chain f residue 540 ASP Chi-restraints excluded: chain f residue 546 LEU Chi-restraints excluded: chain f residue 568 CYS Chi-restraints excluded: chain f residue 606 VAL Chi-restraints excluded: chain g residue 9 ASP Chi-restraints excluded: chain g residue 29 VAL Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 108 VAL Chi-restraints excluded: chain h residue 113 SER Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain i residue 69 VAL Chi-restraints excluded: chain j residue 25 VAL Chi-restraints excluded: chain j residue 46 THR Chi-restraints excluded: chain j residue 76 ASP Chi-restraints excluded: chain j residue 128 SER Chi-restraints excluded: chain j residue 130 THR Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain l residue 14 LEU Chi-restraints excluded: chain m residue 23 ILE Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain n residue 114 ASN Chi-restraints excluded: chain o residue 3 ASP Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain p residue 150 ASP Chi-restraints excluded: chain p residue 158 THR Chi-restraints excluded: chain q residue 14 TRP Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 103 LEU Chi-restraints excluded: chain q residue 148 PHE Chi-restraints excluded: chain q residue 183 ASN Chi-restraints excluded: chain q residue 196 SER Chi-restraints excluded: chain q residue 198 ASP Chi-restraints excluded: chain q residue 213 MET Chi-restraints excluded: chain r residue 3 THR Chi-restraints excluded: chain r residue 14 TRP Chi-restraints excluded: chain r residue 22 ASN Chi-restraints excluded: chain r residue 79 ASP Chi-restraints excluded: chain r residue 207 HIS Chi-restraints excluded: chain r residue 212 VAL Chi-restraints excluded: chain r residue 220 TRP Chi-restraints excluded: chain r residue 234 LEU Chi-restraints excluded: chain r residue 251 LEU Chi-restraints excluded: chain r residue 314 CYS Chi-restraints excluded: chain r residue 315 LEU Chi-restraints excluded: chain s residue 9 VAL Chi-restraints excluded: chain s residue 79 ASP Chi-restraints excluded: chain s residue 108 LEU Chi-restraints excluded: chain s residue 174 VAL Chi-restraints excluded: chain s residue 323 LEU Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 12 ASP Chi-restraints excluded: chain t residue 64 LEU Chi-restraints excluded: chain t residue 85 ASP Chi-restraints excluded: chain t residue 144 HIS Chi-restraints excluded: chain t residue 178 THR Chi-restraints excluded: chain t residue 264 THR Chi-restraints excluded: chain t residue 288 ASP Chi-restraints excluded: chain t residue 290 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 40 PHE Chi-restraints excluded: chain u residue 155 LEU Chi-restraints excluded: chain u residue 210 VAL Chi-restraints excluded: chain u residue 283 THR Chi-restraints excluded: chain u residue 289 THR Chi-restraints excluded: chain u residue 320 TRP Chi-restraints excluded: chain v residue 14 TRP Chi-restraints excluded: chain v residue 47 LEU Chi-restraints excluded: chain v residue 126 LYS Chi-restraints excluded: chain v residue 130 PHE Chi-restraints excluded: chain v residue 147 LEU Chi-restraints excluded: chain v residue 282 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1308 random chunks: chunk 425 optimal weight: 10.0000 chunk 1138 optimal weight: 9.9990 chunk 249 optimal weight: 0.0570 chunk 742 optimal weight: 20.0000 chunk 312 optimal weight: 20.0000 chunk 1265 optimal weight: 30.0000 chunk 1050 optimal weight: 0.7980 chunk 585 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 418 optimal weight: 8.9990 chunk 664 optimal weight: 5.9990 overall best weight: 3.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 153 GLN ** P 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 137 GLN ** 4 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 294 ASN ** U 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 2 GLN ** c 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 361 HIS ** t 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 69 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 152388 Z= 0.298 Angle : 0.641 12.290 216756 Z= 0.287 Chirality : 0.043 0.424 18750 Planarity : 0.005 0.057 28482 Dihedral : 18.294 115.393 25011 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.58 % Favored : 96.39 % Rotamer: Outliers : 3.51 % Allowed : 16.77 % Favored : 79.73 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.23 (0.07), residues: 13287 helix: 0.98 (0.06), residues: 7809 sheet: -2.32 (0.19), residues: 654 loop : -0.75 (0.10), residues: 4824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP u 220 HIS 0.039 0.002 HIS b 144 PHE 0.045 0.002 PHE p 86 TYR 0.022 0.002 TYR F 56 ARG 0.013 0.000 ARG q 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26574 Ramachandran restraints generated. 13287 Oldfield, 0 Emsley, 13287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26574 Ramachandran restraints generated. 13287 Oldfield, 0 Emsley, 13287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1358 residues out of total 10437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 366 poor density : 992 time to evaluate : 9.687 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 51 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8952 (tp) REVERT: A 104 LEU cc_start: 0.8288 (tp) cc_final: 0.8038 (tp) REVERT: A 155 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.6988 (mm-30) REVERT: A 315 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8636 (mp) REVERT: A 547 HIS cc_start: 0.8670 (OUTLIER) cc_final: 0.8195 (m90) REVERT: A 680 TYR cc_start: 0.8742 (m-80) cc_final: 0.8368 (m-80) REVERT: B 520 HIS cc_start: 0.8653 (OUTLIER) cc_final: 0.8123 (m90) REVERT: J 25 ILE cc_start: 0.8377 (mt) cc_final: 0.8092 (mt) REVERT: K 50 GLN cc_start: 0.7400 (mm110) cc_final: 0.6863 (mp10) REVERT: M 26 GLU cc_start: 0.8052 (tp30) cc_final: 0.7764 (tp30) REVERT: 1 200 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5788 (mp) REVERT: 2 207 HIS cc_start: 0.7228 (OUTLIER) cc_final: 0.6424 (m170) REVERT: 2 326 MET cc_start: 0.6795 (OUTLIER) cc_final: 0.6559 (mpt) REVERT: 3 332 ARG cc_start: 0.5351 (tmt170) cc_final: 0.4324 (tpt170) REVERT: 4 45 PHE cc_start: 0.0398 (OUTLIER) cc_final: -0.0487 (m-80) REVERT: 5 312 PHE cc_start: 0.6205 (t80) cc_final: 0.5768 (t80) REVERT: G 13 LYS cc_start: 0.6425 (OUTLIER) cc_final: 0.6123 (tptt) REVERT: G 172 MET cc_start: 0.8224 (mmt) cc_final: 0.7862 (mmt) REVERT: H 437 TYR cc_start: 0.9229 (OUTLIER) cc_final: 0.8089 (m-80) REVERT: H 520 HIS cc_start: 0.8543 (OUTLIER) cc_final: 0.8105 (m90) REVERT: H 568 CYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8487 (m) REVERT: H 574 ASP cc_start: 0.8155 (m-30) cc_final: 0.7900 (m-30) REVERT: R 116 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7196 (mt-10) REVERT: X 134 ARG cc_start: 0.6539 (mmm-85) cc_final: 0.6321 (mmm-85) REVERT: X 169 LEU cc_start: 0.4867 (tt) cc_final: 0.4544 (mp) REVERT: Z 90 PHE cc_start: 0.7177 (t80) cc_final: 0.6977 (t80) REVERT: Z 207 HIS cc_start: 0.7329 (OUTLIER) cc_final: 0.6453 (m170) REVERT: a 69 HIS cc_start: 0.5624 (OUTLIER) cc_final: 0.4807 (m-70) REVERT: c 4 TYR cc_start: 0.1093 (m-80) cc_final: 0.0739 (m-80) REVERT: c 312 PHE cc_start: 0.6378 (t80) cc_final: 0.5917 (t80) REVERT: e 13 LYS cc_start: 0.6219 (OUTLIER) cc_final: 0.5865 (tptt) REVERT: e 51 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8916 (tp) REVERT: f 216 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7868 (pt) REVERT: f 226 PHE cc_start: 0.7505 (m-10) cc_final: 0.7223 (m-10) REVERT: f 520 HIS cc_start: 0.8764 (OUTLIER) cc_final: 0.8285 (m90) REVERT: f 568 CYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8535 (m) REVERT: f 574 ASP cc_start: 0.8044 (m-30) cc_final: 0.7747 (m-30) REVERT: i 15 GLU cc_start: 0.8015 (pm20) cc_final: 0.7690 (pm20) REVERT: m 23 ILE cc_start: 0.7021 (OUTLIER) cc_final: 0.6126 (tp) REVERT: q 190 TYR cc_start: 0.4720 (OUTLIER) cc_final: 0.3279 (t80) REVERT: q 225 PRO cc_start: 0.4913 (Cg_exo) cc_final: 0.4700 (Cg_endo) REVERT: q 276 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7233 (mp) REVERT: r 207 HIS cc_start: 0.6849 (OUTLIER) cc_final: 0.6077 (m170) REVERT: r 220 TRP cc_start: 0.6498 (OUTLIER) cc_final: 0.6103 (t-100) outliers start: 366 outliers final: 278 residues processed: 1268 average time/residue: 1.2590 time to fit residues: 2804.8163 Evaluate side-chains 1173 residues out of total 10437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 870 time to evaluate : 8.