Starting phenix.real_space_refine on Sun Mar 24 14:17:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1c_12695/03_2024/7o1c_12695_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1c_12695/03_2024/7o1c_12695.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1c_12695/03_2024/7o1c_12695_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1c_12695/03_2024/7o1c_12695_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1c_12695/03_2024/7o1c_12695_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1c_12695/03_2024/7o1c_12695.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1c_12695/03_2024/7o1c_12695.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1c_12695/03_2024/7o1c_12695_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1c_12695/03_2024/7o1c_12695_updated.pdb" } resolution = 2.6 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= 0.001 sd= 0.007 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: 8 Type Number sf(0) Gaussians K 147 8.98 5 Zn 3 6.06 5 P 4638 5.49 5 Mg 339 5.21 5 S 158 5.16 5 C 74035 2.51 5 N 27343 2.21 5 O 41512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "AB GLU 145": "OE1" <-> "OE2" Residue "AB GLU 169": "OE1" <-> "OE2" Residue "AB PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB ARG 225": "NH1" <-> "NH2" Residue "AC PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AC PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AC ASP 93": "OD1" <-> "OD2" Residue "AC GLU 110": "OE1" <-> "OE2" Residue "AC ASP 112": "OD1" <-> "OD2" Residue "AC ARG 131": "NH1" <-> "NH2" Residue "AD GLU 35": "OE1" <-> "OE2" Residue "AD TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AE GLU 13": "OE1" <-> "OE2" Residue "AF ARG 2": "NH1" <-> "NH2" Residue "AF GLU 5": "OE1" <-> "OE2" Residue "AF ASP 41": "OD1" <-> "OD2" Residue "AF TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG GLU 40": "OE1" <-> "OE2" Residue "AH ASP 48": "OD1" <-> "OD2" Residue "AI TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI GLU 36": "OE1" <-> "OE2" Residue "AI GLU 112": "OE1" <-> "OE2" Residue "AI ARG 119": "NH1" <-> "NH2" Residue "AI ARG 124": "NH1" <-> "NH2" Residue "AJ ASP 85": "OD1" <-> "OD2" Residue "AK ASP 18": "OD1" <-> "OD2" Residue "AK GLU 68": "OE1" <-> "OE2" Residue "AK TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AL ARG 56": "NH1" <-> "NH2" Residue "AM TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM ASP 58": "OD1" <-> "OD2" Residue "AM GLU 72": "OE1" <-> "OE2" Residue "AN ASP 17": "OD1" <-> "OD2" Residue "AO GLU 26": "OE1" <-> "OE2" Residue "AO GLU 83": "OE1" <-> "OE2" Residue "AP ARG 28": "NH1" <-> "NH2" Residue "AP PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AQ GLU 49": "OE1" <-> "OE2" Residue "AQ GLU 52": "OE1" <-> "OE2" Residue "AS ASP 64": "OD1" <-> "OD2" Residue "AS GLU 65": "OE1" <-> "OE2" Residue "AS GLU 73": "OE1" <-> "OE2" Residue "AT PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AT GLU 53": "OE1" <-> "OE2" Residue "AU GLU 10": "OE1" <-> "OE2" Residue "AU PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC ARG 52": "NH1" <-> "NH2" Residue "BC ARG 63": "NH1" <-> "NH2" Residue "BC ARG 80": "NH1" <-> "NH2" Residue "BC TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC ASP 114": "OD1" <-> "OD2" Residue "BC ARG 133": "NH1" <-> "NH2" Residue "BC ARG 167": "NH1" <-> "NH2" Residue "BC ARG 177": "NH1" <-> "NH2" Residue "BC ARG 182": "NH1" <-> "NH2" Residue "BC ASP 187": "OD1" <-> "OD2" Residue "BC ARG 189": "NH1" <-> "NH2" Residue "BC GLU 199": "OE1" <-> "OE2" Residue "BC ARG 212": "NH1" <-> "NH2" Residue "BC ASP 264": "OD1" <-> "OD2" Residue "BD ARG 13": "NH1" <-> "NH2" Residue "BD ARG 33": "NH1" <-> "NH2" Residue "BD ARG 59": "NH1" <-> "NH2" Residue "BD GLU 64": "OE1" <-> "OE2" Residue "BD ARG 77": "NH1" <-> "NH2" Residue "BD PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BD ARG 83": "NH1" <-> "NH2" Residue "BD PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BD GLU 168": "OE1" <-> "OE2" Residue "BD ARG 169": "NH1" <-> "NH2" Residue "BD GLU 183": "OE1" <-> "OE2" Residue "BD ARG 184": "NH1" <-> "NH2" Residue "BD ASP 200": "OD1" <-> "OD2" Residue "BE ARG 21": "NH1" <-> "NH2" Residue "BE TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE ARG 44": "NH1" <-> "NH2" Residue "BE ARG 49": "NH1" <-> "NH2" Residue "BE ARG 67": "NH1" <-> "NH2" Residue "BE ARG 88": "NH1" <-> "NH2" Residue "BE ARG 102": "NH1" <-> "NH2" Residue "BE ARG 162": "NH1" <-> "NH2" Residue "BE ARG 170": "NH1" <-> "NH2" Residue "BF ARG 71": "NH1" <-> "NH2" Residue "BF ARG 80": "NH1" <-> "NH2" Residue "BF ARG 92": "NH1" <-> "NH2" Residue "BF ARG 102": "NH1" <-> "NH2" Residue "BF ARG 110": "NH1" <-> "NH2" Residue "BF ARG 112": "NH1" <-> "NH2" Residue "BF ARG 115": "NH1" <-> "NH2" Residue "BF ARG 133": "NH1" <-> "NH2" Residue "BG ARG 3": "NH1" <-> "NH2" Residue "BG GLU 130": "OE1" <-> "OE2" Residue "BG ARG 153": "NH1" <-> "NH2" Residue "BG ARG 163": "NH1" <-> "NH2" Residue "BG ARG 170": "NH1" <-> "NH2" Residue "BH ARG 27": "NH1" <-> "NH2" Residue "BH PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BH GLU 114": "OE1" <-> "OE2" Residue "BH PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BI ARG 49": "NH1" <-> "NH2" Residue "BI ARG 56": "NH1" <-> "NH2" Residue "BI ASP 58": "OD1" <-> "OD2" Residue "BJ ARG 13": "NH1" <-> "NH2" Residue "BJ ASP 19": "OD1" <-> "OD2" Residue "BJ GLU 31": "OE1" <-> "OE2" Residue "BJ ARG 37": "NH1" <-> "NH2" Residue "BJ GLU 43": "OE1" <-> "OE2" Residue "BJ ASP 49": "OD1" <-> "OD2" Residue "BJ ASP 71": "OD1" <-> "OD2" Residue "BJ ARG 96": "NH1" <-> "NH2" Residue "BJ GLU 102": "OE1" <-> "OE2" Residue "BJ ARG 120": "NH1" <-> "NH2" Residue "BK GLU 4": "OE1" <-> "OE2" Residue "BK ASP 37": "OD1" <-> "OD2" Residue "BK GLU 45": "OE1" <-> "OE2" Residue "BK ASP 73": "OD1" <-> "OD2" Residue "BL ARG 21": "NH1" <-> "NH2" Residue "BL ARG 33": "NH1" <-> "NH2" Residue "BL ARG 41": "NH1" <-> "NH2" Residue "BL ARG 47": "NH1" <-> "NH2" Residue "BL GLU 51": "OE1" <-> "OE2" Residue "BL ARG 60": "NH1" <-> "NH2" Residue "BL ASP 81": "OD1" <-> "OD2" Residue "BL ARG 126": "NH1" <-> "NH2" Residue "BM ARG 10": "NH1" <-> "NH2" Residue "BM ARG 18": "NH1" <-> "NH2" Residue "BM ASP 25": "OD1" <-> "OD2" Residue "BM ARG 40": "NH1" <-> "NH2" Residue "BM ARG 44": "NH1" <-> "NH2" Residue "BM ARG 50": "NH1" <-> "NH2" Residue "BM ARG 55": "NH1" <-> "NH2" Residue "BM ARG 59": "NH1" <-> "NH2" Residue "BM GLU 75": "OE1" <-> "OE2" Residue "BM GLU 90": "OE1" <-> "OE2" Residue "BM TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BM ASP 106": "OD1" <-> "OD2" Residue "BM ARG 114": "NH1" <-> "NH2" Residue "BM PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BN ARG 8": "NH1" <-> "NH2" Residue "BN ARG 12": "NH1" <-> "NH2" Residue "BN ARG 17": "NH1" <-> "NH2" Residue "BN ARG 22": "NH1" <-> "NH2" Residue "BN GLU 32": "OE1" <-> "OE2" Residue "BN GLU 43": "OE1" <-> "OE2" Residue "BN ARG 46": "NH1" <-> "NH2" Residue "BN ASP 58": "OD1" <-> "OD2" Residue "BN ARG 63": "NH1" <-> "NH2" Residue "BN ARG 64": "NH1" <-> "NH2" Residue "BN ARG 69": "NH1" <-> "NH2" Residue "BN ARG 71": "NH1" <-> "NH2" Residue "BN ASP 72": "OD1" <-> "OD2" Residue "BN ARG 96": "NH1" <-> "NH2" Residue "BN ARG 118": "NH1" <-> "NH2" Residue "BO ARG 10": "NH1" <-> "NH2" Residue "BO ARG 16": "NH1" <-> "NH2" Residue "BO ARG 25": "NH1" <-> "NH2" Residue "BO GLU 55": "OE1" <-> "OE2" Residue "BO GLU 60": "OE1" <-> "OE2" Residue "BO ARG 81": "NH1" <-> "NH2" Residue "BO ARG 94": "NH1" <-> "NH2" Residue "BO ARG 102": "NH1" <-> "NH2" Residue "BO ARG 111": "NH1" <-> "NH2" Residue "BP ARG 21": "NH1" <-> "NH2" Residue "BP ARG 39": "NH1" <-> "NH2" Residue "BP GLU 44": "OE1" <-> "OE2" Residue "BP ARG 62": "NH1" <-> "NH2" Residue "BP ARG 89": "NH1" <-> "NH2" Residue "BP ARG 101": "NH1" <-> "NH2" Residue "BP ARG 109": "NH1" <-> "NH2" Residue "BQ ARG 3": "NH1" <-> "NH2" Residue "BQ ARG 6": "NH1" <-> "NH2" Residue "BQ ARG 13": "NH1" <-> "NH2" Residue "BQ ARG 33": "NH1" <-> "NH2" Residue "BQ TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BQ ARG 48": "NH1" <-> "NH2" Residue "BQ ARG 70": "NH1" <-> "NH2" Residue "BQ ASP 97": "OD1" <-> "OD2" Residue "BQ ASP 102": "OD1" <-> "OD2" Residue "BR ARG 21": "NH1" <-> "NH2" Residue "BR GLU 23": "OE1" <-> "OE2" Residue "BR ARG 68": "NH1" <-> "NH2" Residue "BR ARG 78": "NH1" <-> "NH2" Residue "BR ARG 79": "NH1" <-> "NH2" Residue "BR ARG 84": "NH1" <-> "NH2" Residue "BR PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BR ASP 95": "OD1" <-> "OD2" Residue "BS GLU 52": "OE1" <-> "OE2" Residue "BS ASP 62": "OD1" <-> "OD2" Residue "BS ARG 84": "NH1" <-> "NH2" Residue "BS ARG 88": "NH1" <-> "NH2" Residue "BS ARG 95": "NH1" <-> "NH2" Residue "BS ARG 110": "NH1" <-> "NH2" Residue "BT GLU 4": "OE1" <-> "OE2" Residue "BT GLU 52": "OE1" <-> "OE2" Residue "BT ARG 73": "NH1" <-> "NH2" Residue "BU ARG 6": "NH1" <-> "NH2" Residue "BU ARG 7": "NH1" <-> "NH2" Residue "BU ARG 82": "NH1" <-> "NH2" Residue "BU ARG 86": "NH1" <-> "NH2" Residue "BU ARG 94": "NH1" <-> "NH2" Residue "BW ARG 11": "NH1" <-> "NH2" Residue "BW GLU 83": "OE1" <-> "OE2" Residue "BX ARG 3": "NH1" <-> "NH2" Residue "BX ARG 11": "NH1" <-> "NH2" Residue "BX ARG 18": "NH1" <-> "NH2" Residue "BX ARG 37": "NH1" <-> "NH2" Residue "BX GLU 43": "OE1" <-> "OE2" Residue "BX ARG 50": "NH1" <-> "NH2" Residue "BX ARG 57": "NH1" <-> "NH2" Residue "BX ASP 65": "OD1" <-> "OD2" Residue "BX GLU 70": "OE1" <-> "OE2" Residue "BX ARG 74": "NH1" <-> "NH2" Residue "BY GLU 12": "OE1" <-> "OE2" Residue "BY ARG 29": "NH1" <-> "NH2" Residue "BY ARG 47": "NH1" <-> "NH2" Residue "BY ARG 52": "NH1" <-> "NH2" Residue "BZ ARG 11": "NH1" <-> "NH2" Residue "BZ ARG 30": "NH1" <-> "NH2" Residue "BZ GLU 37": "OE1" <-> "OE2" Residue "BZ ARG 45": "NH1" <-> "NH2" Residue "B0 ARG 10": "NH1" <-> "NH2" Residue "B0 ARG 16": "NH1" <-> "NH2" Residue "B0 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B0 ARG 52": "NH1" <-> "NH2" Residue "B1 GLU 32": "OE1" <-> "OE2" Residue "B1 ARG 44": "NH1" <-> "NH2" Residue "B2 ARG 12": "NH1" <-> "NH2" Residue "B2 ARG 14": "NH1" <-> "NH2" Residue "B2 ARG 19": "NH1" <-> "NH2" Residue "B2 ARG 21": "NH1" <-> "NH2" Residue "B2 ARG 33": "NH1" <-> "NH2" Residue "B2 ARG 41": "NH1" <-> "NH2" Residue "B3 ARG 13": "NH1" <-> "NH2" Residue "B3 ARG 30": "NH1" <-> "NH2" Residue "B3 ARG 40": "NH1" <-> "NH2" Residue "B3 ARG 42": "NH1" <-> "NH2" Residue "B3 ASP 54": "OD1" <-> "OD2" Residue "B4 ARG 24": "NH1" <-> "NH2" Residue "B9 GLU 114": "OE1" <-> "OE2" Residue "B9 GLU 140": "OE1" <-> "OE2" Residue "B9 PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B9 ASP 238": "OD1" <-> "OD2" Residue "B9 ARG 262": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 148175 Number of models: 1 Model: "" Number of chains: 76 Chain: "AA" Number of atoms: 32930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32930 Classifications: {'RNA': 1534} Modifications used: {'rna2p': 1, 'rna2p_pur': 124, 'rna2p_pyr': 94, 'rna3p': 10, 'rna3p_pur': 745, 'rna3p_pyr': 560} Link IDs: {'rna2p': 219, 'rna3p': 1314} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 7 Chain: "AB" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "AC" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "AD" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "AE" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1144 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain: "AF" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "AG" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "AH" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "AI" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "AJ" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Chain: "AK" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "AL" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AM" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "AN" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 799 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "AO" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "AP" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "AQ" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "AR" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AS" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 656 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "AT" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "AU" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 465 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "BA" Number of atoms: 62209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2897, 62209 Classifications: {'RNA': 2897} Modifications used: {'rna2p': 6, 'rna2p_pur': 285, 'rna2p_pyr': 161, 'rna3p': 17, 'rna3p_pur': 1379, 'rna3p_pyr': 1049} Link IDs: {'rna2p': 452, 'rna3p': 2444} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "BB" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 56, 'rna3p_pyr': 50} Link IDs: {'rna2p': 14, 'rna3p': 105} Chain: "BC" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "BD" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "BE" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "BF" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "BG" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "BH" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1110 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "BI" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "BJ" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "BK" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "BL" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "BM" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "BN" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "BO" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 900 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "BP" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "BQ" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "BR" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "BS" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "BT" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "BU" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "BV" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "BW" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 580 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "BX" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "BY" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "BZ" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "B0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "B1" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 414 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "B3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "B4" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "B5" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 146 Classifications: {'peptide': 17} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 14} Chain: "B7" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 211 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 7} Chain: "B8" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1646 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 32, 'rna3p_pyr': 31} Link IDs: {'rna2p': 13, 'rna3p': 63} Chain: "B9" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2768 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 340} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "AA" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 125 Unusual residues: {' K': 38, ' MG': 87} Classifications: {'undetermined': 125} Link IDs: {None: 124} Chain: "AB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "AM" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "BA" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 362 Unusual residues: {' K': 104, ' MG': 243} Classifications: {'peptide': 1, 'undetermined': 347} Modifications used: {'COO': 1} Link IDs: {None: 347} Chain: "BB" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BC" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BD" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 1, ' MG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "BI" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "BL" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "BM" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "B4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B8" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AA" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 167 Classifications: {'water': 167} Link IDs: {None: 166} Chain: "AK" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AM" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AN" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "BA" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 617 Classifications: {'water': 617} Link IDs: {None: 616} Chain: "BC" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "BD" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "BN" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0JSP SG CYSBI 16 120.090 158.551 232.853 1.00111.26 S ATOM A0JT1 SG CYSBI 18 118.060 160.145 235.528 1.00113.66 S ATOM A0JWZ SG CYSBI 37 116.396 158.959 232.419 1.00110.94 S ATOM A0JXK SG CYSBI 40 118.635 161.953 232.334 1.00113.42 S ATOM A0WBF SG CYSB4 11 54.697 166.398 140.795 1.00 66.67 S ATOM A0WC4 SG CYSB4 14 54.501 162.908 139.659 1.00 63.35 S ATOM A0WEZ SG CYSB4 27 53.900 165.689 137.279 1.00 61.81 S Residues with excluded nonbonded symmetry interactions: 29 residue: pdb=" P ABA 404 " occ=0.60 ... (20 atoms not shown) pdb=" C4 ABA 404 " occ=0.60 residue: pdb=" P UBA2884 " occ=0.47 ... (18 atoms not shown) pdb=" C6 UBA2884 " occ=0.47 residue: pdb=" P GBA2885 " occ=0.47 ... (21 atoms not shown) pdb=" C4 GBA2885 " occ=0.47 residue: pdb=" P ABA2886 " occ=0.47 ... (20 atoms not shown) pdb=" C4 ABA2886 " occ=0.47 residue: pdb=" P ABA2887 " occ=0.47 ... (20 atoms not shown) pdb=" C4 ABA2887 " occ=0.47 residue: pdb=" P CBA2888 " occ=0.47 ... (18 atoms not shown) pdb=" C6 CBA2888 " occ=0.47 residue: pdb=" N MEQBD 150 " occ=0.49 ... (8 atoms not shown) pdb=" NE2 MEQBD 150 " occ=0.49 residue: pdb=" N ARGBW 41 " occ=0.49 ... (9 atoms not shown) pdb=" NH2 ARGBW 41 " occ=0.49 residue: pdb=" N ALABZ 2 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALABZ 2 " occ=0.50 residue: pdb=" N LYSBZ 3 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYSBZ 3 " occ=0.50 residue: pdb=" N THRB5 9 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 THRB5 9 " occ=0.50 residue: pdb=" N SERB5 10 " occ=0.50 ... (4 atoms not shown) pdb=" OG SERB5 10 " occ=0.50 ... (remaining 17 not shown) Time building chain proxies: 57.01, per 1000 atoms: 0.38 Number of scatterers: 148175 At special positions: 0 Unit cell: (238.541, 268.472, 252.146, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 3 29.99 K 147 19.00 S 158 16.00 P 4638 15.00 Mg 339 11.99 O 41512 8.00 N 27343 7.00 C 74035 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 59.56 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNAB 301 " pdb="ZN ZNAB 301 " - pdb=" NE2 HISAB 18 " pdb=" ZNB4 101 " pdb="ZN ZNB4 101 " - pdb=" ND1 HISB4 33 " pdb="ZN ZNB4 101 " - pdb=" SG CYSB4 11 " pdb="ZN ZNB4 101 " - pdb=" SG CYSB4 27 " pdb="ZN ZNB4 101 " - pdb=" SG CYSB4 14 " pdb=" ZNBI 101 " pdb="ZN ZNBI 101 " - pdb=" SG CYSBI 18 " pdb="ZN ZNBI 101 " - pdb=" SG CYSBI 40 " pdb="ZN ZNBI 101 " - pdb=" SG CYSBI 16 " pdb="ZN ZNBI 101 " - pdb=" SG CYSBI 37 " Number of angles added : 9 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11116 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: 183 helices and 74 sheets defined 39.7% alpha, 20.1% beta 1632 base pairs and 2570 stacking pairs defined. Time for finding SS restraints: 77.01 Creating SS restraints... Processing helix chain 'AB' and resid 5 through 13 removed outlier: 3.692A pdb=" N METAB 9 " --> pdb=" O SERAB 5 " (cutoff:3.500A) Processing helix chain 'AB' and resid 27 through 32 removed outlier: 3.583A pdb=" N ILEAB 31 " --> pdb=" O METAB 27 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N PHEAB 32 " --> pdb=" O LYSAB 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'AB' and resid 27 through 32' Processing helix chain 'AB' and resid 42 through 64 removed outlier: 3.545A pdb=" N THRAB 46 " --> pdb=" O ASNAB 42 " (cutoff:3.500A) Proline residue: AB 48 - end of helix removed outlier: 3.583A pdb=" N ARGAB 63 " --> pdb=" O LYSAB 59 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYSAB 64 " --> pdb=" O ILEAB 60 " (cutoff:3.500A) Processing helix chain 'AB' and resid 76 through 88 removed outlier: 4.442A pdb=" N LYSAB 81 " --> pdb=" O SERAB 77 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASPAB 82 " --> pdb=" O GLUAB 78 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALAAB 83 " --> pdb=" O ALAAB 79 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N CYSAB 87 " --> pdb=" O ALAAB 83 " (cutoff:3.500A) Processing helix chain 'AB' and resid 103 through 123 removed outlier: 4.324A pdb=" N GLNAB 109 " --> pdb=" O LYSAB 105 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SERAB 110 " --> pdb=" O THRAB 106 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLNAB 122 " --> pdb=" O GLUAB 118 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASPAB 123 " --> pdb=" O THRAB 119 " (cutoff:3.500A) Processing helix chain 'AB' and resid 130 through 148 removed outlier: 6.236A pdb=" N ALAAB 134 " --> pdb=" O THRAB 130 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEUAB 135 " --> pdb=" O LYSAB 131 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N METAB 136 " --> pdb=" O LYSAB 132 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLUAB 142 " --> pdb=" O THRAB 138 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SERAB 147 " --> pdb=" O LYSAB 143 " (cutoff:3.500A) Processing helix chain 'AB' and resid 165 through 170 Processing helix chain 'AB' and resid 171 through 180 removed outlier: 3.626A pdb=" N LEUAB 179 " --> pdb=" O GLUAB 175 " (cutoff:3.500A) Processing helix chain 'AB' and resid 206 through 227 removed outlier: 3.867A pdb=" N GLYAB 224 " --> pdb=" O THRAB 220 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SERAB 226 " --> pdb=" O ARGAB 222 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLNAB 227 " --> pdb=" O GLUAB 223 " (cutoff:3.500A) Processing helix chain 'AC' and resid 6 through 12 removed outlier: 3.821A pdb=" N ILEAC 10 " --> pdb=" O HISAC 6 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARGAC 11 " --> pdb=" O PROAC 7 " (cutoff:3.500A) Processing helix chain 'AC' and resid 28 through 48 removed outlier: 4.168A pdb=" N ALAAC 48 " --> pdb=" O THRAC 44 " (cutoff:3.500A) Processing helix chain 'AC' and resid 72 through 78 removed outlier: 3.958A pdb=" N VALAC 76 " --> pdb=" O ARGAC 72 " (cutoff:3.500A) Processing helix chain 'AC' and resid 81 through 96 removed outlier: 3.922A pdb=" N GLUAC 85 " --> pdb=" O GLYAC 81 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYSAC 86 " --> pdb=" O GLUAC 82 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASPAC 93 " --> pdb=" O LYSAC 89 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILEAC 94 " --> pdb=" O VALAC 90 " (cutoff:3.500A) Processing helix chain 'AC' and resid 108 through 113 removed outlier: 3.987A pdb=" N ASPAC 112 " --> pdb=" O LYSAC 108 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ALAAC 113 " --> pdb=" O PROAC 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'AC' and resid 108 through 113' Processing helix chain 'AC' and resid 114 through 127 Processing helix chain 'AC' and resid 129 through 145 removed outlier: 3.541A pdb=" N LEUAC 144 " --> pdb=" O ASNAC 140 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLYAC 145 " --> pdb=" O ALAAC 141 " (cutoff:3.500A) Processing helix chain 'AD' and resid 7 through 16 removed outlier: 4.216A pdb=" N LEUAD 11 " --> pdb=" O PROAD 7 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SERAD 12 " --> pdb=" O LYSAD 8 " (cutoff:3.500A) Processing helix chain 'AD' and resid 27 through 32 removed outlier: 3.835A pdb=" N LYSAD 31 " --> pdb=" O ALAAD 27 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYSAD 32 " --> pdb=" O ILEAD 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'AD' and resid 27 through 32' Processing helix chain 'AD' and resid 49 through 66 Processing helix chain 'AD' and resid 68 through 83 removed outlier: 5.166A pdb=" N LYSAD 83 " --> pdb=" O ALAAD 79 " (cutoff:3.500A) Processing helix chain 'AD' and resid 85 through 97 removed outlier: 3.765A pdb=" N ARGAD 97 " --> pdb=" O LEUAD 93 " (cutoff:3.500A) Processing helix chain 'AD' and resid 98 through 106 removed outlier: 3.595A pdb=" N TYRAD 103 " --> pdb=" O ASPAD 99 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLYAD 106 " --> pdb=" O VALAD 102 " (cutoff:3.500A) Processing helix chain 'AD' and resid 110 through 121 removed outlier: 3.676A pdb=" N LYSAD 121 " --> pdb=" O LEUAD 117 " (cutoff:3.500A) Processing helix chain 'AD' and resid 146 through 151 removed outlier: 4.952A pdb=" N LYSAD 151 " --> pdb=" O GLUAD 147 " (cutoff:3.500A) Processing helix chain 'AD' and resid 152 through 166 removed outlier: 3.510A pdb=" N GLUAD 160 " --> pdb=" O LYSAD 156 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEUAD 161 " --> pdb=" O ALAAD 157 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLUAD 163 " --> pdb=" O LEUAD 159 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLNAD 164 " --> pdb=" O GLUAD 160 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARGAD 165 " --> pdb=" O LEUAD 161 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLUAD 166 " --> pdb=" O ALAAD 162 " (cutoff:3.500A) Processing helix chain 'AD' and resid 187 through 192 removed outlier: 5.178A pdb=" N SERAD 192 " --> pdb=" O ARGAD 188 " (cutoff:3.500A) Processing helix chain 'AD' and resid 196 through 206 removed outlier: 3.730A pdb=" N ILEAD 200 " --> pdb=" O ASNAD 196 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VALAD 201 " --> pdb=" O GLUAD 197 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLUAD 202 " --> pdb=" O HISAD 198 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYSAD 206 " --> pdb=" O GLUAD 202 " (cutoff:3.500A) Processing helix chain 'AE' and resid 55 through 71 removed outlier: 3.905A pdb=" N ARGAE 69 " --> pdb=" O GLUAE 65 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASNAE 70 " --> pdb=" O LYSAE 66 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N METAE 71 " --> pdb=" O ALAAE 67 " (cutoff:3.500A) Processing helix chain 'AE' and resid 109 through 119 removed outlier: 4.516A pdb=" N ALAAE 113 " --> pdb=" O GLYAE 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VALAE 114 " --> pdb=" O ALAAE 110 " (cutoff:3.500A) Processing helix chain 'AE' and resid 132 through 148 removed outlier: 3.735A pdb=" N METAE 147 " --> pdb=" O GLYAE 143 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ASNAE 148 " --> pdb=" O LEUAE 144 " (cutoff:3.500A) Processing helix chain 'AE' and resid 149 through 158 removed outlier: 3.942A pdb=" N ALAAE 155 " --> pdb=" O GLUAE 151 " (cutoff:3.500A) Processing helix chain 'AF' and resid 11 through 16 removed outlier: 3.844A pdb=" N SERAF 15 " --> pdb=" O HISAF 11 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLUAF 16 " --> pdb=" O PROAF 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'AF' and resid 11 through 16' Processing helix chain 'AF' and resid 17 through 33 removed outlier: 4.428A pdb=" N GLUAF 23 " --> pdb=" O PROAF 19 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALAAF 28 " --> pdb=" O ARGAF 24 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALAAF 32 " --> pdb=" O ALAAF 28 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLUAF 33 " --> pdb=" O ILEAF 29 " (cutoff:3.500A) Processing helix chain 'AF' and resid 67 through 82 removed outlier: 3.607A pdb=" N ILEAF 71 " --> pdb=" O PROAF 67 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLUAF 73 " --> pdb=" O GLUAF 69 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ASPAF 82 " --> pdb=" O PHEAF 78 " (cutoff:3.500A) Processing helix chain 'AF' and resid 100 through 105 Processing helix chain 'AG' and resid 20 through 31 removed outlier: 3.606A pdb=" N ALAAG 24 " --> pdb=" O SERAG 20 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYSAG 25 " --> pdb=" O GLUAG 21 " (cutoff:3.500A) Processing helix chain 'AG' and resid 35 through 55 removed outlier: 3.566A pdb=" N ALAAG 39 " --> pdb=" O LYSAG 35 " (cutoff:3.500A) Processing helix chain 'AG' and resid 57 through 70 removed outlier: 3.711A pdb=" N PHEAG 62 " --> pdb=" O GLUAG 58 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALAAG 65 " --> pdb=" O ALAAG 61 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASNAG 68 " --> pdb=" O VALAG 64 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VALAG 69 " --> pdb=" O ALAAG 65 " (cutoff:3.500A) Processing helix chain 'AG' and resid 92 through 111 removed outlier: 3.750A pdb=" N ASNAG 97 " --> pdb=" O PROAG 93 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYSAG 110 " --> pdb=" O GLUAG 106 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARGAG 111 " --> pdb=" O ALAAG 107 " (cutoff:3.500A) Processing helix chain 'AG' and resid 115 through 130 removed outlier: 3.565A pdb=" N GLUAG 123 " --> pdb=" O ARGAG 119 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALAAG 128 " --> pdb=" O LEUAG 124 " (cutoff:3.500A) Processing helix chain 'AG' and resid 132 through 149 removed outlier: 3.757A pdb=" N ASNAG 148 " --> pdb=" O METAG 144 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYSAG 149 " --> pdb=" O ALAAG 145 " (cutoff:3.500A) Processing helix chain 'AH' and resid 5 through 21 Processing helix chain 'AH' and resid 30 through 44 Processing helix chain 'AH' and resid 112 through 120 removed outlier: 3.510A pdb=" N GLYAH 120 " --> pdb=" O ALAAH 116 " (cutoff:3.500A) Processing helix chain 'AI' and resid 34 through 40 removed outlier: 4.518A pdb=" N GLYAI 40 " --> pdb=" O GLUAI 36 " (cutoff:3.500A) Processing helix chain 'AI' and resid 41 through 56 removed outlier: 3.541A pdb=" N ARGAI 45 " --> pdb=" O ARGAI 41 " (cutoff:3.500A) Proline residue: AI 51 - end of helix removed outlier: 3.871A pdb=" N ASPAI 56 " --> pdb=" O LEUAI 52 " (cutoff:3.500A) Processing helix chain 'AI' and resid 71 through 92 removed outlier: 3.507A pdb=" N ASPAI 91 " --> pdb=" O LEUAI 87 " (cutoff:3.500A) Processing helix chain 'AI' and resid 94 through 102 removed outlier: 3.691A pdb=" N LEUAI 98 " --> pdb=" O LEUAI 94 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLYAI 102 " --> pdb=" O LEUAI 98 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 14 through 33 removed outlier: 3.525A pdb=" N THRAJ 32 " --> pdb=" O THRAJ 28 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLYAJ 33 " --> pdb=" O ALAAJ 29 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 80 through 90 removed outlier: 4.027A pdb=" N VALAJ 84 " --> pdb=" O THRAJ 80 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASPAJ 85 " --> pdb=" O GLUAJ 81 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALAAJ 86 " --> pdb=" O LYSAJ 82 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N METAJ 88 " --> pdb=" O VALAJ 84 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARGAJ 89 " --> pdb=" O ASPAJ 85 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEUAJ 90 " --> pdb=" O ALAAJ 86 " (cutoff:3.500A) Processing helix chain 'AK' and resid 46 through 51 removed outlier: 3.570A pdb=" N SERAK 50 " --> pdb=" O THRAK 46 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLYAK 51 " --> pdb=" O ALAAK 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'AK' and resid 46 through 51' Processing helix chain 'AK' and resid 54 through 59 removed outlier: 3.853A pdb=" N SERAK 58 " --> pdb=" O GLYAK 54 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THRAK 59 " --> pdb=" O SERAK 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'AK' and resid 54 through 59' Processing helix chain 'AK' and resid 60 through 75 Processing helix chain 'AK' and resid 92 through 104 removed outlier: 3.972A pdb=" N THRAK 96 " --> pdb=" O GLYAK 92 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILEAK 97 " --> pdb=" O ARGAK 93 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALAAK 99 " --> pdb=" O SERAK 95 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEUAK 100 " --> pdb=" O THRAK 96 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLYAK 104 " --> pdb=" O LEUAK 100 " (cutoff:3.500A) Processing helix chain 'AL' and resid 3 through 11 removed outlier: 3.819A pdb=" N ARGAL 9 " --> pdb=" O ASNAL 5 " (cutoff:3.500A) Proline residue: AL 11 - end of helix Processing helix chain 'AL' and resid 113 through 118 removed outlier: 4.266A pdb=" N TYRAL 117 " --> pdb=" O ALAAL 113 " (cutoff:3.500A) Processing helix chain 'AM' and resid 14 through 22 removed outlier: 4.308A pdb=" N THRAM 20 " --> pdb=" O VALAM 16 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SERAM 21 " --> pdb=" O ILEAM 17 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILEAM 22 " --> pdb=" O ALAAM 18 " (cutoff:3.500A) Processing helix chain 'AM' and resid 26 through 38 removed outlier: 4.218A pdb=" N SERAM 30 " --> pdb=" O GLYAM 26 " (cutoff:3.500A) Processing helix chain 'AM' and resid 49 through 64 removed outlier: 3.556A pdb=" N ASPAM 58 " --> pdb=" O ASPAM 54 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLUAM 59 " --> pdb=" O THRAM 55 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALAAM 61 " --> pdb=" O ARGAM 57 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYSAM 62 " --> pdb=" O ASPAM 58 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHEAM 63 " --> pdb=" O GLUAM 59 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N VALAM 64 " --> pdb=" O VALAM 60 " (cutoff:3.500A) Processing helix chain 'AM' and resid 66 through 84 removed outlier: 3.533A pdb=" N GLYAM 84 " --> pdb=" O LEUAM 80 " (cutoff:3.500A) Processing helix chain 'AM' and resid 85 through 94 Processing helix chain 'AM' and resid 106 through 111 Processing helix chain 'AN' and resid 2 through 20 removed outlier: 3.740A pdb=" N LYSAN 6 " --> pdb=" O LYSAN 2 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYSAN 18 " --> pdb=" O ALAAN 14 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYRAN 19 " --> pdb=" O LEUAN 15 " (cutoff:3.500A) Processing helix chain 'AN' and resid 23 through 29 removed outlier: 5.360A pdb=" N LYSAN 27 " --> pdb=" O ARGAN 23 " (cutoff:3.500A) Processing helix chain 'AN' and resid 38 through 51 removed outlier: 3.648A pdb=" N ALAAN 44 " --> pdb=" O ASPAN 40 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLNAN 49 " --> pdb=" O VALAN 45 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THRAN 50 " --> pdb=" O LEUAN 46 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEUAN 51 " --> pdb=" O LYSAN 47 " (cutoff:3.500A) Processing helix chain 'AN' and resid 80 through 91 removed outlier: 3.786A pdb=" N ARGAN 85 " --> pdb=" O ARGAN 81 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARGAN 90 " --> pdb=" O GLUAN 86 " (cutoff:3.500A) Processing helix chain 'AO' and resid 4 through 16 removed outlier: 3.764A pdb=" N ALAAO 9 " --> pdb=" O THRAO 5 " (cutoff:3.500A) Processing helix chain 'AO' and resid 24 through 44 removed outlier: 4.450A pdb=" N GLYAO 41 " --> pdb=" O ASNAO 37 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HISAO 42 " --> pdb=" O HISAO 38 " (cutoff:3.500A) Processing helix chain 'AO' and resid 49 through 74 removed outlier: 3.855A pdb=" N GLYAO 55 " --> pdb=" O HISAO 51 " (cutoff:3.500A) Processing helix chain 'AO' and resid 75 through 86 Processing helix chain 'AP' and resid 53 through 64 removed outlier: 3.532A pdb=" N HISAP 59 " --> pdb=" O ASPAP 55 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLNAP 63 " --> pdb=" O HISAP 59 " (cutoff:3.500A) Processing helix chain 'AP' and resid 68 through 81 Processing helix chain 'AR' and resid 25 through 34 removed outlier: 4.337A pdb=" N ASNAR 31 " --> pdb=" O ALAAR 27 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYRAR 32 " --> pdb=" O THRAR 28 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILEAR 33 " --> pdb=" O LEUAR 29 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N THRAR 34 " --> pdb=" O LYSAR 30 " (cutoff:3.500A) Processing helix chain 'AR' and resid 41 through 46 Processing helix chain 'AR' and resid 48 through 66 Processing helix chain 'AS' and resid 12 through 26 removed outlier: 3.846A pdb=" N LYSAS 18 " --> pdb=" O HISAS 14 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLUAS 24 " --> pdb=" O GLUAS 20 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SERAS 25 " --> pdb=" O LYSAS 21 " (cutoff:3.500A) Processing helix chain 'AS' and resid 70 through 76 removed outlier: 4.960A pdb=" N PHEAS 74 " --> pdb=" O LYSAS 70 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ALAAS 75 " --> pdb=" O LEUAS 71 " (cutoff:3.500A) Proline residue: AS 76 - end of helix No H-bonds generated for 'chain 'AS' and resid 70 through 76' Processing helix chain 'AT' and resid 4 through 41 removed outlier: 3.698A pdb=" N LYSAT 8 " --> pdb=" O ILEAT 4 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYSAT 9 " --> pdb=" O LYSAT 5 " (cutoff:3.500A) Processing helix chain 'AT' and resid 44 through 65 Proline residue: AT 56 - end of helix Processing helix chain 'AT' and resid 68 through 87 Processing helix chain 'AU' and resid 11 through 27 removed outlier: 3.681A pdb=" N ARGAU 17 " --> pdb=" O ASPAU 13 " (cutoff:3.500A) Processing helix chain 'AU' and resid 28 through 37 removed outlier: 3.595A pdb=" N ARGAU 34 " --> pdb=" O ALAAU 30 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLUAU 36 " --> pdb=" O VALAU 32 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N PHEAU 37 " --> pdb=" O ARGAU 33 " (cutoff:3.500A) Processing helix chain 'AU' and resid 40 through 56 removed outlier: 4.240A pdb=" N HISAU 56 " --> pdb=" O ALAAU 52 " (cutoff:3.500A) Processing helix chain 'BC' and resid 10 through 15 removed outlier: 5.241A pdb=" N HISBC 15 " --> pdb=" O PROBC 11 " (cutoff:3.500A) Processing helix chain 'BC' and resid 30 through 35 removed outlier: 3.916A pdb=" N LEUBC 34 " --> pdb=" O PHEBC 30 