Starting phenix.real_space_refine on Fri Mar 22 09:29:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssn_25410/03_2024/7ssn_25410.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssn_25410/03_2024/7ssn_25410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssn_25410/03_2024/7ssn_25410.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssn_25410/03_2024/7ssn_25410.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssn_25410/03_2024/7ssn_25410.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssn_25410/03_2024/7ssn_25410.pdb" } resolution = 3.2 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= -0.022 sd= 1.168 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: 5 Type Number sf(0) Gaussians P 4730 5.49 5 S 144 5.16 5 C 72761 2.51 5 N 27107 2.21 5 O 40693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 99": "OE1" <-> "OE2" Residue "b ASP 120": "OD1" <-> "OD2" Residue "b GLU 144": "OE1" <-> "OE2" Residue "b ASP 167": "OD1" <-> "OD2" Residue "b TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c GLU 17": "OE1" <-> "OE2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 131": "OD1" <-> "OD2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ASP 181": "OD1" <-> "OD2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ASP 22": "OD1" <-> "OD2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d ARG 88": "NH1" <-> "NH2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d GLU 127": "OE1" <-> "OE2" Residue "d ASP 140": "OD1" <-> "OD2" Residue "d GLU 144": "OE1" <-> "OE2" Residue "d ASP 154": "OD1" <-> "OD2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ASP 168": "OD1" <-> "OD2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "d ASP 171": "OD1" <-> "OD2" Residue "e PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 55": "OD1" <-> "OD2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e ARG 101": "NH1" <-> "NH2" Residue "e ARG 109": "NH1" <-> "NH2" Residue "e ARG 111": "NH1" <-> "NH2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e ASP 122": "OD1" <-> "OD2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 139": "OE1" <-> "OE2" Residue "e ASP 143": "OD1" <-> "OD2" Residue "e ASP 152": "OD1" <-> "OD2" Residue "e PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "i ASP 46": "OD1" <-> "OD2" Residue "i ASP 63": "OD1" <-> "OD2" Residue "i PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 122": "OE1" <-> "OE2" Residue "i GLU 129": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ASP 19": "OD1" <-> "OD2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "j TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 37": "OD1" <-> "OD2" Residue "k PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 21": "NH1" <-> "NH2" Residue "l ARG 33": "NH1" <-> "NH2" Residue "l ARG 41": "NH1" <-> "NH2" Residue "l ARG 47": "NH1" <-> "NH2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l GLU 86": "OE1" <-> "OE2" Residue "l GLU 106": "OE1" <-> "OE2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m GLU 90": "OE1" <-> "OE2" Residue "m TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "m PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ASP 58": "OD1" <-> "OD2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o GLU 20": "OE1" <-> "OE2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "p PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p GLU 67": "OE1" <-> "OE2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p ARG 100": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 2": "NH1" <-> "NH2" Residue "q ARG 5": "NH1" <-> "NH2" Residue "q ARG 12": "NH1" <-> "NH2" Residue "q TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 32": "NH1" <-> "NH2" Residue "q TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 47": "NH1" <-> "NH2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "q ASP 90": "OD1" <-> "OD2" Residue "q ASP 101": "OD1" <-> "OD2" Residue "r TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r ASP 55": "OD1" <-> "OD2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r ARG 79": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "r PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 95": "OD1" <-> "OD2" Residue "s GLU 2": "OE1" <-> "OE2" Residue "s ASP 34": "OD1" <-> "OD2" Residue "s ASP 65": "OD1" <-> "OD2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "t GLU 5": "OE1" <-> "OE2" Residue "t GLU 18": "OE1" <-> "OE2" Residue "t PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 52": "OE1" <-> "OE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "t TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "v GLU 11": "OE1" <-> "OE2" Residue "v ASP 45": "OD1" <-> "OD2" Residue "w GLU 13": "OE1" <-> "OE2" Residue "w PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ARG 52": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "C PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 39": "OD1" <-> "OD2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "E TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ASP 20": "OD1" <-> "OD2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "G TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G ASP 87": "OD1" <-> "OD2" Residue "G ARG 107": "NH1" <-> "NH2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "G ASP 152": "OD1" <-> "OD2" Residue "G ASP 158": "OD1" <-> "OD2" Residue "G PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 166": "OD1" <-> "OD2" Residue "G GLU 168": "OE1" <-> "OE2" Residue "G GLU 174": "OE1" <-> "OE2" Residue "G ASP 191": "OD1" <-> "OD2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H ASP 82": "OD1" <-> "OD2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H GLU 160": "OE1" <-> "OE2" Residue "I TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 159": "OE1" <-> "OE2" Residue "I ASP 193": "OD1" <-> "OD2" Residue "I GLU 196": "OE1" <-> "OE2" Residue "J PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 141": "OD1" <-> "OD2" Residue "J GLU 144": "OE1" <-> "OE2" Residue "J GLU 150": "OE1" <-> "OE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "K GLU 5": "OE1" <-> "OE2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "K GLU 23": "OE1" <-> "OE2" Residue "K ASP 41": "OD1" <-> "OD2" Residue "K GLU 69": "OE1" <-> "OE2" Residue "K ASP 72": "OD1" <-> "OD2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 32": "OD1" <-> "OD2" Residue "L GLU 59": "OE1" <-> "OE2" Residue "L GLU 73": "OE1" <-> "OE2" Residue "L ASP 139": "OD1" <-> "OD2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "N GLU 52": "OE1" <-> "OE2" Residue "N GLU 96": "OE1" <-> "OE2" Residue "N GLU 111": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O GLU 24": "OE1" <-> "OE2" Residue "O PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 63": "OD1" <-> "OD2" Residue "O GLU 66": "OE1" <-> "OE2" Residue "O ASP 75": "OD1" <-> "OD2" Residue "P PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 67": "OE1" <-> "OE2" Residue "P TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 111": "OD1" <-> "OD2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "R ASP 53": "OD1" <-> "OD2" Residue "R GLU 58": "OE1" <-> "OE2" Residue "R GLU 65": "OE1" <-> "OE2" Residue "R GLU 71": "OE1" <-> "OE2" Residue "T PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 73": "OD1" <-> "OD2" Residue "U ASP 23": "OD1" <-> "OD2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U ASP 69": "OD1" <-> "OD2" Residue "U GLU 77": "OE1" <-> "OE2" Residue "V PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 59": "OE1" <-> "OE2" Residue "V GLU 79": "OE1" <-> "OE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W GLU 15": "OE1" <-> "OE2" Residue "W TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 26": "OD1" <-> "OD2" Residue "X PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 66": "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: 145435 Number of models: 1 Model: "" Number of chains: 54 Chain: "3" Number of atoms: 33012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33012 Classifications: {'RNA': 1539} Modifications used: {'5*END': 1, 'rna2p_pur': 99, 'rna2p_pyr': 58, 'rna3p_pur': 775, 'rna3p_pyr': 607} Link IDs: {'rna2p': 157, 'rna3p': 1381} Chain: "1" Number of atoms: 62317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62317 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 232, 'rna2p_pyr': 114, 'rna3p_pur': 1442, 'rna3p_pyr': 1115} Link IDs: {'rna2p': 346, 'rna3p': 2556} Chain: "2" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2568 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 3, 'rna3p_pur': 60, 'rna3p_pyr': 52} Link IDs: {'rna2p': 8, 'rna3p': 111} Chain: "5" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1647 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 3, 'rna3p_pur': 31, 'rna3p_pyr': 34} Link IDs: {'rna2p': 12, 'rna3p': 64} Chain: "b" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "c" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "d" 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: "e" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "f" 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: "i" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "j" 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: "k" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "l" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "m" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "n" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "o" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "p" 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: "q" 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: "r" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "s" 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: "t" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "u" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "v" 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: "w" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "x" 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: "y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "z" 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: "B" 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: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 410 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "D" 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: "E" 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: "F" 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: "4" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 413 Classifications: {'RNA': 19} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 14, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "6" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 33, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 65} Chain: "G" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1705 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "H" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "I" 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: "J" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1157 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "K" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "L" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "M" 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: "N" 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: "O" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "P" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 870 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "Q" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "R" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "S" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "T" 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: "U" 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: "V" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "W" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 536 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "X" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "Y" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "Z" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 545 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Time building chain proxies: 56.17, per 1000 atoms: 0.39 Number of scatterers: 145435 At special positions: 0 Unit cell: (245.68, 241.53, 253.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 144 16.00 P 4730 15.00 O 40693 8.00 N 27107 7.00 C 72761 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 11 " - pdb=" SG CYS F 14 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 61.87 Conformation dependent library (CDL) restraints added in 7.5 seconds 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10286 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 72 sheets defined 32.8% alpha, 16.7% beta 1358 base pairs and 2559 stacking pairs defined. Time for finding SS restraints: 54.42 Creating SS restraints... Processing helix chain 'b' and resid 38 through 42 removed outlier: 4.256A pdb=" N GLY b 41 " --> pdb=" O LYS b 38 " (cutoff:3.500A) Processing helix chain 'b' and resid 196 through 202 removed outlier: 4.402A pdb=" N MET b 200 " --> pdb=" O ALA b 197 " (cutoff:3.500A) Processing helix chain 'b' and resid 207 through 211 Processing helix chain 'b' and resid 220 through 224 Processing helix chain 'b' and resid 262 through 266 removed outlier: 3.673A pdb=" N ILE b 266 " --> pdb=" O ASP b 263 " (cutoff:3.500A) Processing helix chain 'c' and resid 61 through 72 removed outlier: 3.677A pdb=" N HIS c 67 " --> pdb=" O PRO c 63 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS c 70 " --> pdb=" O GLY c 66 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA c 71 " --> pdb=" O HIS c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 97 through 104 removed outlier: 3.860A pdb=" N LEU c 100 " --> pdb=" O SER c 97 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP c 103 " --> pdb=" O LEU c 100 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL c 104 " --> pdb=" O PHE c 101 " (cutoff:3.500A) Processing helix chain 'c' and resid 120 through 126 Processing helix chain 'd' and resid 24 through 38 removed outlier: 3.643A pdb=" N VAL d 31 " --> pdb=" O LEU d 27 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 115 removed outlier: 3.657A pdb=" N SER d 110 " --> pdb=" O LYS d 106 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL d 113 " --> pdb=" O LEU d 109 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG d 114 " --> pdb=" O SER d 110 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN d 115 " --> pdb=" O GLU d 111 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 141 Processing helix chain 'd' and resid 154 through 160 removed outlier: 3.760A pdb=" N ALA d 160 " --> pdb=" O ASN d 156 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 181 removed outlier: 3.694A pdb=" N ILE d 181 " --> pdb=" O PRO d 177 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 200 removed outlier: 3.785A pdb=" N LYS d 194 " --> pdb=" O ALA d 190 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN d 195 " --> pdb=" O ASP d 191 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU d 198 " --> pdb=" O LYS d 194 " (cutoff:3.500A) Processing helix chain 'e' and resid 3 through 20 removed outlier: 3.772A pdb=" N LYS e 8 " --> pdb=" O HIS e 4 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS e 13 " --> pdb=" O ASP e 9 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET e 16 " --> pdb=" O VAL e 12 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR e 17 " --> pdb=" O LYS e 13 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 27 Processing helix chain 'e' and resid 47 through 58 removed outlier: 3.705A pdb=" N LEU e 56 " --> pdb=" O ALA e 52 " (cutoff:3.500A) Processing helix chain 'e' and resid 93 through 105 removed outlier: 3.915A pdb=" N GLU e 97 " --> pdb=" O GLU e 93 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE e 98 " --> pdb=" O ARG e 94 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE e 103 " --> pdb=" O PHE e 99 " (cutoff:3.500A) Processing helix chain 'e' and resid 105 through 110 removed outlier: 3.615A pdb=" N ARG e 109 " --> pdb=" O ILE e 105 " (cutoff:3.500A) Processing helix chain 'e' and resid 163 through 171 removed outlier: 3.854A pdb=" N ALA e 167 " --> pdb=" O GLU e 163 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA e 171 " --> pdb=" O ALA e 167 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 80 removed outlier: 4.107A pdb=" N THR f 66 " --> pdb=" O ALA f 62 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER f 73 " --> pdb=" O ALA f 69 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE f 76 " --> pdb=" O ASN f 72 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL f 78 " --> pdb=" O MET f 74 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 149 Processing helix chain 'i' and resid 27 through 31 removed outlier: 4.311A pdb=" N GLN i 30 " --> pdb=" O LEU i 27 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY i 31 " --> pdb=" O GLY i 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 27 through 31' Processing helix chain 'i' and resid 34 through 45 removed outlier: 3.585A pdb=" N LYS i 39 " --> pdb=" O MET i 35 " (cutoff:3.500A) Processing helix chain 'i' and resid 76 through 81 Processing helix chain 'i' and resid 103 through 116 removed outlier: 3.657A pdb=" N GLU i 107 " --> pdb=" O ALA i 103 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA i 109 " --> pdb=" O LEU i 105 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR i 111 " --> pdb=" O GLU i 107 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA i 114 " --> pdb=" O GLN i 110 " (cutoff:3.500A) Processing helix chain 'i' and resid 120 through 134 removed outlier: 3.573A pdb=" N SER i 127 " --> pdb=" O ALA i 123 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE i 128 " --> pdb=" O MET i 124 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU i 129 " --> pdb=" O THR i 125 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLY i 130 " --> pdb=" O ARG i 126 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR i 131 " --> pdb=" O SER i 127 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 removed outlier: 3.905A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG j 35 " --> pdb=" O GLU j 31 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG j 37 " --> pdb=" O ALA j 33 " (cutoff:3.500A) Processing helix chain 'j' and resid 67 through 72 removed outlier: 3.869A pdb=" N LYS j 72 " --> pdb=" O LYS j 68 " (cutoff:3.500A) Processing helix chain 'j' and resid 88 through 93 Processing helix chain 'j' and resid 98 through 107 Processing helix chain 'j' and resid 112 through 120 Processing helix chain 'k' and resid 104 through 108 removed outlier: 3.872A pdb=" N LEU k 107 " --> pdb=" O THR k 104 " (cutoff:3.500A) Processing helix chain 'k' and resid 112 through 119 removed outlier: 3.710A pdb=" N ILE k 116 " --> pdb=" O PHE k 112 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU k 118 " --> pdb=" O LYS k 114 " (cutoff:3.500A) Processing helix chain 'l' and resid 37 through 41 removed outlier: 3.775A pdb=" N ARG l 41 " --> pdb=" O GLN l 38 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 61 removed outlier: 3.815A pdb=" N LEU l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Processing helix chain 'l' and resid 68 through 72 removed outlier: 3.562A pdb=" N ALA l 71 " --> pdb=" O SER l 68 " (cutoff:3.500A) Processing helix chain 'l' and resid 79 through 84 removed outlier: 3.528A pdb=" N LEU l 82 " --> pdb=" O LEU l 79 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA l 83 " --> pdb=" O SER l 80 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS l 84 " --> pdb=" O ASP l 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 79 through 84' Processing helix chain 'l' and resid 128 through 137 removed outlier: 3.756A pdb=" N ALA l 133 " --> pdb=" O LYS l 129 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA l 134 " --> pdb=" O GLY l 130 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE l 135 " --> pdb=" O ALA l 131 " (cutoff:3.500A) Processing helix chain 'm' and resid 43 through 51 Processing helix chain 'm' and resid 53 through 58 removed outlier: 3.911A pdb=" N VAL m 57 " --> pdb=" O MET m 53 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 121 removed outlier: 3.517A pdb=" N PHE m 117 " --> pdb=" O ALA m 113 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LYS m 118 " --> pdb=" O ARG m 114 " (cutoff:3.500A) Processing helix chain 'm' and resid 122 through 124 No H-bonds generated for 'chain 'm' and resid 122 through 124' Processing helix chain 'n' and resid 13 through 32 removed outlier: 3.910A pdb=" N ASN n 23 " --> pdb=" O ALA n 19 