Starting phenix.real_space_refine on Sun Mar 24 10:36:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7st6_25420/03_2024/7st6_25420.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7st6_25420/03_2024/7st6_25420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7st6_25420/03_2024/7st6_25420.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7st6_25420/03_2024/7st6_25420.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7st6_25420/03_2024/7st6_25420.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7st6_25420/03_2024/7st6_25420.pdb" } resolution = 3.0 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= 0.009 sd= 0.866 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 4805 5.49 5 S 151 5.16 5 C 74067 2.51 5 N 27572 2.21 5 O 41387 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b GLU 34": "OE1" <-> "OE2" Residue "b GLU 78": "OE1" <-> "OE2" Residue "b ASP 120": "OD1" <-> "OD2" Residue "b TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c GLU 28": "OE1" <-> "OE2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ASP 43": "OD1" <-> "OD2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c GLU 89": "OE1" <-> "OE2" Residue "c ASP 103": "OD1" <-> "OD2" Residue "c ASP 131": "OD1" <-> "OD2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ASP 176": "OD1" <-> "OD2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d GLU 16": "OE1" <-> "OE2" Residue "d PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 21": "NH1" <-> "NH2" 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 TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d ASP 116": "OD1" <-> "OD2" Residue "d ASP 140": "OD1" <-> "OD2" Residue "d ASP 145": "OD1" <-> "OD2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "d PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 197": "OE1" <-> "OE2" 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 ARG 132": "NH1" <-> "NH2" Residue "e TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 146": "OD1" <-> "OD2" Residue "e PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f ASP 15": "OD1" <-> "OD2" Residue "f TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 136": "OD1" <-> "OD2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f GLU 154": "OE1" <-> "OE2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 166": "OE1" <-> "OE2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "i ASP 46": "OD1" <-> "OD2" Residue "i PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 120": "OD1" <-> "OD2" Residue "i GLU 129": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" 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 "j ASP 141": "OD1" <-> "OD2" Residue "k GLU 45": "OE1" <-> "OE2" Residue "k ASP 80": "OD1" <-> "OD2" 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 GLU 51": "OE1" <-> "OE2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "l GLU 136": "OE1" <-> "OE2" 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 GLU 47": "OE1" <-> "OE2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m GLU 75": "OE1" <-> "OE2" Residue "m GLU 90": "OE1" <-> "OE2" Residue "m TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 114": "NH1" <-> "NH2" 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 GLU 49": "OE1" <-> "OE2" 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 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 GLU 10": "OE1" <-> "OE2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p GLU 26": "OE1" <-> "OE2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 61": "NH1" <-> "NH2" 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 ARG 47": "NH1" <-> "NH2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 31": "OE1" <-> "OE2" Residue "r GLU 34": "OE1" <-> "OE2" Residue "r ASP 55": "OD1" <-> "OD2" Residue "r ARG 68": "NH1" <-> "NH2" 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 ASP 68": "OD1" <-> "OD2" Residue "s PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u GLU 9": "OE1" <-> "OE2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "u PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 11": "OD1" <-> "OD2" Residue "w PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 52": "OD1" <-> "OD2" Residue "w ASP 60": "OD1" <-> "OD2" Residue "w PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 28": "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 GLU 36": "OE1" <-> "OE2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "A ASP 4": "OD1" <-> "OD2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "A ASP 58": "OD1" <-> "OD2" Residue "A PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "C PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 31": "OE1" <-> "OE2" 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 PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "G PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G GLU 77": "OE1" <-> "OE2" Residue "G ASP 87": "OD1" <-> "OD2" Residue "G ARG 107": "NH1" <-> "NH2" Residue "G ASP 115": "OD1" <-> "OD2" Residue "G ASP 122": "OD1" <-> "OD2" Residue "G ASP 158": "OD1" <-> "OD2" Residue "G ASP 164": "OD1" <-> "OD2" Residue "G PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 187": "OD1" <-> "OD2" Residue "G ASP 191": "OD1" <-> "OD2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 33": "OD1" <-> "OD2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "H ASP 111": "OD1" <-> "OD2" Residue "H ASP 117": "OD1" <-> "OD2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 182": "OD1" <-> "OD2" Residue "I GLU 14": "OE1" <-> "OE2" Residue "I ASP 49": "OD1" <-> "OD2" Residue "I GLU 68": "OE1" <-> "OE2" Residue "I PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 87": "OE1" <-> "OE2" Residue "I GLU 171": "OE1" <-> "OE2" Residue "J GLU 54": "OE1" <-> "OE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "K ASP 41": "OD1" <-> "OD2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 98": "OE1" <-> "OE2" Residue "L ASP 14": "OD1" <-> "OD2" Residue "L PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 32": "OD1" <-> "OD2" Residue "L GLU 39": "OE1" <-> "OE2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "M GLU 57": "OE1" <-> "OE2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "N PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 96": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O ASP 60": "OD1" <-> "OD2" Residue "O ASP 91": "OD1" <-> "OD2" Residue "P TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 40": "OE1" <-> "OE2" Residue "R ASP 67": "OD1" <-> "OD2" Residue "S GLU 38": "OE1" <-> "OE2" Residue "T PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 20": "OD1" <-> "OD2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 53": "OD1" <-> "OD2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 63": "OD1" <-> "OD2" Residue "Y PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 42": "OD1" <-> "OD2" Residue "Z GLU 9": "OE1" <-> "OE2" Residue "Z ARG 66": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 147982 Number of models: 1 Model: "" Number of chains: 58 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': 101, 'rna2p_pyr': 56, 'rna3p_pur': 773, 'rna3p_pyr': 609} 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': 231, 'rna2p_pyr': 104, 'rna3p_pur': 1443, 'rna3p_pyr': 1125} Link IDs: {'rna2p': 335, 'rna3p': 2567} 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': 4, 'rna3p_pur': 60, 'rna3p_pyr': 51} Link IDs: {'rna2p': 9, 'rna3p': 110} 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': 5, 'rna3p_pur': 31, 'rna3p_pyr': 32} Link IDs: {'rna2p': 14, 'rna3p': 62} Chain: "7" 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': 10, 'rna3p': 66} 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: "g" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 400 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} 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: "A" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 523 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 63} 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: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 390 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna3p_pur': 14, 'rna3p_pyr': 4} Link IDs: {'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': 4, 'rna3p_pur': 33, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 67} 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} Chain: "5" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Time building chain proxies: 57.20, per 1000 atoms: 0.39 Number of scatterers: 147982 At special positions: 0 Unit cell: (245.68, 249.83, 256.47, 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 151 16.00 P 4805 15.00 O 41387 8.00 N 27572 7.00 C 74067 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 62.58 Conformation dependent library (CDL) restraints added in 8.1 seconds 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10506 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 73 sheets defined 32.4% alpha, 18.0% beta 1174 base pairs and 2701 stacking pairs defined. Time for finding SS restraints: 51.63 Creating SS restraints... Processing helix chain 'b' and resid 29 through 31 No H-bonds generated for 'chain 'b' and resid 29 through 31' Processing helix chain 'b' and resid 196 through 200 removed outlier: 3.828A pdb=" N MET b 200 " --> pdb=" O ALA b 197 " (cutoff:3.500A) Processing helix chain 'b' and resid 206 through 212 removed outlier: 3.704A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 224 Processing helix chain 'c' and resid 61 through 72 Processing helix chain 'c' and resid 98 through 102 Processing helix chain 'c' and resid 120 through 126 Processing helix chain 'd' and resid 15 through 20 Processing helix chain 'd' and resid 24 through 38 removed outlier: 3.664A pdb=" N VAL d 33 " --> pdb=" O HIS d 29 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 115 Processing helix chain 'd' and resid 130 through 140 removed outlier: 3.522A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 161 Processing helix chain 'd' and resid 176 through 183 removed outlier: 3.794A pdb=" N LEU d 180 " --> pdb=" O ASP d 176 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE d 181 " --> pdb=" O PRO d 177 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 198 removed outlier: 3.640A pdb=" N LYS d 194 " --> pdb=" O ALA d 190 " (cutoff:3.500A) Processing helix chain 'e' and resid 2 through 8 Processing helix chain 'e' and resid 9 through 19 removed outlier: 3.642A pdb=" N LYS e 13 " --> pdb=" O ASP e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 40 through 44 removed outlier: 4.109A pdb=" N ILE e 43 " --> pdb=" O GLY e 40 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA e 44 " --> pdb=" O GLU e 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 40 through 44' Processing helix chain 'e' and resid 45 through 60 removed outlier: 3.877A pdb=" N LEU e 49 " --> pdb=" O ASP e 45 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE e 59 " --> pdb=" O ASP e 55 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 104 removed outlier: 3.831A pdb=" N TRP e 96 " --> pdb=" O GLY e 92 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR e 104 " --> pdb=" O GLU e 100 " (cutoff:3.500A) Processing helix chain 'e' and resid 106 through 110 removed outlier: 3.799A pdb=" N ILE e 110 " --> pdb=" O VAL e 107 " (cutoff:3.500A) Processing helix chain 'e' and resid 161 through 172 removed outlier: 3.880A pdb=" N ALA e 167 " --> pdb=" O GLU e 163 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU e 168 " --> pdb=" O GLU e 164 " (cutoff:3.500A) Processing helix chain 'f' and resid 2 through 6 Processing helix chain 'f' and resid 59 through 78 removed outlier: 3.751A pdb=" N ALA f 69 " --> pdb=" O GLY f 65 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 149 removed outlier: 3.541A pdb=" N ILE f 140 " --> pdb=" O ASP f 136 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA f 144 " --> pdb=" O ILE f 140 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 28 Processing helix chain 'g' and resid 29 through 34 Processing helix chain 'g' and resid 40 through 48 Processing helix chain 'i' and resid 23 through 28 removed outlier: 3.869A pdb=" N LEU i 27 " --> pdb=" O VAL i 23 " (cutoff:3.500A) Processing helix chain 'i' and resid 37 through 43 removed outlier: 3.797A pdb=" N PHE i 41 " --> pdb=" O PHE i 37 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA i 43 " --> pdb=" O LYS i 39 " (cutoff:3.500A) Processing helix chain 'i' and resid 44 through 48 removed outlier: 3.874A pdb=" N SER i 47 " --> pdb=" O LYS i 44 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 79 Processing helix chain 'i' and resid 102 through 113 removed outlier: 3.811A pdb=" N GLN i 106 " --> pdb=" O ARG i 102 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE i 108 " --> pdb=" O GLN i 104 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN i 110 " --> pdb=" O GLN i 106 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N THR i 111 " --> pdb=" O GLU i 107 " (cutoff:3.500A) Processing helix chain 'i' and resid 121 through 126 removed outlier: 3.544A pdb=" N MET i 124 " --> pdb=" O ILE i 121 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ARG i 126 " --> pdb=" O ALA i 123 " (cutoff:3.500A) Processing helix chain 'i' and resid 127 through 136 removed outlier: 4.003A pdb=" N THR i 131 " --> pdb=" O SER i 127 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA i 132 " --> pdb=" O ILE i 128 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG i 133 " --> pdb=" O GLU i 129 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER i 134 " --> pdb=" O GLY i 130 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 removed outlier: 3.769A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 67 through 72 Processing helix chain 'j' and resid 89 through 96 Processing helix chain 'j' and resid 97 through 107 removed outlier: 4.457A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU j 102 " --> pdb=" O GLU j 98 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 118 Processing helix chain 'j' and resid 132 through 136 Processing helix chain 'k' and resid 112 through 119 Processing helix chain 'l' and resid 37 through 41 removed outlier: 3.722A pdb=" N ARG l 41 " --> pdb=" O GLN l 38 " (cutoff:3.500A) Processing helix chain 'l' and resid 69 through 73 Processing helix chain 'l' and resid 79 through 83 removed outlier: 3.585A pdb=" N ALA l 83 " --> pdb=" O SER l 80 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 138 removed outlier: 3.537A pdb=" N ALA l 133 " --> pdb=" O LYS l 129 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA l 134 " --> pdb=" O GLY l 130 " (cutoff:3.500A) Processing helix chain 'm' and resid 43 through 56 removed outlier: 3.604A pdb=" N ALA m 49 " --> pdb=" O GLN m 45 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 122 removed outlier: 3.775A pdb=" N ALA m 122 " --> pdb=" O LYS m 118 " (cutoff:3.500A) Processing helix chain 'n' and resid 13 through 32 removed outlier: 3.501A pdb=" N ALA n 25 " --> pdb=" O PHE n 21 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS n 31 " --> pdb=" O SER n 27 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 42 Processing helix chain 'n' and resid 44 through 55 Proline residue: n 50 - end of helix Processing helix chain 'n' and resid 59 through 69 removed outlier: 3.581A pdb=" N ARG n 69 " --> pdb=" O LEU n 65 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 79 Processing helix chain 'o' and resid 3 through 20 removed outlier: 3.692A pdb=" N ARG o 7 " --> pdb=" O LYS o 3 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 85 removed outlier: 3.917A pdb=" N ALA o 79 " --> pdb=" O GLY o 75 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU o 84 " --> pdb=" O GLU o 80 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 113 Processing helix chain 'p' and resid 2 through 9 removed outlier: 3.509A pdb=" N LEU p 7 " --> pdb=" O ILE p 3 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN p 9 " --> pdb=" O LYS p 5 " (cutoff:3.500A) Processing helix chain 'p' and resid 52 through 55 Processing helix chain 'p' and resid 96 through 101 removed outlier: 3.614A pdb=" N ARG p 100 " --> pdb=" O TYR p 97 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU p 101 " --> pdb=" O TYR p 98 " (cutoff:3.500A) Processing helix chain 'q' and resid 6 through 20 removed outlier: 3.558A pdb=" N ALA q 11 " --> pdb=" O VAL q 7 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE q 16 " --> pdb=" O ARG q 12 " (cutoff:3.500A) Processing helix chain 'q' and resid 30 through 71 removed outlier: 5.108A pdb=" N GLN q 36 " --> pdb=" O ARG q 32 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE q 39 " --> pdb=" O PHE q 35 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG q 54 " --> pdb=" O ARG q 50 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG q 57 " --> pdb=" O LYS q 53 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 85 removed outlier: 3.674A pdb=" N ASN q 80 " --> pdb=" O SER q 76 " (cutoff:3.500A) Processing helix chain 'q' and resid 90 through 101 Processing helix chain 'q' and resid 101 through 117 removed outlier: 3.601A pdb=" N LEU q 108 " --> pdb=" O ALA q 104 