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain A residue 595 CYS Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 520 HIS Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain L residue 4 ASP Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 114 ASN Chi-restraints excluded: chain M residue 3 ASP Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 150 ASP Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain 1 residue 103 LEU Chi-restraints excluded: chain 1 residue 148 PHE Chi-restraints excluded: chain 1 residue 155 LEU Chi-restraints excluded: chain 1 residue 183 ASN Chi-restraints excluded: chain 1 residue 190 TYR Chi-restraints excluded: chain 1 residue 196 SER Chi-restraints excluded: chain 1 residue 198 ASP Chi-restraints excluded: chain 1 residue 200 LEU Chi-restraints excluded: chain 1 residue 213 MET Chi-restraints excluded: chain 1 residue 270 GLU Chi-restraints excluded: chain 2 residue 3 THR Chi-restraints excluded: chain 2 residue 22 ASN Chi-restraints excluded: chain 2 residue 52 TRP Chi-restraints excluded: chain 2 residue 79 ASP Chi-restraints excluded: chain 2 residue 207 HIS Chi-restraints excluded: chain 2 residue 212 VAL Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 315 LEU Chi-restraints excluded: chain 2 residue 326 MET Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 3 residue 79 ASP Chi-restraints excluded: chain 3 residue 174 VAL Chi-restraints excluded: chain 3 residue 289 THR Chi-restraints excluded: chain 4 residue 3 THR Chi-restraints excluded: chain 4 residue 45 PHE Chi-restraints excluded: chain 4 residue 64 LEU Chi-restraints excluded: chain 4 residue 85 ASP Chi-restraints excluded: chain 4 residue 144 HIS Chi-restraints excluded: chain 4 residue 178 THR Chi-restraints excluded: chain 4 residue 202 ASP Chi-restraints excluded: chain 4 residue 259 PHE Chi-restraints excluded: chain 4 residue 290 VAL Chi-restraints excluded: chain 4 residue 323 LEU Chi-restraints excluded: chain 5 residue 3 THR Chi-restraints excluded: chain 5 residue 40 PHE Chi-restraints excluded: chain 5 residue 111 THR Chi-restraints excluded: chain 5 residue 155 LEU Chi-restraints excluded: chain 5 residue 187 ILE Chi-restraints excluded: chain 6 residue 14 TRP Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 6 residue 130 PHE Chi-restraints excluded: chain 6 residue 147 LEU Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 209 SER Chi-restraints excluded: chain G residue 228 ASP Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 383 TYR Chi-restraints excluded: chain G residue 406 ILE Chi-restraints excluded: chain G residue 547 HIS Chi-restraints excluded: chain G residue 595 CYS Chi-restraints excluded: chain G residue 713 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 437 TYR Chi-restraints excluded: chain H residue 458 VAL Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 478 LEU Chi-restraints excluded: chain H residue 482 ASP Chi-restraints excluded: chain H residue 489 SER Chi-restraints excluded: chain H residue 512 ILE Chi-restraints excluded: chain H residue 520 HIS Chi-restraints excluded: chain H residue 568 CYS Chi-restraints excluded: chain H residue 606 VAL Chi-restraints excluded: chain N residue 9 ASP Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain R residue 25 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 76 ASP Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 153 GLU Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 30 ILE Chi-restraints excluded: chain V residue 5 VAL Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 114 ASN Chi-restraints excluded: chain V residue 158 ILE Chi-restraints excluded: chain W residue 3 ASP Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 117 VAL Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 158 THR Chi-restraints excluded: chain Y residue 14 TRP Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 148 PHE Chi-restraints excluded: chain Y residue 183 ASN Chi-restraints excluded: chain Y residue 190 TYR Chi-restraints excluded: chain Y residue 196 SER Chi-restraints excluded: chain Y residue 198 ASP Chi-restraints excluded: chain Y residue 270 GLU Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 22 ASN Chi-restraints excluded: chain Z residue 52 TRP Chi-restraints excluded: chain Z residue 103 LEU Chi-restraints excluded: chain Z residue 190 TYR Chi-restraints excluded: chain Z residue 207 HIS Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 251 LEU Chi-restraints excluded: chain Z residue 314 CYS Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 69 HIS Chi-restraints excluded: chain a residue 174 VAL Chi-restraints excluded: chain a residue 229 TRP Chi-restraints excluded: chain a residue 235 ILE Chi-restraints excluded: chain b residue 3 THR Chi-restraints excluded: chain b residue 64 LEU Chi-restraints excluded: chain b residue 85 ASP Chi-restraints excluded: chain b residue 178 THR Chi-restraints excluded: chain b residue 259 PHE Chi-restraints excluded: chain b residue 290 VAL Chi-restraints excluded: chain c residue 40 PHE Chi-restraints excluded: chain c residue 111 THR Chi-restraints excluded: chain c residue 155 LEU Chi-restraints excluded: chain c residue 198 ASP Chi-restraints excluded: chain d residue 14 TRP Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 56 ASP Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 130 PHE Chi-restraints excluded: chain d residue 147 LEU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 51 LEU Chi-restraints excluded: chain e residue 129 ASP Chi-restraints excluded: chain e residue 141 SER Chi-restraints excluded: chain e residue 228 ASP Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain e residue 288 THR Chi-restraints excluded: chain e residue 383 TYR Chi-restraints excluded: chain e residue 406 ILE Chi-restraints excluded: chain e residue 471 ASP Chi-restraints excluded: chain e residue 595 CYS Chi-restraints excluded: chain f residue 96 PHE Chi-restraints excluded: chain f residue 144 ILE Chi-restraints excluded: chain f residue 216 LEU Chi-restraints excluded: chain f residue 246 THR Chi-restraints excluded: chain f residue 467 SER Chi-restraints excluded: chain f residue 478 LEU Chi-restraints excluded: chain f residue 482 ASP Chi-restraints excluded: chain f residue 489 SER Chi-restraints excluded: chain f residue 512 ILE Chi-restraints excluded: chain f residue 520 HIS Chi-restraints excluded: chain f residue 540 ASP Chi-restraints excluded: chain f residue 546 LEU Chi-restraints excluded: chain f residue 568 CYS Chi-restraints excluded: chain f residue 606 VAL Chi-restraints excluded: chain f residue 725 LEU Chi-restraints excluded: chain g residue 9 ASP Chi-restraints excluded: chain g residue 29 VAL Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 108 VAL Chi-restraints excluded: chain h residue 113 SER Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain i residue 69 VAL Chi-restraints excluded: chain j residue 25 VAL Chi-restraints excluded: chain j residue 46 THR Chi-restraints excluded: chain j residue 72 ASP Chi-restraints excluded: chain j residue 76 ASP Chi-restraints excluded: chain j residue 128 SER Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain l residue 14 LEU Chi-restraints excluded: chain m residue 20 LEU Chi-restraints excluded: chain m residue 23 ILE Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain n residue 114 ASN Chi-restraints excluded: chain o residue 3 ASP Chi-restraints excluded: chain p residue 14 THR Chi-restraints excluded: chain p residue 150 ASP Chi-restraints excluded: chain p residue 158 THR Chi-restraints excluded: chain q residue 14 TRP Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 103 LEU Chi-restraints excluded: chain q residue 148 PHE Chi-restraints excluded: chain q residue 183 ASN Chi-restraints excluded: chain q residue 190 TYR Chi-restraints excluded: chain q residue 198 ASP Chi-restraints excluded: chain q residue 213 MET Chi-restraints excluded: chain q residue 270 GLU Chi-restraints excluded: chain q residue 276 LEU Chi-restraints excluded: chain q residue 307 HIS Chi-restraints excluded: chain r residue 3 THR Chi-restraints excluded: chain r residue 14 TRP Chi-restraints excluded: chain r residue 22 ASN Chi-restraints excluded: chain r residue 52 TRP Chi-restraints excluded: chain r residue 79 ASP Chi-restraints excluded: chain r residue 207 HIS Chi-restraints excluded: chain r residue 212 VAL Chi-restraints excluded: chain r residue 220 TRP Chi-restraints excluded: chain r residue 234 LEU Chi-restraints excluded: chain r residue 251 LEU Chi-restraints excluded: chain r residue 314 CYS Chi-restraints excluded: chain r residue 315 LEU Chi-restraints excluded: chain s residue 9 VAL Chi-restraints excluded: chain s residue 79 ASP Chi-restraints excluded: chain s residue 108 LEU Chi-restraints excluded: chain s residue 174 VAL Chi-restraints excluded: chain s residue 323 LEU Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 12 ASP Chi-restraints excluded: chain t residue 85 ASP Chi-restraints excluded: chain t residue 131 ASP Chi-restraints excluded: chain t residue 178 THR Chi-restraints excluded: chain t residue 259 PHE Chi-restraints excluded: chain t residue 264 THR Chi-restraints excluded: chain t residue 288 ASP Chi-restraints excluded: chain t residue 290 VAL Chi-restraints excluded: chain u residue 40 PHE Chi-restraints excluded: chain u residue 111 THR Chi-restraints excluded: chain u residue 155 LEU Chi-restraints excluded: chain u residue 289 THR Chi-restraints excluded: chain v residue 1 MET Chi-restraints excluded: chain v residue 14 TRP Chi-restraints excluded: chain v residue 47 LEU Chi-restraints excluded: chain v residue 126 LYS Chi-restraints excluded: chain v residue 130 PHE Chi-restraints excluded: chain v residue 147 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1308 random chunks: chunk 1220 optimal weight: 30.0000 chunk 142 optimal weight: 0.6980 chunk 721 optimal weight: 6.9990 chunk 924 optimal weight: 0.9980 chunk 716 optimal weight: 20.0000 chunk 1065 optimal weight: 9.9990 chunk 706 optimal weight: 9.9990 chunk 1260 optimal weight: 0.1980 chunk 788 optimal weight: 30.0000 chunk 768 optimal weight: 2.9990 chunk 582 optimal weight: 0.7980 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 363 GLN B 496 ASN L 153 GLN ** P 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 ASN ** U 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 137 GLN ** c 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 166 HIS ** t 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 69 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 152388 Z= 0.173 Angle : 0.572 14.459 216756 Z= 0.259 Chirality : 0.040 0.383 18750 Planarity : 0.004 0.056 28482 Dihedral : 17.627 110.392 25011 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.27 % Favored : 96.70 % Rotamer: Outliers : 2.84 % Allowed : 17.90 % Favored : 79.27 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.07), residues: 13287 helix: 1.29 (0.06), residues: 7752 sheet: -1.78 (0.22), residues: 504 loop : -0.74 (0.09), residues: 5031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 167 HIS 0.033 0.001 HIS b 144 PHE 0.034 0.001 PHE p 86 TYR 0.022 0.001 TYR 4 258 ARG 0.014 0.000 ARG q 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26574 Ramachandran restraints generated. 