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER n 27 " --> pdb=" O ASN n 23 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG n 30 " --> pdb=" O GLY n 26 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 56 removed outlier: 3.981A pdb=" N ARG n 45 " --> pdb=" O ALA n 41 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 50 - end of helix Processing helix chain 'n' and resid 59 through 69 removed outlier: 3.593A pdb=" N ARG n 64 " --> pdb=" O VAL n 60 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG n 69 " --> pdb=" O LEU n 65 " (cutoff:3.500A) Processing helix chain 'n' and resid 74 through 79 Processing helix chain 'n' and resid 84 through 88 removed outlier: 3.586A pdb=" N PHE n 87 " --> pdb=" O GLY n 84 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 22 removed outlier: 4.861A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG o 15 " --> pdb=" O ALA o 11 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS o 17 " --> pdb=" O ARG o 13 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 60 removed outlier: 3.784A pdb=" N ALA o 59 " --> pdb=" O GLU o 55 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 83 removed outlier: 3.521A pdb=" N ALA o 73 " --> pdb=" O ASP o 69 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 112 removed outlier: 3.699A pdb=" N GLU o 112 " --> pdb=" O ASP o 108 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 7 Processing helix chain 'p' and resid 52 through 55 Processing helix chain 'p' and resid 96 through 101 removed outlier: 3.534A pdb=" N GLU p 101 " --> pdb=" O TYR p 98 " (cutoff:3.500A) Processing helix chain 'p' and resid 103 through 108 removed outlier: 3.699A pdb=" N ARG p 108 " --> pdb=" O LYS p 105 " (cutoff:3.500A) Processing helix chain 'q' and resid 6 through 20 removed outlier: 3.512A pdb=" N HIS q 13 " --> pdb=" O ALA q 9 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN q 19 " --> pdb=" O LYS q 15 " (cutoff:3.500A) Processing helix chain 'q' and resid 24 through 29 Processing helix chain 'q' and resid 30 through 48 removed outlier: 4.419A pdb=" N GLN q 36 " --> pdb=" O ARG q 32 " (cutoff:3.500A) Processing helix chain 'q' and resid 50 through 68 removed outlier: 3.542A pdb=" N ARG q 54 " --> pdb=" O ARG q 50 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG q 57 " --> pdb=" O LYS q 53 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA q 62 " --> pdb=" O GLN q 58 " (cutoff:3.500A) Processing helix chain 'q' and resid 69 through 71 No H-bonds generated for 'chain 'q' and resid 69 through 71' Processing helix chain 'q' and resid 78 through 86 Processing helix chain 'q' and resid 92 through 101 removed outlier: 3.535A pdb=" N ASP q 96 " --> pdb=" O LYS q 92 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA q 98 " --> pdb=" O LEU q 94 " (cutoff:3.500A) Processing helix chain 'q' and resid 101 through 117 removed outlier: 3.509A pdb=" N LYS q 111 " --> pdb=" O ALA q 107 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA q 117 " --> pdb=" O LYS q 113 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 22 removed outlier: 3.694A pdb=" N LEU s 19 " --> pdb=" O GLN s 15 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 38 removed outlier: 3.778A pdb=" N ASP s 34 " --> pdb=" O SER s 30 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE s 35 " --> pdb=" O GLN s 31 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU s 36 " --> pdb=" O ALA s 32 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 removed outlier: 3.655A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS s 49 " --> pdb=" O VAL s 45 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) Processing helix chain 't' and resid 2 through 7 removed outlier: 4.182A pdb=" N ARG t 6 " --> pdb=" O ILE t 2 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 28 removed outlier: 3.800A pdb=" N LYS t 26 " --> pdb=" O THR t 22 " (cutoff:3.500A) Processing helix chain 't' and resid 39 through 52 removed outlier: 3.559A pdb=" N ALA t 46 " --> pdb=" O GLU t 42 " (cutoff:3.500A) Processing helix chain 'v' and resid 13 through 22 removed outlier: 3.542A pdb=" N SER v 17 " --> pdb=" O GLY v 13 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG v 18 " --> pdb=" O LYS v 14 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG v 21 " --> pdb=" O SER v 17 " (cutoff:3.500A) Processing helix chain 'v' and resid 44 through 52 removed outlier: 3.998A pdb=" N ASN v 49 " --> pdb=" O ASP v 45 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA v 52 " --> pdb=" O MET v 48 " (cutoff:3.500A) Processing helix chain 'v' and resid 53 through 58 removed outlier: 3.752A pdb=" N TYR v 57 " --> pdb=" O ALA v 54 " (cutoff:3.500A) Processing helix chain 'x' and resid 52 through 59 removed outlier: 3.509A pdb=" N ILE x 58 " --> pdb=" O GLY x 54 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP x 59 " --> pdb=" O MET x 55 " (cutoff:3.500A) Processing helix chain 'x' and resid 62 through 73 removed outlier: 3.588A pdb=" N ARG x 73 " --> pdb=" O GLU x 69 " (cutoff:3.500A) Processing helix chain 'y' and resid 1 through 5 removed outlier: 4.102A pdb=" N GLU y 5 " --> pdb=" O LYS y 2 " (cutoff:3.500A) Processing helix chain 'y' and resid 11 through 22 removed outlier: 3.591A pdb=" N ASN y 15 " --> pdb=" O VAL y 11 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU y 18 " --> pdb=" O LEU y 14 " (cutoff:3.500A) Processing helix chain 'y' and resid 23 through 32 removed outlier: 4.444A pdb=" N ARG y 29 " --> pdb=" O GLN y 25 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET y 30 " --> pdb=" O PHE y 26 " (cutoff:3.500A) Processing helix chain 'y' and resid 41 through 57 removed outlier: 3.729A pdb=" N GLN y 45 " --> pdb=" O HIS y 41 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP y 49 " --> pdb=" O GLN y 45 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA y 51 " --> pdb=" O ARG y 47 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU y 56 " --> pdb=" O ARG y 52 " (cutoff:3.500A) Processing helix chain 'z' and resid 11 through 15 removed outlier: 4.355A pdb=" N GLY z 14 " --> pdb=" O SER z 11 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 27 removed outlier: 3.566A pdb=" N LEU z 23 " --> pdb=" O HIS z 19 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 50 removed outlier: 3.648A pdb=" N VAL z 50 " --> pdb=" O MET z 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 16 removed outlier: 3.507A pdb=" N ARG B 12 " --> pdb=" O THR B 8 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY B 13 " --> pdb=" O ARG B 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 17 removed outlier: 3.580A pdb=" N ASN D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER D 15 " --> pdb=" O LYS D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 24 through 37 removed outlier: 3.509A pdb=" N LEU D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG D 33 " --> pdb=" O GLN D 29 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 11 removed outlier: 3.601A pdb=" N LYS E 11 " --> pdb=" O ARG E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 43 removed outlier: 3.622A pdb=" N HIS E 42 " --> pdb=" O LYS E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 61 removed outlier: 3.600A pdb=" N CYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 33 Processing helix chain 'G' and resid 23 through 27 Processing helix chain 'G' and resid 41 through 62 removed outlier: 3.734A pdb=" N VAL G 46 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Proline residue: G 47 - end of helix removed outlier: 3.673A pdb=" N ASN G 57 " --> pdb=" O LEU G 53 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE G 59 " --> pdb=" O GLU G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 87 removed outlier: 3.802A pdb=" N VAL G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS G 80 " --> pdb=" O SER G 76 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER G 85 " --> pdb=" O ASP G 81 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP G 87 " --> pdb=" O ALA G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 107 Processing helix chain 'G' and resid 107 through 120 removed outlier: 3.905A pdb=" N THR G 118 " --> pdb=" O LYS G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 146 removed outlier: 3.784A pdb=" N THR G 137 " --> pdb=" O ALA G 133 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU G 144 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN G 145 " --> pdb=" O GLU G 141 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 176 Processing helix chain 'G' and resid 205 through 217 removed outlier: 4.123A pdb=" N LEU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR G 212 " --> pdb=" O ALA G 208 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA G 215 " --> pdb=" O LEU G 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 10 removed outlier: 3.913A pdb=" N ARG H 10 " --> pdb=" O PRO H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 46 removed outlier: 3.964A pdb=" N ASN H 31 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR H 41 " --> pdb=" O LYS H 37 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU H 42 " --> pdb=" O VAL H 38 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS H 44 " --> pdb=" O GLN H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 removed outlier: 4.015A pdb=" N VAL H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 94 removed outlier: 3.686A pdb=" N GLU H 84 " --> pdb=" O GLY H 80 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL H 89 " --> pdb=" O LYS H 85 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL H 90 " --> pdb=" O LEU H 86 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 removed outlier: 3.590A pdb=" N GLN H 122 " --> pdb=" O SER H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 142 removed outlier: 3.519A pdb=" N ALA H 132 " --> pdb=" O MET H 128 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS H 134 " --> pdb=" O ARG H 130 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG H 135 " --> pdb=" O ARG H 131 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL H 137 " --> pdb=" O MET H 133 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN H 138 " --> pdb=" O LYS H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 159 Processing helix chain 'I' and resid 6 through 15 removed outlier: 3.813A pdb=" N LEU I 10 " --> pdb=" O PRO I 6 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG I 13 " --> pdb=" O LYS I 9 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU I 14 " --> pdb=" O LEU I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.586A pdb=" N CYS I 31 " --> pdb=" O ASP I 28 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS I 32 " --> pdb=" O THR I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 48 through 65 removed outlier: 3.675A pdb=" N TYR I 64 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 81 removed outlier: 3.600A pdb=" N ASN I 73 " --> pdb=" O ARG I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 95 removed outlier: 3.671A pdb=" N ASN I 88 " --> pdb=" O ASN I 84 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU I 93 " --> pdb=" O LEU I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 104 removed outlier: 3.808A pdb=" N TYR I 102 " --> pdb=" O ASP I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 119 removed outlier: 3.904A pdb=" N LEU I 116 " --> pdb=" O GLU I 112 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 161 removed outlier: 3.918A pdb=" N LEU I 160 " --> pdb=" O ALA I 156 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA I 161 " --> pdb=" O ALA I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 164 No H-bonds generated for 'chain 'I' and resid 162 through 164' Processing helix chain 'I' and resid 196 through 201 removed outlier: 3.581A pdb=" N GLU I 201 " --> pdb=" O HIS I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 205 Processing helix chain 'J' and resid 54 through 68 removed outlier: 3.648A pdb=" N GLU J 64 " --> pdb=" O GLN J 60 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA J 66 " --> pdb=" O ALA J 62 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG J 67 " --> pdb=" O MET J 63 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG J 68 " --> pdb=" O GLU J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 118 removed outlier: 3.581A pdb=" N VAL J 116 " --> pdb=" O ALA J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 145 removed outlier: 3.724A pdb=" N ARG J 137 " --> pdb=" O ILE J 133 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE J 140 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN J 145 " --> pdb=" O ASP J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 153 removed outlier: 3.520A pdb=" N VAL J 152 " --> pdb=" O SER J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 165 removed outlier: 3.546A pdb=" N LEU J 164 " --> pdb=" O VAL J 160 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY J 165 " --> pdb=" O GLU J 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 160 through 165' Processing helix chain 'K' and resid 17 through 31 removed outlier: 3.942A pdb=" N GLU K 23 " --> pdb=" O PRO K 19 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG K 24 " --> pdb=" O GLY K 20 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR K 25 " --> pdb=" O MET K 21 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA K 28 " --> pdb=" O ARG K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 80 removed outlier: 3.644A pdb=" N ILE K 71 " --> pdb=" O PRO K 67 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU K 75 " --> pdb=" O ILE K 71 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 30 removed outlier: 3.577A pdb=" N ASN L 27 " --> pdb=" O ALA L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 49 removed outlier: 3.515A pdb=" N VAL L 42 " --> pdb=" O ALA L 38 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER L 44 " --> pdb=" O SER L 40 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU L 47 " --> pdb=" O TYR L 43 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU L 49 " --> pdb=" O ALA L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 58 through 66 removed outlier: 3.787A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 107 removed outlier: 3.574A pdb=" N ARG L 95 " --> pdb=" O ARG L 91 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASN L 96 " --> pdb=" O PRO L 92 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG L 101 " --> pdb=" O ALA L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 126 removed outlier: 3.694A pdb=" N SER L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 143 removed outlier: 3.594A pdb=" N HIS L 141 " --> pdb=" O ARG L 137 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET L 143 " --> pdb=" O ASP L 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 19 Processing helix chain 'M' and resid 31 through 42 removed outlier: 3.511A pdb=" N VAL M 38 " --> pdb=" O ALA M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 119 removed outlier: 3.678A pdb=" N GLN M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 38 Processing helix chain 'N' and resid 44 through 48 removed outlier: 3.823A pdb=" N VAL N 47 " --> pdb=" O ARG N 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 54 removed outlier: 3.883A pdb=" N LEU N 53 " --> pdb=" O PRO N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 86 removed outlier: 3.512A pdb=" N ALA N 77 " --> pdb=" O GLY N 73 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG N 79 " --> pdb=" O ALA N 75 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR N 83 " --> pdb=" O ARG N 79 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG N 84 " --> pdb=" O HIS N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 100 removed outlier: 3.782A pdb=" N LYS N 99 " --> pdb=" O SER N 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 22 removed outlier: 3.501A pdb=" N ILE O 18 " --> pdb=" O ASP O 14 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 30 Processing helix chain 'O' and resid 80 through 85 removed outlier: 3.730A pdb=" N VAL O 84 " --> pdb=" O THR O 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 50 Processing helix chain 'P' and resid 53 through 58 removed outlier: 4.387A pdb=" N SER P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR P 58 " --> pdb=" O SER P 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 53 through 58' Processing helix chain 'P' and resid 58 through 71 removed outlier: 3.643A pdb=" N ALA P 65 " --> pdb=" O ALA P 61 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP P 71 " --> pdb=" O GLU P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 102 removed outlier: 3.523A pdb=" N ALA P 98 " --> pdb=" O SER P 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 9 removed outlier: 3.893A pdb=" N LEU Q 6 " --> pdb=" O THR Q 2 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG Q 8 " --> pdb=" O ASN Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 114 through 118 removed outlier: 3.787A pdb=" N GLY Q 117 " --> pdb=" O SER Q 114 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL Q 118 " --> pdb=" O LYS Q 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 114 through 118' Processing helix chain 'R' and resid 13 through 18 Processing helix chain 'R' and resid 19 through 21 No H-bonds generated for 'chain 'R' and resid 19 through 21' Processing helix chain 'R' and resid 28 through 35 Processing helix chain 'R' and resid 48 through 59 removed outlier: 3.819A pdb=" N ILE R 52 " --> pdb=" O SER R 48 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP R 53 " --> pdb=" O GLU R 49 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP R 57 " --> pdb=" O ASP R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 62 No H-bonds generated for 'chain 'R' and resid 60 through 62' Processing helix chain 'R' and resid 64 through 83 removed outlier: 3.514A pdb=" N GLY R 83 " --> pdb=" O LEU R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 92 removed outlier: 3.673A pdb=" N ARG R 89 " --> pdb=" O TYR R 85 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG R 92 " --> pdb=" O LEU R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 110 removed outlier: 4.032A pdb=" N LYS R 109 " --> pdb=" O ALA R 105 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 15 removed outlier: 3.596A pdb=" N ALA S 7 " --> pdb=" O GLN S 3 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU S 9 " --> pdb=" O MET S 5 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL S 10 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS S 11 " --> pdb=" O ALA S 7 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG S 12 " --> pdb=" O ARG S 8 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU S 15 " --> pdb=" O LYS S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 29 removed outlier: 3.551A pdb=" N ILE S 29 " --> pdb=" O GLU S 25 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 47 removed outlier: 3.662A pdb=" N TRP S 41 " --> pdb=" O ASP S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 48 through 50 No H-bonds generated for 'chain 'S' and resid 48 through 50' Processing helix chain 'S' and resid 51 through 55 removed outlier: 3.521A pdb=" N SER S 54 " --> pdb=" O PRO S 51 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER S 55 " --> pdb=" O ARG S 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 51 through 55' Processing helix chain 'S' and resid 79 through 88 removed outlier: 4.048A pdb=" N ARG S 84 " --> pdb=" O ARG S 80 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU S 85 " --> pdb=" O ILE S 81 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA S 86 " --> pdb=" O LYS S 82 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 15 Processing helix chain 'T' and resid 23 through 44 removed outlier: 3.724A pdb=" N HIS T 37 " --> pdb=" O ALA T 33 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 73 removed outlier: 4.781A pdb=" N GLY T 54 " --> pdb=" O HIS T 50 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER T 60 " --> pdb=" O LEU T 56 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG T 62 " --> pdb=" O MET T 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 85 removed outlier: 3.576A pdb=" N TYR T 77 " --> pdb=" O ASP T 73 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU T 82 " --> pdb=" O THR T 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 62 removed outlier: 3.550A pdb=" N GLY U 62 " --> pdb=" O ALA U 58 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 76 Processing helix chain 'W' and resid 24 through 29 removed outlier: 3.560A pdb=" N LEU W 28 " --> pdb=" O ASP W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 30 through 32 No H-bonds generated for 'chain 'W' and resid 30 through 32' Processing helix chain 'W' and resid 40 through 45 removed outlier: 