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL q 109 " --> pdb=" O PHE q 105 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU q 110 " --> pdb=" O THR q 106 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS q 111 " --> pdb=" O ALA q 107 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 22 removed outlier: 4.285A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP s 22 " --> pdb=" O ARG s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 29 through 38 removed outlier: 3.782A pdb=" N ILE s 35 " --> pdb=" O GLN s 31 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR s 38 " --> pdb=" O ASP s 34 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 removed outlier: 4.036A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU s 46 " --> pdb=" O LYS s 42 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS s 49 " --> pdb=" O VAL s 45 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN s 57 " --> pdb=" O SER s 53 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA s 58 " --> pdb=" O ALA s 54 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU s 59 " --> pdb=" O ILE s 55 " (cutoff:3.500A) Processing helix chain 's' and resid 65 through 68 removed outlier: 3.717A pdb=" N ASP s 68 " --> pdb=" O ASP s 65 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 65 through 68' Processing helix chain 's' and resid 89 through 91 No H-bonds generated for 'chain 's' and resid 89 through 91' Processing helix chain 't' and resid 2 through 8 removed outlier: 3.978A pdb=" N LEU t 7 " --> pdb=" O ARG t 3 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU t 8 " --> pdb=" O GLU t 4 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 26 Processing helix chain 't' and resid 39 through 48 Processing helix chain 'v' and resid 13 through 23 removed outlier: 3.529A pdb=" N ARG v 18 " --> pdb=" O LYS v 14 " (cutoff:3.500A) Processing helix chain 'v' and resid 44 through 51 removed outlier: 4.051A pdb=" N ASN v 49 " --> pdb=" O ASP v 45 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 61 removed outlier: 3.555A pdb=" N ILE x 58 " --> pdb=" O GLY x 54 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP x 59 " --> pdb=" O MET x 55 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS x 60 " --> pdb=" O ARG x 56 " (cutoff:3.500A) Processing helix chain 'x' and resid 62 through 73 Processing helix chain 'y' and resid 9 through 23 removed outlier: 4.132A pdb=" N ASN y 15 " --> pdb=" O VAL y 11 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N THR y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN y 20 " --> pdb=" O THR y 16 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU y 21 " --> pdb=" O GLU y 17 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU y 22 " --> pdb=" O LEU y 18 " (cutoff:3.500A) Processing helix chain 'y' and resid 23 through 35 removed outlier: 3.622A pdb=" N ASN y 27 " --> pdb=" O ARG y 23 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG y 29 " --> pdb=" O GLN y 25 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA y 33 " --> pdb=" O ARG y 29 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER y 34 " --> pdb=" O MET y 30 " (cutoff:3.500A) Processing helix chain 'y' and resid 40 through 61 removed outlier: 3.943A pdb=" N LYS y 44 " --> pdb=" O SER y 40 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA y 51 " --> pdb=" O ARG y 47 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG y 52 " --> pdb=" O ARG y 48 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN y 58 " --> pdb=" O LYS y 54 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 27 removed outlier: 3.552A pdb=" N THR z 22 " --> pdb=" O LYS z 18 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU z 24 " --> pdb=" O LYS z 20 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 48 Processing helix chain 'A' and resid 44 through 52 removed outlier: 3.735A pdb=" N GLN A 48 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASP A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL A 51 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 44 through 52' Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'B' and resid 8 through 16 removed outlier: 3.575A pdb=" N ARG B 16 " --> pdb=" O ARG B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 20 removed outlier: 4.121A pdb=" N ALA B 20 " --> pdb=" O SER B 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 17 through 20' Processing helix chain 'D' and resid 8 through 17 removed outlier: 3.866A pdb=" N SER D 15 " --> pdb=" O LYS D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 22 removed outlier: 3.556A pdb=" N ARG D 21 " --> pdb=" O GLY D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 37 Processing helix chain 'E' and resid 8 through 12 Processing helix chain 'E' and resid 36 through 43 removed outlier: 3.544A pdb=" N LEU E 43 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 61 Processing helix chain 'G' and resid 23 through 27 Processing helix chain 'G' and resid 41 through 61 removed outlier: 3.929A pdb=" N THR G 45 " --> pdb=" O ASN G 41 " (cutoff:3.500A) Proline residue: G 47 - end of helix removed outlier: 3.598A pdb=" N ALA G 54 " --> pdb=" O ASN G 50 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN G 57 " --> pdb=" O LEU G 53 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE G 59 " --> pdb=" O GLU G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 87 removed outlier: 3.557A pdb=" N VAL G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS G 80 " --> pdb=" O SER G 76 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU G 84 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N CYS G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 122 removed outlier: 5.427A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER G 109 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR G 118 " --> pdb=" O LYS G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 147 removed outlier: 3.874A pdb=" N GLU G 141 " --> pdb=" O THR G 137 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS G 142 " --> pdb=" O ARG G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 176 removed outlier: 3.729A pdb=" N ILE G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 224 removed outlier: 3.661A pdb=" N LEU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR G 212 " --> pdb=" O ALA G 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 46 removed outlier: 3.552A pdb=" N ARG H 39 " --> pdb=" O ASP H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 76 removed outlier: 3.709A pdb=" N VAL H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE H 76 " --> pdb=" O PRO H 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 71 through 76' Processing helix chain 'H' and resid 82 through 95 removed outlier: 3.705A pdb=" N LYS H 88 " --> pdb=" O GLU H 84 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL H 89 " --> pdb=" O LYS H 85 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 110 Processing helix chain 'H' and resid 111 through 118 Processing helix chain 'H' and resid 122 through 126 removed outlier: 3.747A pdb=" N ARG H 126 " --> pdb=" O LEU H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 143 Processing helix chain 'H' and resid 156 through 159 removed outlier: 3.874A pdb=" N ALA H 159 " --> pdb=" O LEU H 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 156 through 159' Processing helix chain 'I' and resid 8 through 15 Processing helix chain 'I' and resid 48 through 65 removed outlier: 3.502A pdb=" N VAL I 52 " --> pdb=" O SER I 48 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU I 56 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR I 64 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 81 removed outlier: 3.813A pdb=" N ASN I 73 " --> pdb=" O ARG I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 94 removed outlier: 3.627A pdb=" N LEU I 89 " --> pdb=" O THR I 85 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 104 removed outlier: 3.736A pdb=" N TYR I 102 " --> pdb=" O ASP I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 119 Processing helix chain 'I' and resid 146 through 149 Processing helix chain 'I' and resid 157 through 162 removed outlier: 3.660A pdb=" N ALA I 161 " --> pdb=" O ALA I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 203 removed outlier: 3.731A pdb=" N ILE I 199 " --> pdb=" O ASN I 195 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL I 200 " --> pdb=" O GLU I 196 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU I 201 " --> pdb=" O HIS I 197 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU I 202 " --> pdb=" O LEU I 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 69 removed outlier: 3.690A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG J 68 " --> pdb=" O GLU J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 118 removed outlier: 3.525A pdb=" N ALA J 117 " --> pdb=" O VAL J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 145 removed outlier: 3.638A pdb=" N ILE J 140 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP J 141 " --> pdb=" O ARG J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 154 Processing helix chain 'K' and resid 12 through 16 removed outlier: 3.607A pdb=" N SER K 15 " --> pdb=" O PRO K 12 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU K 16 " --> pdb=" O ASP K 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 12 through 16' Processing helix chain 'K' and resid 17 through 32 removed outlier: 4.240A pdb=" N MET K 21 " --> pdb=" O GLN K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 54 Processing helix chain 'K' and resid 67 through 80 removed outlier: 3.842A pdb=" N ILE K 71 " --> pdb=" O PRO K 67 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP K 72 " --> pdb=" O GLN K 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 30 removed outlier: 3.699A pdb=" N ASN L 27 " --> pdb=" O ALA L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 45 Processing helix chain 'L' and resid 46 through 54 removed outlier: 3.731A pdb=" N GLN L 51 " --> pdb=" O GLU L 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 58 through 63 Processing helix chain 'L' and resid 91 through 108 removed outlier: 3.601A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL L 104 " --> pdb=" O MET L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 125 Processing helix chain 'L' and resid 126 through 128 No H-bonds generated for 'chain 'L' and resid 126 through 128' Processing helix chain 'L' and resid 131 through 145 removed outlier: 3.692A pdb=" N MET L 143 " --> pdb=" O ASP L 139 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 148 No H-bonds generated for 'chain 'L' and resid 146 through 148' Processing helix chain 'M' and resid 4 through 19 Processing helix chain 'M' and resid 30 through 43 removed outlier: 3.781A pdb=" N VAL M 38 " --> pdb=" O ALA M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 94 through 98 Processing helix chain 'M' and resid 111 through 118 Processing helix chain 'N' and resid 10 through 12 No H-bonds generated for 'chain 'N' and resid 10 through 12' Processing helix chain 'N' and resid 34 through 38 Processing helix chain 'N' and resid 43 through 48 removed outlier: 4.277A pdb=" N VAL N 46 " --> pdb=" O ALA N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 54 removed outlier: 3.544A pdb=" N LEU N 53 " --> pdb=" O PRO N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 85 removed outlier: 3.659A pdb=" N ARG N 79 " --> pdb=" O ALA N 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 99 removed outlier: 5.619A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU N 97 " --> pdb=" O LEU N 93 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 28 removed outlier: 3.784A pdb=" N GLN O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA O 21 " --> pdb=" O LEU O 17 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA O 23 " --> pdb=" O ASP O 19 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU O 24 " --> pdb=" O GLN O 20 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL O 26 " --> pdb=" O THR O 22 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 68 Processing helix chain 'Q' and resid 2 through 9 Processing helix chain 'Q' and resid 114 through 118 removed outlier: 4.522A pdb=" N VAL Q 118 " --> pdb=" O LYS Q 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 19 Processing helix chain 'R' and resid 25 through 37 removed outlier: 3.547A pdb=" N SER R 29 " --> pdb=" O GLY R 25 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS R 30 " --> pdb=" O LYS R 26 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA R 35 " --> pdb=" O ALA R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 57 removed outlier: 3.677A pdb=" N ILE R 52 " --> pdb=" O SER R 48 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 83 removed outlier: 3.948A pdb=" N ARG R 70 " --> pdb=" O GLY R 66 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER R 73 " --> pdb=" O ARG R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 93 Processing helix chain 'R' and resid 105 through 110 Processing helix chain 'S' and resid 2 through 19 removed outlier: 3.591A pdb=" N GLU S 9 " --> pdb=" O MET S 5 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG S 12 " --> pdb=" O ARG S 8 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA S 14 " --> pdb=" O VAL S 10 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 29 removed outlier: 3.547A pdb=" N ILE S 29 " --> pdb=" O GLU S 25 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 47 Processing helix chain 'S' and resid 55 through 59 Processing helix chain 'S' and resid 79 through 90 removed outlier: 3.648A pdb=" N ARG S 84 " --> pdb=" O ARG S 80 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA S 86 " --> pdb=" O LYS S 82 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG S 89 " --> pdb=" O GLU S 85 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 15 removed outlier: 3.660A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE T 10 " --> pdb=" O ALA T 6 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 45 removed outlier: 3.567A pdb=" N GLN T 39 " --> pdb=" O ILE T 35 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA T 43 " --> pdb=" O GLN T 39 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLU T 44 " --> pdb=" O GLY T 40 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N HIS T 45 " --> pdb=" O HIS T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 73 removed outlier: 3.625A pdb=" N ARG T 52 " --> pdb=" O ASP T 48 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG T 53 " --> pdb=" O HIS T 49 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY T 54 " --> pdb=" O HIS T 50 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU T 55 " --> pdb=" O SER T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 85 removed outlier: 3.567A pdb=" N ILE T 81 " --> pdb=" O TYR T 77 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLU T 82 " --> pdb=" O THR T 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 61 Processing helix chain 'U' and resid 68 through 76 Processing helix chain 'W' and resid 24 through 29 removed outlier: 3.722A pdb=" N LEU W 28 " --> pdb=" O ASP W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 45 removed outlier: 3.587A pdb=" N THR W 44 " --> pdb=" O PRO W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 64 removed outlier: 4.040A pdb=" N LEU W 54 " --> pdb=" O TYR W 50 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 23 removed outlier: 3.800A pdb=" N LEU X 15 " --> pdb=" O ASP X 11 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS X 20 " --> pdb=" O LYS X 16 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU X 23 " --> pdb=" O GLU X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 44 removed outlier: 3.849A pdb=" N ILE X 44 " --> pdb=" O PRO X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 73 Processing helix chain 'Y' and resid 7 through 41 removed outlier: 3.995A pdb=" N ILE Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS Y 18 " --> pdb=" O GLU Y 14 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER Y 22 " --> pdb=" O LYS Y 18 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG Y 23 " --> pdb=" O HIS Y 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE Y 30 " --> pdb=" O MET Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 64 removed outlier: 3.759A pdb=" N ALA Y 49 " --> pdb=" O ALA Y 45 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU Y 52 " --> pdb=" O LYS Y 48 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN Y 54 " --> pdb=" O PHE Y 50 " (cutoff:3.500A) Proline residue: Y 55 - end of helix removed outlier: 3.743A pdb=" N GLN Y 60 " --> pdb=" O ILE Y 56 " (cutoff:3.500A) Processing helix chain 'Y' and resid 69 through 86 removed outlier: 3.577A pdb=" N LEU Y 85 " --> pdb=" O GLN Y 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 22 removed outlier: 3.600A pdb=" N CYS Z 22 " --> pdb=" O PHE Z 18 " (cutoff:3.500A) Processing helix chain 'Z' and resid 38 through 57 removed outlier: 3.571A pdb=" N ARG Z 44 " --> pdb=" O PRO Z 40 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA Z 47 " --> pdb=" O GLU Z 43 " (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 23 through 24 removed