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLUBC 35 " --> pdb=" O ALABC 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'BC' and resid 30 through 35' Processing helix chain 'BC' and resid 131 through 136 removed outlier: 3.733A pdb=" N ILEBC 135 " --> pdb=" O PROBC 131 " (cutoff:3.500A) Proline residue: BC 136 - end of helix No H-bonds generated for 'chain 'BC' and resid 131 through 136' Processing helix chain 'BC' and resid 207 through 215 removed outlier: 3.917A pdb=" N ALABC 211 " --> pdb=" O LYSBC 207 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARGBC 212 " --> pdb=" O ALABC 208 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARGBC 214 " --> pdb=" O ALABC 210 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLYBC 215 " --> pdb=" O ALABC 211 " (cutoff:3.500A) Processing helix chain 'BC' and resid 221 through 226 removed outlier: 4.067A pdb=" N METBC 225 " --> pdb=" O ARGBC 221 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ASNBC 226 " --> pdb=" O GLYBC 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'BC' and resid 221 through 226' Processing helix chain 'BC' and resid 260 through 268 removed outlier: 3.795A pdb=" N ASPBC 264 " --> pdb=" O ASNBC 260 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LYSBC 265 " --> pdb=" O LYSBC 261 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHEBC 266 " --> pdb=" O ARGBC 262 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILEBC 267 " --> pdb=" O THRBC 263 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VALBC 268 " --> pdb=" O ASPBC 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'BC' and resid 260 through 268' Processing helix chain 'BC' and resid 197 through 202 removed outlier: 4.552A pdb=" N METBC 201 " --> pdb=" O ALABC 198 " (cutoff:3.500A) Processing helix chain 'BD' and resid 56 through 61 removed outlier: 3.667A pdb=" N VALBD 60 " --> pdb=" O LYSBD 56 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THRBD 61 " --> pdb=" O ALABD 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'BD' and resid 56 through 61' Processing helix chain 'BD' and resid 62 through 72 removed outlier: 3.867A pdb=" N ALABD 71 " --> pdb=" O HISBD 67 " (cutoff:3.500A) Processing helix chain 'BD' and resid 98 through 103 removed outlier: 4.463A pdb=" N ALABD 102 " --> pdb=" O VALBD 98 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ASPBD 103 " --> pdb=" O GLUBD 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'BD' and resid 98 through 103' Processing helix chain 'BD' and resid 120 through 125 Processing helix chain 'BE' and resid 15 through 20 Processing helix chain 'BE' and resid 24 through 40 removed outlier: 3.525A pdb=" N GLNBE 30 " --> pdb=" O ALABE 26 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALABE 39 " --> pdb=" O TYRBE 35 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARGBE 40 " --> pdb=" O ALABE 36 " (cutoff:3.500A) Processing helix chain 'BE' and resid 97 through 116 removed outlier: 3.509A pdb=" N ARGBE 114 " --> pdb=" O SERBE 110 " (cutoff:3.500A) Processing helix chain 'BE' and resid 130 through 142 Processing helix chain 'BE' and resid 154 through 163 removed outlier: 3.762A pdb=" N LEUBE 159 " --> pdb=" O GLUBE 155 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARGBE 162 " --> pdb=" O PHEBE 158 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ASNBE 163 " --> pdb=" O LEUBE 159 " (cutoff:3.500A) Processing helix chain 'BE' and resid 176 through 184 removed outlier: 5.849A pdb=" N ASPBE 184 " --> pdb=" O LEUBE 180 " (cutoff:3.500A) Processing helix chain 'BE' and resid 189 through 201 removed outlier: 3.555A pdb=" N LYSBE 194 " --> pdb=" O ALABE 190 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLNBE 195 " --> pdb=" O ASPBE 191 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLUBE 198 " --> pdb=" O LYSBE 194 " (cutoff:3.500A) Processing helix chain 'BF' and resid 2 through 21 removed outlier: 3.541A pdb=" N ASPBF 6 " --> pdb=" O ALABF 2 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYRBF 7 " --> pdb=" O LYSBF 3 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VALBF 13 " --> pdb=" O LYSBF 9 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LYSBF 14 " --> pdb=" O ASPBF 10 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLUBF 19 " --> pdb=" O LYSBF 15 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHEBF 20 " --> pdb=" O LEUBF 16 " (cutoff:3.500A) Processing helix chain 'BF' and resid 42 through 47 removed outlier: 3.794A pdb=" N ASPBF 46 " --> pdb=" O GLUBF 42 " (cutoff:3.500A) Processing helix chain 'BF' and resid 48 through 62 removed outlier: 3.535A pdb=" N LEUBF 57 " --> pdb=" O ALABF 53 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALABF 58 " --> pdb=" O ALABF 54 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALABF 59 " --> pdb=" O ALABF 55 " (cutoff:3.500A) Processing helix chain 'BF' and resid 93 through 111 removed outlier: 3.504A pdb=" N ILEBF 106 " --> pdb=" O ARGBF 102 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VALBF 108 " --> pdb=" O ILEBF 104 " (cutoff:3.500A) Proline residue: BF 109 - end of helix Processing helix chain 'BF' and resid 162 through 174 removed outlier: 3.645A pdb=" N PHEBF 173 " --> pdb=" O LEUBF 169 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASPBF 174 " --> pdb=" O LEUBF 170 " (cutoff:3.500A) Processing helix chain 'BF' and resid 134 through 139 removed outlier: 3.943A pdb=" N ILEBF 137 " --> pdb=" O GLUBF 134 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHEBF 138 " --> pdb=" O GLNBF 135 " (cutoff:3.500A) Proline residue: BF 139 - end of helix No H-bonds generated for 'chain 'BF' and resid 134 through 139' Processing helix chain 'BG' and resid 2 through 8 removed outlier: 3.585A pdb=" N ALABG 7 " --> pdb=" O ARGBG 3 " (cutoff:3.500A) Proline residue: BG 8 - end of helix Processing helix chain 'BG' and resid 60 through 81 removed outlier: 3.585A pdb=" N ILEBG 77 " --> pdb=" O ASNBG 73 " (cutoff:3.500A) Processing helix chain 'BG' and resid 137 through 153 removed outlier: 3.957A pdb=" N TYRBG 151 " --> pdb=" O ASPBG 147 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARGBG 152 " --> pdb=" O LEUBG 148 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARGBG 153 " --> pdb=" O ARGBG 149 " (cutoff:3.500A) Processing helix chain 'BH' and resid 22 through 29 Processing helix chain 'BH' and resid 42 through 47 Processing helix chain 'BH' and resid 48 through 74 removed outlier: 4.950A pdb=" N ALABH 52 " --> pdb=" O GLUBH 48 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLUBH 53 " --> pdb=" O ALABH 49 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALABH 56 " --> pdb=" O ALABH 52 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALABH 59 " --> pdb=" O GLUBH 55 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VALBH 61 " --> pdb=" O LYSBH 57 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALABH 64 " --> pdb=" O GLUBH 60 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYSBH 71 " --> pdb=" O ALABH 67 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILEBH 72 " --> pdb=" O ARGBH 68 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALABH 74 " --> pdb=" O GLUBH 70 " (cutoff:3.500A) Processing helix chain 'BH' and resid 95 through 107 removed outlier: 3.786A pdb=" N ALABH 102 " --> pdb=" O ASPBH 98 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VALBH 103 " --> pdb=" O ILEBH 99 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALABH 105 " --> pdb=" O ASPBH 101 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALABH 106 " --> pdb=" O ALABH 102 " (cutoff:3.500A) Processing helix chain 'BI' and resid 56 through 65 removed outlier: 4.070A pdb=" N PHEBI 64 " --> pdb=" O PHEBI 60 " (cutoff:3.500A) Processing helix chain 'BI' and resid 44 through 49 removed outlier: 5.050A pdb=" N LYSBI 47 " --> pdb=" O PHEBI 44 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLNBI 48 " --> pdb=" O THRBI 45 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ARGBI 49 " --> pdb=" O GLYBI 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'BI' and resid 44 through 49' Processing helix chain 'BJ' and resid 24 through 38 removed outlier: 4.603A pdb=" N GLUBJ 31 " --> pdb=" O ARGBJ 27 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 88 through 96 Processing helix chain 'BJ' and resid 97 through 110 removed outlier: 4.299A pdb=" N ILEBJ 101 " --> pdb=" O PROBJ 97 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N METBJ 108 " --> pdb=" O ALABJ 104 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEUBJ 109 " --> pdb=" O VALBJ 105 " (cutoff:3.500A) Proline residue: BJ 110 - end of helix Processing helix chain 'BJ' and resid 112 through 122 removed outlier: 3.663A pdb=" N ARGBJ 120 " --> pdb=" O ARGBJ 116 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYSBJ 121 " --> pdb=" O ALABJ 117 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEUBJ 122 " --> pdb=" O METBJ 118 " (cutoff:3.500A) Processing helix chain 'BK' and resid 104 through 109 removed outlier: 4.737A pdb=" N ARGBK 108 " --> pdb=" O THRBK 104 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N SERBK 109 " --> pdb=" O ARGBK 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'BK' and resid 104 through 109' Processing helix chain 'BK' and resid 112 through 119 removed outlier: 3.610A pdb=" N LEUBK 118 " --> pdb=" O LYSBK 114 " (cutoff:3.500A) Processing helix chain 'BL' and resid 37 through 42 removed outlier: 4.411A pdb=" N ARGBL 41 " --> pdb=" O GLYBL 37 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N SERBL 42 " --> pdb=" O GLNBL 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'BL' and resid 37 through 42' Processing helix chain 'BL' and resid 56 through 62 removed outlier: 3.600A pdb=" N LEUBL 61 " --> pdb=" O LEUBL 57 " (cutoff:3.500A) Proline residue: BL 62 - end of helix Processing helix chain 'BL' and resid 68 through 75 removed outlier: 4.148A pdb=" N ALABL 72 " --> pdb=" O SERBL 68 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILEBL 73 " --> pdb=" O ARGBL 69 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THRBL 74 " --> pdb=" O LYSBL 70 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ALABL 75 " --> pdb=" O ALABL 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'BL' and resid 68 through 75' Processing helix chain 'BL' and resid 78 through 85 removed outlier: 3.874A pdb=" N LEUBL 82 " --> pdb=" O ARGBL 78 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALABL 83 " --> pdb=" O LEUBL 79 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYSBL 84 " --> pdb=" O SERBL 80 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VALBL 85 " --> pdb=" O ASPBL 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'BL' and resid 78 through 85' Processing helix chain 'BL' and resid 91 through 99 Processing helix chain 'BL' and resid 128 through 139 removed outlier: 3.597A pdb=" N ALABL 137 " --> pdb=" O ALABL 133 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALABL 138 " --> pdb=" O ALABL 134 " (cutoff:3.500A) Processing helix chain 'BM' and resid 42 through 58 removed outlier: 3.607A pdb=" N ARGBM 55 " --> pdb=" O ARGBM 51 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALABM 56 " --> pdb=" O ALABM 52 " (cutoff:3.500A) Processing helix chain 'BM' and resid 109 through 125 removed outlier: 3.844A pdb=" N GLUBM 115 " --> pdb=" O GLUBM 111 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALABM 122 " --> pdb=" O LYSBM 118 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYSBM 123 " --> pdb=" O LEUBM 119 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEUBM 124 " --> pdb=" O ALABM 120 " (cutoff:3.500A) Proline residue: BM 125 - end of helix Processing helix chain 'BN' and resid 13 through 32 Processing helix chain 'BN' and resid 37 through 57 removed outlier: 3.744A pdb=" N ARGBN 45 " --> pdb=" O ALABN 41 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARGBN 46 " --> pdb=" O LYSBN 42 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VALBN 47 " --> pdb=" O GLUBN 43 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLUBN 49 " --> pdb=" O ARGBN 45 " (cutoff:3.500A) Proline residue: BN 50 - end of helix removed outlier: 4.583A pdb=" N THRBN 57 " --> pdb=" O THRBN 53 " (cutoff:3.500A) Processing helix chain 'BN' and resid 59 through 71 removed outlier: 3.525A pdb=" N ALABN 68 " --> pdb=" O ARGBN 64 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARGBN 69 " --> pdb=" O LEUBN 65 " (cutoff:3.500A) Processing helix chain 'BN' and resid 72 through 88 removed outlier: 3.639A pdb=" N LYSBN 78 " --> pdb=" O GLUBN 74 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEUBN 83 " --> pdb=" O LEUBN 79 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLYBN 84 " --> pdb=" O PHEBN 80 " (cutoff:3.500A) Proline residue: BN 85 - end of helix Processing helix chain 'BO' and resid 2 through 22 removed outlier: 4.691A pdb=" N ARGBO 13 " --> pdb=" O ARGBO 9 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ALABO 14 " --> pdb=" O ARGBO 10 " (cutoff:3.500A) Processing helix chain 'BO' and resid 55 through 63 removed outlier: 6.002A pdb=" N GLUBO 60 " --> pdb=" O LYSBO 56 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLNBO 61 " --> pdb=" O ALABO 57 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEUBO 62 " --> pdb=" O ILEBO 58 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LYSBO 63 " --> pdb=" O ALABO 59 " (cutoff:3.500A) Processing helix chain 'BO' and resid 67 through 86 removed outlier: 3.586A pdb=" N GLUBO 84 " --> pdb=" O GLUBO 80 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYSBO 85 " --> pdb=" O ARGBO 81 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLYBO 86 " --> pdb=" O ALABO 82 " (cutoff:3.500A) Processing helix chain 'BO' and resid 101 through 114 removed outlier: 3.600A pdb=" N ALABO 113 " --> pdb=" O ALABO 109 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLYBO 114 " --> pdb=" O ALABO 110 " (cutoff:3.500A) Processing helix chain 'BP' and resid 2 through 13 removed outlier: 3.653A pdb=" N GLUBP 11 " --> pdb=" O GLNBP 7 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLNBP 12 " --> pdb=" O LEUBP 8 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N METBP 13 " --> pdb=" O GLUBP 9 " (cutoff:3.500A) Processing helix chain 'BP' and resid 97 through 104 removed outlier: 4.819A pdb=" N ARGBP 101 " --> pdb=" O LEUBP 97 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLUBP 102 " --> pdb=" O TYRBP 98 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARGBP 103 " --> pdb=" O TYRBP 99 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N THRBP 104 " --> pdb=" O LEUBP 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'BP' and resid 97 through 104' Processing helix chain 'BQ' and resid 7 through 22 removed outlier: 3.871A pdb=" N ILEBQ 17 " --> pdb=" O ARGBQ 13 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLNBQ 20 " --> pdb=" O LYSBQ 16 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYSBQ 22 " --> pdb=" O LEUBQ 18 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 26 through 31 removed outlier: 3.832A pdb=" N ARGBQ 30 " --> pdb=" O GLYBQ 26 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 39 through 73 removed outlier: 3.961A pdb=" N ARGBQ 51 " --> pdb=" O TYRBQ 47 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLNBQ 52 " --> pdb=" O ARGBQ 48 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYSBQ 54 " --> pdb=" O ARGBQ 50 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARGBQ 55 " --> pdb=" O ARGBQ 51 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARGBQ 58 " --> pdb=" O LYSBQ 54 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALABQ 63 " --> pdb=" O GLNBQ 59 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALABQ 67 " --> pdb=" O ALABQ 63 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLNBQ 71 " --> pdb=" O ALABQ 67 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASNBQ 72 " --> pdb=" O ALABQ 68 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 75 through 87 Processing helix chain 'BQ' and resid 91 through 102 removed outlier: 3.579A pdb=" N ASPBQ 97 " --> pdb=" O LYSBQ 93 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VALBQ 100 " --> pdb=" O ALABQ 96 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 103 through 118 Processing helix chain 'BS' and resid 13 through 25 removed outlier: 3.684A pdb=" N LEUBS 19 " --> pdb=" O GLNBS 15 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VALBS 20 " --> pdb=" O LYSBS 16 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEUBS 23 " --> pdb=" O LEUBS 19 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILEBS 24 " --> pdb=" O VALBS 20 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARGBS 25 " --> pdb=" O ALABS 21 " (cutoff:3.500A) Processing helix chain 'BS' and resid 28 through 40 removed outlier: 3.578A pdb=" N ASPBS 34 " --> pdb=" O SERBS 30 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYRBS 38 " --> pdb=" O ASPBS 34 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THRBS 39 " --> pdb=" O ILEBS 35 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ASNBS 40 " --> pdb=" O LEUBS 36 " (cutoff:3.500A) Processing helix chain 'BS' and resid 41 through 61 removed outlier: 3.938A pdb=" N VALBS 45 " --> pdb=" O LYSBS 41 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEUBS 46 " --> pdb=" O LYSBS 42 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLUBS 59 " --> pdb=" O ILEBS 55 " (cutoff:3.500A) Processing helix chain 'BT' and resid 3 through 11 removed outlier: 3.590A pdb=" N LEUBT 7 " --> pdb=" O ARGBT 3 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEUBT 8 " --> pdb=" O GLUBT 4 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYSBT 9 " --> pdb=" O GLUBT 5 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VALBT 10 " --> pdb=" O ARGBT 6 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEUBT 11 " --> pdb=" O LEUBT 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'BT' and resid 3 through 11' Processing helix chain 'BT' and resid 17 through 27 removed outlier: 3.500A pdb=" N GLUBT 25 " --> pdb=" O SERBT 21 " (cutoff:3.500A) Processing helix chain 'BT' and resid 39 through 51 removed outlier: 3.516A pdb=" N LYSBT 49 " --> pdb=" O ALABT 45 " (cutoff:3.500A) Processing helix chain 'BU' and resid 66 through 71 removed outlier: 4.079A pdb=" N VALBU 70 " --> pdb=" O GLNBU 66 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ALABU 71 " --> pdb=" O VALBU 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'BU' and resid 66 through 71' Processing helix chain 'BV' and resid 13 through 24 removed outlier: 3.786A pdb=" N SERBV 17 " --> pdb=" O GLYBV 13 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARGBV 18 " --> pdb=" O LYSBV 14 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARGBV 21 " --> pdb=" O SERBV 17 " (cutoff:3.500A) Processing helix chain 'BV' and resid 43 through 53 removed outlier: 3.686A pdb=" N ALABV 52 " --> pdb=" O METBV 48 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYSBV 53 " --> pdb=" O ASNBV 49 " (cutoff:3.500A) Processing helix chain 'BV' and resid 54 through 59 removed outlier: 4.318A pdb=" N SERBV 