3.689A pdb=" N THR W 44 " --> pdb=" O PRO W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 64 removed outlier: 3.578A pdb=" N GLN W 51 " --> pdb=" O ARG W 47 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG W 52 " --> pdb=" O ALA W 48 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN W 53 " --> pdb=" O LYS W 49 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 21 removed outlier: 3.903A pdb=" N GLU X 19 " --> pdb=" O LEU X 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 44 removed outlier: 3.687A pdb=" N ILE X 44 " --> pdb=" O PRO X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 74 Processing helix chain 'Y' and resid 7 through 12 removed outlier: 3.724A pdb=" N ILE Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) Processing helix chain 'Y' and resid 13 through 39 removed outlier: 3.764A pdb=" N HIS Y 19 " --> pdb=" O LYS Y 15 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE Y 30 " --> pdb=" O MET Y 26 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS Y 32 " --> pdb=" O ARG Y 28 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA Y 37 " --> pdb=" O LYS Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 51 removed outlier: 3.821A pdb=" N ALA Y 46 " --> pdb=" O ASP Y 42 " (cutoff:3.500A) Processing helix chain 'Y' and resid 53 through 58 removed outlier: 3.940A pdb=" N ASP Y 58 " --> pdb=" O GLN Y 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 58 through 63 Processing helix chain 'Y' and resid 67 through 86 removed outlier: 3.879A pdb=" N LYS Y 75 " --> pdb=" O ALA Y 71 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR Y 79 " --> pdb=" O LYS Y 75 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU Y 85 " --> pdb=" O GLN Y 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 38 through 59 removed outlier: 3.848A pdb=" N ARG Z 46 " --> pdb=" O THR Z 42 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA Z 51 " --> pdb=" O ALA Z 47 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS Z 53 " --> pdb=" O ALA Z 49 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG Z 54 " --> pdb=" O SER Z 50 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N HIS Z 55 " --> pdb=" O ALA Z 51 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'b' and resid 33 through 34 Processing sheet with id=AA3, first strand: chain 'b' and resid 100 through 104 removed outlier: 6.917A pdb=" N ILE b 90 " --> pdb=" O LEU b 80 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU b 80 " --> pdb=" O ILE b 90 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 128 through 130 removed outlier: 3.777A pdb=" N SER b 138 " --> pdb=" O ILE b 163 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN b 162 " --> pdb=" O ARG b 174 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THR b 172 " --> pdb=" O VAL b 164 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ARG b 166 " --> pdb=" O TYR b 170 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TYR b 170 " --> pdb=" O ARG b 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 106 through 107 removed outlier: 6.699A pdb=" N VAL c 177 " --> pdb=" O LYS c 190 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LYS c 190 " --> pdb=" O VAL c 177 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE c 22 " --> pdb=" O ARG c 13 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG c 13 " --> pdb=" O ILE c 22 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL c 24 " --> pdb=" O MET c 11 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N MET c 11 " --> pdb=" O VAL c 24 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL c 26 " --> pdb=" O VAL c 9 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 79 through 83 removed outlier: 6.270A pdb=" N THR c 51 " --> pdb=" O VAL c 34 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N VAL c 34 " --> pdb=" O THR c 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 110 through 112 Processing sheet with id=AA8, first strand: chain 'c' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'd' and resid 2 through 3 Processing sheet with id=AB1, first strand: chain 'd' and resid 118 through 121 removed outlier: 3.533A pdb=" N THR d 189 " --> pdb=" O ILE d 149 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG d 170 " --> pdb=" O ILE d 148 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'e' and resid 85 through 88 removed outlier: 4.400A pdb=" N LYS e 32 " --> pdb=" O THR e 156 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'f' and resid 8 through 9 Processing sheet with id=AB4, first strand: chain 'f' and resid 15 through 18 Processing sheet with id=AB5, first strand: chain 'f' and resid 121 through 123 removed outlier: 3.606A pdb=" N VAL f 89 " --> pdb=" O GLY f 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'f' and resid 97 through 98 Processing sheet with id=AB7, first strand: chain 'i' and resid 97 through 100 removed outlier: 5.587A pdb=" N GLY i 98 " --> pdb=" O VAL i 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'j' and resid 122 through 124 removed outlier: 6.465A pdb=" N TYR j 16 " --> pdb=" O ILE j 55 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU j 57 " --> pdb=" O TYR j 16 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL j 18 " --> pdb=" O LEU j 57 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN j 138 " --> pdb=" O TRP j 15 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'j' and resid 76 through 77 Processing sheet with id=AC1, first strand: chain 'k' and resid 7 through 10 removed outlier: 4.145A pdb=" N VAL k 10 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLU k 45 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL k 19 " --> pdb=" O ILE k 43 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE k 43 " --> pdb=" O VAL k 19 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N CYS k 21 " --> pdb=" O ILE k 41 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE k 41 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS k 23 " --> pdb=" O ILE k 39 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE k 39 " --> pdb=" O LYS k 23 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS k 59 " --> pdb=" O LEU k 87 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA k 83 " --> pdb=" O VAL k 63 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N CYS k 84 " --> pdb=" O MET k 7 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASN k 9 " --> pdb=" O CYS k 84 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU k 86 " --> pdb=" O ASN k 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'l' and resid 74 through 75 removed outlier: 3.713A pdb=" N LYS l 109 " --> pdb=" O ALA l 75 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'l' and resid 122 through 123 removed outlier: 6.160A pdb=" N VAL l 122 " --> pdb=" O GLU l 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'm' and resid 62 through 65 removed outlier: 3.570A pdb=" N LYS m 62 " --> pdb=" O ASP m 106 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU m 33 " --> pdb=" O LEU m 102 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU m 104 " --> pdb=" O PHE m 31 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N PHE m 31 " --> pdb=" O GLU m 104 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL m 131 " --> pdb=" O GLY m 32 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'm' and resid 39 through 42 removed outlier: 3.845A pdb=" N ASN m 88 " --> pdb=" O GLU m 75 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE m 73 " --> pdb=" O GLU m 90 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TRP m 92 " --> pdb=" O LYS m 71 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LYS m 71 " --> pdb=" O TRP m 92 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'n' and resid 33 through 37 removed outlier: 6.925A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'o' and resid 47 through 52 removed outlier: 3.808A pdb=" N VAL o 49 " --> pdb=" O VAL o 39 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG o 25 " --> pdb=" O ILE o 40 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LEU o 26 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'p' and resid 67 through 74 removed outlier: 3.775A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ARG p 61 " --> pdb=" O VAL p 46 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N VAL p 46 " --> pdb=" O ARG p 61 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ILE p 63 " --> pdb=" O GLY p 44 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N GLY p 44 " --> pdb=" O ILE p 63 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS p 28 " --> pdb=" O ASP p 81 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'p' and resid 67 through 74 removed outlier: 3.775A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ARG p 61 " --> pdb=" O VAL p 46 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N VAL p 46 " --> pdb=" O ARG p 61 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ILE p 63 " --> pdb=" O GLY p 44 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N GLY p 44 " --> pdb=" O ILE p 63 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR p 24 " --> pdb=" O LYS p 86 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'p' and resid 89 through 90 removed outlier: 4.465A pdb=" N LYS p 110 " --> pdb=" O ALA p 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'r' and resid 11 through 15 removed outlier: 6.963A pdb=" N TYR r 2 " --> pdb=" O ILE r 41 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE r 41 " --> pdb=" O TYR r 2 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL r 4 " --> pdb=" O LEU r 39 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'r' and resid 19 through 22 removed outlier: 6.693A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'r' and resid 72 through 78 removed outlier: 4.443A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 's' and resid 3 through 10 removed outlier: 5.432A pdb=" N SER s 101 " --> pdb=" O HIS s 9 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASP s 94 " --> pdb=" O ILE s 85 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE s 85 " --> pdb=" O ASP s 94 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE s 96 " --> pdb=" O LYS s 83 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LYS s 83 " --> pdb=" O ILE s 96 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LYS s 98 " --> pdb=" O SER s 81 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER s 81 " --> pdb=" O LYS s 98 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N THR s 100 " --> pdb=" O GLY s 79 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER s 108 " --> pdb=" O VAL s 71 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N VAL s 71 " --> pdb=" O SER s 108 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 't' and resid 11 through 14 removed outlier: 6.666A pdb=" N LYS t 33 " --> pdb=" O ARG t 12 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL t 31 " --> pdb=" O PRO t 14 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL t 57 " --> pdb=" O THR t 86 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 't' and resid 67 through 70 Processing sheet with id=AD8, first strand: chain 'u' and resid 64 through 65 removed outlier: 6.737A pdb=" N LYS u 32 " --> pdb=" O VAL u 27 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N VAL u 27 " --> pdb=" O LYS u 32 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ILE u 34 " --> pdb=" O LYS u 25 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY u 22 " --> pdb=" O VAL u 10 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'u' and resid 43 through 44 Processing sheet with id=AE1, first strand: chain 'u' and resid 82 through 84 removed outlier: 3.616A pdb=" N ARG u 93 " --> pdb=" O ILE u 102 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'v' and resid 3 through 8 removed outlier: 8.085A pdb=" N ASN v 5 " --> pdb=" O ASP v 43 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ASP v 43 " --> pdb=" O ASN v 5 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU v 42 " --> pdb=" O PHE v 26 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N LYS v 25 " --> pdb=" O GLN v 87 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N ILE v 89 " --> pdb=" O LYS v 25 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N PHE v 91 " --> pdb=" O PRO v 27 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE v 29 " --> pdb=" O PHE v 91 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL v 92 " --> pdb=" O ALA v 74 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ALA v 74 " --> pdb=" O VAL v 92 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE v 4 " --> pdb=" O VAL v 64 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'w' and resid 18 through 19 removed outlier: 6.996A pdb=" N LEU w 55 " --> pdb=" O ILE w 33 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'w' and resid 26 through 27 removed outlier: 3.689A pdb=" N GLY w 61 " --> pdb=" O VAL w 27 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU w 66 " --> pdb=" O PHE w 75 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE w 75 " --> pdb=" O GLU w 66 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE w 78 " --> pdb=" O GLY w 44 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'x' and resid 12 through 15 removed outlier: 3.675A pdb=" N ARG x 26 " --> pdb=" O GLY x 14 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'x' and resid 32 through 39 Processing sheet with id=AE7, first strand: chain 'z' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AE9, first strand: chain 'C' and resid 20 through 24 removed outlier: 3.592A pdb=" N GLU C 6 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN C 44 " --> pdb=" O ASP C 39 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 14 through 15 Processing sheet with id=AF2, first strand: chain 'F' and resid 2 through 3 removed outlier: 6.806A pdb=" N LYS F 2 " --> pdb=" O ARG F 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'F' and resid 15 through 19 Processing sheet with id=AF4, first strand: chain 'G' and resid 31 through 32 Processing sheet with id=AF5, first strand: chain 'G' and resid 89 through 90 removed outlier: 3.801A pdb=" N PHE G 89 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU G 160 " --> pdb=" O PHE G 183 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE G 185 " --> pdb=" O LEU G 160 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL G 162 " --> pdb=" O ILE G 185 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VAL G 182 " --> pdb=" O PHE G 197 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE G 199 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ALA G 184 " --> pdb=" O ILE G 199 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 51 through 57 removed outlier: 3.506A pdb=" N ARG H 53 " --> pdb=" O HIS H 68 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL H 65 " --> pdb=" O ASN H 101 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ALA H 103 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE H 67 " --> pdb=" O ALA H 103 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 163 through 170 removed outlier: 3.785A pdb=" N GLY H 154 " --> pdb=" O ARG H 163 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL H 150 " --> pdb=" O TYR H 167 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASP H 180 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 122 through 124 removed outlier: 3.575A pdb=" N VAL I 142 " --> pdb=" O GLY I 179 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY I 179 " --> pdb=" O VAL I 142 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 13 through 21 removed outlier: 7.021A pdb=" N LEU J 35 " --> pdb=" O ILE J 15 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL J 17 " --> pdb=" O THR J 33 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR J 33 " --> pdb=" O VAL J 17 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ARG J 19 " --> pdb=" O SER J 31 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER J 31 " --> pdb=" O ARG J 19 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 84 through 85 removed outlier: 3.503A pdb=" N TYR J 127 " --> pdb=" O ARG J 92 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 2 through 3 removed outlier: 3.561A pdb=" N ARG K 2 " --> pdb=" O ALA K 66 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 41 through 45 removed outlier: 4.982A pdb=" N ASP K 41 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU K 61 " --> pdb=" O ASP K 41 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY K 43 " --> pdb=" O TYR K 59 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET K 9 " --> pdb=" O ARG K 86 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ARG K 86 " --> pdb=" O MET K 9 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 72 through 75 Processing sheet with id=AG5, first strand: chain 'M' and resid 23 through 27 removed outlier: 3.893A pdb=" N ASP M 47 " --> pdb=" O THR M 61 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 73 through 74 removed outlier: 6.542A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TYR M 127 " --> pdb=" O ILE M 100 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE M 100 " --> pdb=" O TYR M 127 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.528A pdb=" N GLY N 7 " --> pdb=" O VAL N 18 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL N 28 " --> pdb=" O ILE N 64 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'O' and resid 71 through 72 removed outlier: 3.569A pdb=" N ARG O 7 " --> pdb=" O SER O 101 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'O' and resid 45 through 52 removed outlier: 3.622A pdb=" N THR O 69 " --> pdb=" O ARG O 45 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR O 65 " --> pdb=" O PHE O 49 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL O 51 " --> pdb=" O ASP O 63 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU O 66 " --> pdb=" O LYS S 96 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS S 96 " --> pdb=" O GLU O 66 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'P' and resid 40 through 44 removed outlier: 6.161A pdb=" N LEU P 81 " --> pdb=" O ILE P 106 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN P 108 " --> pdb=" O LEU P 81 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL Z 5 " --> pdb=" O ILE P 109 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Q' and resid 29 through 31 Processing sheet with id=AH3, first strand: chain 'Q' and resid 34 through 39 removed outlier: 5.139A pdb=" N VAL Q 36 " --> pdb=" O VAL Q 51 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL Q 51 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N THR Q 38 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG Q 49 " --> pdb=" O THR Q 38 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU Q 56 " --> pdb=" O PHE Q 60 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N PHE Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'U' and resid 32 through 35 removed outlier: 6.691A pdb=" N VAL U 21 " --> pdb=" O ILE U 33 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'U' and resid 8 through 11 Processing sheet with id=AH6, first strand: chain 'U' and resid 37 through 39 Processing sheet with id=AH7, first strand: chain 'V' and resid 10 through 13 removed outlier: 6.871A pdb=" N VAL V 21 " --> pdb=" O VAL V 12 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'V' and resid 56 through 62 removed outlier: 8.059A pdb=" N VAL V 57 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N VAL V 77 " --> pdb=" O VAL V 57 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'X' and resid 31 through 32 removed outlier: 3.625A pdb=" N HIS X 51 " --> pdb=" O THR X 32 " (cutoff:3.500A) 1362 hydrogen bonds defined for protein. 3738 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3320 hydrogen bonds 5260 hydrogen bond angles 0 basepair planarities 1358 basepair parallelities 2559 stacking parallelities Total time for adding SS restraints: 260.22 Time building geometry restraints manager: 67.