13287 Oldfield, 0 Emsley, 13287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26574 Ramachandran restraints generated. 13287 Oldfield, 0 Emsley, 13287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1365 residues out of total 10437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 1069 time to evaluate : 9.757 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 51 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8935 (tp) REVERT: A 104 LEU cc_start: 0.8122 (tp) cc_final: 0.7830 (tp) REVERT: A 315 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8646 (mp) REVERT: A 363 GLN cc_start: 0.8478 (mm110) cc_final: 0.8012 (mm-40) REVERT: A 547 HIS cc_start: 0.8577 (OUTLIER) cc_final: 0.8342 (m90) REVERT: B 361 ILE cc_start: 0.9008 (tt) cc_final: 0.8678 (tt) REVERT: B 520 HIS cc_start: 0.8519 (OUTLIER) cc_final: 0.8046 (m90) REVERT: B 568 CYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8487 (m) REVERT: K 50 GLN cc_start: 0.7358 (mm110) cc_final: 0.6750 (mp10) REVERT: M 26 GLU cc_start: 0.7970 (tp30) cc_final: 0.7552 (tp30) REVERT: 1 200 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5710 (mp) REVERT: 1 307 HIS cc_start: 0.6727 (OUTLIER) cc_final: 0.6171 (m90) REVERT: 2 207 HIS cc_start: 0.7163 (OUTLIER) cc_final: 0.6350 (m170) REVERT: 2 326 MET cc_start: 0.6756 (OUTLIER) cc_final: 0.6536 (mpt) REVERT: 3 136 LYS cc_start: 0.7490 (ttpp) cc_final: 0.7220 (tttm) REVERT: 3 332 ARG cc_start: 0.5364 (tmt170) cc_final: 0.4246 (tpt170) REVERT: 4 45 PHE cc_start: 0.0630 (OUTLIER) cc_final: -0.0192 (m-80) REVERT: 5 97 LEU cc_start: 0.6967 (mt) cc_final: 0.6557 (pp) REVERT: 5 312 PHE cc_start: 0.6188 (t80) cc_final: 0.5755 (t80) REVERT: 6 335 LYS cc_start: 0.6367 (mttm) cc_final: 0.6023 (pptt) REVERT: G 13 LYS cc_start: 0.6387 (OUTLIER) cc_final: 0.6079 (tptt) REVERT: G 51 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8940 (tp) REVERT: G 196 MET cc_start: 0.7795 (tpp) cc_final: 0.7330 (ttt) REVERT: H 437 TYR cc_start: 0.9207 (OUTLIER) cc_final: 0.7976 (m-80) REVERT: H 520 HIS cc_start: 0.8441 (OUTLIER) cc_final: 0.8029 (m90) REVERT: H 574 ASP cc_start: 0.8011 (m-30) cc_final: 0.7797 (m-30) REVERT: R 116 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7159 (mt-10) REVERT: X 169 LEU cc_start: 0.4712 (tt) cc_final: 0.4466 (mp) REVERT: Y 307 HIS cc_start: 0.6772 (OUTLIER) cc_final: 0.4343 (m90) REVERT: Y 320 TRP cc_start: 0.6198 (OUTLIER) cc_final: 0.5109 (t-100) REVERT: Z 207 HIS cc_start: 0.7291 (OUTLIER) cc_final: 0.6411 (m170) REVERT: a 69 HIS cc_start: 0.5698 (OUTLIER) cc_final: 0.4753 (m-70) REVERT: c 312 PHE cc_start: 0.6424 (t80) cc_final: 0.5958 (t80) REVERT: e 13 LYS cc_start: 0.6099 (OUTLIER) cc_final: 0.5787 (tptt) REVERT: e 51 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8908 (tp) REVERT: f 216 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7788 (pt) REVERT: f 520 HIS cc_start: 0.8674 (OUTLIER) cc_final: 0.8241 (m90) REVERT: f 568 CYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8423 (m) REVERT: f 574 ASP cc_start: 0.7912 (m-30) cc_final: 0.7691 (m-30) REVERT: i 15 GLU cc_start: 0.7970 (pm20) cc_final: 0.7625 (pm20) REVERT: m 23 ILE cc_start: 0.7163 (OUTLIER) cc_final: 0.6340 (tp) REVERT: q 190 TYR cc_start: 0.4521 (OUTLIER) cc_final: 0.3171 (t80) REVERT: q 276 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7121 (mp) REVERT: r 207 HIS cc_start: 0.6791 (OUTLIER) cc_final: 0.6055 (m170) REVERT: r 326 MET cc_start: 0.6821 (mpp) cc_final: 0.6612 (mpt) REVERT: u 198 ASP cc_start: 0.6557 (m-30) cc_final: 0.6177 (m-30) REVERT: v 215 ILE cc_start: 0.4955 (pt) cc_final: 0.4506 (mt) outliers start: 296 outliers final: 216 residues processed: 1291 average time/residue: 1.2901 time to fit residues: 2920.5982 Evaluate side-chains 1166 residues out of total 10437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 923 time to evaluate : 11.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain A residue 595 CYS Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 520 HIS Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain M residue 3 ASP Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 150 ASP Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain 1 residue 103 LEU Chi-restraints excluded: chain 1 residue 148 PHE Chi-restraints excluded: chain 1 residue 183 ASN Chi-restraints excluded: chain 1 residue 190 TYR Chi-restraints excluded: chain 1 residue 196 SER Chi-restraints excluded: chain 1 residue 198 ASP Chi-restraints excluded: chain 1 residue 200 LEU Chi-restraints excluded: chain 1 residue 213 MET Chi-restraints excluded: chain 1 residue 270 GLU Chi-restraints excluded: chain 1 residue 307 HIS Chi-restraints excluded: chain 2 residue 22 ASN Chi-restraints excluded: chain 2 residue 52 TRP Chi-restraints excluded: chain 2 residue 207 HIS Chi-restraints excluded: chain 2 residue 212 VAL Chi-restraints excluded: chain 2 residue 326 MET Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 3 residue 174 VAL Chi-restraints excluded: chain 3 residue 289 THR Chi-restraints excluded: chain 4 residue 45 PHE Chi-restraints excluded: chain 4 residue 64 LEU Chi-restraints excluded: chain 4 residue 85 ASP Chi-restraints excluded: chain 4 residue 131 ASP Chi-restraints excluded: chain 4 residue 144 HIS Chi-restraints excluded: chain 4 residue 178 THR Chi-restraints excluded: chain 4 residue 202 ASP Chi-restraints excluded: chain 4 residue 259 PHE Chi-restraints excluded: chain 5 residue 40 PHE Chi-restraints excluded: chain 5 residue 111 THR Chi-restraints excluded: chain 5 residue 155 LEU Chi-restraints excluded: chain 5 residue 187 ILE Chi-restraints excluded: chain 6 residue 14 TRP Chi-restraints excluded: chain 6 residue 126 LYS Chi-restraints excluded: chain 6 residue 130 PHE Chi-restraints excluded: chain 6 residue 147 LEU Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain G residue 209 SER Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 383 TYR Chi-restraints excluded: chain G residue 595 CYS Chi-restraints excluded: chain G residue 713 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain H residue 437 TYR Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 478 LEU Chi-restraints excluded: chain H residue 489 SER Chi-restraints excluded: chain H residue 512 ILE Chi-restraints excluded: chain H residue 520 HIS Chi-restraints excluded: chain H residue 606 VAL Chi-restraints excluded: chain H residue 649 MET Chi-restraints excluded: chain N residue 9 ASP Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 76 ASP Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 114 ASN Chi-restraints excluded: chain W residue 3 ASP Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 117 VAL Chi-restraints excluded: chain X residue 158 THR Chi-restraints excluded: chain Y residue 14 TRP Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 183 ASN Chi-restraints excluded: chain Y residue 190 TYR Chi-restraints excluded: chain Y residue 196 SER Chi-restraints excluded: chain Y residue 198 ASP Chi-restraints excluded: chain Y residue 201 GLU Chi-restraints excluded: chain Y residue 307 HIS Chi-restraints excluded: chain Y residue 320 TRP Chi-restraints excluded: chain Z residue 22 ASN Chi-restraints excluded: chain Z residue 52 TRP Chi-restraints excluded: chain Z residue 79 ASP Chi-restraints excluded: chain Z residue 103 LEU Chi-restraints excluded: chain Z residue 190 TYR Chi-restraints excluded: chain Z residue 207 HIS Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 251 LEU Chi-restraints excluded: chain Z residue 314 CYS Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 69 HIS Chi-restraints excluded: chain a residue 174 VAL Chi-restraints excluded: chain a residue 229 TRP Chi-restraints excluded: chain a residue 235 ILE Chi-restraints excluded: chain b residue 3 THR Chi-restraints excluded: chain b residue 64 LEU Chi-restraints excluded: chain b residue 85 ASP Chi-restraints excluded: chain b residue 178 THR Chi-restraints excluded: chain b residue 259 PHE Chi-restraints excluded: chain c residue 111 THR Chi-restraints excluded: chain c residue 155 LEU Chi-restraints excluded: chain c residue 198 ASP Chi-restraints excluded: chain d residue 14 TRP Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 56 ASP Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 130 PHE Chi-restraints excluded: chain d residue 147 LEU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 51 LEU Chi-restraints excluded: chain e residue 129 ASP Chi-restraints excluded: chain e residue 141 SER Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain e residue 383 TYR Chi-restraints excluded: chain e residue 595 CYS Chi-restraints excluded: chain e residue 713 VAL Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 96 PHE Chi-restraints excluded: chain f residue 144 ILE Chi-restraints excluded: chain f residue 216 LEU Chi-restraints excluded: chain f residue 246 THR Chi-restraints excluded: chain f residue 352 MET Chi-restraints excluded: chain f residue 467 SER Chi-restraints excluded: chain f residue 478 LEU Chi-restraints excluded: chain f residue 482 ASP Chi-restraints excluded: chain f residue 512 ILE Chi-restraints excluded: chain f residue 520 HIS Chi-restraints excluded: chain f residue 540 ASP Chi-restraints excluded: chain f residue 546 LEU Chi-restraints excluded: chain f residue 568 CYS Chi-restraints excluded: chain f residue 606 VAL Chi-restraints excluded: chain f residue 725 LEU Chi-restraints excluded: chain g residue 9 ASP Chi-restraints excluded: chain g residue 29 VAL Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 108 VAL Chi-restraints excluded: chain h residue 113 SER Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain j residue 46 THR Chi-restraints excluded: chain j residue 128 SER Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain l residue 14 LEU Chi-restraints excluded: chain m residue 20 LEU Chi-restraints excluded: chain m residue 23 ILE Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain n residue 83 VAL Chi-restraints excluded: chain n residue 114 ASN Chi-restraints excluded: chain n residue 166 HIS Chi-restraints excluded: chain o residue 3 ASP Chi-restraints excluded: chain p residue 14 THR Chi-restraints excluded: chain p residue 150 ASP Chi-restraints excluded: chain p residue 158 THR Chi-restraints excluded: chain q residue 14 TRP Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 103 LEU Chi-restraints excluded: chain q residue 148 PHE Chi-restraints excluded: chain q residue 183 ASN Chi-restraints excluded: chain q residue 190 TYR Chi-restraints excluded: chain q residue 196 SER Chi-restraints excluded: chain q residue 198 ASP Chi-restraints excluded: chain q residue 213 MET Chi-restraints excluded: chain q residue 270 GLU Chi-restraints excluded: chain q residue 276 LEU Chi-restraints excluded: chain q residue 288 ASP Chi-restraints excluded: chain r residue 22 ASN Chi-restraints excluded: chain r residue 207 HIS Chi-restraints excluded: chain r residue 212 VAL Chi-restraints excluded: chain r residue 234 LEU Chi-restraints excluded: chain r residue 251 LEU Chi-restraints excluded: chain r residue 314 CYS Chi-restraints excluded: chain r residue 315 LEU Chi-restraints excluded: chain s residue 9 VAL Chi-restraints excluded: chain s residue 79 ASP Chi-restraints excluded: chain s residue 108 LEU Chi-restraints excluded: chain s residue 174 VAL Chi-restraints excluded: chain s residue 323 LEU Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 85 ASP Chi-restraints excluded: chain t residue 144 HIS Chi-restraints excluded: chain t residue 178 THR Chi-restraints excluded: chain t residue 259 PHE Chi-restraints excluded: chain t residue 288 ASP Chi-restraints excluded: chain t residue 290 VAL Chi-restraints excluded: chain u residue 40 PHE Chi-restraints excluded: chain u residue 111 THR Chi-restraints excluded: chain u residue 155 LEU Chi-restraints excluded: chain u residue 289 THR Chi-restraints excluded: chain v residue 14 TRP Chi-restraints excluded: chain v residue 47 LEU Chi-restraints excluded: chain v residue 147 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1308 random chunks: chunk 779 optimal weight: 0.6980 chunk 503 optimal weight: 7.9990 chunk 752 optimal weight: 20.0000 chunk 379 optimal weight: 0.8980 chunk 247 optimal weight: 30.0000 chunk 244 optimal weight: 0.8980 chunk 801 optimal weight: 6.9990 chunk 858 optimal weight: 0.5980 chunk 623 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 990 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 153 GLN ** P 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 636 ASN ** U 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 91 GLN ** Z 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 153 GLN n 166 HIS ** t 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 152388 Z= 0.158 Angle : 0.564 15.826 216756 Z= 0.255 Chirality : 0.039 0.378 18750 Planarity : 0.004 0.059 28482 Dihedral : 17.110 107.516 25011 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.12 % Favored : 96.86 % Rotamer: Outliers : 2.74 % Allowed : 18.31 % Favored : 78.95 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.02 % 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: 0.67 (0.07), residues: 13287 helix: 1.33 (0.06), residues: 7863 sheet: -1.75 (0.22), residues: 510 loop : -0.71 (0.09), residues: 4914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP B 167 HIS 0.032 0.001 HIS b 144 PHE 0.032 0.001 PHE p 86 TYR 0.031 0.001 TYR F 56 ARG 0.013 0.000 ARG q 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26574 Ramachandran restraints generated. 13287 Oldfield, 0 Emsley, 13287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26574 Ramachandran restraints generated. 13287 Oldfield, 0 Emsley, 13287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1330 residues out of total 10437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 1044 time to evaluate : 9.805 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: A 51 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8914 (tp) REVERT: A 155 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.6870 (mm-30) REVERT: A 363 GLN cc_start: 0.8456 (mm110) cc_final: 0.7965 (mm-40) REVERT: A 547 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.8368 (m90) REVERT: B 361 ILE cc_start: 0.8988 (tt) cc_final: 0.8676 (tt) REVERT: B 490 LEU cc_start: 0.8545 (tt) cc_final: 0.8283 (tp) REVERT: B 520 HIS cc_start: 0.8497 (OUTLIER) cc_final: 0.8010 (m90) REVERT: B 568 CYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8396 (m) REVERT: K 50 GLN cc_start: 0.7296 (mm110) cc_final: 0.6722 (mp10) REVERT: L 45 ARG cc_start: 0.8989 (tpt90) cc_final: 0.8754 (tpt90) REVERT: 1 200 LEU cc_start: 0.5923 (OUTLIER) cc_final: 0.5595 (mp) REVERT: 1 307 HIS cc_start: 0.6712 (OUTLIER) cc_final: 0.6150 (m90) REVERT: 1 326 MET cc_start: 0.5679 (mmm) cc_final: 0.4472 (mtt) REVERT: 2 207 HIS cc_start: 0.7077 (OUTLIER) cc_final: 0.6295 (m170) REVERT: 2 326 MET cc_start: 0.6838 (OUTLIER) cc_final: 0.6561 (mpt) REVERT: 3 69 HIS cc_start: 0.5885 (OUTLIER) cc_final: 0.5004 (m-70) REVERT: 3 136 LYS cc_start: 0.7443 (ttpp) cc_final: 0.7187 (tttm) REVERT: 3 332 ARG cc_start: 0.5268 (tmt170) cc_final: 0.4203 (tpt170) REVERT: 4 45 PHE cc_start: 0.0598 (OUTLIER) cc_final: -0.0204 (m-80) REVERT: 5 312 PHE cc_start: 0.6207 (t80) cc_final: 0.5811 (t80) REVERT: 6 59 MET cc_start: 0.5472 (ttt) cc_final: 0.5158 (mtm) REVERT: 6 335 LYS cc_start: 0.6325 (mttm) cc_final: 0.6008 (pptt) REVERT: G 13 LYS cc_start: 0.6283 (OUTLIER) cc_final: 0.5998 (tptt) REVERT: G 51 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8955 (tp) REVERT: H 437 TYR cc_start: 0.9188 (OUTLIER) cc_final: 0.7954 (m-80) REVERT: H 520 HIS cc_start: 0.8415 (OUTLIER) cc_final: 0.8008 (m90) REVERT: X 66 TRP cc_start: 0.7240 (m100) cc_final: 0.7038 (m100) REVERT: X 169 LEU cc_start: 0.4631 (tt) cc_final: 0.4365 (mp) REVERT: Y 148 PHE cc_start: 0.6334 (OUTLIER) cc_final: 0.6084 (t80) REVERT: Y 179 GLU cc_start: 0.5881 (tp30) cc_final: 0.5350 (pt0) REVERT: Y 307 HIS cc_start: 0.6679 (OUTLIER) cc_final: 0.4162 (m90) REVERT: Y 326 MET cc_start: 0.5058 (mmm) cc_final: 0.3923 (mtt) REVERT: Z 90 PHE cc_start: 0.7260 (t80) cc_final: 0.6927 (t80) REVERT: Z 207 HIS cc_start: 0.7256 (OUTLIER) cc_final: 0.6428 (m170) REVERT: a 69 HIS cc_start: 0.5928 (OUTLIER) cc_final: 0.4919 (m-70) REVERT: b 134 ASP cc_start: 0.3200 (t70) cc_final: 0.2975 (t70) REVERT: c 228 GLN cc_start: 0.3765 (pm20) cc_final: 0.3497 (tm-30) REVERT: c 312 PHE cc_start: 0.6406 (t80) cc_final: 0.5945 (t80) REVERT: e 13 LYS cc_start: 0.5980 (OUTLIER) cc_final: 0.5660 (tptt) REVERT: e 51 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8877 (tp) REVERT: f 216 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7740 (pt) REVERT: f 520 HIS cc_start: 0.8640 (OUTLIER) cc_final: 0.8193 (m90) REVERT: i 11 ILE cc_start: 0.9018 (mm) cc_final: 0.8779 (mm) REVERT: i 15 GLU cc_start: 0.7981 (pm20) cc_final: 0.7653 (pm20) REVERT: j 109 ASP cc_start: 0.6342 (t0) cc_final: 0.6117 (p0) REVERT: q 190 TYR cc_start: 0.4648 (OUTLIER) cc_final: 0.3445 (t80) REVERT: q 201 GLU cc_start: 0.6314 (mp0) cc_final: 0.6026 (mp0) REVERT: q 276 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7009 (mp) REVERT: q 326 MET cc_start: 0.5001 (mmm) cc_final: 0.4360 (mtt) REVERT: r 207 HIS cc_start: 0.6849 (OUTLIER) cc_final: 0.6146 (m170) REVERT: r 326 MET cc_start: 0.6821 (mpp) cc_final: 0.6595 (mpt) REVERT: u 198 ASP cc_start: 0.6592 (m-30) cc_final: 0.6321 (m-30) outliers start: 286 outliers final: 205 residues processed: 1257 average time/residue: 1.2634 time to fit residues: 2787.0036 Evaluate side-chains 1175 residues out of total 10437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 944 time to evaluate : 9.