58 " --> pdb=" O ALABV 54 " (cutoff:3.500A) Processing helix chain 'BX' and resid 52 through 63 removed outlier: 3.586A pdb=" N ARGBX 57 " --> pdb=" O ALABX 53 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASPBX 60 " --> pdb=" O METBX 56 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYSBX 61 " --> pdb=" O ARGBX 57 " (cutoff:3.500A) Processing helix chain 'BX' and resid 64 through 75 removed outlier: 3.710A pdb=" N ALABX 69 " --> pdb=" O ASPBX 65 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLUBX 70 " --> pdb=" O THRBX 66 " (cutoff:3.500A) Processing helix chain 'BY' and resid 2 through 10 removed outlier: 6.119A pdb=" N LEUBY 6 " --> pdb=" O LYSBY 2 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARGBY 7 " --> pdb=" O ALABY 3 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLUBY 8 " --> pdb=" O LYSBY 4 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYSBY 9 " --> pdb=" O GLUBY 5 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N SERBY 10 " --> pdb=" O LEUBY 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'BY' and resid 2 through 10' Processing helix chain 'BY' and resid 11 through 35 removed outlier: 3.500A pdb=" N GLUBY 17 " --> pdb=" O GLUBY 13 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARGBY 23 " --> pdb=" O LEUBY 19 " (cutoff:3.500A) Processing helix chain 'BY' and resid 39 through 62 removed outlier: 4.761A pdb=" N LEUBY 43 " --> pdb=" O GLNBY 39 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYSBY 44 " --> pdb=" O SERBY 40 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALABY 51 " --> pdb=" O ARGBY 47 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARGBY 52 " --> pdb=" O ARGBY 48 " (cutoff:3.500A) Processing helix chain 'BZ' and resid 17 through 28 Processing helix chain 'BZ' and resid 41 through 52 Processing helix chain 'B0' and resid 9 through 19 removed outlier: 3.657A pdb=" N GLYB0 14 " --> pdb=" O ARGB0 10 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N HISB0 19 " --> pdb=" O METB0 15 " (cutoff:3.500A) Processing helix chain 'B2' and resid 8 through 16 Processing helix chain 'B2' and resid 17 through 24 removed outlier: 3.585A pdb=" N ALAB2 23 " --> pdb=" O ARGB2 19 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THRB2 24 " --> pdb=" O ALAB2 20 " (cutoff:3.500A) Processing helix chain 'B2' and resid 25 through 38 Processing helix chain 'B3' and resid 7 through 14 removed outlier: 3.735A pdb=" N LYSB3 12 " --> pdb=" O ARGB3 8 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARGB3 13 " --> pdb=" O GLYB3 9 " (cutoff:3.500A) Processing helix chain 'B3' and resid 32 through 37 removed outlier: 4.425A pdb=" N LYSB3 36 " --> pdb=" O ILEB3 32 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ALAB3 37 " --> pdb=" O LEUB3 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'B3' and resid 32 through 37' Processing helix chain 'B3' and resid 38 through 46 removed outlier: 3.521A pdb=" N LEUB3 44 " --> pdb=" O ARGB3 40 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARGB3 45 " --> pdb=" O LYSB3 41 " (cutoff:3.500A) Proline residue: B3 46 - end of helix Processing helix chain 'B3' and resid 51 through 63 removed outlier: 4.529A pdb=" N GLYB3 56 " --> pdb=" O LYSB3 52 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LEUB3 57 " --> pdb=" O GLYB3 53 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VALB3 58 " --> pdb=" O ASPB3 54 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N CYSB3 61 " --> pdb=" O LEUB3 57 " (cutoff:3.500A) Proline residue: B3 63 - end of helix Processing helix chain 'B5' and resid 11 through 17 removed outlier: 3.739A pdb=" N ILEB5 15 " --> pdb=" O LYSB5 11 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASNB5 17 " --> pdb=" O PHEB5 13 " (cutoff:3.500A) Processing helix chain 'B9' and resid 6 through 26 removed outlier: 4.765A pdb=" N ARGB9 10 " --> pdb=" O PROB9 6 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEUB9 21 " --> pdb=" O ARGB9 17 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARGB9 22 " --> pdb=" O SERB9 18 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLYB9 23 " --> pdb=" O ASPB9 19 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYRB9 24 " --> pdb=" O VALB9 20 " (cutoff:3.500A) Processing helix chain 'B9' and resid 27 through 42 removed outlier: 3.650A pdb=" N GLUB9 35 " --> pdb=" O LYSB9 31 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLUB9 36 " --> pdb=" O GLUB9 32 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLUB9 40 " --> pdb=" O GLUB9 36 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLUB9 42 " --> pdb=" O ASNB9 38 " (cutoff:3.500A) Processing helix chain 'B9' and resid 49 through 90 removed outlier: 4.323A pdb=" N SERB9 61 " --> pdb=" O GLYB9 57 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SERB9 62 " --> pdb=" O LYSB9 58 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VALB9 66 " --> pdb=" O SERB9 62 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THRB9 69 " --> pdb=" O ALAB9 65 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLNB9 75 " --> pdb=" O ASPB9 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEUB9 83 " --> pdb=" O ASPB9 79 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEUB9 86 " --> pdb=" O GLYB9 82 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALAB9 90 " --> pdb=" O LEUB9 86 " (cutoff:3.500A) Processing helix chain 'B9' and resid 92 through 120 removed outlier: 4.942A pdb=" N VALB9 100 " --> pdb=" O PHEB9 96 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALAB9 101 " --> pdb=" O ASNB9 97 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLUB9 107 " --> pdb=" O LEUB9 103 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLNB9 112 " --> pdb=" O GLUB9 108 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ARGB9 116 " --> pdb=" O GLNB9 112 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ARGB9 117 " --> pdb=" O LEUB9 113 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N METB9 118 " --> pdb=" O GLUB9 114 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N SERB9 120 " --> pdb=" O ARGB9 116 " (cutoff:3.500A) Processing helix chain 'B9' and resid 138 through 160 removed outlier: 3.828A pdb=" N METB9 151 " --> pdb=" O METB9 147 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLUB9 157 " --> pdb=" O LEUB9 153 " (cutoff:3.500A) Processing helix chain 'B9' and resid 187 through 193 removed outlier: 3.589A pdb=" N TRPB9 191 " --> pdb=" O TYRB9 187 " (cutoff:3.500A) Processing helix chain 'B9' and resid 235 through 240 removed outlier: 3.850A pdb=" N LEUB9 239 " --> pdb=" O ASNB9 235 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ARGB9 240 " --> pdb=" O PROB9 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'B9' and resid 235 through 240' Processing helix chain 'B9' and resid 279 through 315 removed outlier: 3.692A pdb=" N METB9 288 " --> pdb=" O LYSB9 284 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N SERB9 315 " --> pdb=" O GLUB9 311 " (cutoff:3.500A) Processing helix chain 'B9' and resid 344 through 351 Processing helix chain 'B9' and resid 353 through 362 removed outlier: 4.201A pdb=" N GLUB9 358 " --> pdb=" O ASPB9 354 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALAB9 359 " --> pdb=" O GLNB9 355 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LYSB9 362 " --> pdb=" O GLUB9 358 " (cutoff:3.500A) Processing helix chain 'B9' and resid 43 through 48 removed outlier: 3.784A pdb=" N VALB9 46 " --> pdb=" O GLNB9 43 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRPB9 47 " --> pdb=" O PROB9 44 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASNB9 48 " --> pdb=" O ASPB9 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'B9' and resid 43 through 48' Processing sheet with id= 1, first strand: chain 'AB' and resid 15 through 18 removed outlier: 5.375A pdb=" N HISAB 15 " --> pdb=" O ILEAB 41 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N HISAB 39 " --> pdb=" O GLYAB 17 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'AB' and resid 67 through 71 Processing sheet with id= 3, first strand: chain 'AC' and resid 54 through 59 removed outlier: 3.585A pdb=" N ARGAC 54 " --> pdb=" O HISAC 69 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THRAC 70 " --> pdb=" O ALAAC 104 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VALAC 106 " --> pdb=" O THRAC 70 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'AC' and resid 164 through 169 removed outlier: 5.957A pdb=" N ARGAC 164 " --> pdb=" O GLYAC 155 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASPAC 181 " --> pdb=" O LYSAC 204 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLUAC 206 " --> pdb=" O ARGAC 179 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ARGAC 179 " --> pdb=" O GLUAC 206 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'AD' and resid 141 through 144 removed outlier: 4.166A pdb=" N ASPAD 141 " --> pdb=" O PHEAD 182 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'AE' and resid 11 through 16 removed outlier: 6.793A pdb=" N LEUAE 36 " --> pdb=" O ILEAE 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'AE' and resid 84 through 88 removed outlier: 3.997A pdb=" N ALAAE 99 " --> pdb=" O ASNAE 122 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ASNAE 122 " --> pdb=" O ALAAE 99 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'AE' and resid 32 through 41 removed outlier: 6.951A pdb=" N ARGAE 45 " --> pdb=" O ASPAE 41 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'AF' and resid 38 through 42 removed outlier: 3.630A pdb=" N ARGAF 38 " --> pdb=" O ASNAF 63 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N TYRAF 59 " --> pdb=" O TRPAF 42 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N HISAF 3 " --> pdb=" O THRAF 92 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLUAF 5 " --> pdb=" O METAF 90 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARGAF 86 " --> pdb=" O METAF 9 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'AF' and resid 43 through 47 removed outlier: 4.037A pdb=" N GLYAF 43 " --> pdb=" O TYRAF 59 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEUAF 47 " --> pdb=" O HISAF 55 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N HISAF 55 " --> pdb=" O LEUAF 47 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'AG' and resid 72 through 79 removed outlier: 6.975A pdb=" N THRAG 72 " --> pdb=" O VALAG 91 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'AH' and resid 23 through 29 removed outlier: 6.671A pdb=" N ALAAH 23 " --> pdb=" O LEUAH 63 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASPAH 48 " --> pdb=" O THRAH 62 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'AH' and resid 74 through 77 removed outlier: 3.661A pdb=" N CYSAH 127 " --> pdb=" O VALAH 103 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VALAH 103 " --> pdb=" O ILEAH 126 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLUAH 124 " --> pdb=" O SERAH 105 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'AI' and resid 5 through 11 Processing sheet with id= 15, first strand: chain 'AJ' and resid 39 through 42 removed outlier: 4.684A pdb=" N LEUAJ 71 " --> pdb=" O LEUAJ 42 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'AJ' and resid 44 through 52 Processing sheet with id= 17, first strand: chain 'AK' and resid 30 through 35 removed outlier: 3.538A pdb=" N GLYAK 19 " --> pdb=" O ASNAK 81 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'AL' and resid 29 through 32 removed outlier: 5.240A pdb=" N LEUAL 81 " --> pdb=" O VALAL 98 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'AL' and resid 36 through 41 removed outlier: 5.283A pdb=" N LYSAL 51 " --> pdb=" O ILEAL 67 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'AP' and resid 4 through 10 removed outlier: 3.585A pdb=" N GLYAP 37 " --> pdb=" O VALAP 19 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'AQ' and resid 7 through 11 removed outlier: 6.984A pdb=" N GLUAQ 60 " --> pdb=" O VALAQ 76 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'AQ' and resid 19 through 30 No H-bonds generated for sheet with id= 22 Processing sheet with id= 23, first strand: chain 'AS' and resid 30 through 34 removed outlier: 4.228A pdb=" N LEUAS 47 " --> pdb=" O VALAS 62 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'BC' and resid 2 through 6 removed outlier: 5.854A pdb=" N VALBC 16 " --> pdb=" O CYSBC 6 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'BC' and resid 80 through 83 removed outlier: 3.592A pdb=" N ARGBC 80 " --> pdb=" O LEUBC 93 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEUBC 93 " --> pdb=" O GLUBC 79 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILEBC 74 " --> pdb=" O SERBC 118 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N SERBC 118 " --> pdb=" O ILEBC 74 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASPBC 114 " --> pdb=" O VALBC 78 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLYBC 127 " --> pdb=" O GLNBC 115 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLNBC 117 " --> pdb=" O GLYBC 127 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'BC' and resid 138 through 142 removed outlier: 4.361A pdb=" N SERBC 139 " --> pdb=" O ILEBC 164 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLNBC 163 " --> pdb=" O ARGBC 175 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THRBC 173 " --> pdb=" O VALBC 165 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLUBC 180 " --> pdb=" O LEUBC 176 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'BC' and resid 91 through 96 removed outlier: 4.154A pdb=" N GLUBC 100 " --> pdb=" O TYRBC 96 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'BD' and resid 11 through 16 removed outlier: 3.907A pdb=" N VALBD 20 " --> pdb=" O THRBD 16 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VALBD 26 " --> pdb=" O VALBD 9 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEUBD 201 " --> pdb=" O GLYBD 6 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SERBD 199 " --> pdb=" O LYSBD 8 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASPBD 200 " --> pdb=" O THRBD 112 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N THRBD 112 " --> pdb=" O ASPBD 200 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLUBD 168 " --> pdb=" O SERBD 113 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'BD' and resid 36 through 40 removed outlier: 3.887A pdb=" N LEUBD 40 " --> pdb=" O TYRBD 45 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N TYRBD 45 " --> pdb=" O LEUBD 40 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLNBD 49 " --> pdb=" O THRBD 35 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLNBD 94 " --> pdb=" O VALBD 34 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'BD' and resid 179 through 182 Processing sheet with id= 31, first strand: chain 'BD' and resid 24 through 28 Processing sheet with id= 32, first strand: chain 'BD' and resid 46 through 51 removed outlier: 5.763A pdb=" N ARGBD 46 " --> pdb=" O LEUBD 84 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'BD' and resid 105 through 108 removed outlier: 6.692A pdb=" N LYSBD 105 " --> pdb=" O VALBD 177 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'BE' and resid 1 through 6 removed outlier: 3.587A pdb=" N LEUBE 5 " --> pdb=" O SERBE 10 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N SERBE 10 " --> pdb=" O LEUBE 5 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'BE' and resid 117 through 120 removed outlier: 3.714A pdb=" N LYSBE 185 " --> pdb=" O ASPBE 145 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'BF' and resid 65 through 69 removed outlier: 3.519A pdb=" N GLYBF 86 " --> pdb=" O THRBF 68 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILEBF 85 " --> pdb=" O VALBF 40 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N GLYBF 39 " --> pdb=" O GLYBF 151 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N GLYBF 151 " --> pdb=" O GLYBF 39 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'BG' and resid 16 through 19 Processing sheet with id= 38, first strand: chain 'BG' and resid 41 through 45 removed outlier: 3.543A pdb=" N LYSBG 44 " --> pdb=" O THRBG 51 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'BG' and resid 94 through 99 removed outlier: 3.636A pdb=" N VALBG 102 " --> pdb=" O LYSBG 99 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASNBG 101 " --> pdb=" O LEUBG 117 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VALBG 113 " --> pdb=" O LEUBG 105 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'BG' and resid 121 through 125 removed outlier: 5.893A pdb=" N THRBG 129 " --> pdb=" O LEUBG 89 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VALBG 90 " --> pdb=" O GLYBG 161 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'BH' and resid 17 through 20 removed outlier: 4.855A pdb=" N ASPBH 17 " --> pdb=" O LEUBH 5 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLNBH 2 " --> pdb=" O ALABH 39 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'BH' and resid 114 through 117 removed outlier: 5.543A pdb=" N GLUBH 114 " --> pdb=" O GLNBH 133 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARGBH 116 " --> pdb=" O SERBH 131 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SERBH 131 " --> pdb=" O ARGBH 116 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'BI' and resid 11 through 16 removed outlier: 4.200A pdb=" N ASNBI 20 " --> pdb=" O CYSBI 16 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'BJ' and resid 52 through 57 removed outlier: 4.862A pdb=" N ASPBJ 19 " --> pdb=" O LEUBJ 140 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'BJ' and resid 74 through 78 removed outlier: 7.421A pdb=" N GLYBJ 83 " --> pdb=" O THRBJ 78 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'BK' and resid 56 through 60 removed outlier: 4.595A pdb=" N ASPBK 56 " --> pdb=" O ILEBK 43 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYSBK 40 " --> pdb=" O ILEBK 22 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THRBK 6 " --> pdb=" O CYSBK 21 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ASNBK 82 " --> pdb=" O METBK 7 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'BM' and resid 37 through 40 No H-bonds generated for sheet with id= 47 Processing sheet with id= 48, first strand: chain 'BM' and resid 62 through 65 removed outlier: 3.862A pdb=" N TYRBM 103 " --> pdb=" O LEUBM 33 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEUBM 33 " --> pdb=" O LEUBM 102 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYSBM 100 " --> pdb=" O ALABM 35 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'BM' and resid 30 through 36 removed outlier: 7.545A pdb=" N SERBM 30 " --> pdb=" O LYSBM 133 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYSBM 127 " --> pdb=" O VALBM 36 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'BN' and resid 33 through 36 removed outlier: 4.258A pdb=" N METBN 110 " --> pdb=" O CYSBN 100 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N TYRBN 94 " --> pdb=" O VALBN 116 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'BO' and resid 49 through 53 removed