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 18355 1.32 - 1.45: 70554 1.45 - 1.58: 59596 1.58 - 1.70: 9453 1.70 - 1.83: 259 Bond restraints: 158217 Sorted by residual: bond pdb=" C PRO i 21 " pdb=" N PRO i 22 " ideal model delta sigma weight residual 1.336 1.378 -0.042 1.20e-02 6.94e+03 1.24e+01 bond pdb=" C HIS b 229 " pdb=" N PRO b 230 " ideal model delta sigma weight residual 1.334 1.310 0.023 8.40e-03 1.42e+04 7.64e+00 bond pdb=" O5' A 4 13 " pdb=" C5' A 4 13 " ideal model delta sigma weight residual 1.420 1.458 -0.038 1.50e-02 4.44e+03 6.38e+00 bond pdb=" O5' U 4 11 " pdb=" C5' U 4 11 " ideal model delta sigma weight residual 1.420 1.458 -0.038 1.50e-02 4.44e+03 6.27e+00 bond pdb=" O5' A 4 8 " pdb=" C5' A 4 8 " ideal model delta sigma weight residual 1.420 1.457 -0.037 1.50e-02 4.44e+03 6.25e+00 ... (remaining 158212 not shown) Histogram of bond angle deviations from ideal: 98.37 - 105.97: 26149 105.97 - 113.57: 97971 113.57 - 121.17: 71379 121.17 - 128.77: 37002 128.77 - 136.37: 4591 Bond angle restraints: 237092 Sorted by residual: angle pdb=" N GLU l 86 " pdb=" CA GLU l 86 " pdb=" C GLU l 86 " ideal model delta sigma weight residual 114.75 106.22 8.53 1.26e+00 6.30e-01 4.58e+01 angle pdb=" C ASN K 52 " pdb=" N LYS K 53 " pdb=" CA LYS K 53 " ideal model delta sigma weight residual 121.54 133.94 -12.40 1.91e+00 2.74e-01 4.21e+01 angle pdb=" N VAL r 51 " pdb=" CA VAL r 51 " pdb=" C VAL r 51 " ideal model delta sigma weight residual 109.02 103.23 5.79 9.30e-01 1.16e+00 3.88e+01 angle pdb=" C VAL d 83 " pdb=" N THR d 84 " pdb=" CA THR d 84 " ideal model delta sigma weight residual 121.54 133.21 -11.67 1.91e+00 2.74e-01 3.73e+01 angle pdb=" C GLU Z 35 " pdb=" N PHE Z 36 " pdb=" CA PHE Z 36 " ideal model delta sigma weight residual 121.54 131.89 -10.35 1.91e+00 2.74e-01 2.93e+01 ... (remaining 237087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 89129 35.98 - 71.96: 10974 71.96 - 107.94: 1335 107.94 - 143.93: 19 143.93 - 179.91: 26 Dihedral angle restraints: 101483 sinusoidal: 85534 harmonic: 15949 Sorted by residual: dihedral pdb=" CA LYS K 53 " pdb=" C LYS K 53 " pdb=" N LEU K 54 " pdb=" CA LEU K 54 " ideal model delta harmonic sigma weight residual 180.00 126.37 53.63 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CA HIS E 30 " pdb=" C HIS E 30 " pdb=" N ILE E 31 " pdb=" CA ILE E 31 " ideal model delta harmonic sigma weight residual 180.00 -128.99 -51.01 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" CA PRO Z 10 " pdb=" C PRO Z 10 " pdb=" N PHE Z 11 " pdb=" CA PHE Z 11 " ideal model delta harmonic sigma weight residual -180.00 -132.69 -47.31 0 5.00e+00 4.00e-02 8.95e+01 ... (remaining 101480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 28493 0.084 - 0.168: 1708 0.168 - 0.253: 112 0.253 - 0.337: 22 0.337 - 0.421: 4 Chirality restraints: 30339 Sorted by residual: chirality pdb=" CB ILE p 63 " pdb=" CA ILE p 63 " pdb=" CG1 ILE p 63 " pdb=" CG2 ILE p 63 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CB ILE N 29 " pdb=" CA ILE N 29 " pdb=" CG1 ILE N 29 " pdb=" CG2 ILE N 29 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" C3' U 5 43 " pdb=" C4' U 5 43 " pdb=" O3' U 5 43 " pdb=" C2' U 5 43 " both_signs ideal model delta sigma weight residual False -2.48 -2.08 -0.40 2.00e-01 2.50e+01 3.93e+00 ... (remaining 30336 not shown) Planarity restraints: 12448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 4 5 " 0.067 2.00e-02 2.50e+03 3.07e-02 2.60e+01 pdb=" N9 A 4 5 " -0.004 2.00e-02 2.50e+03 pdb=" C8 A 4 5 " -0.028 2.00e-02 2.50e+03 pdb=" N7 A 4 5 " -0.029 2.00e-02 2.50e+03 pdb=" C5 A 4 5 " -0.014 2.00e-02 2.50e+03 pdb=" C6 A 4 5 " 0.009 2.00e-02 2.50e+03 pdb=" N6 A 4 5 " 0.056 2.00e-02 2.50e+03 pdb=" N1 A 4 5 " -0.007 2.00e-02 2.50e+03 pdb=" C2 A 4 5 " -0.016 2.00e-02 2.50e+03 pdb=" N3 A 4 5 " -0.016 2.00e-02 2.50e+03 pdb=" C4 A 4 5 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 31540 " 0.051 2.00e-02 2.50e+03 2.87e-02 1.85e+01 pdb=" N1 U 31540 " 0.000 2.00e-02 2.50e+03 pdb=" C2 U 31540 " -0.010 2.00e-02 2.50e+03 pdb=" O2 U 31540 " -0.020 2.00e-02 2.50e+03 pdb=" N3 U 31540 " -0.010 2.00e-02 2.50e+03 pdb=" C4 U 31540 " -0.011 2.00e-02 2.50e+03 pdb=" O4 U 31540 " 0.052 2.00e-02 2.50e+03 pdb=" C5 U 31540 " -0.029 2.00e-02 2.50e+03 pdb=" C6 U 31540 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY i 24 " -0.071 5.00e-02 4.00e+02 1.07e-01 1.83e+01 pdb=" N PRO i 25 " 0.185 5.00e-02 4.00e+02 pdb=" CA PRO i 25 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO i 25 " -0.059 5.00e-02 4.00e+02 ... (remaining 12445 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 26440 2.76 - 3.29: 122556 3.29 - 3.83: 310132 3.83 - 4.36: 372358 4.36 - 4.90: 495197 Nonbonded interactions: 1326683 Sorted by model distance: nonbonded pdb=" O2' G 1 370 " pdb=" OP1 G 1 424 " model vdw 2.222 2.440 nonbonded pdb=" O ARG d 21 " pdb=" OG SER d 110 " model vdw 2.227 2.440 nonbonded pdb=" O2' G 3 35 " pdb=" O SER Q 114 " model vdw 2.246 2.440 nonbonded pdb=" OP1 G 3 126 " pdb=" O2' U 3 605 " model vdw 2.249 2.440 nonbonded pdb=" OP1 G 11296 " pdb=" O2' G 12709 " model vdw 2.251 2.440 ... (remaining 1326678 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=0.50 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: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 24.820 Check model and map are aligned: 1.610 Set scattering table: 0.960 Process input model: 537.530 Find NCS groups from input model: 3.080 Set up NCS constraints: 0.440 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 575.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 : 0.007 0.123 158217 Z= 0.427 Angle : 0.827 14.666 237092 Z= 0.424 Chirality : 0.045 0.421 30339 Planarity : 0.006 0.107 12448 Dihedral : 23.478 179.908 91194 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.32 % Favored : 90.54 % Rotamer: Outliers : 0.61 % Allowed : 11.45 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -5.01 (0.09), residues: 5506 helix: -4.32 (0.06), residues: 1561 sheet: -2.68 (0.15), residues: 968 loop : -3.00 (0.09), residues: 2977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP b 212 HIS 0.015 0.002 HIS j 80 PHE 0.050 0.003 PHE Z 36 TYR 0.017 0.002 TYR W 69 ARG 0.019 0.001 ARG W 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1629 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1601 time to evaluate : 8.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 144 GLU cc_start: 0.7255 (mt-10) cc_final: 0.7021 (mt-10) REVERT: c 103 ASP cc_start: 0.7579 (t0) cc_final: 0.7117 (t0) REVERT: d 1 MET cc_start: 0.4050 (mtt) cc_final: 0.3260 (tpt) REVERT: d 111 GLU cc_start: 0.8824 (tp30) cc_final: 0.8351 (tp30) REVERT: d 163 ASN cc_start: 0.8076 (t0) cc_final: 0.7825 (t0) REVERT: d 181 ILE cc_start: 0.9187 (tp) cc_final: 0.8934 (tp) REVERT: e 50 ASP cc_start: 0.8241 (t70) cc_final: 0.8023 (t0) REVERT: e 97 GLU cc_start: 0.7732 (pp20) cc_final: 0.7489 (tp30) REVERT: f 138 GLN cc_start: 0.9041 (tm-30) cc_final: 0.8513 (tm-30) REVERT: j 19 ASP cc_start: 0.8326 (t0) cc_final: 0.8116 (t0) REVERT: j 36 LEU cc_start: 0.9049 (mt) cc_final: 0.8377 (mp) REVERT: j 49 ASP cc_start: 0.8211 (p0) cc_final: 0.7859 (p0) REVERT: j 91 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7829 (mp0) REVERT: j 102 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7379 (mt-10) REVERT: j 114 LEU cc_start: 0.9296 (tp) cc_final: 0.8927 (tt) REVERT: m 3 GLN cc_start: 0.8618 (tt0) cc_final: 0.8323 (pp30) REVERT: m 36 VAL cc_start: 0.8876 (t) cc_final: 0.8653 (p) REVERT: m 110 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7559 (tp30) REVERT: n 62 ASN cc_start: 0.8290 (m-40) cc_final: 0.8075 (m-40) REVERT: n 99 LYS cc_start: 0.9003 (mppt) cc_final: 0.8769 (mptt) REVERT: o 91 SER cc_start: 0.8311 (t) cc_final: 0.7949 (p) REVERT: p 4 ILE cc_start: 0.8604 (mt) cc_final: 0.7627 (tt) REVERT: r 31 GLU cc_start: 0.8157 (mp0) cc_final: 0.7685 (mp0) REVERT: r 45 GLU cc_start: 0.7740 (pp20) cc_final: 0.7337 (pp20) REVERT: r 85 LYS cc_start: 0.8908 (tttt) cc_final: 0.8557 (tttt) REVERT: r 97 LYS cc_start: 0.8980 (ttpt) cc_final: 0.8732 (ttpp) REVERT: s 23 LEU cc_start: 0.8424 (mt) cc_final: 0.8166 (mp) REVERT: t 1 MET cc_start: 0.3909 (tpt) cc_final: 0.3228 (ptp) REVERT: t 74 ILE cc_start: 0.8569 (mt) cc_final: 0.8345 (mt) REVERT: u 72 PHE cc_start: 0.7440 (t80) cc_final: 0.6941 (t80) REVERT: y 45 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8305 (tm-30) REVERT: z 2 LYS cc_start: 0.7713 (pttm) cc_final: 0.7154 (mptt) REVERT: z 5 LYS cc_start: 0.9227 (mppt) cc_final: 0.8850 (mttp) REVERT: z 29 ARG cc_start: 0.8432 (mtt-85) cc_final: 0.8224 (mtt90) REVERT: z 48 ASN cc_start: 0.8255 (t0) cc_final: 0.7915 (t0) REVERT: z 57 GLU cc_start: 0.8237 (pt0) cc_final: 0.7837 (pt0) REVERT: B 51 ARG cc_start: 0.8282 (tpp80) cc_final: 0.7981 (ttp80) REVERT: G 55 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7007 (mt-10) REVERT: G 73 ARG cc_start: 0.6593 (ptt-90) cc_final: 0.5946 (tmt-80) REVERT: G 136 ARG cc_start: 0.7747 (mtp85) cc_final: 0.7365 (mmp80) REVERT: G 158 ASP cc_start: 0.8020 (m-30) cc_final: 0.7721 (m-30) REVERT: H 33 ASP cc_start: 0.8073 (t0) cc_final: 0.7808 (t0) REVERT: H 99 GLN cc_start: 0.7691 (tt0) cc_final: 0.7399 (tt0) REVERT: H 106 ARG cc_start: 0.7851 (ptt-90) cc_final: 0.7240 (mmp80) REVERT: H 129 PHE cc_start: 0.7937 (p90) cc_final: 0.7629 (p90) REVERT: H 167 TYR cc_start: 0.6788 (t80) cc_final: 0.6548 (t80) REVERT: H 182 ASP cc_start: 0.8226 (t70) cc_final: 0.7750 (t70) REVERT: I 40 HIS cc_start: 0.7912 (m90) cc_final: 0.7181 (m-70) REVERT: I 70 GLN cc_start: 0.8575 (mt0) cc_final: 0.8205 (mt0) REVERT: I 71 PHE cc_start: 0.8568 (t80) cc_final: 0.8202 (t80) REVERT: I 74 TYR cc_start: 0.8721 (m-10) cc_final: 0.8237 (m-10) REVERT: J 137 ARG cc_start: 0.8276 (mtt-85) cc_final: 0.7988 (ttm170) REVERT: J 149 PRO cc_start: 0.8949 (Cg_exo) cc_final: 0.8721 (Cg_endo) REVERT: K 42 TRP cc_start: 0.6285 (m100) cc_final: 0.5890 (m100) REVERT: K 53 LYS cc_start: 0.8336 (ptpp) cc_final: 0.7879 (mmtm) REVERT: K 88 MET cc_start: 0.8238 (ttt) cc_final: 0.8029 (ttp) REVERT: M 26 MET cc_start: 0.7770 (ptt) cc_final: 0.7566 (ptm) REVERT: M 72 GLU cc_start: 0.7787 (pt0) cc_final: 0.7583 (pm20) REVERT: M 110 MET cc_start: 0.7856 (ptp) cc_final: 0.7651 (ptp) REVERT: M 120 LEU cc_start: 0.7660 (pt) cc_final: 0.7427 (pt) REVERT: N 19 PHE cc_start: 0.7549 (m-80) cc_final: 0.7098 (m-80) REVERT: N 24 ASN cc_start: 0.7595 (t0) cc_final: 0.7257 (t0) REVERT: N 27 ILE cc_start: 0.9091 (mm) cc_final: 0.8878 (mm) REVERT: N 35 GLU cc_start: 0.8280 (mp0) cc_final: 0.8061 (mp0) REVERT: N 48 ARG cc_start: 0.7870 (mtt180) cc_final: 0.7556 (mtt90) REVERT: N 99 LYS cc_start: 0.9146 (mtpt) cc_final: 0.8932 (mttm) REVERT: N 106 ASP cc_start: 0.8748 (t70) cc_final: 0.8001 (t0) REVERT: O 8 ILE cc_start: 0.8786 (mm) cc_final: 0.8472 (mm) REVERT: O 10 LEU cc_start: 0.9063 (mt) cc_final: 0.8655 (mm) REVERT: O 18 ILE cc_start: 0.8891 (tp) cc_final: 0.8634 (mt) REVERT: O 46 LYS cc_start: 0.8888 (mttt) cc_final: 0.8500 (mtpp) REVERT: P 97 ARG cc_start: 0.8568 (ttm-80) cc_final: 0.8091 (mtp-110) REVERT: Q 18 SER cc_start: 0.7720 (t) cc_final: 0.7463 (p) REVERT: Q 37 TYR cc_start: 0.7600 (p90) cc_final: 0.7353 (p90) REVERT: Q 48 LEU cc_start: 0.7973 (tp) cc_final: 0.7679 (mt) REVERT: R 52 ILE cc_start: 0.8611 (pt) cc_final: 0.8248 (mt) REVERT: R 80 MET cc_start: 0.7654 (mmm) cc_final: 0.7417 (mmm) REVERT: S 48 GLN cc_start: 0.7891 (pt0) cc_final: 0.7598 (pt0) REVERT: S 72 PHE cc_start: 0.8280 (t80) cc_final: 0.7964 (t80) REVERT: T 25 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7543 (mt-10) REVERT: T 81 ILE cc_start: 0.8469 (pt) cc_final: 0.8123 (mt) REVERT: U 35 ARG cc_start: 0.7482 (ptm-80) cc_final: 0.7135 (ptt90) REVERT: U 40 ASN cc_start: 0.8318 (t0) cc_final: 0.8016 (t0) REVERT: V 71 SER cc_start: 0.8397 (m) cc_final: 0.8044 (m) REVERT: W 23 LYS cc_start: 0.8396 (mtmm) cc_final: 0.7895 (mmtt) REVERT: W 56 ARG cc_start: 0.8213 (ttm-80) cc_final: 0.7828 (ttm110) REVERT: W 72 ARG cc_start: 0.7666 (mmm160) cc_final: 0.7303 (mpt180) REVERT: X 72 GLU cc_start: 0.8159 (tt0) cc_final: 0.7901 (tt0) REVERT: Y 17 ARG cc_start: 0.8022 (ttp-110) cc_final: 0.7330 (ttp-110) REVERT: Y 42 ASP cc_start: 0.7687 (t70) cc_final: 0.7397 (t0) REVERT: Y 69 ASN cc_start: 0.8565 (t0) cc_final: 0.8008 (t0) REVERT: Z 43 GLU cc_start: 0.7686 (pt0) cc_final: 0.6989 (mt-10) outliers start: 28 outliers final: 15 residues processed: 1617 average time/residue: 1.4120 time to fit residues: 3924.3030 Evaluate side-chains 1178 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1163 time to evaluate : 5.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain V residue 24 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 852 optimal weight: 5.9990 chunk 764 optimal weight: 10.0000 chunk 424 optimal weight: 10.0000 chunk 261 optimal weight: 50.0000 chunk 515 optimal weight: 3.9990 chunk 408 optimal weight: 10.0000 chunk 790 optimal weight: 5.9990 chunk 306 optimal weight: 30.0000 chunk 480 optimal weight: 2.9990 chunk 588 optimal weight: 2.9990 chunk 916 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 24 HIS b 69 ASN ** c 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 30 GLN d 62 GLN d 92 HIS d 94 GLN d 97 ASN ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 37 ASN f 63 GLN f 103 ASN f 142 GLN i 29 GLN i 30 GLN j 80 HIS j 128 ASN m 13 HIS ** m 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 31 HIS o 38 GLN p 11 GLN p 74 GLN q 19 GLN q 55 GLN q 71 ASN r 11 GLN r 91 GLN t 15 HIS t 48 GLN v 49 ASN w 72 ASN x 35 HIS ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 25 GLN y 27 ASN B 5 ASN C 25 ASN C 44 GLN D 13 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 HIS G 88 GLN ** G 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN G 167 HIS G 176 ASN ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 ASN H 139 ASN I 53 GLN I 58 GLN I 197 HIS J 60 GLN J 96 GLN J 121 ASN ** K 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN L 8 GLN L 27 ASN L 129 ASN M 3 GLN M 66 GLN N 36 GLN N 49 GLN O 64 GLN P 100 ASN Q 95 HIS Q 111 GLN S 59 GLN S 65 GLN S 70 HIS T 34 GLN U 18 GLN ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 ASN Y 54 GLN Y 67 HIS Y 74 HIS Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 158217 Z= 0.216 Angle : 0.626 11.898 237092 Z= 0.322 Chirality : 0.037 0.354 30339 Planarity : 0.005 0.092 12448 Dihedral : 23.785 179.562 80163 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.54 % Favored : 91.32 % Rotamer: Outliers : 3.76 % Allowed : 19.62 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.10), residues: 5506 helix: -2.56 (0.10), residues: 1629 sheet: -2.24 (0.15), residues: 1000 loop : -2.60 (0.10), residues: 2877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 200 HIS 0.007 0.001 HIS E 30 PHE 0.033 0.002 PHE Z 36 TYR 0.019 0.002 TYR W 50 ARG 0.011 0.001 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1413 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1241 time to evaluate : 6.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 94 GLN cc_start: 0.7756 (tp40) cc_final: 0.6995 (tm-30) REVERT: c 96 ILE cc_start: 0.8667 (mm) cc_final: 0.7972 (mt) REVERT: d 1 MET cc_start: 0.4031 (mtt) cc_final: 0.3185 (tpt) REVERT: d 181 ILE cc_start: 0.9205 (tp) cc_final: 0.8909 (tp) REVERT: e 25 MET cc_start: 0.8910 (tpp) cc_final: 0.7481 (mmm) REVERT: e 37 MET cc_start: 0.8290 (ttp) cc_final: 0.8064 (ttp) REVERT: e 116 LEU cc_start: 0.7558 (mt) cc_final: 0.7284 (mt) REVERT: e 151 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8077 (pp) REVERT: f 36 LEU cc_start: 0.8589 (mm) cc_final: 0.8209 (mp) REVERT: f 115 GLN cc_start: 0.7115 (tp-100) cc_final: 0.6848 (tp-100) REVERT: f 138 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8617 (tm-30) REVERT: j 36 LEU cc_start: 0.9065 (mt) cc_final: 0.8781 (mp) REVERT: j 43 GLU cc_start: 0.8497 (pm20) cc_final: 0.8079 (pm20) REVERT: j 49 ASP cc_start: 0.8196 (p0) cc_final: 0.7890 (p0) REVERT: j 114 LEU cc_start: 0.9215 (tp) cc_final: 0.8901 (tt) REVERT: k 13 ASN cc_start: 0.7635 (p0) cc_final: 0.7422 (p0) REVERT: m 110 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7269 (tp30) REVERT: m 136 MET cc_start: 0.7745 (ppp) cc_final: 0.7421 (ppp) REVERT: n 99 LYS cc_start: 0.9036 (mppt) cc_final: 0.8729 (mttt) REVERT: n 114 GLU cc_start: 0.6760 (pt0) cc_final: 0.6475 (pt0) REVERT: o 40 ILE cc_start: 0.9123 (mm) cc_final: 0.8914 (mm) REVERT: o 91 SER cc_start: 0.8232 (t) cc_final: 0.7824 (p) REVERT: p 4 ILE cc_start: 0.8553 (mt) cc_final: 0.8099 (tt) REVERT: q 111 LYS cc_start: 0.8923 (tttp) cc_final: 0.8672 (tptt) REVERT: r 34 GLU cc_start: 0.8717 (tt0) cc_final: 0.7987 (tp30) REVERT: r 45 GLU cc_start: 0.7603 (pp20) cc_final: 0.7210 (pp20) REVERT: r 97 LYS cc_start: 0.9018 (ttpt) cc_final: 0.8752 (ttpp) REVERT: s 15 GLN cc_start: 0.8685 (tt0) cc_final: 0.8468 (tt0) REVERT: s 23 LEU cc_start: 0.8326 (mt) cc_final: 0.8126 (mp) REVERT: s 77 ASP cc_start: 0.8113 (p0) cc_final: 0.7685 (p0) REVERT: t 1 MET cc_start: 0.4303 (tpt) cc_final: 0.3189 (ptp) REVERT: u 9 GLU cc_start: 0.7515 (tp30) cc_final: 0.7108 (tp30) REVERT: u 72 PHE cc_start: 0.7265 (t80) cc_final: 0.7024 (t80) REVERT: v 46 LYS cc_start: 0.9120 (mmmm) cc_final: 0.8850 (mmtp) REVERT: w 64 LYS cc_start: 0.8360 (tptm) cc_final: 0.8120 (tppp) REVERT: z 2 LYS cc_start: 0.7740 (pttm) cc_final: 0.7126 (mptt) REVERT: z 48 ASN cc_start: 0.8516 (t0) cc_final: 0.8170 (t0) REVERT: B 10 SER cc_start: 0.8912 (p) cc_final: 0.8518 (t) REVERT: B 24 VAL cc_start: 0.7189 (m) cc_final: 0.6947 (t) REVERT: B 31 LYS cc_start: 0.8584 (tttt) cc_final: 0.8146 (mttp) REVERT: D 1 MET cc_start: 0.8651 (pmm) cc_final: 0.8248 (pmm) REVERT: G 73 ARG cc_start: 0.6651 (ptt-90) cc_final: 0.6156 (tmt-80) REVERT: G 135 MET cc_start: 0.7074 (mmm) cc_final: 0.6457 (mmm) REVERT: G 138 ARG cc_start: 0.7219 (tpt170) cc_final: 0.6861 (ttp80) REVERT: G 158 ASP cc_start: 0.7771 (m-30) cc_final: 0.7523 (m-30) REVERT: H 31 ASN cc_start: 0.8541 (m-40) cc_final: 0.8321 (t0) REVERT: H 106 ARG cc_start: 0.7955 (ptt-90) cc_final: 0.7242 (mmp80) REVERT: H 129 PHE cc_start: 0.7863 (p90) cc_final: 0.7348 (p90) REVERT: H 182 ASP cc_start: 0.8246 (t70) cc_final: 0.7811 (t70) REVERT: I 71 PHE cc_start: 0.8577 (t80) cc_final: 0.8342 (t80) REVERT: J 11 GLN cc_start: 0.8236 (tp40) cc_final: 0.7991 (tp40) REVERT: J 137 ARG cc_start: 0.8283 (mtt-85) cc_final: 0.7872 (ttm170) REVERT: J 150 GLU cc_start: 0.8786 (mp0) cc_final: 0.8580 (mp0) REVERT: K 1 MET cc_start: 0.6315 (mtt) cc_final: 0.6040 (mtm) REVERT: K 4 TYR cc_start: 0.7348 (m-10) cc_final: 0.7058 (m-10) REVERT: K 42 TRP cc_start: 0.6178 (m100) cc_final: 0.5887 (m100) REVERT: K 45 ARG cc_start: 0.8569 (ttm-80) cc_final: 0.8332 (mmm-85) REVERT: K 91 ARG cc_start: 0.6634 (ptp90) cc_final: 0.6424 (ptp90) REVERT: L 121 ASN cc_start: 0.6994 (t0) cc_final: 0.6631 (t0) REVERT: M 42 GLU cc_start: 0.8226 (tp30) cc_final: 0.7684 (tp30) REVERT: M 120 LEU cc_start: 0.8152 (pt) cc_final: 0.7890 (pt) REVERT: N 19 PHE cc_start: 0.7341 (m-80) cc_final: 0.7014 (m-80) REVERT: N 24 ASN cc_start: 0.7449 (t0) cc_final: 0.7065 (t0) REVERT: N 27 ILE cc_start: 0.9139 (mm) cc_final: 0.8892 (mm) REVERT: N 48 ARG cc_start: 0.7680 (mtt180) cc_final: 0.7331 (mtt90) REVERT: N 63 TYR cc_start: 0.7722 (t80) cc_final: 0.7430 (t80) REVERT: O 10 LEU cc_start: 0.8970 (mt) cc_final: 0.8551 (mp) REVERT: O 46 LYS cc_start: 0.8680 (mttt) cc_final: 0.8381 (mtpp) REVERT: O 87 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8079 (pt) REVERT: O 88 MET cc_start: 0.7389 (ppp) cc_final: 0.7087 (ppp) REVERT: P 97 ARG cc_start: 0.8609 (ttm-80) cc_final: 0.8114 (mtp-110) REVERT: Q 18 SER cc_start: 0.7777 (t) cc_final: 0.7513 (p) REVERT: Q 37 TYR cc_start: 0.7753 (p90) cc_final: 0.7388 (p90) REVERT: R 13 HIS cc_start: 0.6288 (m170) cc_final: 0.5808 (m170) REVERT: R 80 MET cc_start: 0.7563 (mmm) cc_final: 0.7313 (mmm) REVERT: S 72 PHE cc_start: 0.8301 (t80) cc_final: 0.7971 (t80) REVERT: T 16 ARG cc_start: 0.6907 (mtt180) cc_final: 0.6282 (mmt90) REVERT: T 25 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7052 (mt-10) REVERT: U 2 VAL cc_start: 0.7886 (OUTLIER) cc_final: 0.7666 (t) REVERT: U 55 ASP cc_start: 0.6725 (OUTLIER) cc_final: 0.6257 (p0) REVERT: V 39 ARG cc_start: 0.8059 (mtp85) cc_final: 0.7855 (mtp85) REVERT: W 23 LYS cc_start: 0.8273 (mtmm) cc_final: 0.7865 (mmtt) REVERT: W 56 ARG cc_start: 0.8367 (ttm-80) cc_final: 0.8079 (ttm110) REVERT: W 72 ARG cc_start: 0.7734 (mmm160) cc_final: 0.6997 (mtt180) REVERT: Y 17 ARG cc_start: 0.8342 (ttp-110) cc_final: 0.7648 (ttp-110) REVERT: Y 35 TYR cc_start: 0.7742 (OUTLIER) cc_final: 0.6971 (m-80) REVERT: Y 54 GLN cc_start: 0.8152 (tt0) cc_final: 0.7287 (mt0) REVERT: Y 56 ILE cc_start: 0.8106 (tt) cc_final: 0.7523 (mm) REVERT: Y 69 ASN cc_start: 0.8346 (t0) cc_final: 0.7680 (t0) REVERT: Z 43 GLU cc_start: 0.7224 (pt0) cc_final: 0.5694 (mt-10) REVERT: Z 44 ARG cc_start: 0.8324 (mpt180) cc_final: 0.8003 (mmt180) outliers start: 172 outliers final: 115 residues processed: 1320 average time/residue: 1.2342 time to fit residues: 2846.6685 Evaluate side-chains 1230 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1110 time to evaluate : 5.