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain A residue 595 CYS Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 520 HIS Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 114 ASN Chi-restraints excluded: chain M residue 3 ASP Chi-restraints excluded: chain P residue 150 ASP Chi-restraints excluded: chain 1 residue 103 LEU Chi-restraints excluded: chain 1 residue 148 PHE Chi-restraints excluded: chain 1 residue 183 ASN Chi-restraints excluded: chain 1 residue 190 TYR Chi-restraints excluded: chain 1 residue 196 SER Chi-restraints excluded: chain 1 residue 198 ASP Chi-restraints excluded: chain 1 residue 200 LEU Chi-restraints excluded: chain 1 residue 213 MET Chi-restraints excluded: chain 1 residue 270 GLU Chi-restraints excluded: chain 1 residue 307 HIS Chi-restraints excluded: chain 2 residue 22 ASN Chi-restraints excluded: chain 2 residue 52 TRP Chi-restraints excluded: chain 2 residue 79 ASP Chi-restraints excluded: chain 2 residue 207 HIS Chi-restraints excluded: chain 2 residue 212 VAL Chi-restraints excluded: chain 2 residue 283 THR Chi-restraints excluded: chain 2 residue 326 MET Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 3 residue 69 HIS Chi-restraints excluded: chain 3 residue 174 VAL Chi-restraints excluded: chain 4 residue 45 PHE Chi-restraints excluded: chain 4 residue 64 LEU Chi-restraints excluded: chain 4 residue 85 ASP Chi-restraints excluded: chain 4 residue 131 ASP Chi-restraints excluded: chain 4 residue 144 HIS Chi-restraints excluded: chain 4 residue 178 THR Chi-restraints excluded: chain 4 residue 202 ASP Chi-restraints excluded: chain 4 residue 259 PHE Chi-restraints excluded: chain 4 residue 290 VAL Chi-restraints excluded: chain 5 residue 40 PHE Chi-restraints excluded: chain 5 residue 111 THR Chi-restraints excluded: chain 5 residue 155 LEU Chi-restraints excluded: chain 5 residue 187 ILE Chi-restraints excluded: chain 5 residue 198 ASP Chi-restraints excluded: chain 6 residue 14 TRP Chi-restraints excluded: chain 6 residue 130 PHE Chi-restraints excluded: chain 6 residue 147 LEU Chi-restraints excluded: chain 6 residue 282 VAL Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain G residue 209 SER Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 383 TYR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain H residue 437 TYR Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 478 LEU Chi-restraints excluded: chain H residue 489 SER Chi-restraints excluded: chain H residue 512 ILE Chi-restraints excluded: chain H residue 520 HIS Chi-restraints excluded: chain H residue 606 VAL Chi-restraints excluded: chain N residue 9 ASP Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 114 ASN Chi-restraints excluded: chain W residue 3 ASP Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 158 THR Chi-restraints excluded: chain Y residue 14 TRP Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 148 PHE Chi-restraints excluded: chain Y residue 183 ASN Chi-restraints excluded: chain Y residue 190 TYR Chi-restraints excluded: chain Y residue 196 SER Chi-restraints excluded: chain Y residue 198 ASP Chi-restraints excluded: chain Y residue 307 HIS Chi-restraints excluded: chain Z residue 22 ASN Chi-restraints excluded: chain Z residue 52 TRP Chi-restraints excluded: chain Z residue 79 ASP Chi-restraints excluded: chain Z residue 103 LEU Chi-restraints excluded: chain Z residue 190 TYR Chi-restraints excluded: chain Z residue 207 HIS Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 251 LEU Chi-restraints excluded: chain Z residue 314 CYS Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 69 HIS Chi-restraints excluded: chain a residue 174 VAL Chi-restraints excluded: chain a residue 229 TRP Chi-restraints excluded: chain a residue 235 ILE Chi-restraints excluded: chain b residue 3 THR Chi-restraints excluded: chain b residue 64 LEU Chi-restraints excluded: chain b residue 85 ASP Chi-restraints excluded: chain b residue 144 HIS Chi-restraints excluded: chain b residue 178 THR Chi-restraints excluded: chain b residue 259 PHE Chi-restraints excluded: chain b residue 290 VAL Chi-restraints excluded: chain c residue 40 PHE Chi-restraints excluded: chain c residue 111 THR Chi-restraints excluded: chain c residue 155 LEU Chi-restraints excluded: chain d residue 14 TRP Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 56 ASP Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 130 PHE Chi-restraints excluded: chain d residue 147 LEU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 51 LEU Chi-restraints excluded: chain e residue 129 ASP Chi-restraints excluded: chain e residue 141 SER Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain e residue 383 TYR Chi-restraints excluded: chain e residue 595 CYS Chi-restraints excluded: chain e residue 713 VAL Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 96 PHE Chi-restraints excluded: chain f residue 166 SER Chi-restraints excluded: chain f residue 216 LEU Chi-restraints excluded: chain f residue 246 THR Chi-restraints excluded: chain f residue 467 SER Chi-restraints excluded: chain f residue 476 VAL Chi-restraints excluded: chain f residue 478 LEU Chi-restraints excluded: chain f residue 482 ASP Chi-restraints excluded: chain f residue 489 SER Chi-restraints excluded: chain f residue 520 HIS Chi-restraints excluded: chain f residue 540 ASP Chi-restraints excluded: chain f residue 546 LEU Chi-restraints excluded: chain f residue 606 VAL Chi-restraints excluded: chain f residue 725 LEU Chi-restraints excluded: chain g residue 9 ASP Chi-restraints excluded: chain g residue 29 VAL Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 108 VAL Chi-restraints excluded: chain h residue 113 SER Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain j residue 46 THR Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain l residue 36 LEU Chi-restraints excluded: chain m residue 20 LEU Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain n residue 83 VAL Chi-restraints excluded: chain n residue 114 ASN Chi-restraints excluded: chain o residue 3 ASP Chi-restraints excluded: chain p residue 150 ASP Chi-restraints excluded: chain p residue 158 THR Chi-restraints excluded: chain q residue 14 TRP Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 148 PHE Chi-restraints excluded: chain q residue 183 ASN Chi-restraints excluded: chain q residue 190 TYR Chi-restraints excluded: chain q residue 196 SER Chi-restraints excluded: chain q residue 198 ASP Chi-restraints excluded: chain q residue 270 GLU Chi-restraints excluded: chain q residue 276 LEU Chi-restraints excluded: chain q residue 288 ASP Chi-restraints excluded: chain r residue 22 ASN Chi-restraints excluded: chain r residue 207 HIS Chi-restraints excluded: chain r residue 212 VAL Chi-restraints excluded: chain r residue 234 LEU Chi-restraints excluded: chain r residue 251 LEU Chi-restraints excluded: chain r residue 314 CYS Chi-restraints excluded: chain r residue 315 LEU Chi-restraints excluded: chain s residue 79 ASP Chi-restraints excluded: chain s residue 108 LEU Chi-restraints excluded: chain s residue 174 VAL Chi-restraints excluded: chain t residue 131 ASP Chi-restraints excluded: chain t residue 144 HIS Chi-restraints excluded: chain t residue 178 THR Chi-restraints excluded: chain t residue 259 PHE Chi-restraints excluded: chain t residue 288 ASP Chi-restraints excluded: chain u residue 40 PHE Chi-restraints excluded: chain u residue 111 THR Chi-restraints excluded: chain u residue 155 LEU Chi-restraints excluded: chain u residue 289 THR Chi-restraints excluded: chain v residue 14 TRP Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 147 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1308 random chunks: chunk 1146 optimal weight: 20.0000 chunk 1207 optimal weight: 20.0000 chunk 1101 optimal weight: 20.0000 chunk 1174 optimal weight: 5.9990 chunk 707 optimal weight: 4.9990 chunk 511 optimal weight: 3.9990 chunk 922 optimal weight: 5.9990 chunk 360 optimal weight: 0.9980 chunk 1061 optimal weight: 9.9990 chunk 1111 optimal weight: 9.9990 chunk 1170 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN L 153 GLN ** P 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 172 GLN ** 5 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 633 ASN H 636 ASN ** U 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 137 GLN b 228 GLN ** c 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 361 HIS f 633 ASN ** m 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 153 GLN s 82 GLN ** t 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 69 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 152388 Z= 0.390 Angle : 0.713 16.158 216756 Z= 0.317 Chirality : 0.045 0.422 18750 Planarity : 0.005 0.061 28482 Dihedral : 17.954 116.228 25011 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.21 % Favored : 95.77 % Rotamer: Outliers : 2.99 % Allowed : 18.30 % Favored : 78.71 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.07), residues: 13287 helix: 1.05 (0.06), residues: 7785 sheet: -1.83 (0.22), residues: 507 loop : -0.68 (0.09), residues: 4995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP B 167 HIS 0.032 0.002 HIS b 144 PHE 0.031 0.002 PHE p 86 TYR 0.024 0.002 TYR f 577 ARG 0.016 0.001 ARG q 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26574 Ramachandran restraints generated. 13287 Oldfield, 0 Emsley, 13287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26574 Ramachandran restraints generated. 