outlier: 6.711A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU b 80 " --> pdb=" O ILE b 90 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE b 90 " --> pdb=" O LEU b 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'b' and resid 23 through 24 Processing sheet with id=AA4, first strand: chain 'b' and resid 33 through 34 Processing sheet with id=AA5, first strand: chain 'b' and resid 128 through 130 removed outlier: 6.034A pdb=" N ILE b 163 " --> pdb=" O ARG b 174 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG b 174 " --> pdb=" O ILE b 163 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET b 180 " --> pdb=" O VAL b 267 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 4 through 15 removed outlier: 5.824A pdb=" N LYS c 8 " --> pdb=" O GLU c 28 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU c 28 " --> pdb=" O LYS c 8 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY c 10 " --> pdb=" O VAL c 26 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU c 186 " --> pdb=" O VAL c 180 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL c 180 " --> pdb=" O LEU c 186 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU c 188 " --> pdb=" O VAL c 178 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ASP c 176 " --> pdb=" O LYS c 190 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N THR c 171 " --> pdb=" O GLY c 111 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLY c 111 " --> pdb=" O THR c 171 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N GLN c 173 " --> pdb=" O VAL c 109 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL c 109 " --> pdb=" O GLN c 173 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR c 112 " --> pdb=" O ASP c 200 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP c 200 " --> pdb=" O THR c 112 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 79 through 83 removed outlier: 6.254A pdb=" N ALA c 47 " --> pdb=" O VAL c 37 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL c 37 " --> pdb=" O ALA c 47 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'c' and resid 117 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 120 removed outlier: 3.630A pdb=" N MET d 188 " --> pdb=" O ILE d 119 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'e' and resid 65 through 68 removed outlier: 3.712A pdb=" N GLY e 85 " --> pdb=" O THR e 67 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS e 32 " --> pdb=" O THR e 156 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'f' and resid 17 through 18 removed outlier: 3.586A pdb=" N LYS f 17 " --> pdb=" O THR f 24 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR f 24 " --> pdb=" O LYS f 17 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'f' and resid 40 through 43 removed outlier: 3.822A pdb=" N LYS f 43 " --> pdb=" O THR f 50 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR f 50 " --> pdb=" O LYS f 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'f' and resid 86 through 89 Processing sheet with id=AB6, first strand: chain 'f' and resid 96 through 98 removed outlier: 3.577A pdb=" N VAL f 112 " --> pdb=" O LEU f 104 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'f' and resid 121 through 123 Processing sheet with id=AB8, first strand: chain 'g' and resid 18 through 20 Processing sheet with id=AB9, first strand: chain 'i' and resid 9 through 10 Processing sheet with id=AC1, first strand: chain 'i' and resid 59 through 60 removed outlier: 3.725A pdb=" N THR i 59 " --> pdb=" O THR i 67 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR i 67 " --> pdb=" O THR i 59 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'i' and resid 99 through 100 Processing sheet with id=AC3, first strand: chain 'j' and resid 122 through 124 removed outlier: 6.643A pdb=" N ILE j 54 " --> pdb=" O LYS j 123 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N TYR j 16 " --> pdb=" O ILE j 55 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU j 57 " --> pdb=" O TYR j 16 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL j 18 " --> pdb=" O LEU j 57 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN j 138 " --> pdb=" O TRP j 15 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'j' and resid 73 through 77 Processing sheet with id=AC5, first strand: chain 'k' and resid 7 through 10 removed outlier: 6.962A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA k 16 " --> pdb=" O ALA k 46 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA k 46 " --> pdb=" O ALA k 16 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ARG k 18 " --> pdb=" O LYS k 44 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS k 40 " --> pdb=" O ILE k 22 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL k 24 " --> pdb=" O ILE k 38 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ILE k 38 " --> pdb=" O VAL k 24 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ALA k 60 " --> pdb=" O LEU k 87 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU k 87 " --> pdb=" O ALA k 60 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL k 62 " --> pdb=" O VAL k 85 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N VAL k 85 " --> pdb=" O VAL k 62 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N CYS k 84 " --> pdb=" O MET k 7 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASN k 9 " --> pdb=" O CYS k 84 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N LEU k 86 " --> pdb=" O ASN k 9 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'k' and resid 69 through 70 removed outlier: 3.672A pdb=" N VAL k 69 " --> pdb=" O ILE k 77 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE k 77 " --> pdb=" O VAL k 69 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL k 76 " --> pdb=" O VAL p 72 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG p 61 " --> pdb=" O VAL p 46 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL p 46 " --> pdb=" O ARG p 61 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N ILE p 63 " --> pdb=" O GLY p 44 " (cutoff:3.500A) removed outlier: 9.105A pdb=" N GLY p 44 " --> pdb=" O ILE p 63 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASP p 23 " --> pdb=" O VAL p 46 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR p 24 " --> pdb=" O LYS p 86 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER p 82 " --> pdb=" O LYS p 28 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TRP p 30 " --> pdb=" O VAL p 80 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL p 80 " --> pdb=" O TRP p 30 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'm' and resid 62 through 65 removed outlier: 6.465A pdb=" N LEU m 33 " --> pdb=" O LEU m 102 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU m 104 " --> pdb=" O PHE m 31 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHE m 31 " --> pdb=" O GLU m 104 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'm' and resid 39 through 42 removed outlier: 5.748A pdb=" N VAL m 89 " --> pdb=" O GLU m 75 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLU m 75 " --> pdb=" O VAL m 89 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR m 91 " --> pdb=" O ILE m 73 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'n' and resid 33 through 37 removed outlier: 6.748A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'o' and resid 47 through 50 removed outlier: 6.526A pdb=" N VAL o 39 " --> pdb=" O LEU o 48 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ALA o 50 " --> pdb=" O ALA o 37 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ALA o 37 " --> pdb=" O ALA o 50 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG o 25 " --> pdb=" O ILE o 40 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL o 28 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'r' and resid 11 through 14 removed outlier: 6.390A 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 23 removed outlier: 6.820A pdb=" N PHE r 93 " --> pdb=" O HIS r 66 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N HIS r 66 " --> pdb=" O PHE r 93 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ILE r 101 " --> pdb=" O VAL r 58 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL r 58 " --> pdb=" O ILE r 101 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'r' and resid 72 through 73 Processing sheet with id=AD5, first strand: chain 'r' and resid 76 through 78 removed outlier: 3.567A pdb=" N ARG r 78 " --> pdb=" O TYR r 83 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 's' and resid 4 through 10 removed outlier: 5.578A pdb=" N ILE s 4 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL s 107 " --> pdb=" O ILE s 4 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LYS s 6 " --> pdb=" O VAL s 105 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL s 105 " --> pdb=" O LYS s 6 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ARG s 8 " --> pdb=" O ILE s 103 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE s 103 " --> pdb=" O ARG s 8 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG s 92 " --> pdb=" O ARG s 88 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N HIS s 102 " --> pdb=" O GLU s 78 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLU s 78 " --> pdb=" O HIS s 102 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR s 104 " --> pdb=" O VAL s 76 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL s 76 " --> pdb=" O THR s 104 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL s 106 " --> pdb=" O ILE s 74 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ILE s 74 " --> pdb=" O VAL s 106 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N SER s 108 " --> pdb=" O THR s 72 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N THR s 72 " --> pdb=" O SER s 108 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS s 27 " --> pdb=" O VAL s 71 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 't' and resid 11 through 14 removed outlier: 6.785A pdb=" N LYS t 33 " --> pdb=" O ARG t 12 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL t 31 " --> pdb=" O PRO t 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL t 34 " --> pdb=" O LYS t 81 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP t 80 " --> pdb=" O VAL t 62 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VAL t 62 " --> pdb=" O TRP t 80 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS t 82 " --> pdb=" O THR t 60 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR t 60 " --> pdb=" O LYS t 82 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR t 84 " --> pdb=" O VAL t 58 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL t 58 " --> pdb=" O TYR t 84 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR t 86 " --> pdb=" O GLU t 56 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 't' and resid 67 through 70 Processing sheet with id=AD9, first strand: chain 'u' and resid 21 through 22 removed outlier: 4.156A pdb=" N ILE u 71 " --> pdb=" O ASP u 80 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'u' and resid 24 through 27 removed outlier: 6.725A pdb=" N ILE u 34 " --> pdb=" O LYS u 25 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL u 27 " --> pdb=" O LYS u 32 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS u 32 " --> pdb=" O VAL u 27 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'u' and resid 40 through 44 removed outlier: 3.540A pdb=" N VAL u 41 " --> pdb=" O LYS u 60 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS u 60 " --> pdb=" O VAL u 41 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'u' and resid 82 through 85 removed outlier: 3.548A pdb=" N VAL u 92 " --> pdb=" O ARG u 85 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'v' and resid 3 through 5 removed outlier: 6.003A pdb=" N ILE v 4 " --> pdb=" O VAL v 64 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL v 72 " --> pdb=" O ARG v 93 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ARG v 93 " --> pdb=" O VAL v 72 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ALA v 74 " --> pdb=" O PHE v 91 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE v 91 " --> pdb=" O ALA v 74 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP v 76 " --> pdb=" O ILE v 89 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ILE v 89 " --> pdb=" O ASP v 76 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLN v 78 " --> pdb=" O GLN v 87 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N LYS v 25 " --> pdb=" O GLN v 87 " (cutoff:3.500A) removed outlier: 9.878A pdb=" N ILE v 89 " --> pdb=" O LYS v 25 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N PHE v 91 " --> pdb=" O PRO v 27 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE v 29 " --> pdb=" O PHE v 91 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ARG v 93 " --> pdb=" O ILE v 29 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR v 31 " --> pdb=" O ARG v 93 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU v 42 " --> pdb=" O PHE v 26 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'w' and resid 18 through 19 removed outlier: 6.352A pdb=" N ILE w 32 " --> pdb=" O ALA w 57 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA w 57 " --> pdb=" O ILE w 32 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE w 56 " --> pdb=" O GLY w 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'w' and resid 26 through 27 removed outlier: 7.196A pdb=" N ILE w 78 " --> pdb=" O GLY w 44 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'x' and resid 12 through 14 Processing sheet with id=AE8, first strand: chain 'x' and resid 33 through 39 Processing sheet with id=AE9, first strand: chain 'z' and resid 34 through 38 Processing sheet with id=AF1, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AF2, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AF3, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AF4, first strand: chain 'C' and resid 19 through 24 removed outlier: 3.603A pdb=" N GLN C 44 " --> pdb=" O ASP C 39 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP C 39 " --> pdb=" O GLN C 44 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 35 " --> pdb=" O TYR C 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 14 through 15 Processing sheet with id=AF6, first strand: chain 'F' and resid 15 through 19 Processing sheet with id=AF7, first strand: chain 'G' and resid 89 through 91 removed outlier: 6.242A pdb=" N ILE G 66 " --> pdb=" O PHE G 89 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL G 91 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE G 68 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU G 67 " --> pdb=" O PHE G 161 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 19 through 20 removed outlier: 6.671A pdb=" N HIS H 68 " --> pdb=" O SER H 52 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE H 54 " --> pdb=" O THR H 66 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N THR H 66 " --> pdb=" O ILE H 54 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE H 56 " --> pdb=" O ARG H 64 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ARG H 64 " --> pdb=" O ILE H 56 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 163 through 170 Processing sheet with id=AG1, first strand: chain 'I' and resid 122 through 124 Processing sheet with id=AG2, first strand: chain 'I' and resid 170 through 172 Processing sheet with id=AG3, first strand: chain 'J' and resid 13 through 23 removed outlier: 4.834A pdb=" N LEU J 14 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL J 37 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL J 20 " --> pdb=" O SER J 31 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 13 through 23 removed outlier: 4.834A pdb=" N LEU J 14 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL J 37 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL J 20 " --> pdb=" O SER J 31 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY J 48 " --> pdb=" O THR J 36 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 84 through 85 Processing sheet with id=AG6, first strand: chain 'K' and resid 2 through 4 Processing sheet with id=AG7, first strand: chain 'K' and resid 41 through 45 removed outlier: 5.124A pdb=" N ASP K 41 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU K 61 " --> pdb=" O ASP K 41 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY K 43 " --> pdb=" O TYR K 59 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE K 8 " --> pdb=" O VAL K 60 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL K 7 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N SER K 87 " --> pdb=" O VAL K 7 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 72 through 76 Processing sheet with id=AG9, first strand: chain 'M' and resid 25 through 27 Processing sheet with id=AH1, first strand: chain 'M' and resid 74 through 76 Processing sheet with id=AH2, first strand: chain 'M' and resid 74 through 76 removed outlier: 7.283A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR M 127 " --> pdb=" O ILE M 100 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE M 100 " --> pdb=" O TYR M 127 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.594A pdb=" N LYS N 21 " --> pdb=" O ASP N 61 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N