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 22 GLU Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 80 LEU Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain e residue 23 SER Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 101 VAL Chi-restraints excluded: chain i residue 125 THR Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain k residue 14 SER Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 55 GLN Chi-restraints excluded: chain r residue 10 LYS Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 34 ILE Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 21 TYR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 139 ASN Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain O residue 24 GLU Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 111 GLN Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 29 ILE Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Y residue 35 TYR Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Z residue 5 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 509 optimal weight: 40.0000 chunk 284 optimal weight: 10.0000 chunk 762 optimal weight: 8.9990 chunk 623 optimal weight: 5.9990 chunk 252 optimal weight: 20.0000 chunk 917 optimal weight: 0.0010 chunk 991 optimal weight: 30.0000 chunk 817 optimal weight: 20.0000 chunk 910 optimal weight: 0.9980 chunk 312 optimal weight: 20.0000 chunk 736 optimal weight: 2.9990 overall best weight: 3.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 89 ASN d 92 HIS ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 114 HIS j 128 ASN k 3 GLN ** m 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 43 GLN ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 70 HIS y 36 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN ** G 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN I 53 GLN I 135 GLN I 197 HIS K 63 ASN ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 GLN S 65 GLN T 61 GLN ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 GLN X 56 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 158217 Z= 0.189 Angle : 0.568 12.899 237092 Z= 0.295 Chirality : 0.034 0.292 30339 Planarity : 0.005 0.090 12448 Dihedral : 23.617 179.791 80159 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.43 % Favored : 91.43 % Rotamer: Outliers : 5.26 % Allowed : 21.95 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.10), residues: 5506 helix: -1.66 (0.12), residues: 1636 sheet: -2.05 (0.15), residues: 1000 loop : -2.34 (0.10), residues: 2870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP X 33 HIS 0.011 0.001 HIS d 165 PHE 0.035 0.002 PHE N 38 TYR 0.017 0.002 TYR K 4 ARG 0.041 0.001 ARG Z 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1472 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1231 time to evaluate : 6.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 94 GLN cc_start: 0.7889 (tp40) cc_final: 0.7347 (tm-30) REVERT: c 96 ILE cc_start: 0.8704 (mm) cc_final: 0.8080 (mt) REVERT: d 1 MET cc_start: 0.4076 (mtt) cc_final: 0.3196 (tpt) REVERT: d 181 ILE cc_start: 0.9156 (tp) cc_final: 0.8876 (tp) REVERT: e 25 MET cc_start: 0.8757 (tpp) cc_final: 0.7425 (mmm) REVERT: e 116 LEU cc_start: 0.7579 (mt) cc_final: 0.7193 (mt) REVERT: e 134 GLN cc_start: 0.8518 (pm20) cc_final: 0.8241 (pm20) REVERT: f 129 GLU cc_start: 0.8477 (tp30) cc_final: 0.8267 (tp30) REVERT: f 138 GLN cc_start: 0.9056 (tm-30) cc_final: 0.8653 (tm-30) REVERT: j 43 GLU cc_start: 0.8394 (pm20) cc_final: 0.8054 (pm20) REVERT: j 99 ARG cc_start: 0.8333 (mmm-85) cc_final: 0.8108 (mmm-85) REVERT: j 114 LEU cc_start: 0.9138 (tp) cc_final: 0.8910 (tt) REVERT: k 7 MET cc_start: 0.8766 (mmm) cc_final: 0.8429 (mmt) REVERT: k 13 ASN cc_start: 0.7597 (p0) cc_final: 0.7326 (p0) REVERT: m 110 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7273 (tp30) REVERT: m 136 MET cc_start: 0.7943 (ppp) cc_final: 0.7581 (ppp) REVERT: n 99 LYS cc_start: 0.9036 (mppt) cc_final: 0.8777 (mppt) REVERT: n 114 GLU cc_start: 0.6990 (pt0) cc_final: 0.6782 (pt0) REVERT: o 91 SER cc_start: 0.8138 (t) cc_final: 0.7673 (p) REVERT: o 98 GLN cc_start: 0.8958 (tp40) cc_final: 0.8753 (tp40) REVERT: p 4 ILE cc_start: 0.8636 (mt) cc_final: 0.8402 (mm) REVERT: p 8 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7147 (pm20) REVERT: p 9 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.6816 (mp10) REVERT: r 45 GLU cc_start: 0.7841 (pp20) cc_final: 0.7038 (pp20) REVERT: r 60 LYS cc_start: 0.8596 (ptmm) cc_final: 0.8084 (ptmm) REVERT: r 97 LYS cc_start: 0.8948 (ttpt) cc_final: 0.8687 (ttpp) REVERT: s 15 GLN cc_start: 0.8750 (tt0) cc_final: 0.8517 (tt0) REVERT: t 1 MET cc_start: 0.4089 (tpt) cc_final: 0.2951 (ptp) REVERT: t 48 GLN cc_start: 0.7692 (tp40) cc_final: 0.7447 (tp-100) REVERT: u 9 GLU cc_start: 0.7674 (tp30) cc_final: 0.7243 (tp30) REVERT: u 72 PHE cc_start: 0.7239 (t80) cc_final: 0.6976 (t80) REVERT: v 45 ASP cc_start: 0.8149 (m-30) cc_final: 0.7785 (m-30) REVERT: v 48 MET cc_start: 0.8543 (tpt) cc_final: 0.8159 (tpt) REVERT: v 51 GLN cc_start: 0.8319 (pp30) cc_final: 0.8022 (pp30) REVERT: w 67 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8395 (m) REVERT: x 60 LYS cc_start: 0.8014 (tptm) cc_final: 0.7294 (tppt) REVERT: x 76 LYS cc_start: 0.7645 (tppt) cc_final: 0.7079 (pttp) REVERT: z 2 LYS cc_start: 0.7874 (pttm) cc_final: 0.7184 (mptt) REVERT: z 46 MET cc_start: 0.8619 (mtp) cc_final: 0.8289 (mtt) REVERT: z 48 ASN cc_start: 0.8648 (t0) cc_final: 0.8293 (t0) REVERT: B 10 SER cc_start: 0.8820 (p) cc_final: 0.8321 (t) REVERT: B 31 LYS cc_start: 0.8558 (tttt) cc_final: 0.8129 (mttt) REVERT: B 47 TYR cc_start: 0.8948 (m-80) cc_final: 0.8112 (m-80) REVERT: B 52 LYS cc_start: 0.9099 (tttm) cc_final: 0.8871 (tttm) REVERT: D 22 MET cc_start: 0.8144 (mmm) cc_final: 0.7890 (mmm) REVERT: G 63 LYS cc_start: 0.8628 (tmtt) cc_final: 0.8303 (tptt) REVERT: G 73 ARG cc_start: 0.6562 (ptt-90) cc_final: 0.6057 (tmt-80) REVERT: G 99 MET cc_start: 0.7773 (ptp) cc_final: 0.7498 (ptp) REVERT: G 108 GLN cc_start: 0.8486 (mt0) cc_final: 0.7865 (mt0) REVERT: G 138 ARG cc_start: 0.7166 (tpt170) cc_final: 0.6907 (ttp80) REVERT: G 158 ASP cc_start: 0.7691 (m-30) cc_final: 0.7437 (m-30) REVERT: H 24 ASN cc_start: 0.8459 (m-40) cc_final: 0.7888 (m110) REVERT: H 31 ASN cc_start: 0.8598 (m-40) cc_final: 0.8388 (t0) REVERT: H 106 ARG cc_start: 0.8020 (ptt-90) cc_final: 0.7321 (mmp80) REVERT: H 182 ASP cc_start: 0.8218 (t70) cc_final: 0.7895 (t70) REVERT: I 89 LEU cc_start: 0.8797 (mt) cc_final: 0.8367 (mt) REVERT: J 32 PHE cc_start: 0.9239 (m-80) cc_final: 0.8937 (m-80) REVERT: J 137 ARG cc_start: 0.8330 (mtt-85) cc_final: 0.8042 (ttm170) REVERT: K 14 GLN cc_start: 0.8493 (mm-40) cc_final: 0.8120 (mm-40) REVERT: K 62 MET cc_start: 0.8414 (mmm) cc_final: 0.8181 (mmm) REVERT: L 84 TYR cc_start: 0.6203 (OUTLIER) cc_final: 0.5645 (m-10) REVERT: L 121 ASN cc_start: 0.7335 (t0) cc_final: 0.7134 (t0) REVERT: M 42 GLU cc_start: 0.8389 (tp30) cc_final: 0.7949 (tp30) REVERT: M 120 LEU cc_start: 0.8341 (pt) cc_final: 0.8073 (pt) REVERT: M 126 CYS cc_start: 0.8293 (p) cc_final: 0.7804 (p) REVERT: N 5 TYR cc_start: 0.7590 (m-80) cc_final: 0.7143 (m-80) REVERT: N 24 ASN cc_start: 0.7572 (t0) cc_final: 0.7187 (t0) REVERT: N 27 ILE cc_start: 0.9170 (mm) cc_final: 0.8938 (mm) REVERT: N 29 ILE cc_start: 0.8810 (tt) cc_final: 0.8595 (tp) REVERT: N 35 GLU cc_start: 0.8408 (mp0) cc_final: 0.8147 (mm-30) REVERT: N 117 LEU cc_start: 0.8048 (mm) cc_final: 0.7634 (tp) REVERT: O 10 LEU cc_start: 0.8874 (mt) cc_final: 0.8633 (mp) REVERT: O 46 LYS cc_start: 0.8675 (mttt) cc_final: 0.8469 (mtpp) REVERT: O 87 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8098 (pt) REVERT: O 88 MET cc_start: 0.7600 (ppp) cc_final: 0.7235 (ppp) REVERT: P 25 SER cc_start: 0.8762 (p) cc_final: 0.8428 (p) REVERT: P 97 ARG cc_start: 0.8617 (ttm-80) cc_final: 0.8067 (mtp-110) REVERT: P 100 ASN cc_start: 0.5942 (m-40) cc_final: 0.5670 (m110) REVERT: Q 18 SER cc_start: 0.7745 (t) cc_final: 0.7333 (p) REVERT: Q 37 TYR cc_start: 0.7774 (p90) cc_final: 0.7371 (p90) REVERT: R 7 ASN cc_start: 0.7629 (t0) cc_final: 0.7425 (t0) REVERT: R 13 HIS cc_start: 0.6560 (m170) cc_final: 0.6176 (m170) REVERT: R 67 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7534 (p0) REVERT: R 74 MET cc_start: 0.8529 (mpp) cc_final: 0.8282 (mpp) REVERT: R 80 MET cc_start: 0.7616 (mmm) cc_final: 0.7356 (mmm) REVERT: S 18 LYS cc_start: 0.8445 (ttmm) cc_final: 0.8214 (ttmm) REVERT: S 72 PHE cc_start: 0.8268 (t80) cc_final: 0.8016 (t80) REVERT: T 25 GLU cc_start: 0.8136 (mt-10) cc_final: 0.6964 (mt-10) REVERT: T 61 GLN cc_start: 0.7968 (mm110) cc_final: 0.7765 (mm-40) REVERT: U 1 MET cc_start: 0.6715 (tpp) cc_final: 0.6198 (tmm) REVERT: U 55 ASP cc_start: 0.6793 (OUTLIER) cc_final: 0.6231 (p0) REVERT: V 64 ARG cc_start: 0.8358 (ttp80) cc_final: 0.8124 (ttp-110) REVERT: W 47 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8860 (mtt-85) REVERT: W 56 ARG cc_start: 0.8444 (ttm-80) cc_final: 0.8106 (ttm110) REVERT: W 72 ARG cc_start: 0.7727 (mmm160) cc_final: 0.7056 (mtt180) REVERT: Y 17 ARG cc_start: 0.8474 (ttp-110) cc_final: 0.7906 (ttp-110) REVERT: Y 20 ASN cc_start: 0.8327 (m-40) cc_final: 0.7899 (m110) REVERT: Y 50 PHE cc_start: 0.7780 (t80) cc_final: 0.7526 (t80) REVERT: Y 53 MET cc_start: 0.8098 (ppp) cc_final: 0.7857 (ppp) REVERT: Y 56 ILE cc_start: 0.8241 (tt) cc_final: 0.7654 (mm) REVERT: Y 69 ASN cc_start: 0.8300 (t0) cc_final: 0.7612 (t0) REVERT: Y 81 GLN cc_start: 0.8640 (tp40) cc_final: 0.8342 (mp10) REVERT: Z 43 GLU cc_start: 0.7066 (pt0) cc_final: 0.6695 (mt-10) REVERT: Z 44 ARG cc_start: 0.8313 (mpt180) cc_final: 0.7724 (mmt180) REVERT: Z 45 LYS cc_start: 0.8825 (tppt) cc_final: 0.8624 (tppp) outliers start: 241 outliers final: 150 residues processed: 1363 average time/residue: 1.1872 time to fit residues: 2838.3037 Evaluate side-chains 1262 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1104 time to evaluate : 5.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 22 GLU Chi-restraints excluded: chain b residue 80 LEU Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 23 SER Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 101 VAL Chi-restraints excluded: chain f residue 120 ILE Chi-restraints excluded: chain f residue 170 THR Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain i residue 125 THR Chi-restraints excluded: chain i residue 127 SER Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain k residue 14 SER Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain p residue 9 GLN Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain r residue 10 LYS Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 34 ILE Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 7 ARG Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 36 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 21 TYR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 84 TYR Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 29 ILE Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 41 SER Chi-restraints excluded: chain W residue 47 ARG Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 5 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 906 optimal weight: 8.9990 chunk 690 optimal weight: 7.9990 chunk 476 optimal weight: 9.9990 chunk 101 optimal weight: 30.0000 chunk 438 optimal weight: 20.0000 chunk 616 optimal weight: 7.9990 chunk 921 optimal weight: 6.9990 chunk 975 optimal weight: 20.0000 chunk 481 optimal weight: 10.0000 chunk 873 optimal weight: 0.9980 chunk 262 optimal weight: 50.0000 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 162 GLN c 67 HIS ** d 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 136 GLN ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 26 GLN ** f 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 128 ASN ** m 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 3 HIS ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 65 ASN ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 70 HIS ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN E 27 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN N 49 GLN O 58 ASN P 21 HIS P 118 ASN Q 4 ASN ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 ASN ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 158217 Z= 0.272 Angle : 0.618 12.424 237092 Z= 0.317 Chirality : 0.036 0.280 30339 Planarity : 0.005 0.082 12448 Dihedral : 23.623 178.925 80154 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.41 % Favored : 90.48 % Rotamer: Outliers : 5.94 % Allowed : 23.72 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.11), residues: 5506 helix: -1.26 (0.12), residues: 1644 sheet: -1.83 (0.16), residues: 983 loop : -2.22 (0.11), residues: 2879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 103 HIS 0.008 0.001 HIS T 41 PHE 0.039 0.002 PHE X 73 TYR 0.020 0.002 TYR R 22 ARG 0.012 0.001 ARG X 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1436 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1164 time to evaluate : 6.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 94 GLN cc_start: 0.8103 (tp40) cc_final: 0.7800 (tp40) REVERT: d 1 MET cc_start: 0.4129 (mtt) cc_final: 0.3015 (tpp) REVERT: d 181 ILE cc_start: 0.9170 (tp) cc_final: 0.8931 (tp) REVERT: e 25 MET cc_start: 0.8843 (tpp) cc_final: 0.7998 (mmm) REVERT: f 41 GLU cc_start: 0.6537 (tp30) cc_final: 0.6314 (tp30) REVERT: f 74 MET cc_start: 0.8579 (ttm) cc_final: 0.8322 (mtt) REVERT: f 100 ASN cc_start: 0.8123 (p0) cc_final: 0.7748 (p0) REVERT: f 138 GLN cc_start: 0.9029 (tm-30) cc_final: 0.8608 (tm-30) REVERT: i 64 ARG cc_start: -0.1920 (OUTLIER) cc_final: -0.2641 (tpt170) REVERT: j 43 GLU cc_start: 0.8378 (pm20) cc_final: 0.8084 (pm20) REVERT: j 93 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.9087 (tp) REVERT: j 114 LEU cc_start: 0.9266 (tp) cc_final: 0.8841 (tt) REVERT: k 7 MET cc_start: 0.8721 (mmm) cc_final: 0.8306 (mmt) REVERT: m 136 MET cc_start: 0.7868 (ppp) cc_final: 0.7578 (ppp) REVERT: o 3 LYS cc_start: 0.7861 (ptmt) cc_final: 0.7585 (pttt) REVERT: p 9 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7720 (mp10) REVERT: r 34 GLU cc_start: 0.8659 (tt0) cc_final: 0.7752 (tp30) REVERT: r 45 GLU cc_start: 0.7937 (pp20) cc_final: 0.7158 (pp20) REVERT: r 97 LYS cc_start: 0.9011 (ttpt) cc_final: 0.8763 (ttpp) REVERT: s 15 GLN cc_start: 0.8819 (tt0) cc_final: 0.8605 (tt0) REVERT: t 1 MET cc_start: 0.4174 (tpt) cc_final: 0.2746 (ptp) REVERT: t 7 LEU cc_start: 0.9051 (mt) cc_final: 0.8809 (mm) REVERT: u 9 GLU cc_start: 0.7511 (tp30) cc_final: 0.7092 (tp30) REVERT: u 72 PHE cc_start: 0.7293 (t80) cc_final: 0.7043 (t80) REVERT: v 41 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7278 (tm-30) REVERT: v 45 ASP cc_start: 0.8241 (m-30) cc_final: 0.7945 (m-30) REVERT: v 48 MET cc_start: 0.8603 (tpt) cc_final: 0.8381 (tpt) REVERT: x 60 LYS cc_start: 0.8106 (tptm) cc_final: 0.7353 (tppt) REVERT: y 6 LEU cc_start: 0.4113 (OUTLIER) cc_final: 0.3776 (mp) REVERT: z 36 GLU cc_start: 0.7738 (pm20) cc_final: 0.7423 (pm20) REVERT: z 48 ASN cc_start: 0.8672 (t0) cc_final: 0.8395 (t0) REVERT: B 10 SER cc_start: 0.8853 (p) cc_final: 0.8438 (t) REVERT: B 31 LYS cc_start: 0.8606 (tttt) cc_final: 0.8191 (mttp) REVERT: B 47 TYR cc_start: 0.9004 (m-80) cc_final: 0.8725 (m-10) REVERT: D 22 MET cc_start: 0.8072 (mmm) cc_final: 0.7621 (mmm) REVERT: G 108 GLN cc_start: 0.8435 (mt0) cc_final: 0.7737 (mt0) REVERT: G 138 ARG cc_start: 0.7112 (tpt170) cc_final: 0.6848 (ttp80) REVERT: H 74 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8309 (mm) REVERT: H 106 ARG cc_start: 0.8160 (ptt-90) cc_final: 0.7452 (mmp80) REVERT: H 182 ASP cc_start: 0.8205 (t70) cc_final: 0.7889 (t70) REVERT: I 2 ARG cc_start: 0.4348 (OUTLIER) cc_final: 0.4006 (mtp-110) REVERT: I 75 TYR cc_start: 0.8611 (t80) cc_final: 0.8236 (t80) REVERT: I 89 LEU cc_start: 0.8859 (mt) cc_final: 0.8453 (mt) REVERT: J 100 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7937 (mm-30) REVERT: J 137 ARG cc_start: 0.8429 (mtt-85) cc_final: 0.8001 (mtt90) REVERT: L 84 TYR cc_start: 0.6352 (OUTLIER) cc_final: 0.5399 (m-10) REVERT: L 140 VAL cc_start: 0.8404 (OUTLIER) cc_final: 0.8157 (t) REVERT: M 42 GLU cc_start: 0.8536 (tp30) cc_final: 0.8136 (tp30) REVERT: N 27 ILE cc_start: 0.9193 (mm) cc_final: 0.8931 (mm) REVERT: N 90 ASP cc_start: 0.7775 (p0) cc_final: 0.7563 (p0) REVERT: O 10 LEU cc_start: 0.8966 (mt) cc_final: 0.8661 (mp) REVERT: O 87 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8134 (pt) REVERT: O 88 MET cc_start: 0.7508 (ppp) cc_final: 0.7101 (ppp) REVERT: P 57 SER cc_start: 0.8517 (p) cc_final: 0.8047 (m) REVERT: P 97 ARG cc_start: 0.8610 (ttm-80) cc_final: 0.8057 (mtp-110) REVERT: Q 18 SER cc_start: 0.7688 (t) cc_final: 0.7291 (p) REVERT: Q 37 TYR cc_start: 0.7720 (p90) cc_final: 0.7367 (p90) REVERT: R 13 HIS cc_start: 0.6677 (m170) cc_final: 0.6179 (m170) REVERT: R 67 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7722 (p0) REVERT: R 74 MET cc_start: 0.8489 (mpp) cc_final: 0.8142 (mpp) REVERT: R 80 MET cc_start: 0.7708 (mmm) cc_final: 0.7477 (mmm) REVERT: S 19 TYR cc_start: 0.7379 (m-80) cc_final: 0.7026 (m-80) REVERT: S 72 PHE cc_start: 0.8354 (t80) cc_final: 0.8062 (t80) REVERT: S 88 MET cc_start: 0.8230 (mmt) cc_final: 0.7914 (mmm) REVERT: T 16 ARG cc_start: 0.6930 (mtt180) cc_final: 0.6464 (mmt90) REVERT: T 25 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7694 (mt-10) REVERT: U 55 ASP cc_start: 0.6690 (OUTLIER) cc_final: 0.6196 (p0) REVERT: V 64 ARG cc_start: 0.8293 (ttp80) cc_final: 0.8069 (ttp-110) REVERT: W 56 ARG cc_start: 0.8469 (ttm-80) cc_final: 0.8145 (ttm110) REVERT: W 58 ILE cc_start: 0.9326 (mt) cc_final: 0.9085 (mt) REVERT: W 72 ARG cc_start: 0.7679 (mmm160) cc_final: 0.7081 (mtt180) REVERT: X 55 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8401 (pm20) REVERT: Y 20 ASN cc_start: 0.8401 (m-40) cc_final: 0.8019 (m110) REVERT: Y 53 MET cc_start: 0.8129 (ppp) cc_final: 0.7856 (ppp) REVERT: Y 69 ASN cc_start: 0.8473 (t0) cc_final: 0.7766 (t0) REVERT: Y 78 LEU cc_start: 0.8634 (mt) cc_final: 0.8221 (mt) REVERT: Z 44 ARG cc_start: 0.8420 (mpt180) cc_final: 0.7967 (mmt180) outliers start: 272 outliers final: 200 residues processed: 1322 average time/residue: 1.2002 time to fit residues: 2803.1162 Evaluate side-chains 1304 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1092 time to evaluate : 5.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 22 GLU Chi-restraints excluded: chain b residue 80 LEU Chi-restraints excluded: chain b residue 162 GLN Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain d residue 197 GLU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 22 ASN Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 70 LEU Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 101 VAL Chi-restraints excluded: chain f residue 115 GLN Chi-restraints excluded: chain f residue 120 ILE Chi-restraints excluded: chain f residue 170 THR Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 64 ARG Chi-restraints excluded: chain i residue 66 PHE Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain i residue 125 THR Chi-restraints excluded: chain i residue 127 SER Chi-restraints excluded: chain j residue 44 TYR Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain k residue 14 SER Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain p residue 9 GLN Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain q residue 51 GLN Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 10 LYS Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 34 ILE Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 66 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain u residue 102 ILE Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 29 ILE Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 1 MET Chi-restraints excluded: chain y residue 6 LEU Chi-restraints excluded: chain y residue 7 ARG Chi-restraints excluded: chain y residue 44 LYS Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 21 TYR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 2 ARG Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 139 ASN Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 84 TYR Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 10 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 29 ILE Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain W residue 9 PHE Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 55 GLN Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 36 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 812 optimal weight: 5.9990 chunk 553 optimal weight: 6.9990 chunk 14 optimal weight: 30.0000 chunk 726 optimal weight: 0.0870 chunk 402 optimal weight: 10.0000 chunk 832 optimal weight: 40.0000 chunk 674 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 498 optimal weight: 4.9990 chunk 875 optimal weight: 9.9990 chunk 246 optimal weight: 20.0000 overall best weight: 5.