13287 Oldfield, 0 Emsley, 13287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1251 residues out of total 10437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 939 time to evaluate : 8.659 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 51 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8985 (tp) REVERT: A 155 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7022 (mm-30) REVERT: A 194 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6676 (mt-10) REVERT: A 289 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.6549 (m-80) REVERT: A 547 HIS cc_start: 0.8714 (OUTLIER) cc_final: 0.8364 (m90) REVERT: A 680 TYR cc_start: 0.8818 (m-80) cc_final: 0.8428 (m-80) REVERT: B 490 LEU cc_start: 0.8616 (tt) cc_final: 0.8355 (tp) REVERT: B 520 HIS cc_start: 0.8681 (OUTLIER) cc_final: 0.8178 (m90) REVERT: B 568 CYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8520 (m) REVERT: K 50 GLN cc_start: 0.7454 (mm110) cc_final: 0.6848 (mp10) REVERT: 1 200 LEU cc_start: 0.5835 (OUTLIER) cc_final: 0.5489 (mp) REVERT: 1 307 HIS cc_start: 0.6933 (OUTLIER) cc_final: 0.6316 (m90) REVERT: 2 207 HIS cc_start: 0.7199 (OUTLIER) cc_final: 0.6411 (m170) REVERT: 2 307 HIS cc_start: 0.7879 (OUTLIER) cc_final: 0.6971 (m170) REVERT: 2 326 MET cc_start: 0.6885 (OUTLIER) cc_final: 0.6585 (mpt) REVERT: 3 69 HIS cc_start: 0.5923 (OUTLIER) cc_final: 0.5164 (m-70) REVERT: 3 136 LYS cc_start: 0.7570 (ttpp) cc_final: 0.7300 (tttm) REVERT: 3 332 ARG cc_start: 0.5444 (tmt170) cc_final: 0.4323 (tpt170) REVERT: 4 45 PHE cc_start: 0.0709 (OUTLIER) cc_final: -0.0423 (m-80) REVERT: 5 312 PHE cc_start: 0.6120 (t80) cc_final: 0.5770 (t80) REVERT: 6 335 LYS cc_start: 0.6389 (mttm) cc_final: 0.5993 (pptt) REVERT: G 13 LYS cc_start: 0.6509 (OUTLIER) cc_final: 0.6176 (tptt) REVERT: G 51 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8958 (tp) REVERT: H 437 TYR cc_start: 0.9245 (OUTLIER) cc_final: 0.8077 (m-80) REVERT: H 520 HIS cc_start: 0.8555 (OUTLIER) cc_final: 0.8021 (m90) REVERT: H 568 CYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8568 (m) REVERT: R 116 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7245 (mt-10) REVERT: X 169 LEU cc_start: 0.4906 (tt) cc_final: 0.4574 (mp) REVERT: Y 179 GLU cc_start: 0.5850 (tp30) cc_final: 0.5256 (pt0) REVERT: Y 307 HIS cc_start: 0.7073 (OUTLIER) cc_final: 0.4860 (m90) REVERT: Z 90 PHE cc_start: 0.7315 (t80) cc_final: 0.7024 (t80) REVERT: Z 207 HIS cc_start: 0.7186 (OUTLIER) cc_final: 0.6347 (m170) REVERT: a 69 HIS cc_start: 0.5682 (OUTLIER) cc_final: 0.4853 (m-70) REVERT: c 312 PHE cc_start: 0.6236 (t80) cc_final: 0.5759 (t80) REVERT: e 13 LYS cc_start: 0.6456 (OUTLIER) cc_final: 0.6096 (tptt) REVERT: e 51 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8945 (tp) REVERT: e 591 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.7371 (ptt90) REVERT: f 520 HIS cc_start: 0.8820 (OUTLIER) cc_final: 0.8361 (m90) REVERT: f 568 CYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8632 (m) REVERT: f 577 TYR cc_start: 0.9270 (OUTLIER) cc_final: 0.9056 (t80) REVERT: i 15 GLU cc_start: 0.8047 (pm20) cc_final: 0.7725 (pm20) REVERT: o 1 MET cc_start: 0.7028 (mtp) cc_final: 0.6734 (mtm) REVERT: q 190 TYR cc_start: 0.4690 (OUTLIER) cc_final: 0.3423 (t80) REVERT: q 201 GLU cc_start: 0.6412 (mp0) cc_final: 0.6088 (mp0) REVERT: q 276 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7159 (mp) REVERT: q 326 MET cc_start: 0.5574 (mmm) cc_final: 0.4805 (mtt) REVERT: r 207 HIS cc_start: 0.6906 (OUTLIER) cc_final: 0.6166 (m170) REVERT: r 326 MET cc_start: 0.6946 (mpp) cc_final: 0.6688 (mpt) REVERT: t 320 TRP cc_start: 0.6439 (t-100) cc_final: 0.5306 (t60) outliers start: 312 outliers final: 243 residues processed: 1184 average time/residue: 1.2494 time to fit residues: 2593.3179 Evaluate side-chains 1150 residues out of total 10437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 876 time to evaluate : 9.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain A residue 595 CYS Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 520 HIS Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 114 ASN Chi-restraints excluded: chain M residue 3 ASP Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 150 ASP Chi-restraints excluded: chain 1 residue 103 LEU Chi-restraints excluded: chain 1 residue 155 LEU Chi-restraints excluded: chain 1 residue 183 ASN Chi-restraints excluded: chain 1 residue 190 TYR Chi-restraints excluded: chain 1 residue 192 THR Chi-restraints excluded: chain 1 residue 198 ASP Chi-restraints excluded: chain 1 residue 200 LEU Chi-restraints excluded: chain 1 residue 213 MET Chi-restraints excluded: chain 1 residue 270 GLU Chi-restraints excluded: chain 1 residue 303 LEU Chi-restraints excluded: chain 1 residue 307 HIS Chi-restraints excluded: chain 2 residue 3 THR Chi-restraints excluded: chain 2 residue 22 ASN Chi-restraints excluded: chain 2 residue 52 TRP Chi-restraints excluded: chain 2 residue 207 HIS Chi-restraints excluded: chain 2 residue 212 VAL Chi-restraints excluded: chain 2 residue 283 THR Chi-restraints excluded: chain 2 residue 307 HIS Chi-restraints excluded: chain 2 residue 326 MET Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 3 residue 69 HIS Chi-restraints excluded: chain 3 residue 79 ASP Chi-restraints excluded: chain 3 residue 174 VAL Chi-restraints excluded: chain 3 residue 208 VAL Chi-restraints excluded: chain 4 residue 45 PHE Chi-restraints excluded: chain 4 residue 85 ASP Chi-restraints excluded: chain 4 residue 131 ASP Chi-restraints excluded: chain 4 residue 144 HIS Chi-restraints excluded: chain 4 residue 178 THR Chi-restraints excluded: chain 4 residue 202 ASP Chi-restraints excluded: chain 4 residue 259 PHE Chi-restraints excluded: chain 4 residue 290 VAL Chi-restraints excluded: chain 5 residue 40 PHE Chi-restraints excluded: chain 5 residue 111 THR Chi-restraints excluded: chain 5 residue 155 LEU Chi-restraints excluded: chain 5 residue 187 ILE Chi-restraints excluded: chain 5 residue 198 ASP Chi-restraints excluded: chain 5 residue 320 TRP Chi-restraints excluded: chain 6 residue 14 TRP Chi-restraints excluded: chain 6 residue 130 PHE Chi-restraints excluded: chain 6 residue 147 LEU Chi-restraints excluded: chain 6 residue 282 VAL Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 209 SER Chi-restraints excluded: chain G residue 228 ASP Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 383 TYR Chi-restraints excluded: chain G residue 406 ILE Chi-restraints excluded: chain G residue 547 HIS Chi-restraints excluded: chain G residue 595 CYS Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain H residue 437 TYR Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 478 LEU Chi-restraints excluded: chain H residue 482 ASP Chi-restraints excluded: chain H residue 489 SER Chi-restraints excluded: chain H residue 512 ILE Chi-restraints excluded: chain H residue 520 HIS Chi-restraints excluded: chain H residue 568 CYS Chi-restraints excluded: chain H residue 606 VAL Chi-restraints excluded: chain N residue 9 ASP Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 76 ASP Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 46 LEU Chi-restraints excluded: chain V residue 5 VAL Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 114 ASN Chi-restraints excluded: chain W residue 3 ASP Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 158 THR Chi-restraints excluded: chain Y residue 14 TRP Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 183 ASN Chi-restraints excluded: chain Y residue 196 SER Chi-restraints excluded: chain Y residue 198 ASP Chi-restraints excluded: chain Y residue 307 HIS Chi-restraints excluded: chain Z residue 22 ASN Chi-restraints excluded: chain Z residue 52 TRP Chi-restraints excluded: chain Z residue 79 ASP Chi-restraints excluded: chain Z residue 103 LEU Chi-restraints excluded: chain Z residue 190 TYR Chi-restraints excluded: chain Z residue 207 HIS Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 251 LEU Chi-restraints excluded: chain Z residue 314 CYS Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 69 HIS Chi-restraints excluded: chain a residue 174 VAL Chi-restraints excluded: chain a residue 229 TRP Chi-restraints excluded: chain a residue 235 ILE Chi-restraints excluded: chain b residue 3 THR Chi-restraints excluded: chain b residue 85 ASP Chi-restraints excluded: chain b residue 144 HIS Chi-restraints excluded: chain b residue 178 THR Chi-restraints excluded: chain b residue 259 PHE Chi-restraints excluded: chain b residue 290 VAL Chi-restraints excluded: chain c residue 40 PHE Chi-restraints excluded: chain c residue 111 THR Chi-restraints excluded: chain c residue 155 LEU Chi-restraints excluded: chain d residue 14 TRP Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 56 ASP Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 130 PHE Chi-restraints excluded: chain d residue 147 LEU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 51 LEU Chi-restraints excluded: chain e residue 129 ASP Chi-restraints excluded: chain e residue 141 SER Chi-restraints excluded: chain e residue 228 ASP Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain e residue 288 THR Chi-restraints excluded: chain e residue 302 LEU Chi-restraints excluded: chain e residue 378 VAL Chi-restraints excluded: chain e residue 383 TYR Chi-restraints excluded: chain e residue 591 ARG Chi-restraints excluded: chain e residue 595 CYS Chi-restraints excluded: chain e residue 713 VAL Chi-restraints excluded: chain f residue 96 PHE Chi-restraints excluded: chain f residue 166 SER Chi-restraints excluded: chain f residue 222 LEU Chi-restraints excluded: chain f residue 246 THR Chi-restraints excluded: chain f residue 467 SER Chi-restraints excluded: chain f residue 478 LEU Chi-restraints excluded: chain f residue 482 ASP Chi-restraints excluded: chain f residue 489 SER Chi-restraints excluded: chain f residue 512 ILE Chi-restraints excluded: chain f residue 520 HIS Chi-restraints excluded: chain f residue 540 ASP Chi-restraints excluded: chain f residue 546 LEU Chi-restraints excluded: chain f residue 568 CYS Chi-restraints excluded: chain f residue 577 TYR Chi-restraints excluded: chain f residue 606 VAL Chi-restraints excluded: chain f residue 725 LEU Chi-restraints excluded: chain g residue 9 ASP Chi-restraints excluded: chain g residue 29 VAL Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 108 VAL Chi-restraints excluded: chain h residue 113 SER Chi-restraints