outlier: 3.638A pdb=" N VALBO 49 " --> pdb=" O VALBO 39 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILEBO 35 " --> pdb=" O THRBO 53 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VALBO 28 " --> pdb=" O ASPBO 93 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'BP' and resid 38 through 44 removed outlier: 6.452A pdb=" N THRBP 25 " --> pdb=" O LYSBP 87 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'BP' and resid 49 through 52 removed outlier: 3.706A pdb=" N ALABP 49 " --> pdb=" O THRBP 60 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N SERBP 57 " --> pdb=" O THRBP 76 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'BR' and resid 11 through 15 removed outlier: 3.738A pdb=" N METBR 40 " --> pdb=" O VALBR 4 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEUBR 39 " --> pdb=" O GLYBR 50 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLUBR 46 " --> pdb=" O ASNBR 43 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'BR' and resid 18 through 23 removed outlier: 4.406A pdb=" N GLNBR 18 " --> pdb=" O ILEBR 98 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASPBR 95 " --> pdb=" O VALBR 64 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LYSBR 60 " --> pdb=" O THRBR 99 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLUBR 31 " --> pdb=" O VALBR 63 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'BR' and resid 57 through 60 Processing sheet with id= 57, first strand: chain 'BR' and resid 65 through 68 removed outlier: 3.871A pdb=" N GLYBR 67 " --> pdb=" O PHEBR 93 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'BR' and resid 71 through 78 removed outlier: 4.177A pdb=" N TYRBR 83 " --> pdb=" O ARGBR 78 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'BS' and resid 2 through 8 Processing sheet with id= 60, first strand: chain 'BT' and resid 28 through 33 removed outlier: 6.353A pdb=" N ASNBT 28 " --> pdb=" O LEUBT 87 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYSBT 68 " --> pdb=" O GLYBT 75 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYSBT 66 " --> pdb=" O ARGBT 77 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASPBT 79 " --> pdb=" O LYSBT 64 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LYSBT 64 " --> pdb=" O ASPBT 79 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LYSBT 81 " --> pdb=" O VALBT 62 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VALBT 62 " --> pdb=" O LYSBT 81 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALABT 83 " --> pdb=" O THRBT 60 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THRBT 60 " --> pdb=" O ALABT 83 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VALBT 85 " --> pdb=" O VALBT 58 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VALBT 58 " --> pdb=" O VALBT 85 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'BU' and resid 40 through 45 removed outlier: 5.719A pdb=" N ASNBU 40 " --> pdb=" O ALABU 63 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'BU' and resid 83 through 86 Processing sheet with id= 63, first strand: chain 'BV' and resid 69 through 72 removed outlier: 6.571A pdb=" N ALABV 39 " --> pdb=" O ARGBV 9 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILEBV 89 " --> pdb=" O PROBV 27 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASPBV 76 " --> pdb=" O ASPBV 90 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'BW' and resid 65 through 71 Processing sheet with id= 65, first strand: chain 'BX' and resid 12 through 19 removed outlier: 4.917A pdb=" N ASNBX 23 " --> pdb=" O SERBX 19 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'BX' and resid 35 through 41 removed outlier: 3.555A pdb=" N ARGBX 45 " --> pdb=" O VALBX 40 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'BZ' and resid 33 through 39 removed outlier: 4.339A pdb=" N HISBZ 34 " --> pdb=" O GLNBZ 9 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N METBZ 54 " --> pdb=" O THRBZ 10 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'B0' and resid 29 through 32 removed outlier: 4.669A pdb=" N GLUB0 36 " --> pdb=" O ASPB0 31 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'B1' and resid 19 through 26 removed outlier: 6.252A pdb=" N HISB1 19 " --> pdb=" O SERB1 13 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILEB1 48 " --> pdb=" O SERB1 14 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEUB1 34 " --> pdb=" O GLUB1 51 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'B3' and resid 22 through 25 removed outlier: 5.636A pdb=" N PHEB3 22 " --> pdb=" O VALB3 50 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'B4' and resid 1 through 5 removed outlier: 3.521A pdb=" N GLYB4 38 " --> pdb=" O ARGB4 4 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HISB4 33 " --> pdb=" O CYSB4 27 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N CYSB4 27 " --> pdb=" O HISB4 33 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILEB4 23 " --> pdb=" O GLNB4 37 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'B9' and resid 161 through 166 removed outlier: 6.734A pdb=" N THRB9 180 " --> pdb=" O ILEB9 166 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LYSB9 177 " --> pdb=" O ALAB9 134 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYSB9 128 " --> pdb=" O ILEB9 183 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ASPB9 127 " --> pdb=" O GLUB9 225 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N PHEB9 217 " --> pdb=" O GLYB9 135 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ARGB9 212 " --> pdb=" O SERB9 205 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARGB9 324 " --> pdb=" O VALB9 198 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VALB9 202 " --> pdb=" O TYRB9 326 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'B9' and resid 241 through 244 removed outlier: 3.717A pdb=" N VALB9 261 " --> pdb=" O CYSB9 274 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYSB9 274 " --> pdb=" O VALB9 261 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILEB9 270 " --> pdb=" O HISB9 265 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'B9' and resid 167 through 170 removed outlier: 3.554A pdb=" N GLUB9 167 " --> pdb=" O THRB9 180 " (cutoff:3.500A) 1920 hydrogen bonds defined for protein. 5670 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4082 hydrogen bonds 6296 hydrogen bond angles 0 basepair planarities 1632 basepair parallelities 2570 stacking parallelities Total time for adding SS restraints: 332.18 Time building geometry restraints manager: 64.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.49: 112640 1.49 - 1.85: 46831 1.85 - 2.21: 0 2.21 - 2.56: 0 2.56 - 2.92: 1 Bond restraints: 159472 Sorted by residual: bond pdb=" O3' UB7 7 " pdb=" P GB7 8 " ideal model delta sigma weight residual 1.607 2.920 -1.313 1.50e-02 4.44e+03 7.66e+03 bond pdb=" C4 5MUBA1939 " pdb=" C5 5MUBA1939 " ideal model delta sigma weight residual 1.802 1.400 0.402 2.00e-02 2.50e+03 4.05e+02 bond pdb=" C4 5MUBA 747 " pdb=" C5 5MUBA 747 " ideal model delta sigma weight residual 1.802 1.419 0.383 2.00e-02 2.50e+03 3.66e+02 bond pdb=" C2' ABA 892 " pdb=" C1' ABA 892 " ideal model delta sigma weight residual 1.529 1.283 0.246 1.50e-02 4.44e+03 2.68e+02 bond pdb=" O4' ABA 892 " pdb=" C1' ABA 892 " ideal model delta sigma weight residual 1.412 1.630 -0.218 1.50e-02 4.44e+03 2.11e+02 ... (remaining 159467 not shown) Histogram of bond angle deviations from ideal: 66.12 - 81.94: 4 81.94 - 97.77: 12 97.77 - 113.60: 125119 113.60 - 129.42: 107144 129.42 - 145.25: 5991 Bond angle restraints: 238270 Sorted by residual: angle pdb=" O3' UB7 7 " pdb=" P GB7 8 " pdb=" O5' GB7 8 " ideal model delta sigma weight residual 104.00 66.12 37.88 1.50e+00 4.44e-01 6.38e+02 angle pdb=" O3' UB7 7 " pdb=" P GB7 8 " pdb=" OP1 GB7 8 " ideal model delta sigma weight residual 108.00 71.81 36.19 3.00e+00 1.11e-01 1.46e+02 angle pdb=" C5' GAA 69 " pdb=" C4' GAA 69 " pdb=" O4' GAA 69 " ideal model delta sigma weight residual 109.80 125.35 -15.55 1.50e+00 4.44e-01 1.07e+02 angle pdb=" O3' UBA 826 " pdb=" P UBA 827 " pdb=" OP1 UBA 827 " ideal model delta sigma weight residual 108.00 77.76 30.24 3.00e+00 1.11e-01 1.02e+02 angle pdb=" O3' UB7 7 " pdb=" P GB7 8 " pdb=" OP2 GB7 8 " ideal model delta sigma weight residual 108.00 77.79 30.21 3.00e+00 1.11e-01 1.01e+02 ... (remaining 238265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 90672 35.75 - 71.49: 10153 71.49 - 107.24: 1152 107.24 - 142.99: 10 142.99 - 178.73: 13 Dihedral angle restraints: 102000 sinusoidal: 84775 harmonic: 17225 Sorted by residual: dihedral pdb=" CA HISB3 31 " pdb=" C HISB3 31 " pdb=" N ILEB3 32 " pdb=" CA ILEB3 32 " ideal model delta harmonic sigma weight residual -180.00 -126.97 -53.03 0 5.00e+00 4.00e-02 1.13e+02 dihedral pdb=" O4' CAA 489 " pdb=" C1' CAA 489 " pdb=" N1 CAA 489 " pdb=" C2 CAA 489 " ideal model delta sinusoidal sigma weight residual -160.00 18.73 -178.73 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' UB8 55 " pdb=" C1' UB8 55 " pdb=" N1 UB8 55 " pdb=" C2 UB8 55 " ideal model delta sinusoidal sigma weight residual 200.00 31.95 168.05 1 1.50e+01 4.44e-03 8.44e+01 ... (remaining 101997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.413: 30298 0.413 - 0.826: 5 0.826 - 1.240: 0 1.240 - 1.653: 0 1.653 - 2.066: 2 Chirality restraints: 30305 Sorted by residual: chirality pdb=" P GAA 117 " pdb=" OP1 GAA 117 " pdb=" OP2 GAA 117 " pdb=" O5' GAA 117 " both_signs ideal model delta sigma weight residual True 2.41 0.34 2.07 2.00e-01 2.50e+01 1.07e+02 chirality pdb=" P UBA 827 " pdb=" OP1 UBA 827 " pdb=" OP2 UBA 827 " pdb=" O5' UBA 827 " both_signs ideal model delta sigma weight residual True 2.41 0.36 2.05 2.00e-01 2.50e+01 1.05e+02 chirality pdb=" C4' GAA 69 " pdb=" C5' GAA 69 " pdb=" O4' GAA 69 " pdb=" C3' GAA 69 " both_signs ideal model delta sigma weight residual False -2.50 -1.68 -0.81 2.00e-01 2.50e+01 1.65e+01 ... (remaining 30302 not shown) Planarity restraints: 12977 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MGBA1835 " 0.043 2.00e-02 2.50e+03 5.81e-01 7.58e+03 pdb=" C4' 2MGBA1835 " 0.424 2.00e-02 2.50e+03 pdb=" O4' 2MGBA1835 " 0.624 2.00e-02 2.50e+03 pdb=" C3' 2MGBA1835 " -0.602 2.00e-02 2.50e+03 pdb=" O3' 2MGBA1835 " -0.583 2.00e-02 2.50e+03 pdb=" C2' 2MGBA1835 " -0.197 2.00e-02 2.50e+03 pdb=" O2' 2MGBA1835 " 0.947 2.00e-02 2.50e+03 pdb=" C1' 2MGBA1835 " 0.224 2.00e-02 2.50e+03 pdb=" N9 2MGBA1835 " -0.880 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMCBA2498 " -0.070 2.00e-02 2.50e+03 5.77e-01 7.48e+03 pdb=" C4' OMCBA2498 " -0.440 2.00e-02 2.50e+03 pdb=" O4' OMCBA2498 " -0.556 2.00e-02 2.50e+03 pdb=" C3' OMCBA2498 " 0.587 2.00e-02 2.50e+03 pdb=" O3' OMCBA2498 " 0.620 2.00e-02 2.50e+03 pdb=" C2' OMCBA2498 " 0.179 2.00e-02 2.50e+03 pdb=" O2' OMCBA2498 " -0.958 2.00e-02 2.50e+03 pdb=" C1' OMCBA2498 " -0.230 2.00e-02 2.50e+03 pdb=" N1 OMCBA2498 " 0.869 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MCAA1407 " -0.055 2.00e-02 2.50e+03 5.75e-01 7.43e+03 pdb=" C4' 5MCAA1407 " -0.437 2.00e-02 2.50e+03 pdb=" O4' 5MCAA1407 " -0.580 2.00e-02 2.50e+03 pdb=" C3' 5MCAA1407 " 0.589 2.00e-02 2.50e+03 pdb=" O3' 5MCAA1407 " 0.604 2.00e-02 2.50e+03 pdb=" C2' 5MCAA1407 " 0.192 2.00e-02 2.50e+03 pdb=" O2' 5MCAA1407 " -0.947 2.00e-02 2.50e+03 pdb=" C1' 5MCAA1407 " -0.228 2.00e-02 2.50e+03 pdb=" N1 5MCAA1407 " 0.862 2.00e-02 2.50e+03 ... (remaining 12974 not shown) Histogram of nonbonded interaction distances: 0.06 - 1.07: 22 1.07 - 2.09: 1065 2.09 - 3.11: 99647 3.11 - 4.12: 553479 4.12 - 5.14: 956880 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1611093 Sorted by model distance: nonbonded pdb=" O HOHBA3531 " pdb=" O HOHBA3553 " model vdw 0.055 2.440 nonbonded pdb=" O HOHBA3805 " pdb=" O HOHBA3817 " model vdw 0.074 2.440 nonbonded pdb=" O HOHBA3517 " pdb=" O HOHBA3642 " model vdw 0.074 2.440 nonbonded pdb=" P ABA 471 " pdb="MG MGBA3196 " model vdw 0.252 2.530 nonbonded pdb=" P CBA 179 " pdb="MG MGBA3138 " model vdw 0.281 2.530 ... (remaining 1611088 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.10 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: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 19.130 Check model and map are aligned: 1.590 Set scattering table: 0.990 Process input model: 657.240 Find NCS groups from input model: 2.880 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:9.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 695.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 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 : 0.018 1.313 159472 Z= 1.104 Angle : 1.899 37.881 238270 Z= 0.733 Chirality : 0.062 2.066 30305 Planarity : 0.018 0.581 12977 Dihedral : 22.518 178.731 90884 Min Nonbonded Distance : 0.055 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.09 % Favored : 94.82 % Rotamer: Outliers : 0.04 % Allowed : 0.55 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.10), residues: 5928 helix: -1.68 (0.11), residues: 1871 sheet: -0.71 (0.14), residues: 1205 loop : -1.16 (0.11), residues: 2852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRPAB 23 HIS 0.021 0.003 HISBC 53 PHE 0.024 0.003 PHEBQ 101 TYR 0.039 0.003 TYRAD 103 ARG 0.033 0.002 ARGBW 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 776 time to evaluate : 6.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 29 PRO cc_start: 0.8103 (Cg_endo) cc_final: 0.7872 (Cg_exo) REVERT: AB 125 THR cc_start: 0.5556 (m) cc_final: 0.5085 (m) REVERT: AC 134 MET cc_start: 0.7322 (ttm) cc_final: 0.6969 (ttm) REVERT: AD 20 PHE cc_start: 0.7860 (m-80) cc_final: 0.7485 (m-80) REVERT: AD 99 ASP cc_start: 0.7420 (p0) cc_final: 0.7019 (p0) REVERT: AD 198 HIS cc_start: 0.6926 (p90) cc_final: 0.6434 (p90) REVERT: AE 45 ARG cc_start: 0.7300 (mtp85) cc_final: 0.6958 (mtp85) REVERT: AE 111 MET cc_start: 0.8457 (mtm) cc_final: 0.7904 (mtp) REVERT: AF 26 THR cc_start: 0.8626 (p) cc_final: 0.8396 (m) REVERT: AG 15 ASP cc_start: 0.6718 (t0) cc_final: 0.6360 (t0) REVERT: AG 20 SER cc_start: 0.7375 (t) cc_final: 0.6920 (p) REVERT: AG 26 PHE cc_start: 0.8908 (t80) cc_final: 0.8367 (t80) REVERT: AG 44 TYR cc_start: 0.6846 (m-10) cc_final: 0.6406 (m-80) REVERT: AG 68 ASN cc_start: 0.8728 (m-40) cc_final: 0.8480 (m-40) REVERT: AH 27 MET cc_start: 0.7269 (ptm) cc_final: 0.6590 (ptm) REVERT: AH 49 PHE cc_start: 0.8718 (p90) cc_final: 0.8291 (p90) REVERT: AH 74 SER cc_start: 0.7414 (t) cc_final: 0.7081 (p) REVERT: AH 91 GLU cc_start: 0.7325 (pm20) cc_final: 0.6984 (mp0) REVERT: AI 14 SER cc_start: 0.8265 (t) cc_final: 0.7923 (p) REVERT: AI 22 LYS cc_start: 0.7257 (ttmm) cc_final: 0.6955 (mttp) REVERT: AJ 17 LEU cc_start: 0.8542 (tp) cc_final: 0.8173 (pp) REVERT: AJ 19 ASP cc_start: 0.7697 (t0) cc_final: 0.7343 (t70) REVERT: AK 83 GLU cc_start: 0.7521 (pm20) cc_final: 0.7282 (pm20) REVERT: AN 60 GLN cc_start: 0.7825 (mt0) cc_final: 0.7560 (pp30) REVERT: AR 21 ILE cc_start: 0.8294 (mm) cc_final: 0.8082 (mm) REVERT: AR 28 THR cc_start: 0.8997 (t) cc_final: 0.8612 (p) REVERT: AT 59 ASP cc_start: 0.7552 (m-30) cc_final: 0.7181 (m-30) REVERT: BC 114 ASP cc_start: 0.7934 (m-30) cc_final: 0.7184 (m-30) REVERT: BD 1 MET cc_start: 0.7570 (tmm) cc_final: 0.7136 (tmt) REVERT: BE 115 GLN cc_start: 0.7720 (mt0) cc_final: 0.7487 (mt0) REVERT: BE 199 MET cc_start: 0.7983 (ttm) cc_final: 0.7674 (ttt) REVERT: BF 7 TYR cc_start: 0.8993 (t80) cc_final: 0.8724 (t80) REVERT: BF 83 TYR cc_start: 0.6853 (m-80) cc_final: 0.6421 (m-80) REVERT: BF 96 MET cc_start: 0.8511 (ttp) cc_final: 0.8275 (ttp) REVERT: BG 62 TRP cc_start: 0.7674 (m100) cc_final: 0.7393 (m100) REVERT: BG 128 GLN cc_start: 0.8088 (mt0) cc_final: 0.7875 (mt0) REVERT: BG 147 ASP cc_start: 0.8262 (m-30) cc_final: 0.7965 (m-30) REVERT: BJ 71 ASP cc_start: 0.7915 (m-30) cc_final: 0.7677 (m-30) REVERT: BP 44 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7274 (mm-30) REVERT: BR 6 GLN cc_start: 0.8050 (tt0) cc_final: 0.7842 (tt0) REVERT: BR 15 SER cc_start: 0.8992 (t) cc_final: 0.8745 (t) REVERT: BR 62 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7564 (tm-30) REVERT: B9 288 MET cc_start: 0.6924 (ptp) cc_final: 0.6281 (pmm) outliers start: 2 outliers final: 2 residues processed: 777 average time/residue: 2.2619 time to fit residues: 2503.7884 Evaluate side-chains 531 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 529 time to evaluate : 6.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AR residue 26 ILE Chi-restraints excluded: chain BK residue 37 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1041 random chunks: chunk 879 optimal weight: 7.9990 chunk 789 optimal weight: 5.9990 chunk 437 optimal weight: 5.9990 chunk 269 optimal weight: 9.9990 chunk 532 optimal weight: 5.9990 chunk 421 optimal weight: 5.9990 chunk 815 optimal weight: 0.9990 chunk 315 optimal weight: 20.0000 chunk 496 optimal weight: 5.9990 chunk 607 optimal weight: 5.9990 chunk 945 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 89 GLN ** AB 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 126 ASN AD 136 GLN AD 152 GLN AE 132 ASN AF 17 GLN AF 68 GLN AG 148 ASN ** AI 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 15 HIS AK 101 ASN ** AK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 52 GLN AN 43 ASN AQ 9 GLN BE 97 ASN ** BE 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 116 GLN BH 18 GLN BH 20 ASN BJ 128 ASN BR 43 ASN BT 48 GLN B4 35 GLN B9 281 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 159472 Z= 0.188 Angle : 0.636 27.296 238270 Z= 0.341 Chirality : 0.040 1.997 30305 Planarity : 0.006 0.128 12977 Dihedral : 22.818 178.990 78998 Min Nonbonded Distance : 0.909 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.58 % Favored : 96.34 % Rotamer: Outliers : 2.08 % Allowed : 10.69 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.03 % 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: -0.92 (0.10), residues: 5928 helix: -0.24 (0.12), residues: 1933 sheet: -0.37 (0.15), residues: 1204 loop : -0.88 (0.11), residues: 2791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRPAB 23 HIS 0.005 0.001 HISBS 60 PHE 0.017 0.001 PHEAG 18 TYR 0.032 0.001 TYRAB 213 ARG 0.006 0.000 ARGB9 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 609 time to evaluate : 6.