VAL N 28 " --> pdb=" O ILE N 64 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL N 66 " --> pdb=" O VAL N 28 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'O' and resid 40 through 52 removed outlier: 4.373A pdb=" N LEU O 71 " --> pdb=" O LEU O 42 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N THR O 44 " --> pdb=" O THR O 69 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR O 69 " --> pdb=" O THR O 44 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS O 46 " --> pdb=" O ILE O 67 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE O 67 " --> pdb=" O LYS O 46 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ARG O 48 " --> pdb=" O TYR O 65 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR O 65 " --> pdb=" O ARG O 48 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N THR O 50 " --> pdb=" O ASP O 63 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASP O 63 " --> pdb=" O THR O 50 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA O 12 " --> pdb=" O HIS O 70 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 40 through 52 removed outlier: 4.373A pdb=" N LEU O 71 " --> pdb=" O LEU O 42 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N THR O 44 " --> pdb=" O THR O 69 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR O 69 " --> pdb=" O THR O 44 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS O 46 " --> pdb=" O ILE O 67 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE O 67 " --> pdb=" O LYS O 46 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ARG O 48 " --> pdb=" O TYR O 65 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR O 65 " --> pdb=" O ARG O 48 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N THR O 50 " --> pdb=" O ASP O 63 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASP O 63 " --> pdb=" O THR O 50 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU O 66 " --> pdb=" O LYS S 96 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS S 96 " --> pdb=" O GLU O 66 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'P' and resid 40 through 45 removed outlier: 7.058A pdb=" N ALA P 40 " --> pdb=" O ASP P 35 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP P 35 " --> pdb=" O ALA P 40 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL P 83 " --> pdb=" O THR P 107 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE P 109 " --> pdb=" O VAL P 83 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N VAL P 85 " --> pdb=" O ILE P 109 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASP P 111 " --> pdb=" O VAL P 85 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Q' and resid 29 through 31 removed outlier: 3.583A pdb=" N ILE Q 79 " --> pdb=" O GLY Q 31 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TYR Q 94 " --> pdb=" O THR Q 63 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR Q 39 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG Q 53 " --> pdb=" O ARG Q 35 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ARG Q 35 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'U' and resid 50 through 52 removed outlier: 3.880A pdb=" N ARG U 51 " --> pdb=" O PHE U 38 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE U 38 " --> pdb=" O ARG U 51 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL U 36 " --> pdb=" O VAL U 19 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL U 19 " --> pdb=" O VAL U 36 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N PHE U 38 " --> pdb=" O TYR U 17 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N TYR U 17 " --> pdb=" O PHE U 38 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL U 2 " --> pdb=" O THR U 66 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'V' and resid 7 through 13 removed outlier: 8.236A pdb=" N GLN V 8 " --> pdb=" O GLU V 25 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLU V 25 " --> pdb=" O GLN V 8 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL V 21 " --> pdb=" O VAL V 12 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP V 72 " --> pdb=" O HIS V 44 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU V 74 " --> pdb=" O HIS V 46 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N VAL V 77 " --> pdb=" O VAL V 57 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL V 57 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU V 7 " --> pdb=" O ILE V 60 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'X' and resid 31 through 32 removed outlier: 8.184A pdb=" N THR X 32 " --> pdb=" O HIS X 51 " (cutoff:3.500A) 1492 hydrogen bonds defined for protein. 4152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2875 hydrogen bonds 4604 hydrogen bond angles 0 basepair planarities 1174 basepair parallelities 2701 stacking parallelities Total time for adding SS restraints: 254.26 Time building geometry restraints manager: 67.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 20155 1.33 - 1.45: 70088 1.45 - 1.58: 60853 1.58 - 1.70: 9601 1.70 - 1.83: 270 Bond restraints: 160967 Sorted by residual: bond pdb=" N PRO 5 101 " pdb=" CD PRO 5 101 " ideal model delta sigma weight residual 1.473 1.293 0.180 1.40e-02 5.10e+03 1.65e+02 bond pdb=" CA PRO 5 101 " pdb=" CB PRO 5 101 " ideal model delta sigma weight residual 1.530 1.316 0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" N PRO 5 101 " pdb=" CA PRO 5 101 " ideal model delta sigma weight residual 1.466 1.618 -0.152 1.50e-02 4.44e+03 1.03e+02 bond pdb=" O3' A 12587 " pdb=" P G 12588 " ideal model delta sigma weight residual 1.607 1.731 -0.124 1.50e-02 4.44e+03 6.82e+01 bond pdb=" C PRO 5 101 " pdb=" O PRO 5 101 " ideal model delta sigma weight residual 1.231 1.385 -0.154 2.00e-02 2.50e+03 5.95e+01 ... (remaining 160962 not shown) Histogram of bond angle deviations from ideal: 64.06 - 85.36: 2 85.36 - 106.66: 30456 106.66 - 127.96: 202368 127.96 - 149.27: 8342 149.27 - 170.57: 1 Bond angle restraints: 241169 Sorted by residual: angle pdb=" O3' C 6 74 " pdb=" P C 6 75 " pdb=" OP2 C 6 75 " ideal model delta sigma weight residual 108.00 170.57 -62.57 3.00e+00 1.11e-01 4.35e+02 angle pdb=" C3' C 6 74 " pdb=" O3' C 6 74 " pdb=" P C 6 75 " ideal model delta sigma weight residual 120.20 90.30 29.90 1.50e+00 4.44e-01 3.97e+02 angle pdb=" O3' C 6 74 " pdb=" P C 6 75 " pdb=" O5' C 6 75 " ideal model delta sigma weight residual 104.00 76.16 27.84 1.50e+00 4.44e-01 3.44e+02 angle pdb=" O3' C 6 74 " pdb=" P C 6 75 " pdb=" OP1 C 6 75 " ideal model delta sigma weight residual 108.00 64.06 43.94 3.00e+00 1.11e-01 2.14e+02 angle pdb=" O3' U 7 55 " pdb=" C3' U 7 55 " pdb=" C2' U 7 55 " ideal model delta sigma weight residual 113.70 130.26 -16.56 1.50e+00 4.44e-01 1.22e+02 ... (remaining 241164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 91162 35.78 - 71.55: 10806 71.55 - 107.33: 1259 107.33 - 143.10: 16 143.10 - 178.88: 19 Dihedral angle restraints: 103262 sinusoidal: 86975 harmonic: 16287 Sorted by residual: dihedral pdb=" C5' G 31032 " pdb=" C4' G 31032 " pdb=" C3' G 31032 " pdb=" O3' G 31032 " ideal model delta sinusoidal sigma weight residual 82.00 -2.78 84.78 1 8.00e+00 1.56e-02 1.36e+02 dihedral pdb=" C5' C 5 75 " pdb=" C4' C 5 75 " pdb=" C3' C 5 75 " pdb=" O3' C 5 75 " ideal model delta sinusoidal sigma weight residual 82.00 5.97 76.03 1 8.00e+00 1.56e-02 1.14e+02 dihedral pdb=" CA GLY d 82 " pdb=" C GLY d 82 " pdb=" N VAL d 83 " pdb=" CA VAL d 83 " ideal model delta harmonic sigma weight residual -180.00 -127.01 -52.99 0 5.00e+00 4.00e-02 1.12e+02 ... (remaining 103259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.776: 30853 0.776 - 1.551: 0 1.551 - 2.327: 0 2.327 - 3.102: 1 3.102 - 3.878: 3 Chirality restraints: 30857 Sorted by residual: chirality pdb=" C3' C 5 75 " pdb=" C4' C 5 75 " pdb=" O3' C 5 75 " pdb=" C2' C 5 75 " both_signs ideal model delta sigma weight residual False -2.48 1.40 -3.88 2.00e-01 2.50e+01 3.76e+02 chirality pdb=" C3' G 31032 " pdb=" C4' G 31032 " pdb=" O3' G 31032 " pdb=" C2' G 31032 " both_signs ideal model delta sigma weight residual False -2.48 1.16 -3.64 2.00e-01 2.50e+01 3.31e+02 chirality pdb=" C3' A 5 76 " pdb=" C4' A 5 76 " pdb=" O3' A 5 76 " pdb=" C2' A 5 76 " both_signs ideal model delta sigma weight residual False -2.48 0.86 -3.34 2.00e-01 2.50e+01 2.79e+02 ... (remaining 30854 not shown) Planarity restraints: 12688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 12034 " -0.193 2.00e-02 2.50e+03 1.13e-01 2.86e+02 pdb=" N1 U 12034 " -0.004 2.00e-02 2.50e+03 pdb=" C2 U 12034 " 0.033 2.00e-02 2.50e+03 pdb=" O2 U 12034 " 0.074 2.00e-02 2.50e+03 pdb=" N3 U 12034 " 0.041 2.00e-02 2.50e+03 pdb=" C4 U 12034 " 0.051 2.00e-02 2.50e+03 pdb=" O4 U 12034 " -0.210 2.00e-02 2.50e+03 pdb=" C5 U 12034 " 0.119 2.00e-02 2.50e+03 pdb=" C6 U 12034 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 1 804 " -0.180 2.00e-02 2.50e+03 8.06e-02 1.79e+02 pdb=" N9 A 1 804 " 0.003 2.00e-02 2.50e+03 pdb=" C8 A 1 804 " 0.067 2.00e-02 2.50e+03 pdb=" N7 A 1 804 " 0.077 2.00e-02 2.50e+03 pdb=" C5 A 1 804 " 0.041 2.00e-02 2.50e+03 pdb=" C6 A 1 804 " -0.027 2.00e-02 2.50e+03 pdb=" N6 A 1 804 " -0.130 2.00e-02 2.50e+03 pdb=" N1 A 1 804 " -0.014 2.00e-02 2.50e+03 pdb=" C2 A 1 804 " 0.039 2.00e-02 2.50e+03 pdb=" N3 A 1 804 " 0.066 2.00e-02 2.50e+03 pdb=" C4 A 1 804 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 11188 " -0.128 2.00e-02 2.50e+03 8.40e-02 1.59e+02 pdb=" N1 U 11188 " -0.005 2.00e-02 2.50e+03 pdb=" C2 U 11188 " 0.027 2.00e-02 2.50e+03 pdb=" O2 U 11188 " 0.034 2.00e-02 2.50e+03 pdb=" N3 U 11188 " 0.053 2.00e-02 2.50e+03 pdb=" C4 U 11188 " 0.060 2.00e-02 2.50e+03 pdb=" O4 U 11188 " -0.172 2.00e-02 2.50e+03 pdb=" C5 U 11188 " 0.084 2.00e-02 2.50e+03 pdb=" C6 U 11188 " 0.046 2.00e-02 2.50e+03 ... (remaining 12685 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.10: 2 2.10 - 2.80: 35905 2.80 - 3.50: 194355 3.50 - 4.20: 471706 4.20 - 4.90: 639399 Nonbonded interactions: 1341367 Sorted by model distance: nonbonded pdb=" O3' A 5 76 " pdb=" C PRO 5 101 " model vdw 1.404 3.270 nonbonded pdb=" N3 G 31032 " pdb=" OP1 G 31033 " model vdw 2.005 3.120 nonbonded pdb=" N1 G 5 2 " pdb=" O6 G 5 72 " model vdw 2.125 2.520 nonbonded pdb=" OP2 A 12448 " pdb=" OP2 C 12498 " model vdw 2.152 3.040 nonbonded pdb=" O3' A 5 76 " pdb=" CA PRO 5 101 " model vdw 2.156 3.470 ... (remaining 1341362 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '6' selection = chain '7' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 25.410 Check model and map are aligned: 1.610 Set scattering table: 1.010 Process input model: 533.570 Find NCS groups from input model: 2.980 Set up NCS constraints: 0.450 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:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 584.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.214 160967 Z= 0.470 Angle : 0.964 62.566 241169 Z= 0.568 Chirality : 0.081 3.878 30857 Planarity : 0.012 0.113 12688 Dihedral : 23.132 178.879 92756 Min Nonbonded Distance : 1.404 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.59 % Favored : 89.00 % Rotamer: Outliers : 0.71 % Allowed : 9.70 % Favored : 89.59 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.44 % 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: -4.95 (0.08), residues: 5620 helix: -3.97 (0.07), residues: 1690 sheet: -2.62 (0.14), residues: 1016 loop : -3.11 (0.09), residues: 2914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP b 212 HIS 0.011 0.002 HIS r 82 PHE 0.030 0.003 PHE Z 36 TYR 0.022 0.002 TYR K 49 ARG 0.011 0.001 ARG b 155 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1632 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1599 time to evaluate : 6.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 65 ASP cc_start: 0.8174 (t0) cc_final: 0.7945 (t0) REVERT: c 36 GLN cc_start: 0.8805 (tt0) cc_final: 0.8604 (tt0) REVERT: c 95 SER cc_start: 0.9051 (m) cc_final: 0.8482 (t) REVERT: c 139 SER cc_start: 0.8470 (m) cc_final: 0.8177 (t) REVERT: d 195 GLN cc_start: 0.8862 (mp-120) cc_final: 0.8404 (mm-40) REVERT: d 198 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7601 (pm20) REVERT: e 21 TYR cc_start: 0.8262 (m-10) cc_final: 0.8019 (m-10) REVERT: f 21 GLN cc_start: 0.7572 (mm110) cc_final: 0.6828 (tp40) REVERT: f 74 MET cc_start: 0.8709 (mtp) cc_final: 0.8364 (ttm) REVERT: f 76 ILE cc_start: 0.9289 (mm) cc_final: 0.9086 (tp) REVERT: i 112 LYS cc_start: -0.0109 (mtmt) cc_final: -0.0763 (ttmt) REVERT: i 124 MET cc_start: 0.1179 (mmp) cc_final: -0.1249 (mmt) REVERT: i 135 MET cc_start: 0.1147 (mmp) cc_final: 0.0571 (mtm) REVERT: j 90 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7829 (tm-30) REVERT: j 106 LYS cc_start: 0.8685 (tttt) cc_final: 0.8117 (ttmm) REVERT: j 114 LEU cc_start: 0.9193 (tp) cc_final: 0.8955 (tp) REVERT: j 125 TYR cc_start: 0.8244 (m-80) cc_final: 0.7945 (m-10) REVERT: k 53 LYS cc_start: 0.8020 (mmtt) cc_final: 0.7754 (mmpt) REVERT: k 73 ASP cc_start: 0.8465 (p0) cc_final: 0.8119 (p0) REVERT: l 105 ILE cc_start: 0.9253 (mm) cc_final: 0.8865 (mp) REVERT: m 119 LEU cc_start: 0.9396 (mt) cc_final: 0.9123 (mp) REVERT: o 17 LYS cc_start: 0.9065 (tptp) cc_final: 0.8842 (tppt) REVERT: o 19 GLN cc_start: 0.8994 (tt0) cc_final: 0.8772 (tt0) REVERT: o 68 LYS cc_start: 0.9269 (mttt) cc_final: 0.8976 (mtmt) REVERT: o 69 ASP cc_start: 0.8353 (p0) cc_final: 0.7586 (p0) REVERT: p 3 ILE cc_start: 0.9499 (mt) cc_final: 0.9227 (mm) REVERT: p 6 GLN cc_start: 0.8970 (mt0) cc_final: 0.8553 (mt0) REVERT: p 64 SER cc_start: 0.8188 (t) cc_final: 0.7154 (t) REVERT: p 98 TYR cc_start: 0.8961 (p90) cc_final: 0.8589 (p90) REVERT: q 113 LYS cc_start: 0.9084 (mtmt) cc_final: 0.8878 (mtpm) REVERT: r 6 GLN cc_start: 0.8516 (pt0) cc_final: 0.8243 (pm20) REVERT: r 97 LYS cc_start: 0.9155 (tppt) cc_final: 0.8943 (tppp) REVERT: s 46 LEU cc_start: 0.9550 (mm) cc_final: 0.9330 (mp) REVERT: s 94 ASP cc_start: 0.7566 (m-30) cc_final: 0.7234 (m-30) REVERT: t 6 ARG cc_start: 0.8813 (tpt170) cc_final: 0.8497 (tpp80) REVERT: t 7 LEU cc_start: 0.9460 (mt) cc_final: 0.9221 (mt) REVERT: t 8 LEU cc_start: 0.9235 (mt) cc_final: 0.8948 (mt) REVERT: u 21 ARG cc_start: 0.8215 (ptm-80) cc_final: 0.7601 (ptm160) REVERT: v 25 LYS cc_start: 0.8735 (mttt) cc_final: 0.8380 (mmmt) REVERT: v 41 GLU cc_start: 0.7166 (pp20) cc_final: 0.6530 (pp20) REVERT: v 42 LEU cc_start: 0.8928 (pt) cc_final: 0.8681 (pp) REVERT: v 78 GLN cc_start: 0.8181 (mt0) cc_final: 0.7866 (mt0) REVERT: x 34 SER cc_start: 0.9024 (m) cc_final: 0.8619 (p) REVERT: x 66 VAL cc_start: 0.9563 (p) cc_final: 0.9260 (p) REVERT: y 29 ARG cc_start: 0.8582 (mtm-85) cc_final: 0.8373 (mtp85) REVERT: y 45 GLN cc_start: 0.8927 (pt0) cc_final: 0.8606 (pt0) REVERT: y 58 ASN cc_start: 0.8888 (t0) cc_final: 0.8576 (t0) REVERT: z 48 ASN cc_start: 0.8942 (t0) cc_final: 0.8509 (t0) REVERT: A 23 LYS cc_start: 0.9398 (pttm) cc_final: 0.9122 (pptt) REVERT: C 47 ILE cc_start: 0.8716 (mm) cc_final: 0.8493 (pt) REVERT: D 22 MET cc_start: 0.8408 (mmm) cc_final: 0.8146 (mmm) REVERT: F 18 LYS cc_start: 0.8696 (tttt) cc_final: 0.8446 (tppp) REVERT: G 29 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8118 (p90) REVERT: G 36 LYS cc_start: 0.9240 (mtmt) cc_final: 0.8916 (tptp) REVERT: G 108 GLN cc_start: 0.9128 (mm110) cc_final: 0.8740 (mp10) REVERT: G 132 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8529 (mp0) REVERT: G 212 TYR cc_start: 0.8241 (m-80) cc_final: 0.7878 (m-80) REVERT: H 5 HIS cc_start: 0.7995 (t-90) cc_final: 0.7629 (t-90) REVERT: H 40 GLN cc_start: 0.8726 (pp30) cc_final: 0.8460 (pp30) REVERT: H 151 GLU cc_start: 0.8149 (tt0) cc_final: 0.7869 (tp30) REVERT: H 182 ASP cc_start: 0.8291 (t0) cc_final: 0.8047 (t0) REVERT: H 183 TYR cc_start: 0.9013 (t80) cc_final: 0.8745 (t80) REVERT: H 184 ASN cc_start: 0.8850 (t0) cc_final: 0.8321 (t0) REVERT: I 50 TYR cc_start: 0.8336 (t80) cc_final: 0.7798 (t80) REVERT: I 82 LYS cc_start: 0.6960 (mttt) cc_final: 0.6628 (mptt) REVERT: I 102 TYR cc_start: 0.8130 (t80) cc_final: 0.7926 (t80) REVERT: I 181 PHE cc_start: 0.8751 (t80) cc_final: 0.7910 (t80) REVERT: J 11 GLN cc_start: 0.8375 (tt0) cc_final: 0.8044 (OUTLIER) REVERT: J 12 GLU cc_start: 0.8124 (pt0) cc_final: 0.7803 (mt-10) REVERT: J 60 GLN cc_start: 0.8846 (tt0) cc_final: 0.8505 (tt0) REVERT: J 61 LYS cc_start: 0.9024 (tttt) cc_final: 0.8584 (ttmt) REVERT: J 96 GLN cc_start: 0.9388 (tt0) cc_final: 0.9121 (tt0) REVERT: J 140 ILE cc_start: 0.9254 (mm) cc_final: 0.8899 (mp) REVERT: J 161 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8343 (tm-30) REVERT: K 1 MET cc_start: 0.7416 (mpp) cc_final: 0.7175 (mpp) REVERT: K 14 GLN cc_start: 0.8830 (mp10) cc_final: 0.8472 (mp10) REVERT: K 35 LYS cc_start: 0.8699 (mtpp) cc_final: 0.8307 (mmmt) REVERT: K 40 GLU cc_start: 0.7344 (tt0) cc_final: 0.6966 (tp30) REVERT: K 61 LEU cc_start: 0.9526 (tp) cc_final: 0.9302 (tm) REVERT: K 97 THR cc_start: 0.8857 (t) cc_final: 0.8626 (m) REVERT: L 46 LEU cc_start: 0.9023 (tp) cc_final: 0.8823 (tm) REVERT: L 85 GLN cc_start: 0.7606 (mp-120) cc_final: 0.6938 (mm-40) REVERT: L 130 LYS cc_start: 0.8875 (pttt) cc_final: 0.8668 (ptmm) REVERT: L 141 HIS cc_start: 0.8446 (m90) cc_final: 0.8157 (m-70) REVERT: L 143 MET cc_start: 0.8583 (tpt) cc_final: 0.8106 (tpt) REVERT: L 147 ASN cc_start: 0.8502 (m110) cc_final: 0.8225 (p0) REVERT: M 4 ASP cc_start: 0.7814 (t0) cc_final: 0.7507 (t0) REVERT: M 15 ASN cc_start: 0.8323 (m-40) cc_final: 0.8008 (m-40) REVERT: M 17 GLN cc_start: 0.8415 (mm110) cc_final: 0.8193 (mm-40) REVERT: M 42 GLU cc_start: 0.8579 (tp30) cc_final: 0.8117 (tp30) REVERT: M 57 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8194 (mm-30) REVERT: M 60 LEU cc_start: 0.9403 (mt) cc_final: 0.8933 (mp) REVERT: N 65 THR cc_start: 0.9397 (OUTLIER) cc_final: 0.8948 (p) REVERT: N 74 GLN cc_start: 0.8459 (mt0) cc_final: 0.8129 (mt0) REVERT: O 25 ILE cc_start: 0.8808 (tp) cc_final: 0.8282 (pp) REVERT: O 71 LEU cc_start: 0.9442 (mp) cc_final: 0.9196 (mt) REVERT: P 63 GLN cc_start: 0.8941 (tt0) cc_final: 0.8535 (tp40) REVERT: P 76 TYR cc_start: 0.8971 (m-80) cc_final: 0.8598 (m-80) REVERT: Q 28 GLN cc_start: 0.8505 (mp10) cc_final: 0.8088 (mp10) REVERT: R 8 ILE cc_start: 0.7062 (mp) cc_final: 0.6772 (mp) REVERT: R 51 GLN cc_start: 0.8713 (mp10) cc_final: 0.8448 (mp10) REVERT: R 74 MET cc_start: 0.9195 (tmm) cc_final: 0.8190 (tmm) REVERT: R 77 LYS cc_start: 0.9559 (tttm) cc_final: 0.9214 (tmmt) REVERT: U 13 LYS cc_start: 0.8607 (mttt) cc_final: 0.8321 (mttt) REVERT: U 23 ASP cc_start: 0.7674 (t0) cc_final: 0.6866 (m-30) REVERT: W 47 ARG cc_start: 0.8164 (mmt-90) cc_final: 0.7927 (mmt180) REVERT: W 56 ARG cc_start: 0.8603 (ttm-80) cc_final: 0.8159 (ptm160) REVERT: X 40 PHE cc_start: 0.8813 (m-10) cc_final: 0.8469 (m-80) REVERT: X 43 MET cc_start: 0.9078 (mmp) cc_final: 0.8777 (mpt) REVERT: X 72 GLU cc_start: 0.8466 (tt0) cc_final: 0.7048 (tm-30) REVERT: Y 23 ARG cc_start: 0.8940 (mmm-85) cc_final: 0.8727 (mmm-85) REVERT: Y 26 MET cc_start: 0.9114 (ttt) cc_final: 0.8806 (tpp) REVERT: Y 54 GLN cc_start: 0.8551 (tt0) cc_final: 0.8158 (tm-30) REVERT: Y 56 ILE cc_start: 0.8995 (tt) cc_final: 0.8761 (tp) REVERT: Y 82 ILE cc_start: 0.8923 (pt) cc_final: 0.8608 (mt) REVERT: Z 24 LYS cc_start: 0.8595 (mttm) cc_final: 0.8029 (mttt) REVERT: Z 45 LYS cc_start: 0.9153 (tptt) cc_final: 0.8917 (ttmm) REVERT: Z 46 ARG cc_start: 0.8014 (tpt90) cc_final: 0.7698 (tpt170) REVERT: Z 57 LYS cc_start: 0.7755 (mptt) cc_final: 0.7532 (tptm) outliers start: 33 outliers final: 24 residues processed: 1624 average time/residue: 2.0543 time to fit residues: 4901.3911 Evaluate side-chains 1237 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1211 time to evaluate : 5.