excluded: chain h residue 140 THR Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain i residue 69 VAL Chi-restraints excluded: chain j residue 46 THR Chi-restraints excluded: chain j residue 128 SER Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain m residue 20 LEU Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain n residue 114 ASN Chi-restraints excluded: chain o residue 3 ASP Chi-restraints excluded: chain p residue 14 THR Chi-restraints excluded: chain p residue 150 ASP Chi-restraints excluded: chain p residue 158 THR Chi-restraints excluded: chain q residue 14 TRP Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 103 LEU Chi-restraints excluded: chain q residue 183 ASN Chi-restraints excluded: chain q residue 190 TYR Chi-restraints excluded: chain q residue 196 SER Chi-restraints excluded: chain q residue 198 ASP Chi-restraints excluded: chain q residue 276 LEU Chi-restraints excluded: chain q residue 288 ASP Chi-restraints excluded: chain q residue 307 HIS Chi-restraints excluded: chain r residue 22 ASN Chi-restraints excluded: chain r residue 207 HIS Chi-restraints excluded: chain r residue 212 VAL Chi-restraints excluded: chain r residue 234 LEU Chi-restraints excluded: chain r residue 251 LEU Chi-restraints excluded: chain r residue 314 CYS Chi-restraints excluded: chain r residue 315 LEU Chi-restraints excluded: chain s residue 9 VAL Chi-restraints excluded: chain s residue 79 ASP Chi-restraints excluded: chain s residue 108 LEU Chi-restraints excluded: chain s residue 174 VAL Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 85 ASP Chi-restraints excluded: chain t residue 131 ASP Chi-restraints excluded: chain t residue 144 HIS Chi-restraints excluded: chain t residue 178 THR Chi-restraints excluded: chain t residue 259 PHE Chi-restraints excluded: chain t residue 288 ASP Chi-restraints excluded: chain t residue 289 THR Chi-restraints excluded: chain t residue 290 VAL Chi-restraints excluded: chain u residue 40 PHE Chi-restraints excluded: chain u residue 70 LEU Chi-restraints excluded: chain u residue 86 THR Chi-restraints excluded: chain u residue 111 THR Chi-restraints excluded: chain u residue 155 LEU Chi-restraints excluded: chain u residue 289 THR Chi-restraints excluded: chain u residue 320 TRP Chi-restraints excluded: chain v residue 14 TRP Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 147 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1308 random chunks: chunk 771 optimal weight: 6.9990 chunk 1242 optimal weight: 10.0000 chunk 758 optimal weight: 9.9990 chunk 589 optimal weight: 0.9990 chunk 863 optimal weight: 40.0000 chunk 1303 optimal weight: 1.9990 chunk 1199 optimal weight: 7.9990 chunk 1037 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 801 optimal weight: 5.9990 chunk 636 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 80 ASN L 153 GLN ** P 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 263 ASN ** b 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 361 HIS ** t 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 263 ASN v 69 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 152388 Z= 0.286 Angle : 0.648 16.250 216756 Z= 0.291 Chirality : 0.043 0.389 18750 Planarity : 0.005 0.063 28482 Dihedral : 17.688 113.625 25011 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.65 % Favored : 96.33 % Rotamer: Outliers : 2.80 % Allowed : 18.81 % Favored : 78.39 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.07), residues: 13287 helix: 1.16 (0.06), residues: 7731 sheet: -1.85 (0.22), residues: 507 loop : -0.66 (0.09), residues: 5049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.002 TRP B 167 HIS 0.031 0.002 HIS b 144 PHE 0.034 0.002 PHE e 275 TYR 0.022 0.002 TYR f 577 ARG 0.015 0.001 ARG q 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26574 Ramachandran restraints generated. 13287 Oldfield, 0 Emsley, 13287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26574 Ramachandran restraints generated. 13287 Oldfield, 0 Emsley, 13287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1220 residues out of total 10437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 928 time to evaluate : 9.838 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: A 51 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8985 (tp) REVERT: A 155 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.6967 (mm-30) REVERT: A 194 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6703 (mt-10) REVERT: A 289 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.6528 (m-80) REVERT: A 547 HIS cc_start: 0.8646 (OUTLIER) cc_final: 0.8212 (m90) REVERT: A 680 TYR cc_start: 0.8765 (m-80) cc_final: 0.8409 (m-80) REVERT: B 490 LEU cc_start: 0.8572 (tt) cc_final: 0.8298 (tp) REVERT: B 520 HIS cc_start: 0.8598 (OUTLIER) cc_final: 0.8076 (m90) REVERT: B 568 CYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8534 (m) REVERT: K 50 GLN cc_start: 0.7459 (mm110) cc_final: 0.7000 (mp10) REVERT: 1 200 LEU cc_start: 0.5743 (OUTLIER) cc_final: 0.5393 (mp) REVERT: 1 307 HIS cc_start: 0.6768 (OUTLIER) cc_final: 0.6194 (m90) REVERT: 2 207 HIS cc_start: 0.7138 (OUTLIER) cc_final: 0.6330 (m170) REVERT: 2 307 HIS cc_start: 0.7785 (OUTLIER) cc_final: 0.6813 (m170) REVERT: 2 326 MET cc_start: 0.6808 (OUTLIER) cc_final: 0.6552 (mpt) REVERT: 3 59 MET cc_start: 0.5657 (tpp) cc_final: 0.5185 (tpp) REVERT: 3 69 HIS cc_start: 0.5855 (OUTLIER) cc_final: 0.5040 (m-70) REVERT: 3 136 LYS cc_start: 0.7587 (ttpp) cc_final: 0.7316 (tttm) REVERT: 3 332 ARG cc_start: 0.5432 (tmt170) cc_final: 0.4317 (tpt170) REVERT: 4 45 PHE cc_start: 0.0195 (OUTLIER) cc_final: -0.0637 (m-80) REVERT: 5 312 PHE cc_start: 0.6151 (t80) cc_final: 0.5821 (t80) REVERT: 6 59 MET cc_start: 0.6294 (mpp) cc_final: 0.6072 (ttt) REVERT: 6 335 LYS cc_start: 0.6372 (mttm) cc_final: 0.5973 (pptt) REVERT: G 13 LYS cc_start: 0.6555 (OUTLIER) cc_final: 0.6276 (tptt) REVERT: G 51 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8952 (tp) REVERT: G 196 MET cc_start: 0.7877 (tpp) cc_final: 0.7153 (ttt) REVERT: G 591 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.7383 (ptt90) REVERT: G 680 TYR cc_start: 0.8810 (m-80) cc_final: 0.8517 (m-80) REVERT: H 437 TYR cc_start: 0.9226 (OUTLIER) cc_final: 0.8079 (m-80) REVERT: H 520 HIS cc_start: 0.8502 (OUTLIER) cc_final: 0.8053 (m90) REVERT: H 568 CYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8457 (m) REVERT: H 574 ASP cc_start: 0.8152 (m-30) cc_final: 0.7949 (m-30) REVERT: R 116 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7213 (mt-10) REVERT: X 138 PHE cc_start: 0.7162 (OUTLIER) cc_final: 0.6500 (t80) REVERT: X 169 LEU cc_start: 0.4910 (tt) cc_final: 0.4568 (mp) REVERT: Y 179 GLU cc_start: 0.5873 (tp30) cc_final: 0.5371 (pt0) REVERT: Y 225 PRO cc_start: 0.4504 (Cg_exo) cc_final: 0.4183 (Cg_endo) REVERT: Y 307 HIS cc_start: 0.7012 (OUTLIER) cc_final: 0.4715 (m90) REVERT: Y 320 TRP cc_start: 0.6410 (OUTLIER) cc_final: 0.5427 (t-100) REVERT: Z 90 PHE cc_start: 0.7240 (t80) cc_final: 0.6957 (t80) REVERT: Z 207 HIS cc_start: 0.7172 (OUTLIER) cc_final: 0.6337 (m170) REVERT: a 69 HIS cc_start: 0.5666 (OUTLIER) cc_final: 0.4806 (m-70) REVERT: b 103 LEU cc_start: 0.4908 (mm) cc_final: 0.4674 (mt) REVERT: b 320 TRP cc_start: 0.5855 (t-100) cc_final: 0.5319 (t-100) REVERT: b 326 MET cc_start: 0.4953 (OUTLIER) cc_final: 0.4431 (tmm) REVERT: c 82 GLN cc_start: 0.4935 (mp10) cc_final: 0.3347 (pt0) REVERT: c 312 PHE cc_start: 0.6306 (t80) cc_final: 0.5885 (t80) REVERT: e 13 LYS cc_start: 0.6413 (OUTLIER) cc_final: 0.6107 (tptt) REVERT: e 51 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8936 (tp) REVERT: e 591 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.7373 (ptt90) REVERT: f 520 HIS cc_start: 0.8751 (OUTLIER) cc_final: 0.8328 (m90) REVERT: i 15 GLU cc_start: 0.8043 (pm20) cc_final: 0.7706 (pm20) REVERT: o 1 MET cc_start: 0.7058 (mtp) cc_final: 0.6763 (mtm) REVERT: q 190 TYR cc_start: 0.4607 (OUTLIER) cc_final: 0.3408 (t80) REVERT: q 276 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7164 (mp) REVERT: q 326 MET cc_start: 0.5460 (mmm) cc_final: 0.4665 (mtt) REVERT: r 207 HIS cc_start: 0.6908 (OUTLIER) cc_final: 0.6199 (m170) REVERT: r 326 MET cc_start: 0.6874 (mpp) cc_final: 0.6657 (mpt) REVERT: t 320 TRP cc_start: 0.6242 (t-100) cc_final: 0.5173 (t60) outliers start: 292 outliers final: 234 residues processed: 1151 average time/residue: 1.2570 time to fit residues: 2537.6180 Evaluate side-chains 1167 residues out of total 10437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 900 time to evaluate : 9.