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 104 TRP cc_start: 0.8408 (t-100) cc_final: 0.8199 (t-100) REVERT: AD 152 GLN cc_start: 0.7462 (mm110) cc_final: 0.7204 (mm-40) REVERT: AD 198 HIS cc_start: 0.6737 (p90) cc_final: 0.6366 (p90) REVERT: AE 45 ARG cc_start: 0.7475 (mtp85) cc_final: 0.6993 (mtp85) REVERT: AE 111 MET cc_start: 0.8112 (mtm) cc_final: 0.7826 (mtp) REVERT: AF 70 VAL cc_start: 0.8589 (p) cc_final: 0.8355 (m) REVERT: AG 20 SER cc_start: 0.7290 (t) cc_final: 0.6921 (p) REVERT: AG 26 PHE cc_start: 0.8799 (t80) cc_final: 0.8453 (t80) REVERT: AG 44 TYR cc_start: 0.7137 (m-10) cc_final: 0.6826 (m-80) REVERT: AG 68 ASN cc_start: 0.8602 (m-40) cc_final: 0.8299 (m-40) REVERT: AH 48 ASP cc_start: 0.7784 (t70) cc_final: 0.7570 (p0) REVERT: AH 49 PHE cc_start: 0.8783 (p90) cc_final: 0.8168 (p90) REVERT: AH 74 SER cc_start: 0.7248 (t) cc_final: 0.6871 (p) REVERT: AI 20 PHE cc_start: 0.6892 (m-80) cc_final: 0.6591 (m-80) REVERT: AI 22 LYS cc_start: 0.7140 (ttmm) cc_final: 0.6834 (mttt) REVERT: AI 30 ILE cc_start: 0.8438 (mm) cc_final: 0.8190 (mm) REVERT: AI 38 TYR cc_start: 0.7244 (t80) cc_final: 0.6918 (t80) REVERT: AJ 19 ASP cc_start: 0.7758 (t0) cc_final: 0.7488 (t70) REVERT: AK 15 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7630 (mm-40) REVERT: AK 97 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8306 (pt) REVERT: AM 31 LYS cc_start: 0.8350 (mttp) cc_final: 0.8049 (mmmm) REVERT: AM 78 LYS cc_start: 0.8778 (tmmt) cc_final: 0.8444 (tmmt) REVERT: AM 80 LEU cc_start: 0.8566 (mp) cc_final: 0.8357 (mp) REVERT: AQ 17 MET cc_start: 0.7804 (ptt) cc_final: 0.7457 (ptp) REVERT: AR 21 ILE cc_start: 0.8287 (mm) cc_final: 0.8043 (mm) REVERT: BC 114 ASP cc_start: 0.7939 (m-30) cc_final: 0.7204 (m-30) REVERT: BD 1 MET cc_start: 0.7490 (tmm) cc_final: 0.7092 (tmt) REVERT: BE 3 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7789 (mm) REVERT: BF 7 TYR cc_start: 0.9011 (t80) cc_final: 0.8733 (t80) REVERT: BF 83 TYR cc_start: 0.6907 (m-80) cc_final: 0.6522 (m-10) REVERT: BG 60 ASP cc_start: 0.7866 (p0) cc_final: 0.7608 (p0) REVERT: BG 62 TRP cc_start: 0.7494 (m100) cc_final: 0.7268 (m100) REVERT: BG 167 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7681 (tt0) REVERT: BG 177 LYS cc_start: 0.2693 (pttm) cc_final: 0.2132 (ptpt) REVERT: BH 70 GLU cc_start: 0.5834 (mm-30) cc_final: 0.5387 (mp0) REVERT: BJ 71 ASP cc_start: 0.7798 (m-30) cc_final: 0.7577 (m-30) REVERT: BO 47 VAL cc_start: 0.8815 (t) cc_final: 0.8449 (p) REVERT: BO 76 LYS cc_start: 0.8936 (tttm) cc_final: 0.8395 (ttmm) REVERT: BQ 111 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7601 (mp0) REVERT: BR 62 GLU cc_start: 0.7426 (tm-30) cc_final: 0.7041 (tm-30) REVERT: BR 97 LYS cc_start: 0.8835 (tttp) cc_final: 0.8617 (tttp) REVERT: BV 58 SER cc_start: 0.8601 (m) cc_final: 0.8365 (p) REVERT: B9 73 MET cc_start: 0.4575 (mmp) cc_final: 0.4252 (mmp) outliers start: 103 outliers final: 29 residues processed: 658 average time/residue: 2.0934 time to fit residues: 2016.0971 Evaluate side-chains 555 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 522 time to evaluate : 6.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AC residue 53 SER Chi-restraints excluded: chain AD residue 140 ASN Chi-restraints excluded: chain AD residue 169 THR Chi-restraints excluded: chain AE residue 80 THR Chi-restraints excluded: chain AI residue 73 SER Chi-restraints excluded: chain AJ residue 50 THR Chi-restraints excluded: chain AJ residue 73 LEU Chi-restraints excluded: chain AK residue 97 ILE Chi-restraints excluded: chain AL residue 109 ASP Chi-restraints excluded: chain AM residue 20 THR Chi-restraints excluded: chain AM residue 89 LEU Chi-restraints excluded: chain AN residue 45 VAL Chi-restraints excluded: chain AO residue 22 THR Chi-restraints excluded: chain AP residue 74 LEU Chi-restraints excluded: chain AR residue 44 ILE Chi-restraints excluded: chain AS residue 43 ASN Chi-restraints excluded: chain AS residue 58 VAL Chi-restraints excluded: chain BD residue 18 ASP Chi-restraints excluded: chain BE residue 3 LEU Chi-restraints excluded: chain BF residue 61 SER Chi-restraints excluded: chain BG residue 2 SER Chi-restraints excluded: chain BG residue 131 ILE Chi-restraints excluded: chain BG residue 167 GLU Chi-restraints excluded: chain BJ residue 131 ASN Chi-restraints excluded: chain BO residue 69 ASP Chi-restraints excluded: chain BQ residue 111 GLU Chi-restraints excluded: chain BS residue 65 ASP Chi-restraints excluded: chain BS residue 68 ASP Chi-restraints excluded: chain BT residue 27 SER Chi-restraints excluded: chain BT residue 93 LEU Chi-restraints excluded: chain BU residue 18 ASP Chi-restraints excluded: chain BU residue 77 THR Chi-restraints excluded: chain B9 residue 75 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1041 random chunks: chunk 525 optimal weight: 20.0000 chunk 293 optimal weight: 10.0000 chunk 786 optimal weight: 20.0000 chunk 643 optimal weight: 10.0000 chunk 260 optimal weight: 20.0000 chunk 947 optimal weight: 20.0000 chunk 1023 optimal weight: 30.0000 chunk 843 optimal weight: 30.0000 chunk 939 optimal weight: 7.9990 chunk 322 optimal weight: 30.0000 chunk 759 optimal weight: 8.9990 overall best weight: 11.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 94 HIS AD 100 ASN AF 94 HIS AH 67 GLN AI 5 GLN ** AK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 73 ASN BG 111 HIS BG 128 GLN BK 3 GLN BM 13 HIS BR 43 ASN BU 40 ASN BU 46 GLN B9 199 HIS B9 281 HIS B9 355 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 159472 Z= 0.340 Angle : 0.692 26.993 238270 Z= 0.365 Chirality : 0.043 2.022 30305 Planarity : 0.007 0.143 12977 Dihedral : 22.804 179.444 78994 Min Nonbonded Distance : 0.856 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.30 % Favored : 95.61 % Rotamer: Outliers : 3.60 % Allowed : 13.21 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.03 % 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: -0.71 (0.11), residues: 5928 helix: 0.15 (0.12), residues: 1949 sheet: -0.20 (0.15), residues: 1203 loop : -0.97 (0.11), residues: 2776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPAB 23 HIS 0.008 0.001 HISB0 42 PHE 0.022 0.002 PHEAU 37 TYR 0.022 0.002 TYRAB 213 ARG 0.011 0.001 ARGBW 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 551 time to evaluate : 6.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AD 99 ASP cc_start: 0.7298 (t0) cc_final: 0.6966 (t0) REVERT: AD 152 GLN cc_start: 0.7485 (mm110) cc_final: 0.7162 (mm110) REVERT: AD 198 HIS cc_start: 0.6864 (p90) cc_final: 0.6417 (p90) REVERT: AE 111 MET cc_start: 0.8047 (mtm) cc_final: 0.7609 (mtp) REVERT: AF 17 GLN cc_start: 0.7393 (mp10) cc_final: 0.6911 (mp-120) REVERT: AG 20 SER cc_start: 0.7465 (t) cc_final: 0.6849 (p) REVERT: AG 26 PHE cc_start: 0.8829 (t80) cc_final: 0.8498 (t80) REVERT: AG 68 ASN cc_start: 0.8576 (m-40) cc_final: 0.8278 (m-40) REVERT: AH 27 MET cc_start: 0.7128 (ptm) cc_final: 0.6899 (ptm) REVERT: AH 49 PHE cc_start: 0.8810 (p90) cc_final: 0.8283 (p90) REVERT: AI 14 SER cc_start: 0.7736 (t) cc_final: 0.7305 (p) REVERT: AI 20 PHE cc_start: 0.6825 (m-80) cc_final: 0.6461 (m-80) REVERT: AI 22 LYS cc_start: 0.7289 (ttmm) cc_final: 0.7008 (mttt) REVERT: AJ 88 MET cc_start: 0.6083 (mmp) cc_final: 0.4941 (mmp) REVERT: AK 97 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8311 (pt) REVERT: AK 109 ASN cc_start: 0.7768 (p0) cc_final: 0.7479 (p0) REVERT: AM 31 LYS cc_start: 0.8258 (mttp) cc_final: 0.8035 (mmmm) REVERT: AM 44 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6969 (mttp) REVERT: AM 80 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8276 (mp) REVERT: AO 17 ARG cc_start: 0.6762 (ttp-110) cc_final: 0.6441 (tmm-80) REVERT: AP 46 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6690 (pttm) REVERT: AQ 17 MET cc_start: 0.8037 (ptt) cc_final: 0.7627 (ptp) REVERT: AQ 57 ASP cc_start: 0.6423 (m-30) cc_final: 0.6172 (m-30) REVERT: AR 21 ILE cc_start: 0.8208 (mm) cc_final: 0.7970 (mm) REVERT: AT 86 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7241 (pp) REVERT: AU 56 HIS cc_start: 0.7081 (OUTLIER) cc_final: 0.6554 (m-70) REVERT: BC 114 ASP cc_start: 0.7893 (m-30) cc_final: 0.7374 (m-30) REVERT: BE 3 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7768 (mm) REVERT: BF 26 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7210 (ttm) REVERT: BF 83 TYR cc_start: 0.6899 (m-80) cc_final: 0.6513 (m-10) REVERT: BG 3 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7388 (mtt-85) REVERT: BG 167 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7740 (tt0) REVERT: BG 177 LYS cc_start: 0.3003 (pttm) cc_final: 0.2350 (ptpt) REVERT: BH 70 GLU cc_start: 0.5764 (mm-30) cc_final: 0.5225 (mp0) REVERT: BJ 71 ASP cc_start: 0.7787 (m-30) cc_final: 0.7564 (m-30) REVERT: BO 76 LYS cc_start: 0.8908 (tttm) cc_final: 0.8376 (ttmm) REVERT: BO 88 LYS cc_start: 0.7939 (ttpt) cc_final: 0.7731 (ttpp) REVERT: BP 44 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7165 (mm-30) REVERT: BR 26 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6783 (p0) REVERT: BR 97 LYS cc_start: 0.8814 (tttp) cc_final: 0.8604 (tttp) REVERT: BV 58 SER cc_start: 0.8574 (m) cc_final: 0.8362 (p) REVERT: BW 25 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.6807 (mtp180) REVERT: BY 5 GLU cc_start: 0.7393 (pm20) cc_final: 0.7141 (pp20) REVERT: BZ 37 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.6154 (pm20) outliers start: 178 outliers final: 76 residues processed: 651 average time/residue: 2.0648 time to fit residues: 1974.6857 Evaluate side-chains 603 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 514 time to evaluate : 6.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AC residue 53 SER Chi-restraints excluded: chain AC residue 56 VAL Chi-restraints excluded: chain AD residue 34 ILE Chi-restraints excluded: chain AD residue 140 ASN Chi-restraints excluded: chain AD residue 169 THR Chi-restraints excluded: chain AD residue 195 ILE Chi-restraints excluded: chain AE residue 56 VAL Chi-restraints excluded: chain AE residue 80 THR Chi-restraints excluded: chain AE residue 141 ILE Chi-restraints excluded: chain AF residue 9 MET Chi-restraints excluded: chain AF residue 18 VAL Chi-restraints excluded: chain AF residue 74 LEU Chi-restraints excluded: chain AF residue 84 VAL Chi-restraints excluded: chain AF residue 97 THR Chi-restraints excluded: chain AG residue 45 SER Chi-restraints excluded: chain AI residue 19 VAL Chi-restraints excluded: chain AI residue 72 ILE Chi-restraints excluded: chain AI residue 73 SER Chi-restraints excluded: chain AJ residue 50 THR Chi-restraints excluded: chain AJ residue 63 ASP Chi-restraints excluded: chain AJ residue 96 VAL Chi-restraints excluded: chain AK residue 36 ASP Chi-restraints excluded: chain AK residue 97 ILE Chi-restraints excluded: chain AL residue 109 ASP Chi-restraints excluded: chain AM residue 20 THR Chi-restraints excluded: chain AM residue 41 GLU Chi-restraints excluded: chain AM residue 44 LYS Chi-restraints excluded: chain AM residue 80 LEU Chi-restraints excluded: chain AM residue 89 LEU Chi-restraints excluded: chain AN residue 45 VAL Chi-restraints excluded: chain AO residue 22 THR Chi-restraints excluded: chain AO residue 83 GLU Chi-restraints excluded: chain AP residue 3 THR Chi-restraints excluded: chain AP residue 46 LYS Chi-restraints excluded: chain AP residue 74 LEU Chi-restraints excluded: chain AQ residue 8 LEU Chi-restraints excluded: chain AQ residue 16 LYS Chi-restraints excluded: chain AR residue 44 ILE Chi-restraints excluded: chain AS residue 33 THR Chi-restraints excluded: chain AS residue 43 ASN Chi-restraints excluded: chain AS residue 58 VAL Chi-restraints excluded: chain AS residue 71 LEU Chi-restraints excluded: chain AS residue 73 GLU Chi-restraints excluded: chain AT residue 59 ASP Chi-restraints excluded: chain AT residue 86 LEU Chi-restraints excluded: chain AU residue 56 HIS Chi-restraints excluded: chain BD residue 18 ASP Chi-restraints excluded: chain BD residue 97 SER Chi-restraints excluded: chain BE residue 3 LEU Chi-restraints excluded: chain BF residue 26 MET Chi-restraints excluded: chain BF residue 61 SER Chi-restraints excluded: chain BF residue 158 THR Chi-restraints excluded: chain BG residue 3 ARG Chi-restraints excluded: chain BG residue 44 LYS Chi-restraints excluded: chain BG residue 103 ILE Chi-restraints excluded: chain BG residue 131 ILE Chi-restraints excluded: chain BG residue 162 VAL Chi-restraints excluded: chain BG residue 167 GLU Chi-restraints excluded: chain BI residue 22 MET Chi-restraints excluded: chain BI residue 40 CYS Chi-restraints excluded: chain BJ residue 142 ILE Chi-restraints excluded: chain BK residue 7 MET Chi-restraints excluded: chain BK residue 37 ASP Chi-restraints excluded: chain BK residue 80 ASP Chi-restraints excluded: chain BL residue 55 MET Chi-restraints excluded: chain BN residue 36 THR Chi-restraints excluded: chain BO residue 58 ILE Chi-restraints excluded: chain BO residue 69 ASP Chi-restraints excluded: chain BQ residue 111 GLU Chi-restraints excluded: chain BR residue 15 SER Chi-restraints excluded: chain BR residue 25 LEU Chi-restraints excluded: chain BR residue 26 ASP Chi-restraints excluded: chain BR residue 40 MET Chi-restraints excluded: chain BS residue 68 ASP Chi-restraints excluded: chain BT residue 1 MET Chi-restraints excluded: chain BT residue 2 ILE Chi-restraints excluded: chain BT residue 27 SER Chi-restraints excluded: chain BT residue 93 LEU Chi-restraints excluded: chain BU residue 77 THR Chi-restraints excluded: chain BV residue 65 VAL Chi-restraints excluded: chain BW residue 25 ARG Chi-restraints excluded: chain BZ residue 37 GLU Chi-restraints excluded: chain BZ residue 57 VAL Chi-restraints excluded: chain B3 residue 29 LEU Chi-restraints excluded: chain B3 residue 32 ILE Chi-restraints excluded: chain B9 residue 75 GLN Chi-restraints excluded: chain B9 residue 77 LEU Chi-restraints excluded: chain B9 residue 327 VAL Chi-restraints excluded: chain B9 residue 338 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1041 random chunks: chunk 935 optimal weight: 30.0000 chunk 712 optimal weight: 6.9990 chunk 491 optimal weight: 50.0000 chunk 104 optimal weight: 50.0000 chunk 451 optimal weight: 10.0000 chunk 635 optimal weight: 10.0000 chunk 950 optimal weight: 20.0000 chunk 1006 optimal weight: 50.0000 chunk 496 optimal weight: 20.0000 chunk 900 optimal weight: 10.0000 chunk 271 optimal weight: 10.0000 overall best weight: 9.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 94 HIS ** AE 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 4 ASN ** AK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 9 GLN BG 128 GLN BH 73 ASN BM 60 GLN BR 43 ASN BU 27 ASN BU 40 ASN B4 13 ASN B5 22 HIS ** B9 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 159472 Z= 0.283 Angle : 0.643 27.209 238270 Z= 0.343 Chirality : 0.041 1.993 30305 Planarity : 0.006 0.136 12977 Dihedral : 22.755 179.788 78994 Min Nonbonded Distance : 0.844 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.88 % Favored : 96.04 % Rotamer: Outliers : 3.78 % Allowed : 15.24 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.03 % 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: -0.49 (0.11), residues: 5928 helix: 0.48 (0.12), residues: 1964 sheet: -0.17 (0.15), residues: 1197 loop : -0.91 (0.11), residues: 2767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRPAN 42 HIS 0.006 0.001 HISB0 42 PHE 0.013 0.002 PHEAD 20 TYR 0.028 0.002 TYRAG 44 ARG 0.011 0.001 ARGBX 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 562 time to evaluate : 5.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AD 152 GLN cc_start: 0.7464 (mm110) cc_final: 0.7212 (mm-40) REVERT: AE 45 ARG cc_start: 0.7421 (mtp85) cc_final: 0.6960 (mtp85) REVERT: AE 111 MET cc_start: 0.8011 (mtm) cc_final: 0.7627 (mtp) REVERT: AF 3 HIS cc_start: 0.7903 (m-70) cc_final: 0.7445 (m170) REVERT: AF 30 THR cc_start: 0.8050 (p) cc_final: 0.7850 (p) REVERT: AG 20 SER cc_start: 0.7477 (t) cc_final: 0.6882 (p) REVERT: AG 26 PHE cc_start: 0.8825 (t80) cc_final: 0.8579 (t80) REVERT: AG 68 ASN cc_start: 0.8560 (m-40) cc_final: 0.8252 (m-40) REVERT: AH 27 MET cc_start: 0.7114 (ptm) cc_final: 0.6854 (ptm) REVERT: AH 49 PHE cc_start: 0.8787 (p90) cc_final: 0.8201 (p90) REVERT: AH 90 ASP cc_start: 0.7820 (t0) cc_final: 0.7595 (t0) REVERT: AI 14 SER cc_start: 0.7607 (t) cc_final: 0.7160 (p) REVERT: AI 20 PHE cc_start: 0.6840 (m-80) cc_final: 0.6478 (m-80) REVERT: AI 22 LYS cc_start: 0.7215 (ttmm) cc_final: 0.6919 (mttt) REVERT: AJ 88 MET cc_start: 0.6242 (mmp) cc_final: 0.6000 (mmp) REVERT: AK 68 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7401 (mt-10) REVERT: AK 109 ASN cc_start: 0.7750 (p0) cc_final: 0.7509 (p0) REVERT: AM 31 LYS cc_start: 0.8199 (mttp) cc_final: 0.7964 (mmtm) REVERT: AM 78 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8597 (tmmt) REVERT: AM 80 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8283 (mp) REVERT: AO 17 ARG cc_start: 0.6955 (ttp-110) cc_final: 0.6588 (tmm-80) REVERT: AP 50 THR cc_start: 0.8065 (m) cc_final: 0.7861 (p) REVERT: AQ 57 ASP cc_start: 0.6363 (m-30) cc_final: 0.6087 (m-30) REVERT: AR 21 ILE cc_start: 0.8110 (mm) cc_final: 0.7902 (mm) REVERT: AR 28 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8687 (p) REVERT: AU 56 HIS cc_start: 0.6966 (OUTLIER) cc_final: 0.6299 (m-70) REVERT: BC 24 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8780 (mp) REVERT: BC 114 ASP cc_start: 0.7875 (m-30) cc_final: 0.7342 (m-30) REVERT: BE 3 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7717 (mt) REVERT: BF 26 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7111 (ttm) REVERT: BF 83 TYR cc_start: 0.6896 (m-80) cc_final: 0.6531 (m-10) REVERT: BG 3 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7420 (mtt-85) REVERT: BG 75 MET cc_start: 0.7019 (mtt) cc_final: 0.6719 (mtp) REVERT: BG 167 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7791 (tt0) REVERT: BG 177 LYS cc_start: 0.2965 (pttm) cc_final: 0.2176 (ptpt) REVERT: BJ 71 ASP cc_start: 0.7768 (m-30) cc_final: 0.7567 (m-30) REVERT: BP 44 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7127 (mm-30) REVERT: BR 26 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6581 (p0) REVERT: BR 97 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8600 (tttp) REVERT: BV 7 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7397 (pt0) REVERT: BV 58 SER cc_start: 0.8572 (m) cc_final: 0.8343 (p) REVERT: BW 25 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.6726 (mtp180) REVERT: BY 5 GLU cc_start: 0.7531 (pm20) cc_final: 0.7161 (pp20) REVERT: B0 36 GLU cc_start: 0.7478 (pt0) cc_final: 0.7277 (pt0) REVERT: B1 5 ILE cc_start: 0.7712 (mp) cc_final: 0.7488 (mp) REVERT: B1 7 GLU cc_start: 0.7671 (pm20) cc_final: 0.7397 (pm20) REVERT: B9 118 MET cc_start: 0.6257 (mtm) cc_final: 0.5936 (mtm) outliers start: 187 outliers final: 86 residues processed: 675 average time/residue: 2.0938 time to fit residues: 2079.2720 Evaluate side-chains 618 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 519 time to evaluate : 6.