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 198 GLU Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain i residue 22 PRO Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 10 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 867 optimal weight: 8.9990 chunk 778 optimal weight: 5.9990 chunk 431 optimal weight: 20.0000 chunk 265 optimal weight: 20.0000 chunk 525 optimal weight: 4.9990 chunk 415 optimal weight: 10.0000 chunk 804 optimal weight: 8.9990 chunk 311 optimal weight: 20.0000 chunk 489 optimal weight: 0.0980 chunk 599 optimal weight: 9.9990 chunk 932 optimal weight: 8.9990 overall best weight: 5.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 24 HIS b 89 ASN b 142 ASN b 259 ASN c 49 GLN c 134 HIS c 150 GLN c 167 ASN ** d 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 47 ASN ** f 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 110 HIS i 29 GLN i 30 GLN ** j 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 136 GLN k 3 GLN k 93 GLN l 4 ASN l 104 GLN m 13 HIS n 11 ASN n 18 GLN o 116 GLN p 114 ASN t 59 ASN t 91 GLN ** t 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 5 GLN x 33 HIS y 31 GLN z 8 GLN A 20 ASN D 16 HIS F 13 ASN G 14 HIS ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN I 135 GLN I 197 HIS J 76 ASN J 121 ASN ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN L 85 GLN M 20 ASN N 4 GLN P 14 GLN Q 4 ASN Q 76 HIS ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 99 GLN S 42 ASN T 39 GLN U 79 ASN V 30 HIS W 18 GLN X 51 HIS Y 2 ASN Y 20 ASN Y 69 ASN Y 77 ASN Y 81 GLN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 160967 Z= 0.240 Angle : 0.656 11.444 241169 Z= 0.342 Chirality : 0.038 0.342 30857 Planarity : 0.006 0.085 12688 Dihedral : 23.468 177.449 81512 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.04 % Favored : 89.70 % Rotamer: Outliers : 6.09 % Allowed : 23.19 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.18 % 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: -3.68 (0.10), residues: 5620 helix: -2.06 (0.10), residues: 1697 sheet: -2.21 (0.15), residues: 1040 loop : -2.78 (0.10), residues: 2883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP b 212 HIS 0.008 0.001 HIS s 60 PHE 0.023 0.002 PHE G 15 TYR 0.023 0.002 TYR l 58 ARG 0.011 0.001 ARG I 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1652 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1367 time to evaluate : 6.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 65 ASP cc_start: 0.8091 (t0) cc_final: 0.7832 (t0) REVERT: b 102 TYR cc_start: 0.8465 (m-10) cc_final: 0.8235 (m-80) REVERT: c 94 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8016 (mt0) REVERT: c 95 SER cc_start: 0.8852 (m) cc_final: 0.8351 (t) REVERT: c 139 SER cc_start: 0.8444 (m) cc_final: 0.8171 (t) REVERT: d 198 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7530 (mt-10) REVERT: e 25 MET cc_start: 0.9207 (mmm) cc_final: 0.8731 (tpp) REVERT: f 29 ASN cc_start: 0.8585 (t0) cc_final: 0.8222 (m110) REVERT: f 87 GLN cc_start: 0.8720 (mt0) cc_final: 0.8514 (mm110) REVERT: f 148 ARG cc_start: 0.8341 (mmm160) cc_final: 0.8046 (mmm160) REVERT: g 11 ASN cc_start: 0.7955 (t0) cc_final: 0.7317 (m110) REVERT: i 135 MET cc_start: 0.1150 (mmp) cc_final: 0.0497 (mtm) REVERT: k 73 ASP cc_start: 0.8502 (p0) cc_final: 0.8224 (p0) REVERT: l 91 ASP cc_start: 0.8795 (t70) cc_final: 0.8470 (t70) REVERT: m 129 THR cc_start: 0.8338 (p) cc_final: 0.8018 (t) REVERT: n 78 LYS cc_start: 0.9213 (tppp) cc_final: 0.8962 (tppp) REVERT: o 19 GLN cc_start: 0.9023 (tt0) cc_final: 0.8822 (tt0) REVERT: o 68 LYS cc_start: 0.9085 (mttt) cc_final: 0.8852 (mttp) REVERT: o 69 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7995 (p0) REVERT: p 6 GLN cc_start: 0.8837 (mt0) cc_final: 0.8600 (mt0) REVERT: p 64 SER cc_start: 0.8063 (t) cc_final: 0.7342 (t) REVERT: p 70 GLU cc_start: 0.7963 (pm20) cc_final: 0.7676 (pm20) REVERT: q 70 GLN cc_start: 0.9015 (tt0) cc_final: 0.8614 (tp40) REVERT: s 33 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8966 (mm) REVERT: t 4 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8341 (tm-30) REVERT: t 6 ARG cc_start: 0.8853 (tpt170) cc_final: 0.8328 (tpp80) REVERT: t 8 LEU cc_start: 0.9238 (mt) cc_final: 0.8790 (mt) REVERT: t 93 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7038 (tp) REVERT: u 58 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8276 (p) REVERT: v 7 GLU cc_start: 0.8472 (pm20) cc_final: 0.8268 (pm20) REVERT: v 69 GLU cc_start: 0.8823 (pp20) cc_final: 0.8568 (tm-30) REVERT: w 62 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8567 (tppp) REVERT: x 66 VAL cc_start: 0.9685 (p) cc_final: 0.9416 (p) REVERT: y 29 ARG cc_start: 0.8696 (mtm-85) cc_final: 0.8423 (mtp85) REVERT: z 48 ASN cc_start: 0.8904 (t0) cc_final: 0.8508 (t0) REVERT: A 23 LYS cc_start: 0.9372 (pttm) cc_final: 0.9092 (pptt) REVERT: A 25 ARG cc_start: 0.7206 (mtm180) cc_final: 0.6931 (mtm180) REVERT: B 14 MET cc_start: 0.8269 (mtm) cc_final: 0.8029 (mtm) REVERT: C 30 PRO cc_start: 0.9077 (Cg_endo) cc_final: 0.8819 (Cg_exo) REVERT: D 22 MET cc_start: 0.8367 (mmm) cc_final: 0.8133 (mmm) REVERT: F 18 LYS cc_start: 0.8619 (tttt) cc_final: 0.8395 (tppt) REVERT: G 26 MET cc_start: 0.8547 (mmm) cc_final: 0.8296 (mmm) REVERT: G 29 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8124 (p90) REVERT: G 36 LYS cc_start: 0.9258 (mtmt) cc_final: 0.9029 (tmtt) REVERT: G 212 TYR cc_start: 0.8320 (m-80) cc_final: 0.7929 (m-80) REVERT: H 167 TYR cc_start: 0.7795 (OUTLIER) cc_final: 0.7037 (m-80) REVERT: H 182 ASP cc_start: 0.8278 (t0) cc_final: 0.8073 (t0) REVERT: I 44 LYS cc_start: 0.8037 (tptp) cc_final: 0.7788 (tppt) REVERT: I 50 TYR cc_start: 0.8193 (t80) cc_final: 0.7730 (t80) REVERT: I 82 LYS cc_start: 0.7145 (mttt) cc_final: 0.6825 (mptt) REVERT: I 181 PHE cc_start: 0.8662 (t80) cc_final: 0.7796 (t80) REVERT: J 11 GLN cc_start: 0.8428 (tt0) cc_final: 0.7427 (OUTLIER) REVERT: J 54 GLU cc_start: 0.7659 (tt0) cc_final: 0.7019 (tt0) REVERT: J 60 GLN cc_start: 0.8729 (tt0) cc_final: 0.8519 (tt0) REVERT: J 61 LYS cc_start: 0.9012 (tttt) cc_final: 0.8520 (ttmt) REVERT: J 115 GLU cc_start: 0.8689 (tt0) cc_final: 0.8308 (tm-30) REVERT: J 127 TYR cc_start: 0.8044 (m-10) cc_final: 0.7816 (m-10) REVERT: J 140 ILE cc_start: 0.9308 (mm) cc_final: 0.9038 (mp) REVERT: J 144 GLU cc_start: 0.8343 (pt0) cc_final: 0.8114 (pt0) REVERT: K 14 GLN cc_start: 0.8701 (mp10) cc_final: 0.8169 (mp10) REVERT: K 35 LYS cc_start: 0.8585 (mtpp) cc_final: 0.8186 (mmmt) REVERT: K 40 GLU cc_start: 0.7207 (tt0) cc_final: 0.6929 (tp30) REVERT: K 97 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8408 (m) REVERT: L 22 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8696 (tm) REVERT: L 25 PHE cc_start: 0.9446 (t80) cc_final: 0.9162 (t80) REVERT: L 85 GLN cc_start: 0.7535 (mp10) cc_final: 0.6875 (mp10) REVERT: L 115 MET cc_start: 0.8684 (tpp) cc_final: 0.8417 (ttm) REVERT: M 4 ASP cc_start: 0.7664 (t0) cc_final: 0.7418 (t0) REVERT: M 17 GLN cc_start: 0.8520 (mm110) cc_final: 0.8146 (mm-40) REVERT: M 42 GLU cc_start: 0.8677 (tp30) cc_final: 0.8399 (tp30) REVERT: M 57 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8153 (mm-30) REVERT: M 60 LEU cc_start: 0.9252 (mt) cc_final: 0.8958 (mp) REVERT: M 64 TYR cc_start: 0.7610 (m-80) cc_final: 0.7305 (m-80) REVERT: N 28 VAL cc_start: 0.8635 (t) cc_final: 0.8423 (p) REVERT: N 46 VAL cc_start: 0.9360 (m) cc_final: 0.9106 (p) REVERT: N 74 GLN cc_start: 0.8443 (mt0) cc_final: 0.8120 (mt0) REVERT: N 96 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8641 (pt0) REVERT: N 119 LYS cc_start: 0.8812 (ttmm) cc_final: 0.8603 (ttmm) REVERT: O 46 LYS cc_start: 0.9142 (mtmm) cc_final: 0.8540 (mtmm) REVERT: O 47 GLU cc_start: 0.6481 (mp0) cc_final: 0.6271 (mp0) REVERT: O 59 LYS cc_start: 0.8592 (ttpt) cc_final: 0.8371 (ttpp) REVERT: P 76 TYR cc_start: 0.8944 (m-80) cc_final: 0.8739 (m-80) REVERT: Q 4 ASN cc_start: 0.8893 (OUTLIER) cc_final: 0.8604 (t0) REVERT: Q 28 GLN cc_start: 0.8609 (mp10) cc_final: 0.8291 (mp10) REVERT: R 43 LYS cc_start: 0.8400 (mtmt) cc_final: 0.8103 (mtmt) REVERT: R 58 GLU cc_start: 0.9276 (mm-30) cc_final: 0.9039 (mm-30) REVERT: R 77 LYS cc_start: 0.9540 (tttm) cc_final: 0.9181 (tmmt) REVERT: S 15 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9038 (tp) REVERT: T 46 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8563 (pttm) REVERT: U 13 LYS cc_start: 0.8532 (mttt) cc_final: 0.8286 (mttt) REVERT: U 23 ASP cc_start: 0.7699 (t0) cc_final: 0.6924 (m-30) REVERT: W 47 ARG cc_start: 0.7976 (mmt-90) cc_final: 0.7744 (mmt180) REVERT: W 56 ARG cc_start: 0.8623 (ttm-80) cc_final: 0.8112 (ptm160) REVERT: X 16 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.9028 (mmtm) REVERT: X 17 LYS cc_start: 0.9161 (mmmt) cc_final: 0.8425 (mmmt) REVERT: X 19 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8318 (tm-30) REVERT: X 20 LYS cc_start: 0.8879 (ptmt) cc_final: 0.8546 (pptt) REVERT: X 43 MET cc_start: 0.9004 (mmt) cc_final: 0.8783 (mpt) REVERT: X 72 GLU cc_start: 0.8557 (tt0) cc_final: 0.7143 (tm-30) REVERT: Y 20 ASN cc_start: 0.8744 (t0) cc_final: 0.8471 (t0) REVERT: Y 27 MET cc_start: 0.8944 (ptm) cc_final: 0.8600 (mtp) REVERT: Y 47 GLN cc_start: 0.8704 (tp-100) cc_final: 0.8360 (tp-100) REVERT: Y 56 ILE cc_start: 0.8880 (tt) cc_final: 0.8663 (tp) REVERT: Z 53 LYS cc_start: 0.7959 (mttt) cc_final: 0.7438 (ttpt) outliers start: 285 outliers final: 118 residues processed: 1482 average time/residue: 1.9205 time to fit residues: 4249.8124 Evaluate side-chains 1340 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1206 time to evaluate : 6.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 94 GLN Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain d residue 198 GLU Chi-restraints excluded: chain e residue 9 ASP Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain i residue 131 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain j residue 118 MET Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 45 SER Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 55 GLU Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 84 SER Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 58 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain w residue 40 LYS Chi-restraints excluded: chain w residue 62 LYS Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 167 TYR Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 110 MET Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 113 THR Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 114 SER Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain T residue 19 ASN Chi-restraints excluded: chain T residue 46 LYS Chi-restraints excluded: chain U residue 32 PHE Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 19 GLU Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 18 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 518 optimal weight: 7.9990 chunk 289 optimal weight: 10.0000 chunk 776 optimal weight: 30.0000 chunk 635 optimal weight: 8.9990 chunk 257 optimal weight: 40.0000 chunk 934 optimal weight: 8.9990 chunk 1009 optimal weight: 9.9990 chunk 832 optimal weight: 5.9990 chunk 926 optimal weight: 0.4980 chunk 318 optimal weight: 10.0000 chunk 749 optimal weight: 6.9990 overall best weight: 6.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 GLN c 49 GLN c 167 ASN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 132 HIS ** t 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN H 122 GLN I 195 ASN ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 20 ASN Q 4 ASN Q 111 GLN S 42 ASN Y 81 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 160967 Z= 0.243 Angle : 0.607 10.294 241169 Z= 0.316 Chirality : 0.035 0.308 30857 Planarity : 0.005 0.078 12688 Dihedral : 23.432 178.814 81490 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.28 % Favored : 89.50 % Rotamer: Outliers : 6.75 % Allowed : 26.12 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.20 % 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: -2.92 (0.10), residues: 5620 helix: -1.03 (0.12), residues: 1706 sheet: -1.94 (0.15), residues: 1041 loop : -2.53 (0.11), residues: 2873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 212 HIS 0.006 0.001 HIS V 46 PHE 0.025 0.002 PHE Z 36 TYR 0.028 0.002 TYR p 98 ARG 0.015 0.001 ARG R 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1601 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 1285 time to evaluate : 6.