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 49 GLN ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 70 HIS v 49 ASN D 29 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN H 7 ASN ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN J 96 GLN ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 ASN P 100 ASN Q 4 ASN ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN U 18 GLN U 26 ASN U 29 ASN Y 12 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 158217 Z= 0.233 Angle : 0.582 13.188 237092 Z= 0.300 Chirality : 0.035 0.294 30339 Planarity : 0.005 0.113 12448 Dihedral : 23.577 179.006 80154 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.90 % Favored : 90.97 % Rotamer: Outliers : 5.90 % Allowed : 25.67 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.11), residues: 5506 helix: -1.05 (0.12), residues: 1650 sheet: -1.68 (0.16), residues: 991 loop : -2.10 (0.11), residues: 2865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 200 HIS 0.008 0.001 HIS E 30 PHE 0.038 0.002 PHE Z 36 TYR 0.017 0.002 TYR n 94 ARG 0.009 0.000 ARG W 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1419 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 1149 time to evaluate : 6.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 94 GLN cc_start: 0.8188 (tp40) cc_final: 0.7910 (tp40) REVERT: d 1 MET cc_start: 0.4169 (mtt) cc_final: 0.3052 (tpt) REVERT: d 181 ILE cc_start: 0.9179 (tp) cc_final: 0.8919 (tp) REVERT: e 25 MET cc_start: 0.8789 (tpp) cc_final: 0.7924 (mmm) REVERT: e 99 PHE cc_start: 0.8562 (t80) cc_final: 0.8284 (t80) REVERT: f 41 GLU cc_start: 0.6617 (tp30) cc_final: 0.6323 (tp30) REVERT: f 100 ASN cc_start: 0.8269 (p0) cc_final: 0.8019 (p0) REVERT: f 129 GLU cc_start: 0.8541 (tp30) cc_final: 0.8289 (tp30) REVERT: f 138 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8594 (tm-30) REVERT: i 64 ARG cc_start: -0.2053 (OUTLIER) cc_final: -0.3406 (tpm170) REVERT: i 66 PHE cc_start: 0.5027 (OUTLIER) cc_final: 0.3558 (t80) REVERT: j 43 GLU cc_start: 0.8319 (pm20) cc_final: 0.8041 (pm20) REVERT: j 114 LEU cc_start: 0.9253 (tp) cc_final: 0.8860 (tt) REVERT: j 118 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7594 (mmt) REVERT: k 7 MET cc_start: 0.8725 (mmm) cc_final: 0.8298 (mmt) REVERT: l 76 GLU cc_start: 0.7524 (pt0) cc_final: 0.7267 (pt0) REVERT: l 81 ASP cc_start: 0.8663 (m-30) cc_final: 0.8225 (t70) REVERT: n 22 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8292 (ptm160) REVERT: o 3 LYS cc_start: 0.7900 (ptmt) cc_final: 0.7615 (pttt) REVERT: p 9 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7728 (mp10) REVERT: r 1 MET cc_start: 0.8188 (tpp) cc_final: 0.7981 (tpt) REVERT: r 2 TYR cc_start: 0.8685 (p90) cc_final: 0.8408 (p90) REVERT: r 45 GLU cc_start: 0.7975 (pp20) cc_final: 0.7174 (pp20) REVERT: r 97 LYS cc_start: 0.8989 (ttpt) cc_final: 0.8755 (ttpp) REVERT: s 15 GLN cc_start: 0.8823 (tt0) cc_final: 0.8591 (tt0) REVERT: t 1 MET cc_start: 0.4224 (tpt) cc_final: 0.2686 (ptp) REVERT: t 7 LEU cc_start: 0.9056 (mt) cc_final: 0.8799 (mm) REVERT: t 48 GLN cc_start: 0.7820 (tp40) cc_final: 0.7597 (tp-100) REVERT: u 9 GLU cc_start: 0.7608 (tp30) cc_final: 0.7165 (tp30) REVERT: u 72 PHE cc_start: 0.7323 (t80) cc_final: 0.7043 (t80) REVERT: v 7 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7481 (pm20) REVERT: v 19 ARG cc_start: 0.8180 (mtm-85) cc_final: 0.7877 (mtm-85) REVERT: v 48 MET cc_start: 0.8568 (tpt) cc_final: 0.8335 (tpt) REVERT: x 60 LYS cc_start: 0.8131 (tptm) cc_final: 0.7609 (tppp) REVERT: x 76 LYS cc_start: 0.7738 (tppt) cc_final: 0.7411 (pttp) REVERT: y 6 LEU cc_start: 0.3879 (OUTLIER) cc_final: 0.3508 (mp) REVERT: z 36 GLU cc_start: 0.7701 (pm20) cc_final: 0.7398 (pm20) REVERT: z 48 ASN cc_start: 0.8701 (t0) cc_final: 0.8472 (t0) REVERT: B 31 LYS cc_start: 0.8587 (tttt) cc_final: 0.8158 (mttt) REVERT: B 47 TYR cc_start: 0.9021 (m-80) cc_final: 0.8577 (m-10) REVERT: D 22 MET cc_start: 0.8027 (mmm) cc_final: 0.7640 (mmm) REVERT: D 42 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8827 (tt) REVERT: G 63 LYS cc_start: 0.8747 (tmtt) cc_final: 0.8410 (tptt) REVERT: G 73 ARG cc_start: 0.6526 (ptt-90) cc_final: 0.5955 (tmt-80) REVERT: G 108 GLN cc_start: 0.8483 (mt0) cc_final: 0.7733 (mt0) REVERT: G 138 ARG cc_start: 0.6996 (tpt170) cc_final: 0.6781 (ttp80) REVERT: H 74 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8304 (mm) REVERT: H 106 ARG cc_start: 0.8232 (ptt-90) cc_final: 0.7514 (mmp80) REVERT: H 182 ASP cc_start: 0.8230 (t70) cc_final: 0.7933 (t70) REVERT: I 2 ARG cc_start: 0.4378 (OUTLIER) cc_final: 0.4125 (mtp-110) REVERT: I 75 TYR cc_start: 0.8589 (t80) cc_final: 0.8258 (t80) REVERT: I 89 LEU cc_start: 0.8886 (mt) cc_final: 0.8514 (mt) REVERT: J 137 ARG cc_start: 0.8372 (mtt-85) cc_final: 0.8040 (mtt90) REVERT: L 84 TYR cc_start: 0.6372 (OUTLIER) cc_final: 0.5424 (m-10) REVERT: L 140 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8226 (t) REVERT: M 4 ASP cc_start: 0.7090 (t70) cc_final: 0.6732 (t70) REVERT: M 15 ASN cc_start: 0.8770 (m-40) cc_final: 0.8561 (m-40) REVERT: M 42 GLU cc_start: 0.8442 (tp30) cc_final: 0.8011 (tp30) REVERT: N 18 VAL cc_start: 0.8637 (t) cc_final: 0.8387 (p) REVERT: N 27 ILE cc_start: 0.9225 (mm) cc_final: 0.8977 (mm) REVERT: N 35 GLU cc_start: 0.8407 (mp0) cc_final: 0.8194 (mm-30) REVERT: N 103 VAL cc_start: 0.8789 (m) cc_final: 0.8526 (p) REVERT: O 10 LEU cc_start: 0.8917 (mt) cc_final: 0.8596 (mm) REVERT: O 87 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8128 (pt) REVERT: O 88 MET cc_start: 0.7561 (ppp) cc_final: 0.7138 (ppp) REVERT: P 25 SER cc_start: 0.8912 (p) cc_final: 0.8622 (p) REVERT: P 57 SER cc_start: 0.8492 (p) cc_final: 0.8029 (m) REVERT: Q 18 SER cc_start: 0.7702 (t) cc_final: 0.7269 (p) REVERT: Q 37 TYR cc_start: 0.7731 (p90) cc_final: 0.7350 (p90) REVERT: R 67 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7656 (p0) REVERT: R 74 MET cc_start: 0.8501 (mpp) cc_final: 0.8138 (mpp) REVERT: R 80 MET cc_start: 0.7921 (mmm) cc_final: 0.7635 (mmm) REVERT: S 19 TYR cc_start: 0.7383 (m-80) cc_final: 0.7089 (m-80) REVERT: S 72 PHE cc_start: 0.8367 (t80) cc_final: 0.8082 (t80) REVERT: T 61 GLN cc_start: 0.7995 (mm110) cc_final: 0.7759 (mm-40) REVERT: U 55 ASP cc_start: 0.6609 (OUTLIER) cc_final: 0.6090 (p0) REVERT: V 15 LYS cc_start: 0.8318 (mtmm) cc_final: 0.7487 (ptpt) REVERT: V 62 GLU cc_start: 0.8570 (tp30) cc_final: 0.8200 (tp30) REVERT: V 64 ARG cc_start: 0.8249 (ttp80) cc_final: 0.7780 (ttt-90) REVERT: W 72 ARG cc_start: 0.7704 (mmm160) cc_final: 0.7152 (mtt180) REVERT: X 55 GLN cc_start: 0.8605 (pt0) cc_final: 0.8404 (pm20) REVERT: Y 12 GLN cc_start: 0.8596 (tt0) cc_final: 0.7831 (mt0) REVERT: Y 20 ASN cc_start: 0.8404 (m-40) cc_final: 0.8016 (m110) REVERT: Y 69 ASN cc_start: 0.8431 (t0) cc_final: 0.7711 (t0) REVERT: Z 44 ARG cc_start: 0.8211 (mpt180) cc_final: 0.7945 (mmt180) REVERT: Z 55 HIS cc_start: 0.7321 (p-80) cc_final: 0.6848 (p-80) outliers start: 270 outliers final: 202 residues processed: 1306 average time/residue: 1.2030 time to fit residues: 2778.7163 Evaluate side-chains 1310 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1093 time to evaluate : 6.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 22 GLU Chi-restraints excluded: chain b residue 80 LEU Chi-restraints excluded: chain b residue 116 GLN Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 165 MET Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 75 SER Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 22 ASN Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 37 MET Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain f residue 37 ASN Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 70 LEU Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 101 VAL Chi-restraints excluded: chain f residue 170 THR Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 64 ARG Chi-restraints excluded: chain i residue 66 PHE Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain i residue 125 THR Chi-restraints excluded: chain i residue 127 SER Chi-restraints excluded: chain j residue 21 THR Chi-restraints excluded: chain j residue 44 TYR Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 67 ASN Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 118 MET Chi-restraints excluded: chain k residue 14 SER Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 108 VAL Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 131 VAL Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 22 ARG Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain p residue 9 GLN Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain r residue 10 LYS Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 34 ILE Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 66 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain u residue 102 ILE Chi-restraints excluded: chain v residue 7 GLU Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 29 ILE Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain y residue 1 MET Chi-restraints excluded: chain y residue 6 LEU Chi-restraints excluded: chain y residue 7 ARG Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 21 TYR Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 161 ILE Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 2 ARG Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 139 ASN Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 84 TYR Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 48 ARG Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 10 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 29 ILE Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 41 SER Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 36 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 328 optimal weight: 10.0000 chunk 878 optimal weight: 5.9990 chunk 192 optimal weight: 20.0000 chunk 572 optimal weight: 7.9990 chunk 240 optimal weight: 20.0000 chunk 976 optimal weight: 5.9990 chunk 810 optimal weight: 4.9990 chunk 452 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 322 optimal weight: 10.0000 chunk 512 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 128 ASN ** m 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 6 GLN ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 70 HIS ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN Q 45 ASN ** T 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 158217 Z= 0.252 Angle : 0.595 12.413 237092 Z= 0.305 Chirality : 0.035 0.295 30339 Planarity : 0.005 0.100 12448 Dihedral : 23.566 179.097 80153 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.28 % Favored : 90.59 % Rotamer: Outliers : 6.57 % Allowed : 26.02 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.11), residues: 5506 helix: -0.94 (0.13), residues: 1666 sheet: -1.65 (0.16), residues: 986 loop : -2.03 (0.11), residues: 2854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 102 HIS 0.010 0.001 HIS m 13 PHE 0.034 0.002 PHE Z 36 TYR 0.020 0.002 TYR n 94 ARG 0.012 0.000 ARG W 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1438 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 1137 time to evaluate : 6.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 94 GLN cc_start: 0.8169 (tp40) cc_final: 0.7916 (tm-30) REVERT: d 1 MET cc_start: 0.4117 (mtt) cc_final: 0.2988 (tpt) REVERT: d 181 ILE cc_start: 0.9172 (tp) cc_final: 0.8913 (tp) REVERT: d 197 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7816 (tm-30) REVERT: e 25 MET cc_start: 0.8827 (tpp) cc_final: 0.7980 (mmm) REVERT: e 51 ASN cc_start: 0.8114 (t0) cc_final: 0.7856 (t0) REVERT: e 99 PHE cc_start: 0.8628 (t80) cc_final: 0.8359 (t80) REVERT: e 127 TYR cc_start: 0.7782 (t80) cc_final: 0.6975 (t80) REVERT: f 41 GLU cc_start: 0.6699 (tp30) cc_final: 0.6379 (tp30) REVERT: f 129 GLU cc_start: 0.8531 (tp30) cc_final: 0.8256 (tp30) REVERT: f 138 GLN cc_start: 0.8976 (tm-30) cc_final: 0.8536 (tm-30) REVERT: i 64 ARG cc_start: -0.1752 (OUTLIER) cc_final: -0.3156 (tpm170) REVERT: i 66 PHE cc_start: 0.5015 (OUTLIER) cc_final: 0.3635 (t80) REVERT: j 43 GLU cc_start: 0.8347 (pm20) cc_final: 0.8055 (pm20) REVERT: j 49 ASP cc_start: 0.7619 (p0) cc_final: 0.7393 (p0) REVERT: j 114 LEU cc_start: 0.9252 (tp) cc_final: 0.8859 (tt) REVERT: j 118 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7609 (mmt) REVERT: k 7 MET cc_start: 0.8726 (mmm) cc_final: 0.8303 (mmt) REVERT: l 81 ASP cc_start: 0.8690 (m-30) cc_final: 0.8275 (t70) REVERT: m 47 GLU cc_start: 0.7407 (tp30) cc_final: 0.7166 (tp30) REVERT: n 22 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8382 (ptm160) REVERT: n 120 GLU cc_start: 0.5733 (OUTLIER) cc_final: 0.5068 (tt0) REVERT: o 3 LYS cc_start: 0.7862 (ptmt) cc_final: 0.7557 (pttt) REVERT: o 58 ILE cc_start: 0.8813 (mm) cc_final: 0.8587 (mp) REVERT: r 45 GLU cc_start: 0.8071 (pp20) cc_final: 0.7353 (pp20) REVERT: r 60 LYS cc_start: 0.8605 (ptmm) cc_final: 0.8369 (ptmm) REVERT: r 97 LYS cc_start: 0.8999 (ttpt) cc_final: 0.8780 (ttpp) REVERT: s 15 GLN cc_start: 0.8814 (tt0) cc_final: 0.8607 (tt0) REVERT: t 1 MET cc_start: 0.4182 (tpt) cc_final: 0.2573 (ptp) REVERT: t 7 LEU cc_start: 0.9084 (mt) cc_final: 0.8846 (mm) REVERT: u 9 GLU cc_start: 0.7584 (tp30) cc_final: 0.7126 (tp30) REVERT: u 72 PHE cc_start: 0.7287 (t80) cc_final: 0.6998 (t80) REVERT: v 7 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7841 (pm20) REVERT: v 48 MET cc_start: 0.8554 (tpt) cc_final: 0.8296 (tpt) REVERT: w 25 GLU cc_start: 0.7072 (pt0) cc_final: 0.6738 (pt0) REVERT: w 66 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6925 (tp30) REVERT: x 60 LYS cc_start: 0.8120 (tptm) cc_final: 0.7630 (tppp) REVERT: x 76 LYS cc_start: 0.7755 (tppt) cc_final: 0.7483 (pttp) REVERT: z 36 GLU cc_start: 0.7759 (pm20) cc_final: 0.7495 (pm20) REVERT: B 31 LYS cc_start: 0.8579 (tttt) cc_final: 0.8171 (mttt) REVERT: B 47 TYR cc_start: 0.9057 (m-80) cc_final: 0.8703 (m-10) REVERT: D 42 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8861 (tt) REVERT: G 108 GLN cc_start: 0.8509 (mt0) cc_final: 0.7727 (mt0) REVERT: G 138 ARG cc_start: 0.7006 (tpt170) cc_final: 0.6798 (ttp80) REVERT: H 31 ASN cc_start: 0.8591 (t0) cc_final: 0.7973 (t0) REVERT: H 74 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8313 (mm) REVERT: H 105 VAL cc_start: 0.8234 (p) cc_final: 0.8023 (p) REVERT: H 106 ARG cc_start: 0.8248 (ptt-90) cc_final: 0.7557 (mmp80) REVERT: H 129 PHE cc_start: 0.7864 (p90) cc_final: 0.7374 (p90) REVERT: H 182 ASP cc_start: 0.8227 (t70) cc_final: 0.7941 (t70) REVERT: I 2 ARG cc_start: 0.4523 (OUTLIER) cc_final: 0.4222 (mtp-110) REVERT: I 39 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8473 (tm-30) REVERT: I 75 TYR cc_start: 0.8577 (t80) cc_final: 0.8293 (t80) REVERT: I 89 LEU cc_start: 0.8885 (mt) cc_final: 0.8489 (mt) REVERT: J 137 ARG cc_start: 0.8395 (mtt-85) cc_final: 0.8057 (mtt90) REVERT: K 14 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8290 (mm-40) REVERT: L 51 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8355 (mp10) REVERT: L 84 TYR cc_start: 0.6441 (OUTLIER) cc_final: 0.5477 (m-10) REVERT: L 140 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8268 (t) REVERT: M 4 ASP cc_start: 0.7213 (t70) cc_final: 0.6724 (t0) REVERT: M 15 ASN cc_start: 0.8746 (m-40) cc_final: 0.8542 (m-40) REVERT: M 42 GLU cc_start: 0.8424 (tp30) cc_final: 0.8007 (tp30) REVERT: M 90 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: N 27 ILE cc_start: 0.9244 (mm) cc_final: 0.8983 (mm) REVERT: N 103 VAL cc_start: 0.8755 (m) cc_final: 0.8515 (p) REVERT: O 10 LEU cc_start: 0.8940 (mt) cc_final: 0.8630 (mm) REVERT: O 87 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8164 (pt) REVERT: O 88 MET cc_start: 0.7544 (ppp) cc_final: 0.7102 (ppp) REVERT: P 25 SER cc_start: 0.8930 (p) cc_final: 0.8632 (p) REVERT: P 57 SER cc_start: 0.8469 (p) cc_final: 0.8011 (m) REVERT: Q 18 SER cc_start: 0.7713 (t) cc_final: 0.7295 (p) REVERT: Q 37 TYR cc_start: 0.7665 (p90) cc_final: 0.7333 (p90) REVERT: R 67 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7679 (p0) REVERT: R 80 MET cc_start: 0.7830 (mmm) cc_final: 0.7563 (mmm) REVERT: S 19 TYR cc_start: 0.7419 (m-80) cc_final: 0.7172 (m-80) REVERT: S 72 PHE cc_start: 0.8413 (t80) cc_final: 0.8134 (t80) REVERT: U 55 ASP cc_start: 0.6636 (OUTLIER) cc_final: 0.6219 (p0) REVERT: V 15 LYS cc_start: 0.8371 (mtmm) cc_final: 0.7472 (ptpp) REVERT: V 62 GLU cc_start: 0.8515 (tp30) cc_final: 0.8227 (tp30) REVERT: W 72 ARG cc_start: 0.7648 (mmm160) cc_final: 0.7152 (mtt180) REVERT: Y 14 GLU cc_start: 0.8647 (pt0) cc_final: 0.8300 (pm20) REVERT: Y 20 ASN cc_start: 0.8393 (m-40) cc_final: 0.8035 (m110) REVERT: Y 58 ASP cc_start: 0.8273 (m-30) cc_final: 0.7998 (m-30) REVERT: Y 69 ASN cc_start: 0.8450 (t0) cc_final: 0.7683 (t0) REVERT: Z 44 ARG cc_start: 0.8261 (mpt180) cc_final: 0.7968 (mmt180) REVERT: Z 48 LYS cc_start: 0.8011 (mtpp) cc_final: 0.7688 (mtpt) REVERT: Z 55 HIS cc_start: 0.7164 (p-80) cc_final: 0.6840 (p-80) outliers start: 301 outliers final: 237 residues processed: 1319 average time/residue: 1.1992 time to fit residues: 2805.5406 Evaluate side-chains 1354 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 1100 time to evaluate : 6.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 22 GLU Chi-restraints excluded: chain b residue 80 LEU Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 200 MET Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 165 MET Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 75 SER Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain d residue 197 GLU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 22 ASN Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 37 ASN Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 70 LEU Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 101 VAL Chi-restraints excluded: chain f residue 170 THR Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 64 ARG Chi-restraints excluded: chain i residue 66 PHE Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain i residue 125 THR Chi-restraints excluded: chain i residue 127 SER Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 21 THR Chi-restraints excluded: chain j residue 44 TYR Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 67 ASN Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 118 MET Chi-restraints excluded: chain k residue 14 SER Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 108 VAL Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 22 ARG Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 120 GLU Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain r residue 10 LYS Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 34 ILE Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 66 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain u residue 102 ILE Chi-restraints excluded: chain v residue 7 GLU Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 29 ILE Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 49 CYS Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain y residue 7 ARG Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 21 TYR Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 161 ILE Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 2 ARG Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 139 ASN Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 51 GLN Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 84 TYR Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 26 MET Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 48 ARG Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 10 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 29 ILE Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 9 PHE Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 41 SER Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 36 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 941 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 chunk 556 optimal weight: 20.0000 chunk 712 optimal weight: 9.9990 chunk 552 optimal weight: 7.9990 chunk 821 optimal weight: 10.0000 chunk 545 optimal weight: 9.9990 chunk 972 optimal weight: 20.0000 chunk 608 optimal weight: 8.9990 chunk 592 optimal weight: 7.9990 chunk 448 optimal weight: 20.0000 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 162 GLN ** d 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 40 HIS k 3 GLN ** m 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 11 GLN r 12 HIS ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 70 HIS ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 36 GLN D 29 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 GLN ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 ASN M 66 GLN Q 45 ASN ** T 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN W 53 GLN ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 54 GLN Z 63 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 158217 Z= 0.349 Angle : 0.675 13.416 237092 Z= 0.344 Chirality : 0.039 0.352 30339 Planarity : 0.005 0.113 12448 Dihedral : 23.659 178.110 80153 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.72 % Favored : 89.18 % Rotamer: Outliers : 7.34 % Allowed : 25.93 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.11), residues: 5506 helix: -1.07 (0.12), residues: 1657 sheet: -1.71 (0.16), residues: 1005 loop : -2.07 (0.11), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP b 212 HIS 0.010 0.001 HIS d 92 PHE 0.035 0.002 PHE Z 36 TYR 0.027 0.002 TYR n 94 ARG 0.013 0.001 ARG W 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1454 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 1118 time to evaluate : 6.