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain A residue 595 CYS Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 520 HIS Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 114 ASN Chi-restraints excluded: chain M residue 3 ASP Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 150 ASP Chi-restraints excluded: chain 1 residue 103 LEU Chi-restraints excluded: chain 1 residue 183 ASN Chi-restraints excluded: chain 1 residue 190 TYR Chi-restraints excluded: chain 1 residue 198 ASP Chi-restraints excluded: chain 1 residue 200 LEU Chi-restraints excluded: chain 1 residue 213 MET Chi-restraints excluded: chain 1 residue 270 GLU Chi-restraints excluded: chain 1 residue 303 LEU Chi-restraints excluded: chain 1 residue 307 HIS Chi-restraints excluded: chain 2 residue 22 ASN Chi-restraints excluded: chain 2 residue 52 TRP Chi-restraints excluded: chain 2 residue 79 ASP Chi-restraints excluded: chain 2 residue 207 HIS Chi-restraints excluded: chain 2 residue 212 VAL Chi-restraints excluded: chain 2 residue 283 THR Chi-restraints excluded: chain 2 residue 307 HIS Chi-restraints excluded: chain 2 residue 326 MET Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 3 residue 69 HIS Chi-restraints excluded: chain 3 residue 79 ASP Chi-restraints excluded: chain 3 residue 174 VAL Chi-restraints excluded: chain 4 residue 45 PHE Chi-restraints excluded: chain 4 residue 85 ASP Chi-restraints excluded: chain 4 residue 144 HIS Chi-restraints excluded: chain 4 residue 178 THR Chi-restraints excluded: chain 4 residue 202 ASP Chi-restraints excluded: chain 4 residue 259 PHE Chi-restraints excluded: chain 4 residue 290 VAL Chi-restraints excluded: chain 5 residue 40 PHE Chi-restraints excluded: chain 5 residue 111 THR Chi-restraints excluded: chain 5 residue 155 LEU Chi-restraints excluded: chain 5 residue 187 ILE Chi-restraints excluded: chain 5 residue 320 TRP Chi-restraints excluded: chain 6 residue 14 TRP Chi-restraints excluded: chain 6 residue 130 PHE Chi-restraints excluded: chain 6 residue 147 LEU Chi-restraints excluded: chain 6 residue 282 VAL Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 209 SER Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 383 TYR Chi-restraints excluded: chain G residue 406 ILE Chi-restraints excluded: chain G residue 547 HIS Chi-restraints excluded: chain G residue 591 ARG Chi-restraints excluded: chain G residue 595 CYS Chi-restraints excluded: chain G residue 713 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain H residue 437 TYR Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 478 LEU Chi-restraints excluded: chain H residue 482 ASP Chi-restraints excluded: chain H residue 489 SER Chi-restraints excluded: chain H residue 512 ILE Chi-restraints excluded: chain H residue 520 HIS Chi-restraints excluded: chain H residue 568 CYS Chi-restraints excluded: chain H residue 606 VAL Chi-restraints excluded: chain N residue 9 ASP Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 46 LEU Chi-restraints excluded: chain V residue 5 VAL Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 109 THR Chi-restraints excluded: chain V residue 114 ASN Chi-restraints excluded: chain W residue 3 ASP Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 117 VAL Chi-restraints excluded: chain X residue 138 PHE Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 158 THR Chi-restraints excluded: chain Y residue 14 TRP Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 183 ASN Chi-restraints excluded: chain Y residue 198 ASP Chi-restraints excluded: chain Y residue 288 ASP Chi-restraints excluded: chain Y residue 307 HIS Chi-restraints excluded: chain Y residue 320 TRP Chi-restraints excluded: chain Z residue 22 ASN Chi-restraints excluded: chain Z residue 52 TRP Chi-restraints excluded: chain Z residue 79 ASP Chi-restraints excluded: chain Z residue 103 LEU Chi-restraints excluded: chain Z residue 190 TYR Chi-restraints excluded: chain Z residue 207 HIS Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 251 LEU Chi-restraints excluded: chain Z residue 314 CYS Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 69 HIS Chi-restraints excluded: chain a residue 174 VAL Chi-restraints excluded: chain a residue 229 TRP Chi-restraints excluded: chain a residue 235 ILE Chi-restraints excluded: chain b residue 3 THR Chi-restraints excluded: chain b residue 85 ASP Chi-restraints excluded: chain b residue 144 HIS Chi-restraints excluded: chain b residue 178 THR Chi-restraints excluded: chain b residue 259 PHE Chi-restraints excluded: chain b residue 290 VAL Chi-restraints excluded: chain b residue 326 MET Chi-restraints excluded: chain c residue 40 PHE Chi-restraints excluded: chain c residue 111 THR Chi-restraints excluded: chain c residue 155 LEU Chi-restraints excluded: chain c residue 210 VAL Chi-restraints excluded: chain d residue 14 TRP Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 56 ASP Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 130 PHE Chi-restraints excluded: chain d residue 147 LEU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 51 LEU Chi-restraints excluded: chain e residue 129 ASP Chi-restraints excluded: chain e residue 141 SER Chi-restraints excluded: chain e residue 205 LEU Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain e residue 286 PHE Chi-restraints excluded: chain e residue 288 THR Chi-restraints excluded: chain e residue 302 LEU Chi-restraints excluded: chain e residue 383 TYR Chi-restraints excluded: chain e residue 406 ILE Chi-restraints excluded: chain e residue 591 ARG Chi-restraints excluded: chain e residue 595 CYS Chi-restraints excluded: chain e residue 713 VAL Chi-restraints excluded: chain f residue 96 PHE Chi-restraints excluded: chain f residue 144 ILE Chi-restraints excluded: chain f residue 166 SER Chi-restraints excluded: chain f residue 222 LEU Chi-restraints excluded: chain f residue 246 THR Chi-restraints excluded: chain f residue 352 MET Chi-restraints excluded: chain f residue 467 SER Chi-restraints excluded: chain f residue 478 LEU Chi-restraints excluded: chain f residue 482 ASP Chi-restraints excluded: chain f residue 489 SER Chi-restraints excluded: chain f residue 512 ILE Chi-restraints excluded: chain f residue 520 HIS Chi-restraints excluded: chain f residue 540 ASP Chi-restraints excluded: chain f residue 546 LEU Chi-restraints excluded: chain f residue 606 VAL Chi-restraints excluded: chain f residue 725 LEU Chi-restraints excluded: chain g residue 9 ASP Chi-restraints excluded: chain g residue 29 VAL Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 108 VAL Chi-restraints excluded: chain h residue 113 SER Chi-restraints excluded: chain h residue 140 THR Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain i residue 69 VAL Chi-restraints excluded: chain j residue 46 THR Chi-restraints excluded: chain j residue 128 SER Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain m residue 20 LEU Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 114 ASN Chi-restraints excluded: chain o residue 3 ASP Chi-restraints excluded: chain p residue 14 THR Chi-restraints excluded: chain p residue 139 VAL Chi-restraints excluded: chain p residue 150 ASP Chi-restraints excluded: chain p residue 158 THR Chi-restraints excluded: chain q residue 14 TRP Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 103 LEU Chi-restraints excluded: chain q residue 183 ASN Chi-restraints excluded: chain q residue 190 TYR Chi-restraints excluded: chain q residue 198 ASP Chi-restraints excluded: chain q residue 213 MET Chi-restraints excluded: chain q residue 276 LEU Chi-restraints excluded: chain q residue 288 ASP Chi-restraints excluded: chain r residue 22 ASN Chi-restraints excluded: chain r residue 207 HIS Chi-restraints excluded: chain r residue 212 VAL Chi-restraints excluded: chain r residue 234 LEU Chi-restraints excluded: chain r residue 251 LEU Chi-restraints excluded: chain r residue 314 CYS Chi-restraints excluded: chain r residue 315 LEU Chi-restraints excluded: chain s residue 9 VAL Chi-restraints excluded: chain s residue 79 ASP Chi-restraints excluded: chain s residue 108 LEU Chi-restraints excluded: chain s residue 174 VAL Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 12 ASP Chi-restraints excluded: chain t residue 131 ASP Chi-restraints excluded: chain t residue 144 HIS Chi-restraints excluded: chain t residue 178 THR Chi-restraints excluded: chain t residue 259 PHE Chi-restraints excluded: chain t residue 288 ASP Chi-restraints excluded: chain t residue 289 THR Chi-restraints excluded: chain u residue 40 PHE Chi-restraints excluded: chain u residue 70 LEU Chi-restraints excluded: chain u residue 86 THR Chi-restraints excluded: chain u residue 111 THR Chi-restraints excluded: chain u residue 155 LEU Chi-restraints excluded: chain u residue 289 THR Chi-restraints excluded: chain v residue 14 TRP Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 69 HIS Chi-restraints excluded: chain v residue 147 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1308 random chunks: chunk 824 optimal weight: 6.9990 chunk 1105 optimal weight: 20.0000 chunk 317 optimal weight: 5.9990 chunk 956 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 288 optimal weight: 6.9990 chunk 1039 optimal weight: 8.9990 chunk 434 optimal weight: 5.9990 chunk 1067 optimal weight: 7.9990 chunk 131 optimal weight: 0.6980 chunk 191 optimal weight: 0.7980 overall best weight: 1.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 80 ASN L 153 GLN ** P 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 263 ASN v 69 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.152789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.114730 restraints weight = 262144.363| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.50 r_work: 0.3074 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 152388 Z= 0.218 Angle : 0.614 19.296 216756 Z= 0.277 Chirality : 0.041 0.384 18750 Planarity : 0.005 0.061 28482 Dihedral : 17.355 110.246 25011 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.70 % Favored : 96.27 % Rotamer: Outliers : 2.76 % Allowed : 18.88 % Favored : 78.37 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.07), residues: 13287 helix: 1.27 (0.06), residues: 7761 sheet: -1.81 (0.22), residues: 507 loop : -0.70 (0.09), residues: 5019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.098 0.002 TRP B 167 HIS 0.030 0.002 HIS b 144 PHE 0.031 0.002 PHE e 275 TYR 0.024 0.001 TYR 4 258 ARG 0.015 0.000 ARG q 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 43199.86 seconds wall clock time: 752 minutes 15.10 seconds (45135.10 seconds total)