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 167 ASP cc_start: 0.7664 (m-30) cc_final: 0.7254 (p0) REVERT: c 94 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8032 (mt0) REVERT: c 95 SER cc_start: 0.8853 (m) cc_final: 0.8380 (t) REVERT: c 139 SER cc_start: 0.8476 (m) cc_final: 0.8210 (t) REVERT: d 149 ILE cc_start: 0.9321 (pp) cc_final: 0.9101 (pp) REVERT: d 195 GLN cc_start: 0.8687 (mm110) cc_final: 0.8369 (mm110) REVERT: e 25 MET cc_start: 0.9148 (mmm) cc_final: 0.8675 (tpp) REVERT: f 29 ASN cc_start: 0.8612 (t0) cc_final: 0.8202 (m-40) REVERT: f 87 GLN cc_start: 0.8698 (mt0) cc_final: 0.8429 (mm110) REVERT: i 116 MET cc_start: 0.0125 (OUTLIER) cc_final: -0.0365 (mmm) REVERT: i 124 MET cc_start: 0.0816 (mmt) cc_final: 0.0346 (tpt) REVERT: i 135 MET cc_start: 0.1277 (mmp) cc_final: 0.0581 (mtm) REVERT: j 91 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7944 (tm-30) REVERT: k 73 ASP cc_start: 0.8512 (p0) cc_final: 0.8269 (p0) REVERT: l 10 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7612 (tm-30) REVERT: l 91 ASP cc_start: 0.8836 (t70) cc_final: 0.8534 (t70) REVERT: m 110 GLU cc_start: 0.7990 (pp20) cc_final: 0.7617 (pp20) REVERT: m 129 THR cc_start: 0.8337 (p) cc_final: 0.8035 (t) REVERT: n 78 LYS cc_start: 0.9211 (tppp) cc_final: 0.8982 (tppp) REVERT: o 4 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8774 (tppt) REVERT: o 17 LYS cc_start: 0.9243 (tppt) cc_final: 0.8908 (tptp) REVERT: o 68 LYS cc_start: 0.9093 (mttt) cc_final: 0.8832 (mtmm) REVERT: o 69 ASP cc_start: 0.8273 (p0) cc_final: 0.8035 (p0) REVERT: o 88 LYS cc_start: 0.8641 (tmtm) cc_final: 0.7964 (tptp) REVERT: p 6 GLN cc_start: 0.8864 (mt0) cc_final: 0.8639 (mt0) REVERT: p 12 MET cc_start: 0.7761 (mtm) cc_final: 0.7415 (mtm) REVERT: p 64 SER cc_start: 0.7993 (t) cc_final: 0.7438 (t) REVERT: q 48 ASP cc_start: 0.7331 (m-30) cc_final: 0.6930 (m-30) REVERT: q 70 GLN cc_start: 0.9042 (tt0) cc_final: 0.8682 (tp-100) REVERT: s 33 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.8948 (mm) REVERT: t 5 GLU cc_start: 0.7973 (pp20) cc_final: 0.7750 (pp20) REVERT: t 6 ARG cc_start: 0.8819 (tpt170) cc_final: 0.8523 (tpp80) REVERT: t 8 LEU cc_start: 0.9259 (mt) cc_final: 0.8957 (mt) REVERT: t 54 GLU cc_start: 0.8648 (pm20) cc_final: 0.8285 (pm20) REVERT: u 17 ASP cc_start: 0.6479 (m-30) cc_final: 0.6078 (m-30) REVERT: u 45 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.7793 (tm-30) REVERT: u 93 ARG cc_start: 0.8438 (mtp180) cc_final: 0.8023 (mtm180) REVERT: v 62 THR cc_start: 0.9394 (m) cc_final: 0.9075 (p) REVERT: w 62 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8627 (tppp) REVERT: y 2 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7814 (pttp) REVERT: y 17 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8348 (pp20) REVERT: y 29 ARG cc_start: 0.8735 (mtm-85) cc_final: 0.8272 (mtp85) REVERT: z 35 VAL cc_start: 0.9316 (OUTLIER) cc_final: 0.9004 (p) REVERT: z 48 ASN cc_start: 0.8918 (t0) cc_final: 0.8529 (t0) REVERT: A 10 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8407 (mm-30) REVERT: A 23 LYS cc_start: 0.9350 (pttm) cc_final: 0.9084 (pptt) REVERT: B 52 LYS cc_start: 0.9161 (tppp) cc_final: 0.8922 (tppp) REVERT: D 22 MET cc_start: 0.8385 (mmm) cc_final: 0.8184 (mmm) REVERT: G 26 MET cc_start: 0.8698 (mmm) cc_final: 0.8392 (mmt) REVERT: G 29 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8082 (p90) REVERT: G 36 LYS cc_start: 0.9245 (mtmt) cc_final: 0.9008 (tmtm) REVERT: G 190 SER cc_start: 0.8766 (t) cc_final: 0.8264 (m) REVERT: G 198 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8618 (m) REVERT: G 212 TYR cc_start: 0.8257 (m-80) cc_final: 0.7839 (m-80) REVERT: H 21 TRP cc_start: 0.8755 (p-90) cc_final: 0.8481 (p-90) REVERT: H 167 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.7088 (m-80) REVERT: H 182 ASP cc_start: 0.8274 (t0) cc_final: 0.8061 (t0) REVERT: H 183 TYR cc_start: 0.9011 (t80) cc_final: 0.8734 (t80) REVERT: I 44 LYS cc_start: 0.7976 (tptp) cc_final: 0.7724 (tppt) REVERT: I 47 LEU cc_start: 0.5928 (OUTLIER) cc_final: 0.5396 (mm) REVERT: I 50 TYR cc_start: 0.8226 (t80) cc_final: 0.7616 (t80) REVERT: I 82 LYS cc_start: 0.7144 (mttt) cc_final: 0.6828 (mptt) REVERT: I 84 ASN cc_start: 0.8828 (t0) cc_final: 0.8449 (p0) REVERT: I 181 PHE cc_start: 0.8617 (t80) cc_final: 0.7760 (t80) REVERT: I 190 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8222 (mm) REVERT: J 11 GLN cc_start: 0.8411 (tt0) cc_final: 0.7697 (tm-30) REVERT: J 22 LYS cc_start: 0.8643 (pttt) cc_final: 0.8356 (ptpt) REVERT: J 54 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7017 (tt0) REVERT: J 61 LYS cc_start: 0.9044 (tttt) cc_final: 0.8490 (ttmt) REVERT: J 115 GLU cc_start: 0.8705 (tt0) cc_final: 0.8386 (pp20) REVERT: J 140 ILE cc_start: 0.9315 (mm) cc_final: 0.8994 (mp) REVERT: K 14 GLN cc_start: 0.8813 (mp10) cc_final: 0.8299 (mp10) REVERT: K 35 LYS cc_start: 0.8588 (mtpp) cc_final: 0.8217 (mmmt) REVERT: K 40 GLU cc_start: 0.7123 (tt0) cc_final: 0.6824 (tp30) REVERT: L 85 GLN cc_start: 0.7393 (mp10) cc_final: 0.6945 (mp10) REVERT: L 124 SER cc_start: 0.9035 (p) cc_final: 0.8829 (m) REVERT: L 143 MET cc_start: 0.9033 (tpp) cc_final: 0.8454 (tpt) REVERT: M 4 ASP cc_start: 0.7697 (t0) cc_final: 0.7458 (t0) REVERT: M 17 GLN cc_start: 0.8480 (mm110) cc_final: 0.8121 (mm-40) REVERT: M 42 GLU cc_start: 0.8640 (tp30) cc_final: 0.8381 (tp30) REVERT: M 58 LEU cc_start: 0.9573 (tp) cc_final: 0.9372 (tm) REVERT: N 5 TYR cc_start: 0.8237 (m-80) cc_final: 0.7985 (m-80) REVERT: N 46 VAL cc_start: 0.9265 (m) cc_final: 0.8882 (p) REVERT: N 49 GLN cc_start: 0.8854 (mt0) cc_final: 0.8560 (mt0) REVERT: N 65 THR cc_start: 0.9445 (t) cc_final: 0.9032 (p) REVERT: N 74 GLN cc_start: 0.8258 (mt0) cc_final: 0.7926 (mt0) REVERT: N 111 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8131 (mp0) REVERT: N 119 LYS cc_start: 0.8789 (ttmm) cc_final: 0.8497 (ttmm) REVERT: O 46 LYS cc_start: 0.9138 (mtmm) cc_final: 0.8558 (mtmm) REVERT: O 47 GLU cc_start: 0.6449 (mp0) cc_final: 0.6188 (mp0) REVERT: O 59 LYS cc_start: 0.8641 (ttpt) cc_final: 0.8348 (ttpp) REVERT: P 76 TYR cc_start: 0.9039 (m-80) cc_final: 0.8740 (m-80) REVERT: Q 28 GLN cc_start: 0.8471 (mp10) cc_final: 0.8151 (mp10) REVERT: Q 54 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8276 (p) REVERT: R 8 ILE cc_start: 0.7124 (OUTLIER) cc_final: 0.6859 (mp) REVERT: R 43 LYS cc_start: 0.8364 (mtmt) cc_final: 0.7750 (mtpm) REVERT: R 46 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7828 (mp0) REVERT: R 77 LYS cc_start: 0.9605 (tttm) cc_final: 0.9242 (tmmt) REVERT: S 15 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9027 (tp) REVERT: S 65 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8487 (mt0) REVERT: T 9 LYS cc_start: 0.9231 (mtpp) cc_final: 0.8940 (mmmt) REVERT: T 46 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8292 (pttm) REVERT: U 13 LYS cc_start: 0.8399 (mttt) cc_final: 0.8125 (mttt) REVERT: U 23 ASP cc_start: 0.7681 (t0) cc_final: 0.6887 (m-30) REVERT: V 74 LEU cc_start: 0.9052 (pt) cc_final: 0.8084 (pt) REVERT: W 56 ARG cc_start: 0.8636 (ttm-80) cc_final: 0.7974 (ptm160) REVERT: X 43 MET cc_start: 0.9032 (mmt) cc_final: 0.8728 (mpt) REVERT: X 72 GLU cc_start: 0.8603 (tt0) cc_final: 0.7117 (tm-30) REVERT: Y 47 GLN cc_start: 0.8835 (tp-100) cc_final: 0.8572 (tp-100) REVERT: Y 73 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8459 (ptp-170) REVERT: Z 24 LYS cc_start: 0.8178 (mttt) cc_final: 0.7578 (mppt) REVERT: 5 101 PRO cc_start: 0.7618 (Cg_exo) cc_final: 0.7376 (Cg_endo) outliers start: 316 outliers final: 154 residues processed: 1438 average time/residue: 1.8933 time to fit residues: 4110.5752 Evaluate side-chains 1364 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1188 time to evaluate : 6.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 193 GLU Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 94 GLN Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 15 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain i residue 116 MET Chi-restraints excluded: chain i residue 131 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 91 GLU Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain n residue 110 MET Chi-restraints excluded: chain o residue 4 LYS Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 45 SER Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 55 GLU Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 59 LEU Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain t residue 42 GLU Chi-restraints excluded: chain t residue 74 ILE Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 45 GLN Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain w residue 40 LYS Chi-restraints excluded: chain w residue 62 LYS Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 2 LYS Chi-restraints excluded: chain y residue 15 ASN Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 35 VAL Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 167 TYR Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 54 GLU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 108 ASP Chi-restraints excluded: chain Q residue 111 GLN Chi-restraints excluded: chain Q residue 114 SER Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 54 THR Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 65 GLN Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain T residue 19 ASN Chi-restraints excluded: chain T residue 46 LYS Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 32 PHE Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 69 ASN Chi-restraints excluded: chain Y residue 73 ARG Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 52 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 923 optimal weight: 40.0000 chunk 702 optimal weight: 2.9990 chunk 484 optimal weight: 20.0000 chunk 103 optimal weight: 50.0000 chunk 445 optimal weight: 20.0000 chunk 627 optimal weight: 30.0000 chunk 937 optimal weight: 7.9990 chunk 992 optimal weight: 9.9990 chunk 489 optimal weight: 20.0000 chunk 888 optimal weight: 7.9990 chunk 267 optimal weight: 20.0000 overall best weight: 9.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 36 ASN ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 ASN d 195 GLN e 4 HIS ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 114 HIS j 136 GLN o 19 GLN ** t 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 20 ASN B 4 GLN C 25 ASN F 13 ASN ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN H 122 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 ASN ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 ASN N 3 ASN ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 58 ASN ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 ASN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 111 GLN S 42 ASN ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 39 GLN ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 81 GLN Z 63 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 160967 Z= 0.357 Angle : 0.676 10.923 241169 Z= 0.349 Chirality : 0.038 0.358 30857 Planarity : 0.005 0.074 12688 Dihedral : 23.524 178.894 81485 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.26 % Favored : 88.51 % Rotamer: Outliers : 7.78 % Allowed : 28.04 % Favored : 64.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.18 % 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: -2.69 (0.11), residues: 5620 helix: -0.72 (0.12), residues: 1705 sheet: -1.88 (0.15), residues: 1018 loop : -2.45 (0.11), residues: 2897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP b 212 HIS 0.008 0.001 HIS d 165 PHE 0.035 0.002 PHE H 129 TYR 0.028 0.002 TYR p 98 ARG 0.018 0.001 ARG Q 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1598 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 364 poor density : 1234 time to evaluate : 6.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 97 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7978 (p0) REVERT: b 167 ASP cc_start: 0.7841 (m-30) cc_final: 0.7378 (p0) REVERT: b 176 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.8095 (tpp-160) REVERT: c 94 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8021 (mt0) REVERT: c 95 SER cc_start: 0.8773 (m) cc_final: 0.8285 (t) REVERT: c 139 SER cc_start: 0.8518 (m) cc_final: 0.8250 (t) REVERT: d 195 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8378 (mm110) REVERT: e 25 MET cc_start: 0.9187 (mmm) cc_final: 0.8668 (tpp) REVERT: e 37 MET cc_start: 0.8298 (ttp) cc_final: 0.8026 (mtm) REVERT: f 29 ASN cc_start: 0.8651 (t0) cc_final: 0.8211 (m-40) REVERT: f 35 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8461 (m) REVERT: f 87 GLN cc_start: 0.8698 (mt0) cc_final: 0.8486 (mm110) REVERT: i 124 MET cc_start: 0.1381 (mmt) cc_final: 0.0505 (tpp) REVERT: i 135 MET cc_start: 0.1543 (mmt) cc_final: 0.0776 (mtm) REVERT: j 53 TYR cc_start: 0.8852 (OUTLIER) cc_final: 0.8206 (m-10) REVERT: j 91 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8014 (tm-30) REVERT: l 10 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7674 (tm-30) REVERT: l 91 ASP cc_start: 0.8885 (t70) cc_final: 0.8598 (t70) REVERT: m 82 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7157 (mmm) REVERT: m 110 GLU cc_start: 0.7922 (pp20) cc_final: 0.7690 (pp20) REVERT: m 129 THR cc_start: 0.8566 (p) cc_final: 0.8254 (t) REVERT: n 43 GLU cc_start: 0.8480 (mt-10) cc_final: 0.7999 (mt-10) REVERT: n 49 GLU cc_start: 0.8496 (mp0) cc_final: 0.8162 (mp0) REVERT: o 55 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8144 (mp0) REVERT: o 68 LYS cc_start: 0.9168 (mttt) cc_final: 0.8854 (mttp) REVERT: o 69 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7995 (p0) REVERT: o 89 ASP cc_start: 0.8034 (m-30) cc_final: 0.7586 (m-30) REVERT: p 6 GLN cc_start: 0.8838 (mt0) cc_final: 0.8621 (mt0) REVERT: q 70 GLN cc_start: 0.9076 (tt0) cc_final: 0.8666 (tp-100) REVERT: s 33 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.8934 (mm) REVERT: t 4 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8531 (tm-30) REVERT: t 6 ARG cc_start: 0.8865 (tpt170) cc_final: 0.8580 (tpp80) REVERT: t 54 GLU cc_start: 0.8731 (pm20) cc_final: 0.8443 (pm20) REVERT: u 93 ARG cc_start: 0.8401 (mtp180) cc_final: 0.8168 (mtm180) REVERT: v 62 THR cc_start: 0.9293 (m) cc_final: 0.9005 (p) REVERT: x 34 SER cc_start: 0.9078 (m) cc_final: 0.8646 (p) REVERT: y 8 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7665 (mp0) REVERT: y 17 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8466 (pp20) REVERT: y 38 GLN cc_start: 0.8592 (tp-100) cc_final: 0.8340 (tp-100) REVERT: y 45 GLN cc_start: 0.8873 (pt0) cc_final: 0.8417 (tm-30) REVERT: y 49 ASP cc_start: 0.8340 (p0) cc_final: 0.7828 (p0) REVERT: A 23 LYS cc_start: 0.9349 (pttm) cc_final: 0.9061 (pptt) REVERT: A 56 ARG cc_start: 0.6792 (mmm-85) cc_final: 0.6484 (mmm-85) REVERT: B 52 LYS cc_start: 0.9226 (tppp) cc_final: 0.9010 (tppp) REVERT: D 1 MET cc_start: 0.7615 (tpp) cc_final: 0.7394 (tpp) REVERT: D 22 MET cc_start: 0.8451 (mmm) cc_final: 0.8102 (mmm) REVERT: F 32 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.8786 (mmpt) REVERT: G 26 MET cc_start: 0.8741 (mmm) cc_final: 0.8474 (mmm) REVERT: G 29 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.7906 (p90) REVERT: G 36 LYS cc_start: 0.9229 (mtmt) cc_final: 0.8834 (tptp) REVERT: G 139 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8566 (tm-30) REVERT: G 198 VAL cc_start: 0.9013 (OUTLIER) cc_final: 0.8706 (m) REVERT: G 212 TYR cc_start: 0.8190 (m-80) cc_final: 0.7735 (m-80) REVERT: H 167 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.7116 (m-80) REVERT: H 182 ASP cc_start: 0.8361 (t0) cc_final: 0.8121 (t0) REVERT: I 44 LYS cc_start: 0.8054 (tptp) cc_final: 0.7802 (tptp) REVERT: I 47 LEU cc_start: 0.5985 (OUTLIER) cc_final: 0.5441 (mm) REVERT: I 50 TYR cc_start: 0.8250 (t80) cc_final: 0.7598 (t80) REVERT: I 82 LYS cc_start: 0.7253 (mttt) cc_final: 0.6976 (mttt) REVERT: I 181 PHE cc_start: 0.8577 (t80) cc_final: 0.7695 (t80) REVERT: I 190 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8328 (mm) REVERT: J 11 GLN cc_start: 0.8381 (tt0) cc_final: 0.7326 (tm-30) REVERT: J 22 LYS cc_start: 0.8553 (pttt) cc_final: 0.8272 (ptpt) REVERT: J 54 GLU cc_start: 0.7690 (tt0) cc_final: 0.7080 (tt0) REVERT: J 61 LYS cc_start: 0.9056 (tttt) cc_final: 0.8291 (ttmt) REVERT: J 65 LYS cc_start: 0.8877 (ptpp) cc_final: 0.8530 (ptpp) REVERT: J 115 GLU cc_start: 0.8762 (tt0) cc_final: 0.8327 (tm-30) REVERT: J 140 ILE cc_start: 0.9301 (mm) cc_final: 0.8962 (mp) REVERT: K 1 MET cc_start: 0.7180 (ptp) cc_final: 0.6686 (ptp) REVERT: K 14 GLN cc_start: 0.8891 (mp10) cc_final: 0.8372 (mp10) REVERT: K 35 LYS cc_start: 0.8546 (mtpp) cc_final: 0.8324 (mmpt) REVERT: K 40 GLU cc_start: 0.7319 (tt0) cc_final: 0.6907 (tp30) REVERT: L 85 GLN cc_start: 0.7556 (mp10) cc_final: 0.7031 (mp10) REVERT: L 115 MET cc_start: 0.8735 (tpp) cc_final: 0.8443 (ttm) REVERT: L 124 SER cc_start: 0.9067 (p) cc_final: 0.8862 (m) REVERT: L 141 HIS cc_start: 0.9056 (OUTLIER) cc_final: 0.8329 (m-70) REVERT: L 143 MET cc_start: 0.9204 (tpp) cc_final: 0.8491 (tpt) REVERT: M 4 ASP cc_start: 0.7575 (t0) cc_final: 0.7311 (t0) REVERT: M 17 GLN cc_start: 0.8519 (mm110) cc_final: 0.8154 (mm-40) REVERT: M 58 LEU cc_start: 0.9595 (tp) cc_final: 0.9390 (tm) REVERT: M 59 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8424 (tm-30) REVERT: M 60 LEU cc_start: 0.9192 (mt) cc_final: 0.8975 (mt) REVERT: M 110 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8221 (ptp) REVERT: N 49 GLN cc_start: 0.8999 (mt0) cc_final: 0.8678 (mt0) REVERT: N 59 LYS cc_start: 0.8958 (mmtp) cc_final: 0.8736 (mmtp) REVERT: N 74 GLN cc_start: 0.8225 (mt0) cc_final: 0.7955 (mt0) REVERT: N 119 LYS cc_start: 0.8716 (ttmm) cc_final: 0.8463 (ttmm) REVERT: O 47 GLU cc_start: 0.6528 (mp0) cc_final: 0.6320 (mp0) REVERT: O 59 LYS cc_start: 0.8727 (ttpt) cc_final: 0.8312 (ttpp) REVERT: O 64 GLN cc_start: 0.8276 (mm-40) cc_final: 0.7979 (mm-40) REVERT: P 76 TYR cc_start: 0.9052 (m-80) cc_final: 0.8807 (m-80) REVERT: R 26 LYS cc_start: 0.9092 (tptp) cc_final: 0.8771 (tptp) REVERT: R 30 LYS cc_start: 0.9463 (mtmm) cc_final: 0.9200 (mtmm) REVERT: R 77 LYS cc_start: 0.9627 (tttm) cc_final: 0.9265 (tmmt) REVERT: T 9 LYS cc_start: 0.9273 (mtpp) cc_final: 0.8982 (mmmt) REVERT: T 46 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8497 (pttm) REVERT: V 10 ARG cc_start: 0.8237 (mtp85) cc_final: 0.7901 (mtp85) REVERT: V 74 LEU cc_start: 0.8824 (pt) cc_final: 0.8591 (pt) REVERT: W 25 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8621 (mp) REVERT: W 37 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8589 (mtpt) REVERT: W 56 ARG cc_start: 0.8658 (ttm-80) cc_final: 0.8006 (ptm160) REVERT: X 17 LYS cc_start: 0.9120 (mmmt) cc_final: 0.8423 (mmmt) REVERT: X 20 LYS cc_start: 0.8912 (ptmt) cc_final: 0.8710 (pptt) REVERT: X 72 GLU cc_start: 0.8671 (tt0) cc_final: 0.7194 (tm-30) REVERT: Y 20 ASN cc_start: 0.8776 (t0) cc_final: 0.8464 (t0) REVERT: Y 24 ARG cc_start: 0.9075 (mtp-110) cc_final: 0.8758 (mtp-110) REVERT: Y 26 MET cc_start: 0.9192 (ttp) cc_final: 0.8734 (tmt) REVERT: Y 47 GLN cc_start: 0.8874 (tp-100) cc_final: 0.8568 (tp-100) REVERT: Y 73 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8437 (ptp-170) REVERT: Z 24 LYS cc_start: 0.8104 (mttt) cc_final: 0.7526 (mppt) REVERT: 5 101 PRO cc_start: 0.7620 (Cg_exo) cc_final: 0.7409 (Cg_endo) outliers start: 364 outliers final: 190 residues processed: 1418 average time/residue: 1.9061 time to fit residues: 4077.7275 Evaluate side-chains 1375 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1162 time to evaluate : 6.