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AC residue 53 SER Chi-restraints excluded: chain AD residue 34 ILE Chi-restraints excluded: chain AD residue 140 ASN Chi-restraints excluded: chain AD residue 143 VAL Chi-restraints excluded: chain AD residue 169 THR Chi-restraints excluded: chain AE residue 56 VAL Chi-restraints excluded: chain AE residue 80 THR Chi-restraints excluded: chain AE residue 141 ILE Chi-restraints excluded: chain AE residue 148 ASN Chi-restraints excluded: chain AF residue 9 MET Chi-restraints excluded: chain AF residue 74 LEU Chi-restraints excluded: chain AF residue 84 VAL Chi-restraints excluded: chain AF residue 97 THR Chi-restraints excluded: chain AG residue 45 SER Chi-restraints excluded: chain AH residue 32 LEU Chi-restraints excluded: chain AH residue 74 SER Chi-restraints excluded: chain AI residue 19 VAL Chi-restraints excluded: chain AI residue 72 ILE Chi-restraints excluded: chain AI residue 73 SER Chi-restraints excluded: chain AJ residue 50 THR Chi-restraints excluded: chain AJ residue 63 ASP Chi-restraints excluded: chain AK residue 36 ASP Chi-restraints excluded: chain AL residue 103 ASP Chi-restraints excluded: chain AL residue 109 ASP Chi-restraints excluded: chain AM residue 20 THR Chi-restraints excluded: chain AM residue 41 GLU Chi-restraints excluded: chain AM residue 78 LYS Chi-restraints excluded: chain AM residue 80 LEU Chi-restraints excluded: chain AM residue 89 LEU Chi-restraints excluded: chain AN residue 31 SER Chi-restraints excluded: chain AN residue 45 VAL Chi-restraints excluded: chain AO residue 22 THR Chi-restraints excluded: chain AO residue 83 GLU Chi-restraints excluded: chain AP residue 3 THR Chi-restraints excluded: chain AP residue 74 LEU Chi-restraints excluded: chain AQ residue 8 LEU Chi-restraints excluded: chain AQ residue 16 LYS Chi-restraints excluded: chain AR residue 28 THR Chi-restraints excluded: chain AR residue 44 ILE Chi-restraints excluded: chain AS residue 33 THR Chi-restraints excluded: chain AS residue 43 ASN Chi-restraints excluded: chain AS residue 58 VAL Chi-restraints excluded: chain AS residue 63 THR Chi-restraints excluded: chain AS residue 71 LEU Chi-restraints excluded: chain AS residue 73 GLU Chi-restraints excluded: chain AT residue 59 ASP Chi-restraints excluded: chain AU residue 13 ASP Chi-restraints excluded: chain AU residue 56 HIS Chi-restraints excluded: chain BC residue 4 VAL Chi-restraints excluded: chain BC residue 24 LEU Chi-restraints excluded: chain BD residue 18 ASP Chi-restraints excluded: chain BD residue 97 SER Chi-restraints excluded: chain BD residue 100 LEU Chi-restraints excluded: chain BE residue 3 LEU Chi-restraints excluded: chain BE residue 51 GLU Chi-restraints excluded: chain BF residue 17 MET Chi-restraints excluded: chain BF residue 26 MET Chi-restraints excluded: chain BF residue 61 SER Chi-restraints excluded: chain BF residue 158 THR Chi-restraints excluded: chain BG residue 3 ARG Chi-restraints excluded: chain BG residue 39 ASP Chi-restraints excluded: chain BG residue 44 LYS Chi-restraints excluded: chain BG residue 88 GLN Chi-restraints excluded: chain BG residue 103 ILE Chi-restraints excluded: chain BG residue 131 ILE Chi-restraints excluded: chain BG residue 162 VAL Chi-restraints excluded: chain BG residue 167 GLU Chi-restraints excluded: chain BI residue 40 CYS Chi-restraints excluded: chain BJ residue 131 ASN Chi-restraints excluded: chain BJ residue 142 ILE Chi-restraints excluded: chain BK residue 7 MET Chi-restraints excluded: chain BK residue 37 ASP Chi-restraints excluded: chain BK residue 80 ASP Chi-restraints excluded: chain BL residue 30 THR Chi-restraints excluded: chain BL residue 55 MET Chi-restraints excluded: chain BM residue 7 THR Chi-restraints excluded: chain BO residue 58 ILE Chi-restraints excluded: chain BO residue 62 LEU Chi-restraints excluded: chain BO residue 69 ASP Chi-restraints excluded: chain BO residue 87 ILE Chi-restraints excluded: chain BQ residue 111 GLU Chi-restraints excluded: chain BR residue 15 SER Chi-restraints excluded: chain BR residue 25 LEU Chi-restraints excluded: chain BR residue 26 ASP Chi-restraints excluded: chain BR residue 40 MET Chi-restraints excluded: chain BR residue 97 LYS Chi-restraints excluded: chain BT residue 2 ILE Chi-restraints excluded: chain BT residue 27 SER Chi-restraints excluded: chain BT residue 93 LEU Chi-restraints excluded: chain BU residue 18 ASP Chi-restraints excluded: chain BV residue 7 GLU Chi-restraints excluded: chain BV residue 65 VAL Chi-restraints excluded: chain BW residue 25 ARG Chi-restraints excluded: chain BZ residue 57 VAL Chi-restraints excluded: chain B3 residue 32 ILE Chi-restraints excluded: chain B9 residue 75 GLN Chi-restraints excluded: chain B9 residue 327 VAL Chi-restraints excluded: chain B9 residue 338 THR Chi-restraints excluded: chain B9 residue 354 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1041 random chunks: chunk 838 optimal weight: 0.2980 chunk 571 optimal weight: 10.0000 chunk 14 optimal weight: 40.0000 chunk 749 optimal weight: 9.9990 chunk 415 optimal weight: 20.0000 chunk 858 optimal weight: 2.9990 chunk 695 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 chunk 513 optimal weight: 20.0000 chunk 903 optimal weight: 10.0000 chunk 253 optimal weight: 8.9990 overall best weight: 6.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 94 HIS AD 198 HIS ** AE 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 128 GLN BR 43 ASN BU 40 ASN B9 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 159472 Z= 0.211 Angle : 0.618 27.097 238270 Z= 0.332 Chirality : 0.040 1.990 30305 Planarity : 0.006 0.132 12977 Dihedral : 22.761 179.900 78994 Min Nonbonded Distance : 0.882 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.00 % Favored : 95.93 % Rotamer: Outliers : 3.50 % Allowed : 17.30 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.03 % 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: -0.29 (0.11), residues: 5928 helix: 0.74 (0.12), residues: 1939 sheet: -0.09 (0.15), residues: 1191 loop : -0.84 (0.11), residues: 2798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRPAN 42 HIS 0.010 0.001 HISAD 198 PHE 0.024 0.001 PHEAD 107 TYR 0.025 0.002 TYRAD 135 ARG 0.011 0.000 ARGBG 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 538 time to evaluate : 6.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AD 28 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7095 (pp) REVERT: AD 152 GLN cc_start: 0.7358 (mm110) cc_final: 0.7137 (mm-40) REVERT: AE 45 ARG cc_start: 0.7405 (mtp85) cc_final: 0.6851 (mtp85) REVERT: AE 111 MET cc_start: 0.8005 (mtm) cc_final: 0.7602 (mtp) REVERT: AF 1 MET cc_start: 0.6637 (tpp) cc_final: 0.6327 (tpp) REVERT: AF 3 HIS cc_start: 0.7897 (m-70) cc_final: 0.7436 (m170) REVERT: AF 17 GLN cc_start: 0.7431 (mp10) cc_final: 0.6901 (mp-120) REVERT: AF 30 THR cc_start: 0.8098 (p) cc_final: 0.7892 (p) REVERT: AG 26 PHE cc_start: 0.8817 (t80) cc_final: 0.8561 (t80) REVERT: AG 68 ASN cc_start: 0.8506 (m-40) cc_final: 0.8196 (m-40) REVERT: AH 27 MET cc_start: 0.7019 (ptm) cc_final: 0.6797 (ptm) REVERT: AH 49 PHE cc_start: 0.8770 (p90) cc_final: 0.8229 (p90) REVERT: AH 61 LEU cc_start: 0.8890 (mp) cc_final: 0.8608 (mt) REVERT: AI 14 SER cc_start: 0.7504 (t) cc_final: 0.7061 (p) REVERT: AI 20 PHE cc_start: 0.6806 (m-80) cc_final: 0.6518 (m-80) REVERT: AI 22 LYS cc_start: 0.7225 (ttmm) cc_final: 0.6916 (mttt) REVERT: AJ 88 MET cc_start: 0.6334 (mmp) cc_final: 0.5946 (mmp) REVERT: AK 68 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7419 (mt-10) REVERT: AM 31 LYS cc_start: 0.8215 (mttp) cc_final: 0.7997 (mmmm) REVERT: AM 80 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8296 (mp) REVERT: AO 17 ARG cc_start: 0.6947 (ttp-110) cc_final: 0.6575 (tmm-80) REVERT: AP 46 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6671 (pttm) REVERT: AP 50 THR cc_start: 0.8041 (m) cc_final: 0.7839 (p) REVERT: AQ 17 MET cc_start: 0.8048 (ptt) cc_final: 0.7656 (ptp) REVERT: AQ 57 ASP cc_start: 0.6265 (m-30) cc_final: 0.6001 (m-30) REVERT: AR 21 ILE cc_start: 0.8102 (mm) cc_final: 0.7894 (mm) REVERT: AR 25 ASP cc_start: 0.7618 (t0) cc_final: 0.7380 (t0) REVERT: AR 28 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8591 (p) REVERT: AS 49 ILE cc_start: 0.7326 (mp) cc_final: 0.7033 (tp) REVERT: AT 86 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7245 (pp) REVERT: BC 24 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8775 (mp) REVERT: BC 114 ASP cc_start: 0.7885 (m-30) cc_final: 0.7309 (m-30) REVERT: BE 136 GLN cc_start: 0.8130 (tp40) cc_final: 0.7917 (mm110) REVERT: BF 26 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7019 (ttm) REVERT: BF 83 TYR cc_start: 0.6912 (m-80) cc_final: 0.6551 (m-10) REVERT: BG 3 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7387 (mtt-85) REVERT: BG 75 MET cc_start: 0.7073 (mtt) cc_final: 0.6764 (mtp) REVERT: BG 128 GLN cc_start: 0.7939 (mt0) cc_final: 0.7707 (mt0) REVERT: BG 167 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: BG 177 LYS cc_start: 0.2934 (pttm) cc_final: 0.2048 (ptpt) REVERT: BJ 71 ASP cc_start: 0.7756 (m-30) cc_final: 0.7552 (m-30) REVERT: BK 7 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7709 (mpp) REVERT: BR 26 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6576 (p0) REVERT: BR 31 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7263 (mm-30) REVERT: BR 48 LYS cc_start: 0.8510 (ptpp) cc_final: 0.8188 (mttp) REVERT: BS 110 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.6041 (ppp80) REVERT: BV 58 SER cc_start: 0.8562 (m) cc_final: 0.8328 (p) REVERT: BW 25 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.6772 (mtp180) REVERT: BY 5 GLU cc_start: 0.7513 (pm20) cc_final: 0.7147 (pp20) REVERT: B9 118 MET cc_start: 0.6254 (mtm) cc_final: 0.6003 (mtm) outliers start: 173 outliers final: 96 residues processed: 643 average time/residue: 2.0162 time to fit residues: 1909.3379 Evaluate side-chains 621 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 511 time to evaluate : 5.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 111 ILE Chi-restraints excluded: chain AC residue 53 SER Chi-restraints excluded: chain AC residue 56 VAL Chi-restraints excluded: chain AD residue 28 ILE Chi-restraints excluded: chain AD residue 125 VAL Chi-restraints excluded: chain AD residue 140 ASN Chi-restraints excluded: chain AD residue 143 VAL Chi-restraints excluded: chain AD residue 169 THR Chi-restraints excluded: chain AE residue 56 VAL Chi-restraints excluded: chain AE residue 80 THR Chi-restraints excluded: chain AF residue 9 MET Chi-restraints excluded: chain AF residue 84 VAL Chi-restraints excluded: chain AF residue 97 THR Chi-restraints excluded: chain AG residue 15 ASP Chi-restraints excluded: chain AG residue 45 SER Chi-restraints excluded: chain AH residue 74 SER Chi-restraints excluded: chain AI residue 72 ILE Chi-restraints excluded: chain AI residue 73 SER Chi-restraints excluded: chain AJ residue 50 THR Chi-restraints excluded: chain AJ residue 63 ASP Chi-restraints excluded: chain AK residue 36 ASP Chi-restraints excluded: chain AL residue 103 ASP Chi-restraints excluded: chain AL residue 109 ASP Chi-restraints excluded: chain AM residue 7 ILE Chi-restraints excluded: chain AM residue 20 THR Chi-restraints excluded: chain AM residue 80 LEU Chi-restraints excluded: chain AM residue 89 LEU Chi-restraints excluded: chain AN residue 31 SER Chi-restraints excluded: chain AN residue 45 VAL Chi-restraints excluded: chain AO residue 22 THR Chi-restraints excluded: chain AO residue 83 GLU Chi-restraints excluded: chain AP residue 46 LYS Chi-restraints excluded: chain AP residue 74 LEU Chi-restraints excluded: chain AQ residue 8 LEU Chi-restraints excluded: chain AQ residue 16 LYS Chi-restraints excluded: chain AQ residue 76 VAL Chi-restraints excluded: chain AR residue 28 THR Chi-restraints excluded: chain AR residue 44 ILE Chi-restraints excluded: chain AS residue 15 LEU Chi-restraints excluded: chain AS residue 33 THR Chi-restraints excluded: chain AS residue 43 ASN Chi-restraints excluded: chain AS residue 58 VAL Chi-restraints excluded: chain AS residue 63 THR Chi-restraints excluded: chain AS residue 71 LEU Chi-restraints excluded: chain AS residue 73 GLU Chi-restraints excluded: chain AT residue 59 ASP Chi-restraints excluded: chain AT residue 86 LEU Chi-restraints excluded: chain AU residue 13 ASP Chi-restraints excluded: chain BC residue 4 VAL Chi-restraints excluded: chain BC residue 24 LEU Chi-restraints excluded: chain BD residue 18 ASP Chi-restraints excluded: chain BD residue 97 SER Chi-restraints excluded: chain BD residue 121 THR Chi-restraints excluded: chain BE residue 51 GLU Chi-restraints excluded: chain BF residue 17 MET Chi-restraints excluded: chain BF residue 26 MET Chi-restraints excluded: chain BF residue 61 SER Chi-restraints excluded: chain BF residue 158 THR Chi-restraints excluded: chain BG residue 3 ARG Chi-restraints excluded: chain BG residue 11 VAL Chi-restraints excluded: chain BG residue 39 ASP Chi-restraints excluded: chain BG residue 44 LYS Chi-restraints excluded: chain BG residue 88 GLN Chi-restraints excluded: chain BG residue 103 ILE Chi-restraints excluded: chain BG residue 131 ILE Chi-restraints excluded: chain BG residue 162 VAL Chi-restraints excluded: chain BG residue 167 GLU Chi-restraints excluded: chain BI residue 22 MET Chi-restraints excluded: chain BI residue 40 CYS Chi-restraints excluded: chain BJ residue 131 ASN Chi-restraints excluded: chain BJ residue 142 ILE Chi-restraints excluded: chain BK residue 1 MET Chi-restraints excluded: chain BK residue 7 MET Chi-restraints excluded: chain BK residue 37 ASP Chi-restraints excluded: chain BL residue 30 THR Chi-restraints excluded: chain BL residue 55 MET Chi-restraints excluded: chain BM residue 7 THR Chi-restraints excluded: chain BO residue 58 ILE Chi-restraints excluded: chain BO residue 62 LEU Chi-restraints excluded: chain BO residue 69 ASP Chi-restraints excluded: chain BO residue 87 ILE Chi-restraints excluded: chain BQ residue 111 GLU Chi-restraints excluded: chain BR residue 15 SER Chi-restraints excluded: chain BR residue 25 LEU Chi-restraints excluded: chain BR residue 26 ASP Chi-restraints excluded: chain BR residue 31 GLU Chi-restraints excluded: chain BR residue 40 MET Chi-restraints excluded: chain BR residue 43 ASN Chi-restraints excluded: chain BS residue 110 ARG Chi-restraints excluded: chain BT residue 2 ILE Chi-restraints excluded: chain BT residue 27 SER Chi-restraints excluded: chain BT residue 93 LEU Chi-restraints excluded: chain BU residue 8 ASP Chi-restraints excluded: chain BU residue 18 ASP Chi-restraints excluded: chain BU residue 72 ILE Chi-restraints excluded: chain BV residue 65 VAL Chi-restraints excluded: chain BV residue 70 ILE Chi-restraints excluded: chain BW residue 25 ARG Chi-restraints excluded: chain BY residue 17 GLU Chi-restraints excluded: chain BY residue 34 SER Chi-restraints excluded: chain BZ residue 57 VAL Chi-restraints excluded: chain B0 residue 46 ASP Chi-restraints excluded: chain B3 residue 32 ILE Chi-restraints excluded: chain B5 residue 8 VAL Chi-restraints excluded: chain B9 residue 40 GLU Chi-restraints excluded: chain B9 residue 75 GLN Chi-restraints excluded: chain B9 residue 85 GLU Chi-restraints excluded: chain B9 residue 327 VAL Chi-restraints excluded: chain B9 residue 338 THR Chi-restraints excluded: chain B9 residue 354 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1041 random chunks: chunk 338 optimal weight: 20.0000 chunk 906 optimal weight: 20.0000 chunk 198 optimal weight: 8.9990 chunk 590 optimal weight: 20.0000 chunk 248 optimal weight: 6.9990 chunk 1007 optimal weight: 20.0000 chunk 836 optimal weight: 0.0670 chunk 466 optimal weight: 20.0000 chunk 83 optimal weight: 40.0000 chunk 333 optimal weight: 20.0000 chunk 528 optimal weight: 20.0000 overall best weight: 11.2130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 94 HIS AD 198 HIS AE 135 ASN AH 118 GLN AJ 56 HIS AK 109 ASN ** AK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AN 43 ASN BC 128 ASN BG 38 ASN BU 40 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 159472 Z= 0.334 Angle : 0.680 27.451 238270 Z= 0.359 Chirality : 0.043 2.009 30305 Planarity : 0.006 0.141 12977 Dihedral : 22.785 179.692 78994 Min Nonbonded Distance : 0.826 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.44 % Favored : 95.50 % Rotamer: Outliers : 3.92 % Allowed : 18.17 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.03 % 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: -0.38 (0.11), residues: 5928 helix: 0.64 (0.12), residues: 1966 sheet: -0.09 (0.15), residues: 1176 loop : -0.91 (0.11), residues: 2786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPAN 42 HIS 0.008 0.001 HISAD 198 PHE 0.018 0.002 PHEAJ 49 TYR 0.019 0.002 TYRAG 44 ARG 0.011 0.001 ARGBG 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 536 time to evaluate : 6.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 29 PRO cc_start: 0.8398 (Cg_endo) cc_final: 0.8189 (Cg_exo) REVERT: AD 28 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7143 (pp) REVERT: AD 103 TYR cc_start: 0.8113 (t80) cc_final: 0.7899 (t80) REVERT: AD 152 GLN cc_start: 0.7428 (mm110) cc_final: 0.7106 (mm110) REVERT: AE 111 MET cc_start: 0.8055 (mtm) cc_final: 0.7746 (mtp) REVERT: AF 3 HIS cc_start: 0.7913 (m-70) cc_final: 0.7410 (m170) REVERT: AF 17 GLN cc_start: 0.7391 (mp10) cc_final: 0.6947 (mp-120) REVERT: AF 30 THR cc_start: 0.8071 (p) cc_final: 0.7870 (p) REVERT: AF 90 MET cc_start: 0.7794 (mtp) cc_final: 0.7534 (mtt) REVERT: AG 26 PHE cc_start: 0.8814 (t80) cc_final: 0.8538 (t80) REVERT: AG 68 ASN cc_start: 0.8530 (m-40) cc_final: 0.8232 (m-40) REVERT: AH 49 PHE cc_start: 0.8839 (p90) cc_final: 0.8517 (p90) REVERT: AH 61 LEU cc_start: 0.8844 (mp) cc_final: 0.8631 (mt) REVERT: AI 14 SER cc_start: 0.7622 (t) cc_final: 0.7161 (p) REVERT: AI 20 PHE cc_start: 0.6941 (m-80) cc_final: 0.6632 (m-80) REVERT: AI 22 LYS cc_start: 0.7267 (ttmm) cc_final: 0.7020 (mttp) REVERT: AJ 88 MET cc_start: 0.6459 (mmp) cc_final: 0.6181 (mmp) REVERT: AK 68 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7419 (mt-10) REVERT: AM 31 LYS cc_start: 0.8241 (mttp) cc_final: 0.8026 (mmmm) REVERT: AM 72 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7548 (tm-30) REVERT: AM 80 LEU cc_start: 0.8525 (mp) cc_final: 0.8302 (mp) REVERT: AQ 6 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.6822 (ttp-170) REVERT: AR 25 ASP cc_start: 0.7615 (t0) cc_final: 0.7329 (t0) REVERT: AR 28 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8608 (p) REVERT: AS 32 ARG cc_start: 0.7081 (mtp-110) cc_final: 0.6788 (mtp-110) REVERT: AU 56 HIS cc_start: 0.6972 (OUTLIER) cc_final: 0.6236 (m-70) REVERT: BC 24 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8790 (mp) REVERT: BC 114 ASP cc_start: 0.7904 (m-30) cc_final: 0.7327 (m-30) REVERT: BF 26 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7137 (ttm) REVERT: BF 83 TYR cc_start: 0.7001 (m-80) cc_final: 0.6716 (m-10) REVERT: BG 3 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7355 (mtt-85) REVERT: BG 167 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: BG 177 LYS cc_start: 0.3496 (pttm) cc_final: 0.2424 (ptpt) REVERT: BH 70 GLU cc_start: 0.5960 (mm-30) cc_final: 0.5204 (mp0) REVERT: BR 26 ASP cc_start: 0.7136 (OUTLIER) cc_final: 0.6643 (p0) REVERT: BR 31 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7248 (mm-30) REVERT: BR 34 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7711 (mm-30) REVERT: BS 110 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.6013 (ppp80) REVERT: BW 25 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.6758 (mtp180) REVERT: BW 83 GLU cc_start: 0.7567 (mp0) cc_final: 0.7337 (mp0) REVERT: BY 5 GLU cc_start: 0.7467 (pm20) cc_final: 0.7145 (pp20) REVERT: B9 115 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.7002 (m-80) outliers start: 194 outliers final: 113 residues processed: 656 average time/residue: 2.0753 time to fit residues: 2001.5702 Evaluate side-chains 641 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 515 time to evaluate : 6.