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 94 GLN cc_start: 0.8191 (tp40) cc_final: 0.7877 (tp-100) REVERT: d 1 MET cc_start: 0.4126 (mtt) cc_final: 0.2919 (tpt) REVERT: d 181 ILE cc_start: 0.9177 (tp) cc_final: 0.8948 (tp) REVERT: e 25 MET cc_start: 0.8875 (tpp) cc_final: 0.7943 (mmm) REVERT: e 51 ASN cc_start: 0.8330 (t0) cc_final: 0.8052 (t0) REVERT: e 99 PHE cc_start: 0.8709 (t80) cc_final: 0.8471 (t80) REVERT: e 127 TYR cc_start: 0.7821 (t80) cc_final: 0.7046 (t80) REVERT: e 174 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7621 (m-10) REVERT: f 41 GLU cc_start: 0.6794 (tp30) cc_final: 0.6498 (tp30) REVERT: f 138 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8456 (tm-30) REVERT: i 64 ARG cc_start: -0.1205 (OUTLIER) cc_final: -0.1768 (tpm170) REVERT: j 43 GLU cc_start: 0.8350 (pm20) cc_final: 0.8055 (pm20) REVERT: j 114 LEU cc_start: 0.9268 (tp) cc_final: 0.8891 (tt) REVERT: j 118 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7730 (mmt) REVERT: k 7 MET cc_start: 0.8716 (mmm) cc_final: 0.8332 (mmt) REVERT: l 81 ASP cc_start: 0.8732 (m-30) cc_final: 0.8355 (t70) REVERT: n 9 GLN cc_start: 0.7139 (pp30) cc_final: 0.6691 (pp30) REVERT: n 22 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8234 (ptm160) REVERT: n 120 GLU cc_start: 0.5817 (OUTLIER) cc_final: 0.5132 (tt0) REVERT: o 58 ILE cc_start: 0.8805 (mm) cc_final: 0.8557 (mp) REVERT: r 45 GLU cc_start: 0.8169 (pp20) cc_final: 0.7430 (pp20) REVERT: r 60 LYS cc_start: 0.8679 (ptmm) cc_final: 0.8358 (ptmm) REVERT: r 97 LYS cc_start: 0.9035 (ttpt) cc_final: 0.8805 (ttpp) REVERT: t 7 LEU cc_start: 0.9183 (mt) cc_final: 0.8973 (mm) REVERT: u 9 GLU cc_start: 0.7565 (tp30) cc_final: 0.7130 (tp30) REVERT: u 72 PHE cc_start: 0.7294 (t80) cc_final: 0.6945 (t80) REVERT: v 7 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7825 (pm20) REVERT: v 19 ARG cc_start: 0.8157 (mtm-85) cc_final: 0.7827 (mtt-85) REVERT: v 48 MET cc_start: 0.8574 (tpt) cc_final: 0.8296 (tpt) REVERT: w 25 GLU cc_start: 0.7222 (pt0) cc_final: 0.6977 (pt0) REVERT: x 60 LYS cc_start: 0.8129 (tptm) cc_final: 0.7623 (tppp) REVERT: y 6 LEU cc_start: 0.4090 (OUTLIER) cc_final: 0.3826 (mp) REVERT: z 36 GLU cc_start: 0.7802 (pm20) cc_final: 0.7562 (pm20) REVERT: B 31 LYS cc_start: 0.8583 (tttt) cc_final: 0.8212 (mttt) REVERT: B 47 TYR cc_start: 0.9084 (m-80) cc_final: 0.8770 (m-10) REVERT: B 48 TYR cc_start: 0.8649 (t80) cc_final: 0.8345 (t80) REVERT: D 22 MET cc_start: 0.8132 (mmm) cc_final: 0.7903 (mmm) REVERT: D 42 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8864 (tt) REVERT: G 29 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8490 (m-80) REVERT: G 108 GLN cc_start: 0.8519 (mt0) cc_final: 0.7746 (mt0) REVERT: G 138 ARG cc_start: 0.7020 (tpt170) cc_final: 0.6717 (ttp80) REVERT: H 74 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8384 (mm) REVERT: H 106 ARG cc_start: 0.8227 (ptt-90) cc_final: 0.7594 (mmp80) REVERT: H 129 PHE cc_start: 0.7888 (p90) cc_final: 0.7529 (p90) REVERT: H 182 ASP cc_start: 0.8207 (t70) cc_final: 0.7925 (t70) REVERT: I 2 ARG cc_start: 0.4520 (OUTLIER) cc_final: 0.4253 (mtp-110) REVERT: I 3 TYR cc_start: 0.7768 (t80) cc_final: 0.7562 (t80) REVERT: I 39 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8658 (tm-30) REVERT: I 75 TYR cc_start: 0.8610 (t80) cc_final: 0.8393 (t80) REVERT: I 89 LEU cc_start: 0.8910 (mt) cc_final: 0.8659 (mt) REVERT: J 137 ARG cc_start: 0.8367 (mtt-85) cc_final: 0.8030 (mtt90) REVERT: K 14 GLN cc_start: 0.8555 (mm-40) cc_final: 0.8352 (mm-40) REVERT: L 51 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8077 (mp10) REVERT: L 84 TYR cc_start: 0.6390 (OUTLIER) cc_final: 0.5419 (m-10) REVERT: L 140 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8325 (t) REVERT: M 42 GLU cc_start: 0.8422 (tp30) cc_final: 0.8031 (tp30) REVERT: M 75 GLN cc_start: 0.8148 (mm110) cc_final: 0.7844 (mm110) REVERT: M 90 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: N 18 VAL cc_start: 0.8728 (t) cc_final: 0.8116 (m) REVERT: N 27 ILE cc_start: 0.9224 (mm) cc_final: 0.8945 (mm) REVERT: N 103 VAL cc_start: 0.8773 (m) cc_final: 0.8497 (p) REVERT: O 10 LEU cc_start: 0.8963 (mt) cc_final: 0.8622 (mm) REVERT: O 46 LYS cc_start: 0.8839 (mtmt) cc_final: 0.8546 (mtpp) REVERT: O 87 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8155 (pt) REVERT: O 88 MET cc_start: 0.7326 (ppp) cc_final: 0.6905 (ppp) REVERT: P 57 SER cc_start: 0.8404 (p) cc_final: 0.7930 (m) REVERT: Q 18 SER cc_start: 0.7735 (t) cc_final: 0.7369 (p) REVERT: Q 37 TYR cc_start: 0.7712 (p90) cc_final: 0.7380 (p90) REVERT: R 80 MET cc_start: 0.7881 (mmm) cc_final: 0.7582 (mmm) REVERT: S 19 TYR cc_start: 0.7376 (m-80) cc_final: 0.7129 (m-80) REVERT: S 72 PHE cc_start: 0.8480 (t80) cc_final: 0.8175 (t80) REVERT: U 55 ASP cc_start: 0.6566 (OUTLIER) cc_final: 0.6172 (p0) REVERT: V 15 LYS cc_start: 0.8413 (mtmm) cc_final: 0.7547 (ptpp) REVERT: V 62 GLU cc_start: 0.8404 (tp30) cc_final: 0.8188 (tp30) REVERT: W 69 TYR cc_start: 0.8470 (m-80) cc_final: 0.8262 (m-10) REVERT: W 72 ARG cc_start: 0.7653 (mmm160) cc_final: 0.7198 (mtt180) REVERT: X 43 MET cc_start: 0.6796 (mpp) cc_final: 0.6338 (mpp) REVERT: X 64 GLU cc_start: 0.7831 (tt0) cc_final: 0.7627 (tt0) REVERT: Y 20 ASN cc_start: 0.8377 (m-40) cc_final: 0.8035 (m-40) REVERT: Y 58 ASP cc_start: 0.8338 (m-30) cc_final: 0.8096 (m-30) REVERT: Y 69 ASN cc_start: 0.8537 (t0) cc_final: 0.7785 (t0) REVERT: Z 44 ARG cc_start: 0.8304 (mpt180) cc_final: 0.8068 (mmt180) REVERT: Z 48 LYS cc_start: 0.8060 (mtpp) cc_final: 0.7791 (mtpp) outliers start: 336 outliers final: 269 residues processed: 1318 average time/residue: 1.2092 time to fit residues: 2839.3783 Evaluate side-chains 1372 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 1086 time to evaluate : 5.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 22 GLU Chi-restraints excluded: chain b residue 80 LEU Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 162 GLN Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 200 MET Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 165 MET Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 75 SER Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain d residue 197 GLU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 22 ASN Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 174 PHE Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 37 ASN Chi-restraints excluded: chain f residue 46 ASP Chi-restraints excluded: chain f residue 70 LEU Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 101 VAL Chi-restraints excluded: chain f residue 120 ILE Chi-restraints excluded: chain f residue 170 THR Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 64 ARG Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain i residue 125 THR Chi-restraints excluded: chain i residue 127 SER Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 21 THR Chi-restraints excluded: chain j residue 44 TYR Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 58 ASN Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 67 ASN Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 118 MET Chi-restraints excluded: chain k residue 14 SER Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 103 ILE Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 131 VAL Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 22 ARG Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 120 GLU Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain q residue 76 SER Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain r residue 10 LYS Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 59 ILE Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 94 ASP Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 34 ILE Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 66 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain u residue 102 ILE Chi-restraints excluded: chain v residue 7 GLU Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 29 ILE Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain y residue 1 MET Chi-restraints excluded: chain y residue 6 LEU Chi-restraints excluded: chain y residue 7 ARG Chi-restraints excluded: chain y residue 36 GLN Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 21 TYR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 161 ILE Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 2 ARG Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 139 ASN Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 51 GLN Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 84 TYR Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 26 MET Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 48 ARG Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain R residue 10 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 29 ILE Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain T residue 2 LEU Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 41 SER Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 36 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 601 optimal weight: 10.0000 chunk 388 optimal weight: 10.0000 chunk 580 optimal weight: 5.9990 chunk 292 optimal weight: 20.0000 chunk 191 optimal weight: 10.0000 chunk 188 optimal weight: 30.0000 chunk 618 optimal weight: 5.9990 chunk 662 optimal weight: 5.9990 chunk 480 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 764 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 89 HIS ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 48 GLN t 70 HIS x 22 ASN y 36 GLN ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 GLN O 20 GLN ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN W 53 GLN Y 47 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 158217 Z= 0.267 Angle : 0.616 13.016 237092 Z= 0.316 Chirality : 0.036 0.321 30339 Planarity : 0.005 0.105 12448 Dihedral : 23.611 178.245 80153 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.54 % Favored : 90.36 % Rotamer: Outliers : 6.82 % Allowed : 26.82 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.11), residues: 5506 helix: -0.94 (0.12), residues: 1660 sheet: -1.64 (0.16), residues: 985 loop : -1.98 (0.11), residues: 2861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 200 HIS 0.010 0.001 HIS f 114 PHE 0.036 0.002 PHE Z 36 TYR 0.021 0.002 TYR n 94 ARG 0.012 0.000 ARG W 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1424 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 1112 time to evaluate : 6.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 94 GLN cc_start: 0.8168 (tp40) cc_final: 0.7951 (tm-30) REVERT: d 1 MET cc_start: 0.4034 (mtt) cc_final: 0.2889 (tpt) REVERT: d 143 LEU cc_start: 0.7091 (mt) cc_final: 0.6630 (tp) REVERT: d 181 ILE cc_start: 0.9180 (tp) cc_final: 0.8944 (tp) REVERT: d 195 GLN cc_start: 0.7913 (mt0) cc_final: 0.7680 (mm-40) REVERT: e 25 MET cc_start: 0.8798 (tpp) cc_final: 0.7906 (mmm) REVERT: e 51 ASN cc_start: 0.8407 (t0) cc_final: 0.8133 (t0) REVERT: e 80 GLN cc_start: 0.8696 (tp40) cc_final: 0.8489 (tp40) REVERT: e 99 PHE cc_start: 0.8673 (t80) cc_final: 0.8379 (t80) REVERT: e 127 TYR cc_start: 0.7788 (t80) cc_final: 0.7111 (t80) REVERT: e 174 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7474 (m-10) REVERT: f 41 GLU cc_start: 0.6827 (tp30) cc_final: 0.6517 (tp30) REVERT: f 129 GLU cc_start: 0.8575 (tp30) cc_final: 0.8342 (tp30) REVERT: f 138 GLN cc_start: 0.8946 (tm-30) cc_final: 0.8489 (tm-30) REVERT: i 64 ARG cc_start: -0.1190 (OUTLIER) cc_final: -0.1659 (tpm170) REVERT: j 43 GLU cc_start: 0.8313 (pm20) cc_final: 0.8028 (pm20) REVERT: j 114 LEU cc_start: 0.9255 (tp) cc_final: 0.8856 (tt) REVERT: j 118 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7668 (mmt) REVERT: k 7 MET cc_start: 0.8730 (mmm) cc_final: 0.8356 (mmt) REVERT: l 81 ASP cc_start: 0.8699 (m-30) cc_final: 0.8319 (t70) REVERT: l 106 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7885 (mp0) REVERT: n 22 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8409 (ptm160) REVERT: n 120 GLU cc_start: 0.5802 (OUTLIER) cc_final: 0.5118 (tt0) REVERT: o 58 ILE cc_start: 0.8805 (mm) cc_final: 0.8554 (mp) REVERT: r 45 GLU cc_start: 0.8176 (pp20) cc_final: 0.7434 (pp20) REVERT: r 60 LYS cc_start: 0.8629 (ptmm) cc_final: 0.8340 (ptmm) REVERT: r 97 LYS cc_start: 0.9017 (ttpt) cc_final: 0.8795 (ttpp) REVERT: t 7 LEU cc_start: 0.9173 (mt) cc_final: 0.8953 (mm) REVERT: u 6 ARG cc_start: 0.7754 (ttt180) cc_final: 0.7005 (ttt90) REVERT: u 9 GLU cc_start: 0.7723 (tp30) cc_final: 0.7157 (tp30) REVERT: u 45 GLN cc_start: 0.8293 (tm-30) cc_final: 0.8047 (tm-30) REVERT: u 72 PHE cc_start: 0.7122 (t80) cc_final: 0.6900 (t80) REVERT: v 7 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7717 (pm20) REVERT: v 48 MET cc_start: 0.8550 (tpt) cc_final: 0.8328 (tpt) REVERT: w 25 GLU cc_start: 0.7059 (pt0) cc_final: 0.6774 (pt0) REVERT: x 60 LYS cc_start: 0.8115 (tptm) cc_final: 0.7643 (tppp) REVERT: y 6 LEU cc_start: 0.4055 (OUTLIER) cc_final: 0.3792 (mp) REVERT: z 36 GLU cc_start: 0.7772 (pm20) cc_final: 0.7535 (pm20) REVERT: B 31 LYS cc_start: 0.8565 (tttt) cc_final: 0.8212 (mttt) REVERT: D 22 MET cc_start: 0.8074 (mmm) cc_final: 0.7771 (mmm) REVERT: D 42 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8838 (tt) REVERT: G 108 GLN cc_start: 0.8514 (mt0) cc_final: 0.7690 (mt0) REVERT: H 74 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8376 (mm) REVERT: H 106 ARG cc_start: 0.8236 (ptt-90) cc_final: 0.7613 (mmp80) REVERT: H 129 PHE cc_start: 0.7873 (p90) cc_final: 0.7422 (p90) REVERT: H 182 ASP cc_start: 0.8219 (t70) cc_final: 0.7947 (t70) REVERT: H 206 ILE cc_start: 0.5877 (OUTLIER) cc_final: 0.5180 (tp) REVERT: I 2 ARG cc_start: 0.4643 (OUTLIER) cc_final: 0.4379 (mtp-110) REVERT: I 39 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8389 (tm-30) REVERT: J 137 ARG cc_start: 0.8364 (mtt-85) cc_final: 0.8030 (mtt90) REVERT: K 14 GLN cc_start: 0.8470 (mm-40) cc_final: 0.8252 (mm-40) REVERT: L 84 TYR cc_start: 0.6417 (OUTLIER) cc_final: 0.5336 (m-10) REVERT: L 140 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8303 (t) REVERT: M 42 GLU cc_start: 0.8425 (tp30) cc_final: 0.7931 (tp30) REVERT: M 75 GLN cc_start: 0.8133 (mm110) cc_final: 0.7835 (mm110) REVERT: M 90 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.6841 (mp0) REVERT: N 18 VAL cc_start: 0.8738 (t) cc_final: 0.8500 (p) REVERT: N 27 ILE cc_start: 0.9278 (mm) cc_final: 0.9053 (mm) REVERT: N 103 VAL cc_start: 0.8730 (m) cc_final: 0.8501 (p) REVERT: O 10 LEU cc_start: 0.8986 (mt) cc_final: 0.8684 (mm) REVERT: O 46 LYS cc_start: 0.8777 (mtmt) cc_final: 0.8491 (mtpp) REVERT: O 87 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8192 (pt) REVERT: Q 18 SER cc_start: 0.7786 (t) cc_final: 0.7343 (p) REVERT: Q 37 TYR cc_start: 0.7697 (p90) cc_final: 0.7336 (p90) REVERT: R 80 MET cc_start: 0.7866 (mmm) cc_final: 0.7557 (mmm) REVERT: S 19 TYR cc_start: 0.7344 (m-80) cc_final: 0.7117 (m-80) REVERT: S 72 PHE cc_start: 0.8458 (t80) cc_final: 0.8231 (t80) REVERT: S 89 ARG cc_start: 0.7577 (mtt90) cc_final: 0.6990 (mtm-85) REVERT: U 54 LEU cc_start: 0.7952 (mm) cc_final: 0.7700 (mt) REVERT: U 55 ASP cc_start: 0.6569 (OUTLIER) cc_final: 0.6200 (p0) REVERT: V 15 LYS cc_start: 0.8419 (mtmm) cc_final: 0.7414 (ptpp) REVERT: V 62 GLU cc_start: 0.8388 (tp30) cc_final: 0.8155 (tp30) REVERT: W 69 TYR cc_start: 0.8433 (m-80) cc_final: 0.8226 (m-10) REVERT: W 72 ARG cc_start: 0.7591 (mmm160) cc_final: 0.7258 (mtt180) REVERT: X 43 MET cc_start: 0.6801 (mpp) cc_final: 0.6400 (mpp) REVERT: Y 20 ASN cc_start: 0.8368 (m-40) cc_final: 0.8037 (m-40) REVERT: Y 69 ASN cc_start: 0.8453 (t0) cc_final: 0.7682 (t0) REVERT: Z 44 ARG cc_start: 0.8283 (mpt180) cc_final: 0.8034 (mmt180) REVERT: Z 48 LYS cc_start: 0.8002 (mtpp) cc_final: 0.7765 (mtpp) outliers start: 312 outliers final: 262 residues processed: 1296 average time/residue: 1.1885 time to fit residues: 2733.9850 Evaluate side-chains 1366 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 1088 time to evaluate : 7.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 22 GLU Chi-restraints excluded: chain b residue 80 LEU Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 116 GLN Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 165 MET Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 75 SER Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 22 ASN Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 174 PHE Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 37 ASN Chi-restraints excluded: chain f residue 46 ASP Chi-restraints excluded: chain f residue 70 LEU Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 101 VAL Chi-restraints excluded: chain f residue 120 ILE Chi-restraints excluded: chain f residue 170 THR Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 64 ARG Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain i residue 125 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 21 THR Chi-restraints excluded: chain j residue 44 TYR Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 67 ASN Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 118 MET Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 10 GLU Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 103 ILE Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 108 VAL Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 131 VAL Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain m residue 136 MET Chi-restraints excluded: chain n residue 22 ARG Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 120 GLU Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain q residue 76 SER Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain r residue 10 LYS Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 59 ILE Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 34 ILE Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 66 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain u residue 102 ILE Chi-restraints excluded: chain v residue 7 GLU Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 29 ILE Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 65 THR Chi-restraints excluded: chain y residue 6 LEU Chi-restraints excluded: chain y residue 36 GLN Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 21 TYR Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 161 ILE Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain I residue 2 ARG Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 139 ASN Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 84 TYR Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 48 ARG Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain R residue 10 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 29 ILE Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain T residue 2 LEU Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 41 SER Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 36 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 884 optimal weight: 5.9990 chunk 931 optimal weight: 20.0000 chunk 850 optimal weight: 30.0000 chunk 906 optimal weight: 10.0000 chunk 545 optimal weight: 30.0000 chunk 394 optimal weight: 10.0000 chunk 711 optimal weight: 8.9990 chunk 278 optimal weight: 10.0000 chunk 818 optimal weight: 8.9990 chunk 857 optimal weight: 6.9990 chunk 903 optimal weight: 10.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 162 GLN ** d 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 70 HIS x 22 ASN ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 ASN D 29 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 45 ASN ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 GLN X 68 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 158217 Z= 0.323 Angle : 0.653 12.967 237092 Z= 0.334 Chirality : 0.038 0.325 30339 Planarity : 0.005 0.109 12448 Dihedral : 23.617 178.278 80153 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.37 % Favored : 89.52 % Rotamer: Outliers : 7.08 % Allowed : 26.80 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.11), residues: 5506 helix: -0.99 (0.12), residues: 1654 sheet: -1.64 (0.16), residues: 1014 loop : -2.03 (0.11), residues: 2838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP b 212 HIS 0.009 0.001 HIS T 41 PHE 0.035 0.002 PHE Z 36 TYR 0.028 0.002 TYR n 94 ARG 0.012 0.001 ARG W 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1413 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 324 poor density : 1089 time to evaluate : 6.