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 36 ASN Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 97 ASP Chi-restraints excluded: chain b residue 176 ARG Chi-restraints excluded: chain b residue 193 GLU Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 37 VAL Chi-restraints excluded: chain c residue 94 GLN Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain e residue 9 ASP Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 15 LEU Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain i residue 131 THR Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 53 TYR Chi-restraints excluded: chain j residue 91 GLU Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 80 ASP Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 63 ILE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 82 MET Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain n residue 110 MET Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 45 SER Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain t residue 42 GLU Chi-restraints excluded: chain t residue 74 ILE Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain w residue 40 LYS Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 8 GLU Chi-restraints excluded: chain y residue 15 ASN Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain F residue 32 LYS Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 167 TYR Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain J residue 77 ASN Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 121 ASN Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 141 HIS Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 58 ASN Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 108 ASP Chi-restraints excluded: chain Q residue 114 SER Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 54 THR Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain T residue 3 SER Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 13 GLU Chi-restraints excluded: chain T residue 19 ASN Chi-restraints excluded: chain T residue 46 LYS Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 32 PHE Chi-restraints excluded: chain U residue 60 TRP Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 37 LYS Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 51 ASN Chi-restraints excluded: chain Y residue 69 ASN Chi-restraints excluded: chain Y residue 73 ARG Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 52 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 826 optimal weight: 20.0000 chunk 563 optimal weight: 9.9990 chunk 14 optimal weight: 30.0000 chunk 739 optimal weight: 20.0000 chunk 409 optimal weight: 10.0000 chunk 847 optimal weight: 0.3980 chunk 686 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 506 optimal weight: 5.9990 chunk 891 optimal weight: 20.0000 chunk 250 optimal weight: 10.0000 overall best weight: 6.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN F 13 ASN ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 HIS G 176 ASN H 31 ASN K 52 ASN ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 GLN O 58 ASN ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 74 GLN S 42 ASN T 39 GLN Y 81 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 160967 Z= 0.257 Angle : 0.614 10.504 241169 Z= 0.318 Chirality : 0.035 0.336 30857 Planarity : 0.005 0.075 12688 Dihedral : 23.477 178.608 81485 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.69 % Favored : 89.13 % Rotamer: Outliers : 6.92 % Allowed : 30.71 % Favored : 62.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.18 % 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: -2.44 (0.11), residues: 5620 helix: -0.42 (0.13), residues: 1700 sheet: -1.78 (0.16), residues: 1025 loop : -2.33 (0.11), residues: 2895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 21 HIS 0.008 0.001 HIS d 165 PHE 0.026 0.002 PHE H 129 TYR 0.028 0.002 TYR p 98 ARG 0.011 0.001 ARG J 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1563 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 324 poor density : 1239 time to evaluate : 6.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 36 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.7992 (p0) REVERT: b 167 ASP cc_start: 0.7739 (m-30) cc_final: 0.7351 (p0) REVERT: c 94 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7986 (mt0) REVERT: c 95 SER cc_start: 0.8777 (m) cc_final: 0.8287 (t) REVERT: c 139 SER cc_start: 0.8502 (m) cc_final: 0.8238 (t) REVERT: d 195 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8427 (mm-40) REVERT: e 25 MET cc_start: 0.9130 (mmm) cc_final: 0.8693 (tpp) REVERT: f 29 ASN cc_start: 0.8587 (t0) cc_final: 0.8174 (m-40) REVERT: i 135 MET cc_start: 0.1639 (mmt) cc_final: 0.0876 (mtm) REVERT: l 10 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7688 (tm-30) REVERT: l 91 ASP cc_start: 0.8865 (t70) cc_final: 0.8561 (t70) REVERT: m 129 THR cc_start: 0.8458 (p) cc_final: 0.8165 (t) REVERT: o 55 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8051 (mp0) REVERT: o 56 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8458 (mptt) REVERT: o 68 LYS cc_start: 0.9152 (mttt) cc_final: 0.8813 (mtmm) REVERT: o 69 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7940 (p0) REVERT: p 6 GLN cc_start: 0.8876 (mt0) cc_final: 0.8630 (mt0) REVERT: q 48 ASP cc_start: 0.7369 (m-30) cc_final: 0.7087 (m-30) REVERT: q 70 GLN cc_start: 0.9076 (tt0) cc_final: 0.8694 (tp-100) REVERT: s 33 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.8984 (mm) REVERT: t 4 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8507 (tm-30) REVERT: t 6 ARG cc_start: 0.8875 (tpt170) cc_final: 0.8557 (tpp80) REVERT: t 54 GLU cc_start: 0.8698 (pm20) cc_final: 0.8439 (pm20) REVERT: u 45 GLN cc_start: 0.8593 (tm-30) cc_final: 0.7758 (tm-30) REVERT: w 62 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8804 (tppp) REVERT: x 34 SER cc_start: 0.9068 (m) cc_final: 0.8623 (p) REVERT: y 45 GLN cc_start: 0.8831 (pt0) cc_final: 0.8361 (tm-30) REVERT: y 49 ASP cc_start: 0.8312 (p0) cc_final: 0.7829 (p0) REVERT: A 23 LYS cc_start: 0.9334 (pttm) cc_final: 0.9060 (pptt) REVERT: A 25 ARG cc_start: 0.7418 (mtm180) cc_final: 0.7156 (mtm180) REVERT: A 56 ARG cc_start: 0.6704 (mmm-85) cc_final: 0.6376 (mmm-85) REVERT: B 52 LYS cc_start: 0.9187 (tppp) cc_final: 0.8835 (tppt) REVERT: D 1 MET cc_start: 0.7620 (tpp) cc_final: 0.7416 (tpp) REVERT: F 32 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.8924 (mmpt) REVERT: G 29 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.7814 (p90) REVERT: G 36 LYS cc_start: 0.9238 (mtmt) cc_final: 0.8997 (tttm) REVERT: G 190 SER cc_start: 0.8739 (t) cc_final: 0.8140 (p) REVERT: G 198 VAL cc_start: 0.8989 (OUTLIER) cc_final: 0.8697 (m) REVERT: G 212 TYR cc_start: 0.8181 (m-80) cc_final: 0.7735 (m-80) REVERT: H 167 TYR cc_start: 0.7812 (OUTLIER) cc_final: 0.7108 (m-80) REVERT: H 182 ASP cc_start: 0.8385 (t0) cc_final: 0.8166 (t0) REVERT: I 44 LYS cc_start: 0.8055 (tptp) cc_final: 0.7809 (tppt) REVERT: I 47 LEU cc_start: 0.5878 (OUTLIER) cc_final: 0.5314 (mm) REVERT: I 50 TYR cc_start: 0.8248 (t80) cc_final: 0.7620 (t80) REVERT: I 82 LYS cc_start: 0.7178 (mttt) cc_final: 0.6780 (mptt) REVERT: I 131 ILE cc_start: 0.6950 (OUTLIER) cc_final: 0.6467 (pt) REVERT: I 181 PHE cc_start: 0.8609 (t80) cc_final: 0.7752 (t80) REVERT: I 190 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8311 (mm) REVERT: J 11 GLN cc_start: 0.8370 (tt0) cc_final: 0.7630 (tm-30) REVERT: J 22 LYS cc_start: 0.8557 (pttt) cc_final: 0.8277 (ptpt) REVERT: J 54 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6948 (tt0) REVERT: J 61 LYS cc_start: 0.9034 (tttt) cc_final: 0.8436 (tttt) REVERT: J 65 LYS cc_start: 0.8826 (ptpp) cc_final: 0.8539 (ptpp) REVERT: J 115 GLU cc_start: 0.8760 (tt0) cc_final: 0.8460 (pp20) REVERT: K 1 MET cc_start: 0.7272 (ptp) cc_final: 0.6729 (ptp) REVERT: K 14 GLN cc_start: 0.8842 (mp10) cc_final: 0.8242 (mp10) REVERT: K 40 GLU cc_start: 0.7216 (tt0) cc_final: 0.6844 (tp30) REVERT: L 3 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7951 (ptp-110) REVERT: L 85 GLN cc_start: 0.7577 (mp10) cc_final: 0.7113 (mp10) REVERT: L 124 SER cc_start: 0.9006 (p) cc_final: 0.8762 (m) REVERT: L 141 HIS cc_start: 0.9058 (OUTLIER) cc_final: 0.8300 (m-70) REVERT: M 17 GLN cc_start: 0.8491 (mm110) cc_final: 0.8111 (mm-40) REVERT: M 42 GLU cc_start: 0.8830 (tp30) cc_final: 0.8550 (tp30) REVERT: M 58 LEU cc_start: 0.9593 (tp) cc_final: 0.9379 (tm) REVERT: M 110 MET cc_start: 0.8543 (ptm) cc_final: 0.8245 (ptp) REVERT: M 123 GLU cc_start: 0.8113 (tt0) cc_final: 0.7687 (pt0) REVERT: N 74 GLN cc_start: 0.8126 (mt0) cc_final: 0.7817 (mt0) REVERT: N 111 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8086 (mp0) REVERT: N 119 LYS cc_start: 0.8695 (ttmm) cc_final: 0.8401 (ttmm) REVERT: N 122 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8145 (tmt-80) REVERT: O 46 LYS cc_start: 0.9163 (mtmm) cc_final: 0.8667 (mtmm) REVERT: O 47 GLU cc_start: 0.6477 (mp0) cc_final: 0.6274 (mp0) REVERT: O 59 LYS cc_start: 0.8622 (ttpt) cc_final: 0.8309 (ttpp) REVERT: O 64 GLN cc_start: 0.8287 (mm-40) cc_final: 0.7961 (mm-40) REVERT: P 76 TYR cc_start: 0.9016 (m-80) cc_final: 0.8724 (m-80) REVERT: R 26 LYS cc_start: 0.9039 (tptp) cc_final: 0.8827 (tptp) REVERT: R 30 LYS cc_start: 0.9430 (mtmm) cc_final: 0.9224 (mtmm) REVERT: R 77 LYS cc_start: 0.9635 (tttm) cc_final: 0.9263 (ttpp) REVERT: S 15 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8732 (tp) REVERT: S 22 LYS cc_start: 0.8397 (mptt) cc_final: 0.8013 (mppt) REVERT: S 53 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.7989 (p0) REVERT: T 9 LYS cc_start: 0.9264 (mtpp) cc_final: 0.9021 (mmmt) REVERT: T 46 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8375 (pttm) REVERT: U 13 LYS cc_start: 0.8549 (mttt) cc_final: 0.8168 (mmtp) REVERT: V 74 LEU cc_start: 0.8740 (pt) cc_final: 0.8462 (pt) REVERT: W 37 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8448 (mtpt) REVERT: W 47 ARG cc_start: 0.8069 (mmt180) cc_final: 0.7848 (mmt180) REVERT: W 56 ARG cc_start: 0.8630 (ttm-80) cc_final: 0.8065 (ptm160) REVERT: X 17 LYS cc_start: 0.9080 (mmmt) cc_final: 0.8323 (mmmt) REVERT: X 72 GLU cc_start: 0.8656 (tt0) cc_final: 0.7176 (tm-30) REVERT: Y 26 MET cc_start: 0.9211 (ttp) cc_final: 0.8687 (tmt) REVERT: Y 47 GLN cc_start: 0.8849 (tp-100) cc_final: 0.8523 (tp-100) REVERT: Z 24 LYS cc_start: 0.7939 (mttt) cc_final: 0.7444 (mppt) outliers start: 324 outliers final: 175 residues processed: 1408 average time/residue: 1.9035 time to fit residues: 4048.4200 Evaluate side-chains 1365 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1169 time to evaluate : 6.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 36 ASN Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 193 GLU Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain c residue 13 ARG Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 37 VAL Chi-restraints excluded: chain c residue 94 GLN Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 198 GLU Chi-restraints excluded: chain e residue 9 ASP Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 112 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 15 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain i residue 131 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain j residue 122 LEU Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain n residue 110 MET Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 45 SER Chi-restraints excluded: chain o residue 56 LYS Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 83 ILE Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain t residue 42 GLU Chi-restraints excluded: chain t residue 74 ILE Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain w residue 40 LYS Chi-restraints excluded: chain w residue 62 LYS Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 15 ASN Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain F residue 32 LYS Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 167 TYR Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 153 ARG Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 54 GLU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 3 ARG Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 141 HIS Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 122 ARG Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 108 ASP Chi-restraints excluded: chain Q residue 114 SER Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain T residue 3 SER Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 19 ASN Chi-restraints excluded: chain T residue 46 LYS Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain U residue 32 PHE Chi-restraints excluded: chain U residue 60 TRP Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 61 ARG Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 37 LYS Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 27 MET Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 8 ASN Chi-restraints excluded: chain Z residue 52 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 333 optimal weight: 10.0000 chunk 893 optimal weight: 0.0370 chunk 196 optimal weight: 20.0000 chunk 582 optimal weight: 0.0470 chunk 245 optimal weight: 20.0000 chunk 993 optimal weight: 9.9990 chunk 824 optimal weight: 9.9990 chunk 460 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 328 optimal weight: 10.0000 chunk 521 optimal weight: 8.9990 overall best weight: 5.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 36 ASN ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 104 GLN ** t 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN F 13 ASN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 HIS H 31 ASN ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 58 ASN ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 111 GLN S 42 ASN T 39 GLN W 30 ASN ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 81 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 160967 Z= 0.231 Angle : 0.604 11.966 241169 Z= 0.311 Chirality : 0.034 0.305 30857 Planarity : 0.005 0.097 12688 Dihedral : 23.440 178.879 81485 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.82 % Favored : 89.00 % Rotamer: Outliers : 7.37 % Allowed : 31.55 % Favored : 61.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.18 % 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: -2.27 (0.11), residues: 5620 helix: -0.20 (0.13), residues: 1697 sheet: -1.69 (0.16), residues: 1012 loop : -2.29 (0.11), residues: 2911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 21 HIS 0.007 0.001 HIS d 165 PHE 0.032 0.002 PHE b 29 TYR 0.031 0.002 TYR p 98 ARG 0.012 0.000 ARG J 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1581 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 345 poor density : 1236 time to evaluate : 6.