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 111 ILE Chi-restraints excluded: chain AB residue 227 GLN Chi-restraints excluded: chain AC residue 31 ASP Chi-restraints excluded: chain AC residue 53 SER Chi-restraints excluded: chain AC residue 56 VAL Chi-restraints excluded: chain AD residue 28 ILE Chi-restraints excluded: chain AD residue 125 VAL Chi-restraints excluded: chain AD residue 143 VAL Chi-restraints excluded: chain AD residue 169 THR Chi-restraints excluded: chain AE residue 56 VAL Chi-restraints excluded: chain AE residue 80 THR Chi-restraints excluded: chain AE residue 148 ASN Chi-restraints excluded: chain AF residue 9 MET Chi-restraints excluded: chain AF residue 70 VAL Chi-restraints excluded: chain AF residue 74 LEU Chi-restraints excluded: chain AF residue 84 VAL Chi-restraints excluded: chain AF residue 97 THR Chi-restraints excluded: chain AG residue 15 ASP Chi-restraints excluded: chain AG residue 20 SER Chi-restraints excluded: chain AG residue 45 SER Chi-restraints excluded: chain AH residue 51 VAL Chi-restraints excluded: chain AH residue 74 SER Chi-restraints excluded: chain AI residue 19 VAL Chi-restraints excluded: chain AI residue 72 ILE Chi-restraints excluded: chain AI residue 73 SER Chi-restraints excluded: chain AJ residue 50 THR Chi-restraints excluded: chain AJ residue 56 HIS Chi-restraints excluded: chain AJ residue 63 ASP Chi-restraints excluded: chain AJ residue 71 LEU Chi-restraints excluded: chain AK residue 36 ASP Chi-restraints excluded: chain AL residue 103 ASP Chi-restraints excluded: chain AL residue 109 ASP Chi-restraints excluded: chain AM residue 7 ILE Chi-restraints excluded: chain AM residue 20 THR Chi-restraints excluded: chain AM residue 89 LEU Chi-restraints excluded: chain AN residue 31 SER Chi-restraints excluded: chain AN residue 45 VAL Chi-restraints excluded: chain AO residue 22 THR Chi-restraints excluded: chain AO residue 83 GLU Chi-restraints excluded: chain AP residue 3 THR Chi-restraints excluded: chain AP residue 46 LYS Chi-restraints excluded: chain AP residue 74 LEU Chi-restraints excluded: chain AQ residue 6 ARG Chi-restraints excluded: chain AQ residue 8 LEU Chi-restraints excluded: chain AQ residue 16 LYS Chi-restraints excluded: chain AQ residue 76 VAL Chi-restraints excluded: chain AR residue 28 THR Chi-restraints excluded: chain AR residue 44 ILE Chi-restraints excluded: chain AS residue 15 LEU Chi-restraints excluded: chain AS residue 33 THR Chi-restraints excluded: chain AS residue 43 ASN Chi-restraints excluded: chain AS residue 58 VAL Chi-restraints excluded: chain AS residue 63 THR Chi-restraints excluded: chain AS residue 71 LEU Chi-restraints excluded: chain AS residue 73 GLU Chi-restraints excluded: chain AT residue 59 ASP Chi-restraints excluded: chain AU residue 56 HIS Chi-restraints excluded: chain BC residue 4 VAL Chi-restraints excluded: chain BC residue 24 LEU Chi-restraints excluded: chain BC residue 137 VAL Chi-restraints excluded: chain BD residue 18 ASP Chi-restraints excluded: chain BD residue 97 SER Chi-restraints excluded: chain BD residue 121 THR Chi-restraints excluded: chain BE residue 51 GLU Chi-restraints excluded: chain BF residue 17 MET Chi-restraints excluded: chain BF residue 26 MET Chi-restraints excluded: chain BF residue 61 SER Chi-restraints excluded: chain BF residue 132 VAL Chi-restraints excluded: chain BF residue 158 THR Chi-restraints excluded: chain BG residue 3 ARG Chi-restraints excluded: chain BG residue 10 VAL Chi-restraints excluded: chain BG residue 11 VAL Chi-restraints excluded: chain BG residue 44 LYS Chi-restraints excluded: chain BG residue 103 ILE Chi-restraints excluded: chain BG residue 131 ILE Chi-restraints excluded: chain BG residue 162 VAL Chi-restraints excluded: chain BG residue 167 GLU Chi-restraints excluded: chain BH residue 20 ASN Chi-restraints excluded: chain BI residue 22 MET Chi-restraints excluded: chain BI residue 40 CYS Chi-restraints excluded: chain BJ residue 131 ASN Chi-restraints excluded: chain BJ residue 142 ILE Chi-restraints excluded: chain BK residue 1 MET Chi-restraints excluded: chain BK residue 7 MET Chi-restraints excluded: chain BK residue 37 ASP Chi-restraints excluded: chain BK residue 80 ASP Chi-restraints excluded: chain BL residue 55 MET Chi-restraints excluded: chain BM residue 7 THR Chi-restraints excluded: chain BO residue 58 ILE Chi-restraints excluded: chain BO residue 62 LEU Chi-restraints excluded: chain BO residue 69 ASP Chi-restraints excluded: chain BO residue 76 LYS Chi-restraints excluded: chain BO residue 87 ILE Chi-restraints excluded: chain BQ residue 111 GLU Chi-restraints excluded: chain BR residue 15 SER Chi-restraints excluded: chain BR residue 25 LEU Chi-restraints excluded: chain BR residue 26 ASP Chi-restraints excluded: chain BR residue 31 GLU Chi-restraints excluded: chain BR residue 40 MET Chi-restraints excluded: chain BR residue 43 ASN Chi-restraints excluded: chain BS residue 110 ARG Chi-restraints excluded: chain BT residue 1 MET Chi-restraints excluded: chain BT residue 2 ILE Chi-restraints excluded: chain BT residue 27 SER Chi-restraints excluded: chain BT residue 93 LEU Chi-restraints excluded: chain BU residue 8 ASP Chi-restraints excluded: chain BU residue 18 ASP Chi-restraints excluded: chain BU residue 72 ILE Chi-restraints excluded: chain BU residue 83 VAL Chi-restraints excluded: chain BV residue 65 VAL Chi-restraints excluded: chain BV residue 70 ILE Chi-restraints excluded: chain BW residue 25 ARG Chi-restraints excluded: chain BY residue 17 GLU Chi-restraints excluded: chain BY residue 34 SER Chi-restraints excluded: chain BZ residue 57 VAL Chi-restraints excluded: chain B0 residue 46 ASP Chi-restraints excluded: chain B2 residue 1 MET Chi-restraints excluded: chain B3 residue 32 ILE Chi-restraints excluded: chain B5 residue 8 VAL Chi-restraints excluded: chain B5 residue 9 THR Chi-restraints excluded: chain B9 residue 75 GLN Chi-restraints excluded: chain B9 residue 85 GLU Chi-restraints excluded: chain B9 residue 115 PHE Chi-restraints excluded: chain B9 residue 327 VAL Chi-restraints excluded: chain B9 residue 338 THR Chi-restraints excluded: chain B9 residue 354 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1041 random chunks: chunk 971 optimal weight: 5.9990 chunk 113 optimal weight: 50.0000 chunk 573 optimal weight: 20.0000 chunk 735 optimal weight: 1.9990 chunk 569 optimal weight: 20.0000 chunk 847 optimal weight: 7.9990 chunk 562 optimal weight: 10.0000 chunk 1003 optimal weight: 30.0000 chunk 627 optimal weight: 10.0000 chunk 611 optimal weight: 30.0000 chunk 463 optimal weight: 10.0000 overall best weight: 7.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 94 HIS AD 198 HIS ** AK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BU 40 ASN BY 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 159472 Z= 0.230 Angle : 0.635 27.148 238270 Z= 0.340 Chirality : 0.040 1.996 30305 Planarity : 0.006 0.134 12977 Dihedral : 22.777 179.682 78994 Min Nonbonded Distance : 0.881 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.07 % Favored : 95.88 % Rotamer: Outliers : 3.46 % Allowed : 19.18 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.27 (0.11), residues: 5928 helix: 0.76 (0.12), residues: 1970 sheet: -0.06 (0.15), residues: 1158 loop : -0.87 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRPAN 42 HIS 0.010 0.001 HISAJ 56 PHE 0.032 0.001 PHEAJ 49 TYR 0.026 0.002 TYRAD 135 ARG 0.014 0.000 ARGBG 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 532 time to evaluate : 6.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 154 MET cc_start: 0.6396 (tpt) cc_final: 0.6169 (tpt) REVERT: AD 28 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7129 (pp) REVERT: AE 111 MET cc_start: 0.8018 (mtm) cc_final: 0.7705 (mtp) REVERT: AF 3 HIS cc_start: 0.7876 (m-70) cc_final: 0.7441 (m170) REVERT: AF 17 GLN cc_start: 0.7480 (mp10) cc_final: 0.7075 (mp-120) REVERT: AF 30 THR cc_start: 0.8095 (p) cc_final: 0.7890 (p) REVERT: AG 20 SER cc_start: 0.7181 (OUTLIER) cc_final: 0.6421 (p) REVERT: AG 26 PHE cc_start: 0.8815 (t80) cc_final: 0.8560 (t80) REVERT: AG 68 ASN cc_start: 0.8519 (m-40) cc_final: 0.8221 (m-40) REVERT: AH 49 PHE cc_start: 0.8820 (p90) cc_final: 0.8311 (p90) REVERT: AI 14 SER cc_start: 0.7588 (t) cc_final: 0.7133 (p) REVERT: AI 20 PHE cc_start: 0.6922 (m-80) cc_final: 0.6718 (m-80) REVERT: AI 22 LYS cc_start: 0.7243 (ttmm) cc_final: 0.6999 (mttp) REVERT: AI 100 LYS cc_start: 0.7975 (mmpt) cc_final: 0.7708 (mmtm) REVERT: AJ 88 MET cc_start: 0.6432 (mmp) cc_final: 0.6045 (mmp) REVERT: AK 68 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7404 (mt-10) REVERT: AM 31 LYS cc_start: 0.8235 (mttp) cc_final: 0.7958 (mmtm) REVERT: AM 72 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7491 (tm-30) REVERT: AM 80 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8281 (mp) REVERT: AN 96 LEU cc_start: 0.8200 (tp) cc_final: 0.7998 (mt) REVERT: AQ 7 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7727 (t) REVERT: AQ 57 ASP cc_start: 0.6316 (m-30) cc_final: 0.6102 (m-30) REVERT: AR 25 ASP cc_start: 0.7629 (t0) cc_final: 0.7324 (t0) REVERT: AR 28 THR cc_start: 0.8875 (OUTLIER) cc_final: 0.8579 (p) REVERT: AS 32 ARG cc_start: 0.7070 (mtp-110) cc_final: 0.6772 (mtp-110) REVERT: AT 86 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7350 (pp) REVERT: AU 56 HIS cc_start: 0.6943 (OUTLIER) cc_final: 0.6098 (m-70) REVERT: BC 24 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8778 (mp) REVERT: BC 114 ASP cc_start: 0.7858 (m-30) cc_final: 0.7281 (m-30) REVERT: BE 123 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7858 (mptp) REVERT: BE 136 GLN cc_start: 0.8164 (tp40) cc_final: 0.7930 (mm110) REVERT: BF 26 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7025 (ttm) REVERT: BF 83 TYR cc_start: 0.6996 (m-80) cc_final: 0.6711 (m-10) REVERT: BG 3 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7348 (mtt-85) REVERT: BG 75 MET cc_start: 0.6807 (mtt) cc_final: 0.6550 (mtp) REVERT: BG 177 LYS cc_start: 0.3444 (pttm) cc_final: 0.2368 (ptpt) REVERT: BH 70 GLU cc_start: 0.6025 (mm-30) cc_final: 0.5317 (mp0) REVERT: BK 7 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7697 (mpp) REVERT: BR 26 ASP cc_start: 0.7115 (OUTLIER) cc_final: 0.6628 (p0) REVERT: BR 31 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7251 (mm-30) REVERT: BW 25 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.6748 (mtp180) REVERT: BW 83 GLU cc_start: 0.7534 (mp0) cc_final: 0.7304 (mp0) REVERT: BY 5 GLU cc_start: 0.7446 (pm20) cc_final: 0.7098 (pp20) REVERT: B1 5 ILE cc_start: 0.7653 (mp) cc_final: 0.7391 (mp) outliers start: 171 outliers final: 106 residues processed: 640 average time/residue: 2.0113 time to fit residues: 1904.9212 Evaluate side-chains 633 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 512 time to evaluate : 6.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 111 ILE Chi-restraints excluded: chain AB residue 153 ASP Chi-restraints excluded: chain AB residue 227 GLN Chi-restraints excluded: chain AC residue 31 ASP Chi-restraints excluded: chain AC residue 53 SER Chi-restraints excluded: chain AC residue 56 VAL Chi-restraints excluded: chain AD residue 28 ILE Chi-restraints excluded: chain AD residue 125 VAL Chi-restraints excluded: chain AD residue 140 ASN Chi-restraints excluded: chain AD residue 143 VAL Chi-restraints excluded: chain AD residue 169 THR Chi-restraints excluded: chain AE residue 56 VAL Chi-restraints excluded: chain AE residue 80 THR Chi-restraints excluded: chain AE residue 148 ASN Chi-restraints excluded: chain AF residue 9 MET Chi-restraints excluded: chain AF residue 74 LEU Chi-restraints excluded: chain AF residue 84 VAL Chi-restraints excluded: chain AF residue 97 THR Chi-restraints excluded: chain AG residue 15 ASP Chi-restraints excluded: chain AG residue 20 SER Chi-restraints excluded: chain AG residue 45 SER Chi-restraints excluded: chain AH residue 51 VAL Chi-restraints excluded: chain AH residue 74 SER Chi-restraints excluded: chain AI residue 19 VAL Chi-restraints excluded: chain AI residue 72 ILE Chi-restraints excluded: chain AI residue 73 SER Chi-restraints excluded: chain AJ residue 56 HIS Chi-restraints excluded: chain AJ residue 63 ASP Chi-restraints excluded: chain AJ residue 71 LEU Chi-restraints excluded: chain AK residue 36 ASP Chi-restraints excluded: chain AL residue 103 ASP Chi-restraints excluded: chain AL residue 109 ASP Chi-restraints excluded: chain AM residue 7 ILE Chi-restraints excluded: chain AM residue 20 THR Chi-restraints excluded: chain AM residue 80 LEU Chi-restraints excluded: chain AM residue 89 LEU Chi-restraints excluded: chain AN residue 31 SER Chi-restraints excluded: chain AN residue 45 VAL Chi-restraints excluded: chain AO residue 22 THR Chi-restraints excluded: chain AO residue 83 GLU Chi-restraints excluded: chain AP residue 3 THR Chi-restraints excluded: chain AP residue 46 LYS Chi-restraints excluded: chain AP residue 74 LEU Chi-restraints excluded: chain AQ residue 7 THR Chi-restraints excluded: chain AQ residue 8 LEU Chi-restraints excluded: chain AQ residue 16 LYS Chi-restraints excluded: chain AQ residue 67 LEU Chi-restraints excluded: chain AQ residue 76 VAL Chi-restraints excluded: chain AR residue 28 THR Chi-restraints excluded: chain AR residue 44 ILE Chi-restraints excluded: chain AS residue 15 LEU Chi-restraints excluded: chain AS residue 33 THR Chi-restraints excluded: chain AS residue 43 ASN Chi-restraints excluded: chain AS residue 58 VAL Chi-restraints excluded: chain AS residue 63 THR Chi-restraints excluded: chain AS residue 71 LEU Chi-restraints excluded: chain AS residue 73 GLU Chi-restraints excluded: chain AT residue 59 ASP Chi-restraints excluded: chain AT residue 86 LEU Chi-restraints excluded: chain AU residue 3 VAL Chi-restraints excluded: chain AU residue 56 HIS Chi-restraints excluded: chain BC residue 4 VAL Chi-restraints excluded: chain BC residue 24 LEU Chi-restraints excluded: chain BC residue 137 VAL Chi-restraints excluded: chain BD residue 18 ASP Chi-restraints excluded: chain BD residue 97 SER Chi-restraints excluded: chain BD residue 121 THR Chi-restraints excluded: chain BE residue 123 LYS Chi-restraints excluded: chain BF residue 17 MET Chi-restraints excluded: chain BF residue 26 MET Chi-restraints excluded: chain BF residue 61 SER Chi-restraints excluded: chain BF residue 132 VAL Chi-restraints excluded: chain BF residue 158 THR Chi-restraints excluded: chain BG residue 3 ARG Chi-restraints excluded: chain BG residue 10 VAL Chi-restraints excluded: chain BG residue 11 VAL Chi-restraints excluded: chain BG residue 44 LYS Chi-restraints excluded: chain BG residue 103 ILE Chi-restraints excluded: chain BG residue 131 ILE Chi-restraints excluded: chain BG residue 162 VAL Chi-restraints excluded: chain BH residue 108 VAL Chi-restraints excluded: chain BI residue 40 CYS Chi-restraints excluded: chain BJ residue 131 ASN Chi-restraints excluded: chain BJ residue 142 ILE Chi-restraints excluded: chain BK residue 1 MET Chi-restraints excluded: chain BK residue 7 MET Chi-restraints excluded: chain BK residue 10 VAL Chi-restraints excluded: chain BK residue 37 ASP Chi-restraints excluded: chain BK residue 80 ASP Chi-restraints excluded: chain BL residue 55 MET Chi-restraints excluded: chain BM residue 7 THR Chi-restraints excluded: chain BM residue 111 GLU Chi-restraints excluded: chain BO residue 24 THR Chi-restraints excluded: chain BO residue 58 ILE Chi-restraints excluded: chain BO residue 62 LEU Chi-restraints excluded: chain BO residue 76 LYS Chi-restraints excluded: chain BO residue 87 ILE Chi-restraints excluded: chain BQ residue 111 GLU Chi-restraints excluded: chain BR residue 25 LEU Chi-restraints excluded: chain BR residue 26 ASP Chi-restraints excluded: chain BR residue 31 GLU Chi-restraints excluded: chain BR residue 40 MET Chi-restraints excluded: chain BT residue 1 MET Chi-restraints excluded: chain BT residue 27 SER Chi-restraints excluded: chain BT residue 93 LEU Chi-restraints excluded: chain BU residue 8 ASP Chi-restraints excluded: chain BU residue 18 ASP Chi-restraints excluded: chain BU residue 83 VAL Chi-restraints excluded: chain BV residue 65 VAL Chi-restraints excluded: chain BV residue 70 ILE Chi-restraints excluded: chain BW residue 25 ARG Chi-restraints excluded: chain BY residue 17 GLU Chi-restraints excluded: chain BY residue 34 SER Chi-restraints excluded: chain BZ residue 57 VAL Chi-restraints excluded: chain B0 residue 46 ASP Chi-restraints excluded: chain B3 residue 32 ILE Chi-restraints excluded: chain B5 residue 8 VAL Chi-restraints excluded: chain B5 residue 9 THR Chi-restraints excluded: chain B9 residue 75 GLN Chi-restraints excluded: chain B9 residue 327 VAL Chi-restraints excluded: chain B9 residue 338 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.0618 > 50: distance: 38 - 39: 19.697 distance: 38 - 169: 4.800 distance: 39 - 40: 11.541 distance: 39 - 42: 6.282 distance: 40 - 41: 19.160 distance: 40 - 43: 23.146 distance: 41 - 166: 29.408 distance: 43 - 44: 8.605 distance: 44 - 45: 23.492 distance: 44 - 47: 13.643 distance: 45 - 46: 25.801 distance: 45 - 50: 6.646 distance: 47 - 48: 16.238 distance: 47 - 49: 14.310 distance: 50 - 51: 32.890 distance: 50 - 153: 30.447 distance: 51 - 52: 17.490 distance: 51 - 54: 21.777 distance: 52 - 53: 10.397 distance: 52 - 57: 29.334 distance: 53 - 150: 23.572 distance: 54 - 55: 9.500 distance: 54 - 56: 44.122 distance: 57 - 58: 20.352 distance: 58 - 59: 24.427 distance: 58 - 61: 15.202 distance: 59 - 60: 14.711 distance: 59 - 66: 16.842 distance: 61 - 62: 10.567 distance: 62 - 63: 55.711 distance: 63 - 64: 3.016 distance: 64 - 65: 12.999 distance: 66 - 67: 23.740 distance: 66 - 139: 10.647 distance: 67 - 68: 31.174 distance: 67 - 70: 27.480 distance: 68 - 69: 25.695 distance: 68 - 72: 23.457 distance: 70 - 71: 27.639 distance: 72 - 73: 52.372 distance: 73 - 74: 5.511 distance: 73 - 76: 26.047 distance: 74 - 75: 28.358 distance: 74 - 81: 9.817 distance: 76 - 77: 44.186 distance: 77 - 78: 43.162 distance: 78 - 79: 38.136 distance: 79 - 80: 37.087 distance: 81 - 82: 17.300 distance: 81 - 87: 11.562 distance: 82 - 83: 38.922 distance: 82 - 85: 29.280 distance: 83 - 84: 24.658 distance: 83 - 88: 21.915 distance: 85 - 86: 23.542 distance: 86 - 87: 23.817 distance: 88 - 89: 27.484 distance: 89 - 90: 10.544 distance: 89 - 92: 7.910 distance: 90 - 91: 30.216 distance: 90 - 95: 16.700 distance: 92 - 93: 6.455 distance: 92 - 94: 14.976 distance: 96 - 97: 4.381 distance: 96 - 99: 10.505 distance: 97 - 98: 7.212 distance: 97 - 101: 29.965 distance: 98 - 122: 20.944 distance: 99 - 100: 25.844