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 1 MET cc_start: 0.3998 (mtt) cc_final: 0.2836 (tpt) REVERT: d 35 TYR cc_start: 0.8635 (t80) cc_final: 0.8423 (t80) REVERT: d 143 LEU cc_start: 0.7133 (mt) cc_final: 0.6630 (tp) REVERT: d 181 ILE cc_start: 0.9182 (tp) cc_final: 0.8954 (tp) REVERT: d 195 GLN cc_start: 0.7946 (mt0) cc_final: 0.7709 (mm110) REVERT: d 197 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7945 (pp20) REVERT: e 25 MET cc_start: 0.8903 (tpp) cc_final: 0.7954 (mmm) REVERT: e 51 ASN cc_start: 0.8429 (t0) cc_final: 0.8134 (t0) REVERT: e 99 PHE cc_start: 0.8680 (t80) cc_final: 0.8419 (t80) REVERT: e 127 TYR cc_start: 0.7805 (t80) cc_final: 0.6776 (t80) REVERT: e 174 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7240 (m-80) REVERT: f 41 GLU cc_start: 0.6856 (tp30) cc_final: 0.6533 (tp30) REVERT: f 129 GLU cc_start: 0.8572 (tp30) cc_final: 0.8320 (tp30) REVERT: f 138 GLN cc_start: 0.8932 (tm-30) cc_final: 0.8473 (tm-30) REVERT: i 64 ARG cc_start: -0.1188 (OUTLIER) cc_final: -0.1595 (tpm170) REVERT: j 43 GLU cc_start: 0.8346 (pm20) cc_final: 0.8037 (pm20) REVERT: j 114 LEU cc_start: 0.9254 (tp) cc_final: 0.8878 (tt) REVERT: j 118 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7712 (mmt) REVERT: k 7 MET cc_start: 0.8743 (mmm) cc_final: 0.8340 (mmt) REVERT: l 81 ASP cc_start: 0.8721 (m-30) cc_final: 0.8359 (t70) REVERT: n 9 GLN cc_start: 0.7108 (pp30) cc_final: 0.6677 (pp30) REVERT: n 22 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8542 (ptm160) REVERT: n 120 GLU cc_start: 0.5812 (OUTLIER) cc_final: 0.5131 (tt0) REVERT: o 58 ILE cc_start: 0.8795 (mm) cc_final: 0.8544 (mp) REVERT: r 45 GLU cc_start: 0.8208 (pp20) cc_final: 0.7460 (pp20) REVERT: r 60 LYS cc_start: 0.8653 (ptmm) cc_final: 0.8350 (ptmm) REVERT: r 97 LYS cc_start: 0.9008 (ttpt) cc_final: 0.8779 (ttpp) REVERT: t 7 LEU cc_start: 0.9217 (mt) cc_final: 0.9005 (mm) REVERT: u 6 ARG cc_start: 0.7774 (ttt180) cc_final: 0.7016 (ttt90) REVERT: u 9 GLU cc_start: 0.7655 (tp30) cc_final: 0.7134 (tp30) REVERT: u 72 PHE cc_start: 0.7147 (t80) cc_final: 0.6897 (t80) REVERT: v 7 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7788 (pm20) REVERT: v 48 MET cc_start: 0.8533 (tpt) cc_final: 0.8270 (tpt) REVERT: w 25 GLU cc_start: 0.7125 (pt0) cc_final: 0.6832 (pt0) REVERT: x 43 LYS cc_start: 0.8254 (mmtp) cc_final: 0.7522 (pttm) REVERT: x 60 LYS cc_start: 0.8130 (tptm) cc_final: 0.7654 (tppp) REVERT: y 6 LEU cc_start: 0.4103 (OUTLIER) cc_final: 0.3839 (mp) REVERT: z 10 ARG cc_start: 0.8293 (ttm-80) cc_final: 0.8080 (ttm-80) REVERT: z 36 GLU cc_start: 0.7804 (pm20) cc_final: 0.7577 (pm20) REVERT: D 22 MET cc_start: 0.8072 (mmm) cc_final: 0.7695 (mmm) REVERT: D 42 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8854 (tt) REVERT: G 108 GLN cc_start: 0.8507 (mt0) cc_final: 0.7724 (mt0) REVERT: H 74 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8387 (mm) REVERT: H 106 ARG cc_start: 0.8312 (ptt-90) cc_final: 0.7655 (mmp80) REVERT: H 129 PHE cc_start: 0.7916 (p90) cc_final: 0.7481 (p90) REVERT: H 182 ASP cc_start: 0.8169 (t70) cc_final: 0.7915 (t70) REVERT: I 2 ARG cc_start: 0.4731 (OUTLIER) cc_final: 0.4489 (mtp-110) REVERT: I 39 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8345 (tm-30) REVERT: I 89 LEU cc_start: 0.8806 (mt) cc_final: 0.8396 (mt) REVERT: J 137 ARG cc_start: 0.8370 (mtt-85) cc_final: 0.8034 (mtt90) REVERT: K 14 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8302 (mm-40) REVERT: L 84 TYR cc_start: 0.6424 (OUTLIER) cc_final: 0.5322 (m-10) REVERT: M 42 GLU cc_start: 0.8416 (tp30) cc_final: 0.7873 (tp30) REVERT: M 75 GLN cc_start: 0.8145 (mm110) cc_final: 0.7850 (mm110) REVERT: M 90 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: N 27 ILE cc_start: 0.9261 (mm) cc_final: 0.9012 (mm) REVERT: N 103 VAL cc_start: 0.8734 (m) cc_final: 0.8522 (p) REVERT: O 10 LEU cc_start: 0.8964 (mt) cc_final: 0.8626 (mm) REVERT: O 46 LYS cc_start: 0.8816 (mtmt) cc_final: 0.8530 (mtpp) REVERT: O 87 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8174 (pt) REVERT: Q 18 SER cc_start: 0.7622 (t) cc_final: 0.7214 (p) REVERT: Q 37 TYR cc_start: 0.7706 (p90) cc_final: 0.7322 (p90) REVERT: R 80 MET cc_start: 0.7838 (mmm) cc_final: 0.7517 (mmm) REVERT: S 72 PHE cc_start: 0.8499 (t80) cc_final: 0.8221 (t80) REVERT: U 55 ASP cc_start: 0.6618 (OUTLIER) cc_final: 0.6251 (p0) REVERT: V 15 LYS cc_start: 0.8437 (mtmm) cc_final: 0.7623 (ptpt) REVERT: W 69 TYR cc_start: 0.8471 (m-80) cc_final: 0.8260 (m-10) REVERT: W 72 ARG cc_start: 0.7587 (mmm160) cc_final: 0.7272 (mtt180) REVERT: X 43 MET cc_start: 0.6702 (OUTLIER) cc_final: 0.6297 (mtm) REVERT: Y 20 ASN cc_start: 0.8390 (m-40) cc_final: 0.8049 (m-40) REVERT: Y 69 ASN cc_start: 0.8492 (t0) cc_final: 0.7729 (t0) REVERT: Z 44 ARG cc_start: 0.8316 (mpt180) cc_final: 0.8072 (mmt180) REVERT: Z 48 LYS cc_start: 0.8025 (mtpp) cc_final: 0.7772 (mtpp) outliers start: 324 outliers final: 285 residues processed: 1279 average time/residue: 1.2088 time to fit residues: 2747.1926 Evaluate side-chains 1376 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 1075 time to evaluate : 6.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 22 GLU Chi-restraints excluded: chain b residue 80 LEU Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 116 GLN Chi-restraints excluded: chain b residue 162 GLN Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 165 MET Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 75 SER Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain d residue 197 GLU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 22 ASN Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 174 PHE Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 37 ASN Chi-restraints excluded: chain f residue 46 ASP Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 101 VAL Chi-restraints excluded: chain f residue 120 ILE Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain f residue 170 THR Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 64 ARG Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain i residue 125 THR Chi-restraints excluded: chain i residue 127 SER Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 21 THR Chi-restraints excluded: chain j residue 44 TYR Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 58 ASN Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 67 ASN Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 118 MET Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 20 MET Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 10 GLU Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain l residue 103 ILE Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 108 VAL Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 131 VAL Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain m residue 136 MET Chi-restraints excluded: chain n residue 22 ARG Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 120 GLU Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain q residue 51 GLN Chi-restraints excluded: chain q residue 76 SER Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain r residue 10 LYS Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 59 ILE Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 94 ASP Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain u residue 12 VAL Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 34 ILE Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 66 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain u residue 102 ILE Chi-restraints excluded: chain v residue 7 GLU Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 29 ILE Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 65 THR Chi-restraints excluded: chain y residue 1 MET Chi-restraints excluded: chain y residue 6 LEU Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 21 TYR Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 161 ILE Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 2 ARG Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 139 ASN Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 84 TYR Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 48 ARG Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain R residue 10 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 29 ILE Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain T residue 2 LEU Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 41 SER Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 43 MET Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 36 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 595 optimal weight: 7.9990 chunk 958 optimal weight: 6.9990 chunk 584 optimal weight: 8.9990 chunk 454 optimal weight: 30.0000 chunk 666 optimal weight: 1.9990 chunk 1005 optimal weight: 5.9990 chunk 925 optimal weight: 10.0000 chunk 800 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 618 optimal weight: 6.9990 chunk 490 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 162 GLN ** d 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 70 HIS ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 ASN ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 58 ASN ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 GLN X 68 HIS ** Y 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.213 158217 Z= 0.287 Angle : 0.669 59.200 237092 Z= 0.346 Chirality : 0.037 0.545 30339 Planarity : 0.005 0.108 12448 Dihedral : 23.619 178.288 80153 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.26 % Favored : 89.63 % Rotamer: Outliers : 6.92 % Allowed : 27.20 % Favored : 65.88 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.11), residues: 5506 helix: -0.98 (0.12), residues: 1653 sheet: -1.65 (0.16), residues: 1014 loop : -2.03 (0.11), residues: 2839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP V 72 HIS 0.010 0.001 HIS L 141 PHE 0.041 0.002 PHE Z 36 TYR 0.072 0.002 TYR B 47 ARG 0.014 0.000 ARG f 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11012 Ramachandran restraints generated. 5506 Oldfield, 0 Emsley, 5506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1396 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 317 poor density : 1079 time to evaluate : 6.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 1 MET cc_start: 0.4023 (mtt) cc_final: 0.2871 (tpt) REVERT: d 35 TYR cc_start: 0.8631 (t80) cc_final: 0.8420 (t80) REVERT: d 143 LEU cc_start: 0.7130 (mt) cc_final: 0.6629 (tp) REVERT: d 181 ILE cc_start: 0.9180 (tp) cc_final: 0.8950 (tp) REVERT: d 195 GLN cc_start: 0.7970 (mt0) cc_final: 0.7728 (mm110) REVERT: e 25 MET cc_start: 0.8901 (tpp) cc_final: 0.7953 (mmm) REVERT: e 51 ASN cc_start: 0.8427 (t0) cc_final: 0.8131 (t0) REVERT: e 99 PHE cc_start: 0.8675 (t80) cc_final: 0.8417 (t80) REVERT: e 127 TYR cc_start: 0.7800 (t80) cc_final: 0.7093 (t80) REVERT: e 174 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7248 (m-80) REVERT: f 41 GLU cc_start: 0.6854 (tp30) cc_final: 0.6531 (tp30) REVERT: f 74 MET cc_start: 0.8496 (ttm) cc_final: 0.8127 (mtm) REVERT: f 129 GLU cc_start: 0.8570 (tp30) cc_final: 0.8327 (tp30) REVERT: f 138 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8473 (tm-30) REVERT: i 64 ARG cc_start: -0.1208 (OUTLIER) cc_final: -0.1597 (tpm170) REVERT: j 43 GLU cc_start: 0.8340 (pm20) cc_final: 0.8031 (pm20) REVERT: j 114 LEU cc_start: 0.9251 (tp) cc_final: 0.8874 (tt) REVERT: j 118 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7705 (mmt) REVERT: k 7 MET cc_start: 0.8740 (mmm) cc_final: 0.8335 (mmt) REVERT: l 81 ASP cc_start: 0.8717 (m-30) cc_final: 0.8352 (t70) REVERT: n 9 GLN cc_start: 0.7124 (pp30) cc_final: 0.6684 (pp30) REVERT: n 22 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8241 (ptm160) REVERT: n 120 GLU cc_start: 0.5814 (OUTLIER) cc_final: 0.5131 (tt0) REVERT: o 58 ILE cc_start: 0.8794 (mm) cc_final: 0.8543 (mp) REVERT: r 45 GLU cc_start: 0.8206 (pp20) cc_final: 0.7460 (pp20) REVERT: r 60 LYS cc_start: 0.8654 (ptmm) cc_final: 0.8350 (ptmm) REVERT: r 97 LYS cc_start: 0.9006 (ttpt) cc_final: 0.8776 (ttpp) REVERT: t 7 LEU cc_start: 0.9214 (mt) cc_final: 0.9003 (mm) REVERT: u 6 ARG cc_start: 0.7769 (ttt180) cc_final: 0.7009 (ttt90) REVERT: u 9 GLU cc_start: 0.7653 (tp30) cc_final: 0.7130 (tp30) REVERT: u 72 PHE cc_start: 0.7144 (t80) cc_final: 0.6895 (t80) REVERT: v 7 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7783 (pm20) REVERT: v 48 MET cc_start: 0.8528 (tpt) cc_final: 0.8265 (tpt) REVERT: w 25 GLU cc_start: 0.7119 (pt0) cc_final: 0.6822 (pt0) REVERT: x 43 LYS cc_start: 0.8221 (mmtp) cc_final: 0.7481 (pttm) REVERT: x 60 LYS cc_start: 0.8130 (tptm) cc_final: 0.7640 (tppp) REVERT: y 6 LEU cc_start: 0.4098 (OUTLIER) cc_final: 0.3833 (mp) REVERT: z 10 ARG cc_start: 0.8286 (ttm-80) cc_final: 0.8073 (ttm-80) REVERT: z 36 GLU cc_start: 0.7801 (pm20) cc_final: 0.7575 (pm20) REVERT: D 22 MET cc_start: 0.8062 (mmm) cc_final: 0.7675 (mmm) REVERT: D 42 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8850 (tt) REVERT: G 108 GLN cc_start: 0.8507 (mt0) cc_final: 0.7722 (mt0) REVERT: H 74 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8386 (mm) REVERT: H 106 ARG cc_start: 0.8310 (ptt-90) cc_final: 0.7654 (mmp80) REVERT: H 129 PHE cc_start: 0.7910 (p90) cc_final: 0.7356 (p90) REVERT: H 182 ASP cc_start: 0.8178 (t70) cc_final: 0.7911 (t70) REVERT: H 206 ILE cc_start: 0.5925 (OUTLIER) cc_final: 0.5172 (tp) REVERT: I 2 ARG cc_start: 0.4730 (OUTLIER) cc_final: 0.4453 (mtp-110) REVERT: I 39 GLN cc_start: 0.8903 (tm-30) cc_final: 0.8346 (tm-30) REVERT: I 89 LEU cc_start: 0.8807 (mt) cc_final: 0.8393 (mt) REVERT: J 137 ARG cc_start: 0.8361 (mtt-85) cc_final: 0.8022 (mtt90) REVERT: K 14 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8281 (mm-40) REVERT: L 84 TYR cc_start: 0.6422 (OUTLIER) cc_final: 0.5322 (m-10) REVERT: M 42 GLU cc_start: 0.8397 (tp30) cc_final: 0.7932 (tp30) REVERT: M 75 GLN cc_start: 0.8142 (mm110) cc_final: 0.7847 (mm110) REVERT: M 90 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: N 27 ILE cc_start: 0.9262 (mm) cc_final: 0.9012 (mm) REVERT: N 103 VAL cc_start: 0.8734 (m) cc_final: 0.8521 (p) REVERT: O 10 LEU cc_start: 0.8964 (mt) cc_final: 0.8625 (mm) REVERT: O 46 LYS cc_start: 0.8816 (mtmt) cc_final: 0.8528 (mtpp) REVERT: O 87 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8173 (pt) REVERT: Q 18 SER cc_start: 0.7617 (t) cc_final: 0.7210 (p) REVERT: Q 37 TYR cc_start: 0.7720 (p90) cc_final: 0.7367 (p90) REVERT: R 80 MET cc_start: 0.7836 (mmm) cc_final: 0.7511 (mmm) REVERT: S 72 PHE cc_start: 0.8496 (t80) cc_final: 0.8220 (t80) REVERT: U 55 ASP cc_start: 0.6614 (OUTLIER) cc_final: 0.6249 (p0) REVERT: V 15 LYS cc_start: 0.8432 (mtmm) cc_final: 0.7617 (ptpt) REVERT: W 69 TYR cc_start: 0.8465 (m-80) cc_final: 0.8252 (m-10) REVERT: W 72 ARG cc_start: 0.7581 (mmm160) cc_final: 0.7269 (mtt180) REVERT: X 43 MET cc_start: 0.6697 (OUTLIER) cc_final: 0.6291 (mtm) REVERT: Y 20 ASN cc_start: 0.8387 (m-40) cc_final: 0.8045 (m-40) REVERT: Y 69 ASN cc_start: 0.8488 (t0) cc_final: 0.7724 (t0) REVERT: Z 44 ARG cc_start: 0.8293 (mpt180) cc_final: 0.8042 (mmt180) REVERT: Z 48 LYS cc_start: 0.8018 (mtpp) cc_final: 0.7763 (mtpp) outliers start: 317 outliers final: 292 residues processed: 1260 average time/residue: 1.1930 time to fit residues: 2674.6016 Evaluate side-chains 1385 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 308 poor density : 1077 time to evaluate : 6.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 22 GLU Chi-restraints excluded: chain b residue 80 LEU Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 116 GLN Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 165 MET Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 75 SER Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 22 ASN Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 156 THR Chi-restraints excluded: chain e residue 174 PHE Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 37 ASN Chi-restraints excluded: chain f residue 46 ASP Chi-restraints excluded: chain f residue 70 LEU Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 101 VAL Chi-restraints excluded: chain f residue 120 ILE Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain f residue 170 THR Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 64 ARG Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain i residue 125 THR Chi-restraints excluded: chain i residue 127 SER Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 21 THR Chi-restraints excluded: chain j residue 44 TYR Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 58 ASN Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 67 ASN Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 118 MET Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain l residue 103 ILE Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 108 VAL Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 131 VAL Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain m residue 136 MET Chi-restraints excluded: chain n residue 22 ARG Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 120 GLU Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 6 GLN Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain q residue 51 GLN Chi-restraints excluded: chain q residue 76 SER Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain r residue 10 LYS Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 59 ILE Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 94 ASP Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain u residue 12 VAL Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 34 ILE Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 66 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain u residue 102 ILE Chi-restraints excluded: chain v residue 7 GLU Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 29 ILE Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 65 THR Chi-restraints excluded: chain y residue 1 MET Chi-restraints excluded: chain y residue 6 LEU Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 21 TYR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 161 ILE Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain I residue 2 ARG Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 139 ASN Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 84 TYR Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 26 MET Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 48 ARG Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain R residue 10 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 29 ILE Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 2 LEU Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 41 SER Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 43 MET Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 36 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 635 optimal weight: 1.9990 chunk 852 optimal weight: 20.0000 chunk 245 optimal weight: 10.0000 chunk 738 optimal weight: 20.0000 chunk 118 optimal weight: 20.0000 chunk 222 optimal weight: 10.0000 chunk 801 optimal weight: 7.9990 chunk 335 optimal weight: 10.0000 chunk 823 optimal weight: 20.0000 chunk 101 optimal weight: 30.0000 chunk 147 optimal weight: 20.0000 overall best weight: 7.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 70 HIS ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 ASN ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 GLN X 68 HIS ** Y 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.077664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.061515 restraints weight = 560694.498| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.64 r_work: 0.3126 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.213 158217 Z= 0.287 Angle : 0.669 59.200 237092 Z= 0.346 Chirality : 0.037 0.545 30339 Planarity : 0.005 0.108 12448 Dihedral : 23.619 178.288 80153 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.26 % Favored : 89.63 % Rotamer: Outliers : 6.73 % Allowed : 27.24 % Favored : 66.03 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.11), residues: 5506 helix: -0.98 (0.12), residues: 1653 sheet: -1.65 (0.16), residues: 1014 loop : -2.03 (0.11), residues: 2839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP V 72 HIS 0.010 0.001 HIS L 141 PHE 0.041 0.002 PHE Z 36 TYR 0.072 0.002 TYR B 47 ARG 0.014 0.000 ARG f 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 43285.26 seconds wall clock time: 754 minutes 1.46 seconds (45241.46 seconds total)