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 167 ASP cc_start: 0.7748 (m-30) cc_final: 0.7413 (p0) REVERT: c 94 GLN cc_start: 0.8374 (tt0) cc_final: 0.8027 (mt0) REVERT: c 95 SER cc_start: 0.8734 (m) cc_final: 0.8240 (t) REVERT: c 139 SER cc_start: 0.8468 (m) cc_final: 0.8214 (t) REVERT: e 25 MET cc_start: 0.9072 (mmm) cc_final: 0.8593 (tpp) REVERT: f 29 ASN cc_start: 0.8610 (t0) cc_final: 0.8168 (m-40) REVERT: f 35 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8544 (m) REVERT: i 135 MET cc_start: 0.1846 (mmt) cc_final: 0.1083 (mtm) REVERT: l 10 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7697 (tm-30) REVERT: l 91 ASP cc_start: 0.8792 (t70) cc_final: 0.8526 (t70) REVERT: m 129 THR cc_start: 0.8432 (p) cc_final: 0.8189 (t) REVERT: o 56 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8449 (mptt) REVERT: o 68 LYS cc_start: 0.9172 (mttt) cc_final: 0.8871 (mttp) REVERT: o 69 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7897 (p0) REVERT: p 6 GLN cc_start: 0.8854 (mt0) cc_final: 0.8615 (mt0) REVERT: q 48 ASP cc_start: 0.7344 (m-30) cc_final: 0.7081 (m-30) REVERT: q 70 GLN cc_start: 0.9080 (tt0) cc_final: 0.8701 (tp-100) REVERT: s 33 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9001 (mm) REVERT: t 4 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8554 (tm-30) REVERT: t 6 ARG cc_start: 0.8853 (tpt170) cc_final: 0.8541 (tpp80) REVERT: t 54 GLU cc_start: 0.8612 (pm20) cc_final: 0.8411 (pm20) REVERT: u 21 ARG cc_start: 0.8617 (ptm160) cc_final: 0.8216 (ttp80) REVERT: u 45 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7734 (tm-30) REVERT: x 34 SER cc_start: 0.9048 (m) cc_final: 0.8613 (p) REVERT: y 17 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8545 (pp20) REVERT: y 45 GLN cc_start: 0.8832 (pt0) cc_final: 0.8360 (tm-30) REVERT: y 49 ASP cc_start: 0.8326 (p0) cc_final: 0.7919 (p0) REVERT: z 10 ARG cc_start: 0.8652 (ttm-80) cc_final: 0.8436 (ttm-80) REVERT: A 23 LYS cc_start: 0.9337 (pttm) cc_final: 0.9100 (pptt) REVERT: A 25 ARG cc_start: 0.7432 (mtm180) cc_final: 0.7150 (mtm180) REVERT: A 56 ARG cc_start: 0.6676 (mmm-85) cc_final: 0.6383 (mmm-85) REVERT: D 1 MET cc_start: 0.7583 (tpp) cc_final: 0.7306 (tpp) REVERT: G 29 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.7871 (p90) REVERT: G 36 LYS cc_start: 0.9244 (mtmt) cc_final: 0.8993 (tttm) REVERT: G 190 SER cc_start: 0.8663 (t) cc_final: 0.8346 (m) REVERT: G 198 VAL cc_start: 0.8976 (OUTLIER) cc_final: 0.8678 (m) REVERT: G 212 TYR cc_start: 0.8181 (m-80) cc_final: 0.7734 (m-80) REVERT: H 167 TYR cc_start: 0.7818 (OUTLIER) cc_final: 0.7109 (m-80) REVERT: H 182 ASP cc_start: 0.8398 (t0) cc_final: 0.8181 (t0) REVERT: I 44 LYS cc_start: 0.8124 (tptp) cc_final: 0.7830 (tppt) REVERT: I 47 LEU cc_start: 0.5858 (OUTLIER) cc_final: 0.5238 (mm) REVERT: I 50 TYR cc_start: 0.8258 (t80) cc_final: 0.7636 (t80) REVERT: I 84 ASN cc_start: 0.8869 (t0) cc_final: 0.8529 (p0) REVERT: I 131 ILE cc_start: 0.6884 (OUTLIER) cc_final: 0.6381 (pt) REVERT: I 144 ILE cc_start: 0.5803 (OUTLIER) cc_final: 0.5330 (mm) REVERT: I 181 PHE cc_start: 0.8589 (t80) cc_final: 0.7711 (t80) REVERT: I 190 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8341 (mm) REVERT: I 199 ILE cc_start: 0.9344 (mm) cc_final: 0.9132 (mp) REVERT: J 11 GLN cc_start: 0.8365 (tt0) cc_final: 0.7689 (tm-30) REVERT: J 14 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8587 (tm) REVERT: J 22 LYS cc_start: 0.8550 (pttt) cc_final: 0.8271 (ptpt) REVERT: J 54 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6952 (tt0) REVERT: J 61 LYS cc_start: 0.9038 (tttt) cc_final: 0.8617 (tttt) REVERT: J 115 GLU cc_start: 0.8718 (tt0) cc_final: 0.8469 (pp20) REVERT: K 1 MET cc_start: 0.7329 (ptp) cc_final: 0.6799 (ptp) REVERT: K 14 GLN cc_start: 0.8786 (mp10) cc_final: 0.8270 (mp10) REVERT: K 40 GLU cc_start: 0.7123 (tt0) cc_final: 0.6839 (tp30) REVERT: L 17 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7336 (p90) REVERT: L 85 GLN cc_start: 0.7555 (mp10) cc_final: 0.7105 (mp10) REVERT: L 124 SER cc_start: 0.9005 (p) cc_final: 0.8753 (m) REVERT: L 141 HIS cc_start: 0.9043 (OUTLIER) cc_final: 0.8261 (m-70) REVERT: L 143 MET cc_start: 0.9191 (tpp) cc_final: 0.8395 (tpp) REVERT: M 17 GLN cc_start: 0.8486 (mm110) cc_final: 0.8102 (mm-40) REVERT: M 42 GLU cc_start: 0.8837 (tp30) cc_final: 0.8599 (tp30) REVERT: M 58 LEU cc_start: 0.9582 (tp) cc_final: 0.9376 (tm) REVERT: M 110 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8260 (ptp) REVERT: M 123 GLU cc_start: 0.8018 (tt0) cc_final: 0.7678 (pt0) REVERT: N 74 GLN cc_start: 0.8119 (mt0) cc_final: 0.7917 (mt0) REVERT: N 111 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8004 (mp0) REVERT: N 119 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8370 (ttmm) REVERT: N 122 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8184 (tmt-80) REVERT: O 46 LYS cc_start: 0.9176 (mtmm) cc_final: 0.8862 (mtmm) REVERT: O 59 LYS cc_start: 0.8665 (ttpt) cc_final: 0.8204 (ttpp) REVERT: O 64 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7960 (mm-40) REVERT: P 76 TYR cc_start: 0.8965 (m-80) cc_final: 0.8708 (m-80) REVERT: R 30 LYS cc_start: 0.9426 (mtmm) cc_final: 0.9154 (mtmm) REVERT: R 43 LYS cc_start: 0.8376 (mtmt) cc_final: 0.8031 (mtmm) REVERT: R 77 LYS cc_start: 0.9649 (tttm) cc_final: 0.9286 (tmmt) REVERT: S 15 LEU cc_start: 0.9336 (mt) cc_final: 0.9004 (tt) REVERT: T 9 LYS cc_start: 0.9249 (mtpp) cc_final: 0.9030 (mmmt) REVERT: T 46 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8486 (pttm) REVERT: U 6 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8681 (tp) REVERT: U 13 LYS cc_start: 0.8513 (mttt) cc_final: 0.8208 (mmtp) REVERT: V 74 LEU cc_start: 0.8501 (pt) cc_final: 0.8270 (pp) REVERT: W 23 LYS cc_start: 0.8565 (mppt) cc_final: 0.8347 (mppt) REVERT: W 37 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8400 (mtpt) REVERT: W 56 ARG cc_start: 0.8620 (ttm-80) cc_final: 0.8035 (ptm160) REVERT: X 72 GLU cc_start: 0.8653 (tt0) cc_final: 0.7172 (tm-30) REVERT: Y 18 LYS cc_start: 0.9402 (mttt) cc_final: 0.9023 (mtpp) REVERT: Y 47 GLN cc_start: 0.8856 (tp-100) cc_final: 0.8518 (tp-100) REVERT: Y 73 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7980 (ptt-90) outliers start: 345 outliers final: 184 residues processed: 1419 average time/residue: 1.8646 time to fit residues: 3991.5644 Evaluate side-chains 1371 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1165 time to evaluate : 5.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 193 GLU Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 13 ARG Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 37 VAL Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 196 VAL Chi-restraints excluded: chain e residue 9 ASP Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 112 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 14 SER Chi-restraints excluded: chain g residue 15 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain i residue 131 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain n residue 110 MET Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 45 SER Chi-restraints excluded: chain o residue 56 LYS Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 83 ILE Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain t residue 42 GLU Chi-restraints excluded: chain t residue 74 ILE Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 45 GLN Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 167 TYR Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 153 ARG Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 54 GLU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain J residue 77 ASN Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 141 HIS Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 122 ARG Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 58 ASN Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 114 SER Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 19 ASN Chi-restraints excluded: chain T residue 46 LYS Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain U residue 32 PHE Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 60 TRP Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 61 ARG Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 37 LYS Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 69 ASN Chi-restraints excluded: chain Y residue 73 ARG Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 8 ASN Chi-restraints excluded: chain Z residue 52 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 958 optimal weight: 3.9990 chunk 112 optimal weight: 30.0000 chunk 566 optimal weight: 8.9990 chunk 725 optimal weight: 20.0000 chunk 562 optimal weight: 30.0000 chunk 836 optimal weight: 30.0000 chunk 554 optimal weight: 5.9990 chunk 989 optimal weight: 8.9990 chunk 619 optimal weight: 1.9990 chunk 603 optimal weight: 0.6980 chunk 457 optimal weight: 40.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 36 ASN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 29 ASN ** f 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 3 GLN ** t 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 HIS H 31 ASN ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 GLN ** O 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 70 HIS ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 111 GLN S 42 ASN ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 81 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 160967 Z= 0.194 Angle : 0.591 12.276 241169 Z= 0.303 Chirality : 0.033 0.332 30857 Planarity : 0.005 0.077 12688 Dihedral : 23.399 178.985 81485 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.25 % Favored : 89.57 % Rotamer: Outliers : 6.24 % Allowed : 33.70 % Favored : 60.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.16 % 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: -2.17 (0.11), residues: 5620 helix: -0.13 (0.13), residues: 1705 sheet: -1.60 (0.16), residues: 1001 loop : -2.23 (0.11), residues: 2914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 21 HIS 0.010 0.001 HIS O 56 PHE 0.036 0.001 PHE H 129 TYR 0.032 0.001 TYR p 98 ARG 0.015 0.000 ARG f 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1540 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 1248 time to evaluate : 6.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8365 (tt0) cc_final: 0.7966 (mt0) REVERT: c 139 SER cc_start: 0.8421 (m) cc_final: 0.8182 (t) REVERT: e 25 MET cc_start: 0.9008 (mmm) cc_final: 0.8553 (tpp) REVERT: e 164 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8372 (mt-10) REVERT: f 29 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8214 (m-40) REVERT: f 35 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8519 (m) REVERT: g 20 ASN cc_start: 0.8874 (t0) cc_final: 0.8633 (t0) REVERT: i 135 MET cc_start: 0.1806 (mmt) cc_final: 0.1081 (mtm) REVERT: k 53 LYS cc_start: 0.8473 (mmpt) cc_final: 0.8053 (mmpt) REVERT: l 10 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7658 (tm-30) REVERT: l 93 ASN cc_start: 0.8768 (p0) cc_final: 0.8226 (p0) REVERT: m 110 GLU cc_start: 0.7683 (pp20) cc_final: 0.7463 (pp20) REVERT: m 129 THR cc_start: 0.8415 (p) cc_final: 0.8202 (t) REVERT: n 43 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8045 (mt-10) REVERT: o 55 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8034 (mp0) REVERT: o 56 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8491 (mtmm) REVERT: p 70 GLU cc_start: 0.8000 (pm20) cc_final: 0.7772 (pm20) REVERT: q 48 ASP cc_start: 0.7323 (m-30) cc_final: 0.7025 (m-30) REVERT: q 70 GLN cc_start: 0.9064 (tt0) cc_final: 0.8715 (tp-100) REVERT: r 23 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8309 (mm-30) REVERT: s 33 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9074 (mm) REVERT: s 35 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.9057 (mt) REVERT: t 4 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8557 (tm-30) REVERT: u 21 ARG cc_start: 0.8600 (ptm160) cc_final: 0.8399 (tmm160) REVERT: u 45 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: u 80 ASP cc_start: 0.7452 (m-30) cc_final: 0.7204 (t0) REVERT: v 7 GLU cc_start: 0.9023 (pm20) cc_final: 0.8442 (pm20) REVERT: x 34 SER cc_start: 0.9046 (m) cc_final: 0.8603 (p) REVERT: y 17 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8496 (pp20) REVERT: y 45 GLN cc_start: 0.8804 (pt0) cc_final: 0.8348 (tm-30) REVERT: y 49 ASP cc_start: 0.8294 (p0) cc_final: 0.7893 (p0) REVERT: B 52 LYS cc_start: 0.8976 (tppp) cc_final: 0.8759 (tppp) REVERT: C 19 PHE cc_start: 0.8802 (p90) cc_final: 0.8345 (p90) REVERT: D 1 MET cc_start: 0.7574 (tpp) cc_final: 0.7327 (tpp) REVERT: G 29 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.7833 (p90) REVERT: G 36 LYS cc_start: 0.9243 (mtmt) cc_final: 0.8991 (tttm) REVERT: G 153 MET cc_start: 0.7858 (ttm) cc_final: 0.7051 (mtp) REVERT: G 190 SER cc_start: 0.8835 (t) cc_final: 0.8341 (m) REVERT: G 198 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8661 (m) REVERT: G 212 TYR cc_start: 0.8187 (m-80) cc_final: 0.7758 (m-80) REVERT: H 138 GLN cc_start: 0.8852 (mt0) cc_final: 0.8580 (mp10) REVERT: H 167 TYR cc_start: 0.7800 (OUTLIER) cc_final: 0.7103 (m-80) REVERT: I 50 TYR cc_start: 0.8255 (t80) cc_final: 0.7536 (t80) REVERT: I 84 ASN cc_start: 0.8850 (t0) cc_final: 0.8529 (p0) REVERT: I 127 ARG cc_start: 0.8270 (mpp80) cc_final: 0.8026 (mpp80) REVERT: I 131 ILE cc_start: 0.6761 (OUTLIER) cc_final: 0.6303 (pt) REVERT: I 181 PHE cc_start: 0.8631 (t80) cc_final: 0.7788 (t80) REVERT: I 190 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8387 (mm) REVERT: I 199 ILE cc_start: 0.9322 (mm) cc_final: 0.9112 (mp) REVERT: J 11 GLN cc_start: 0.8298 (tt0) cc_final: 0.7744 (tm-30) REVERT: J 14 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8587 (tm) REVERT: J 22 LYS cc_start: 0.8416 (pttt) cc_final: 0.8159 (ptpt) REVERT: J 54 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7001 (tt0) REVERT: J 61 LYS cc_start: 0.9065 (tttt) cc_final: 0.8690 (tttt) REVERT: J 115 GLU cc_start: 0.8689 (tt0) cc_final: 0.8449 (pp20) REVERT: K 1 MET cc_start: 0.7334 (ptp) cc_final: 0.6735 (ptp) REVERT: K 14 GLN cc_start: 0.8689 (mp10) cc_final: 0.8258 (mp10) REVERT: K 23 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8725 (mm-30) REVERT: K 65 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7075 (pp20) REVERT: L 17 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7272 (p90) REVERT: L 85 GLN cc_start: 0.7531 (mp10) cc_final: 0.6937 (mm-40) REVERT: L 124 SER cc_start: 0.8998 (p) cc_final: 0.8747 (m) REVERT: L 141 HIS cc_start: 0.9025 (OUTLIER) cc_final: 0.8168 (m-70) REVERT: M 4 ASP cc_start: 0.7853 (t0) cc_final: 0.7150 (m-30) REVERT: M 17 GLN cc_start: 0.8447 (mm110) cc_final: 0.8105 (mm-40) REVERT: M 42 GLU cc_start: 0.8820 (tp30) cc_final: 0.8559 (tp30) REVERT: M 110 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8280 (ptp) REVERT: M 123 GLU cc_start: 0.7980 (tt0) cc_final: 0.7613 (pt0) REVERT: N 111 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7995 (mp0) REVERT: N 119 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8455 (ttmm) REVERT: N 122 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8173 (tmt-80) REVERT: O 46 LYS cc_start: 0.9069 (mtmm) cc_final: 0.8503 (mtmm) REVERT: O 64 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7946 (mm-40) REVERT: P 76 TYR cc_start: 0.8909 (m-80) cc_final: 0.8645 (m-80) REVERT: Q 65 TYR cc_start: 0.7939 (t80) cc_final: 0.7672 (t80) REVERT: Q 102 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.7133 (m-30) REVERT: R 30 LYS cc_start: 0.9433 (mtmm) cc_final: 0.9177 (mtmm) REVERT: R 43 LYS cc_start: 0.8360 (mtmt) cc_final: 0.8117 (mtmt) REVERT: R 77 LYS cc_start: 0.9650 (tttm) cc_final: 0.9282 (tmmt) REVERT: S 15 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9060 (tp) REVERT: S 22 LYS cc_start: 0.8323 (mptt) cc_final: 0.7835 (mppt) REVERT: T 9 LYS cc_start: 0.9247 (mtpp) cc_final: 0.9032 (mmmt) REVERT: T 46 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8424 (pttm) REVERT: U 6 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8566 (tp) REVERT: U 13 LYS cc_start: 0.8480 (mttt) cc_final: 0.8182 (mmtp) REVERT: V 10 ARG cc_start: 0.7969 (mtp85) cc_final: 0.7498 (mtp85) REVERT: V 79 GLU cc_start: 0.7690 (tt0) cc_final: 0.7462 (tt0) REVERT: W 23 LYS cc_start: 0.8579 (mppt) cc_final: 0.8322 (mppt) REVERT: W 37 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8262 (mtpt) REVERT: W 56 ARG cc_start: 0.8615 (ttm-80) cc_final: 0.8018 (ptm160) REVERT: X 72 GLU cc_start: 0.8637 (tt0) cc_final: 0.7148 (tm-30) REVERT: Y 26 MET cc_start: 0.9270 (ttp) cc_final: 0.8803 (tmt) REVERT: Y 47 GLN cc_start: 0.8849 (tp-100) cc_final: 0.8584 (tp-100) REVERT: Y 53 MET cc_start: 0.8598 (ppp) cc_final: 0.8366 (ppp) REVERT: 5 101 PRO cc_start: 0.7295 (Cg_endo) cc_final: 0.7086 (Cg_exo) outliers start: 292 outliers final: 177 residues processed: 1402 average time/residue: 1.8763 time to fit residues: 3979.9226 Evaluate side-chains 1375 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1174 time to evaluate : 6.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 36 ASN Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 193 GLU Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain c residue 13 ARG Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 37 VAL Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain e residue 9 ASP Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 29 ASN Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 112 VAL Chi-restraints excluded: chain f residue 136 ASP Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 15 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain i residue 131 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 80 ASP Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 96 ILE Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 43 GLU Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain n residue 110 MET Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 45 SER Chi-restraints excluded: chain o residue 56 LYS Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 83 ILE Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 35 ILE Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain t residue 42 GLU Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 45 GLN Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain z residue 11 SER Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 128 MET Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 167 TYR Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 153 ARG Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 54 GLU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain J residue 77 ASN Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 65 GLU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 141 HIS Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 122 ARG Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain Q residue 111 GLN Chi-restraints excluded: chain Q residue 114 SER Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 19 ASN Chi-restraints excluded: chain T residue 46 LYS Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain U residue 32 PHE Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 61 ARG Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 37 LYS Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 69 ASN Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 52 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 612 optimal weight: 6.9990 chunk 395 optimal weight: 10.0000 chunk 591 optimal weight: 20.0000 chunk 298 optimal weight: 20.0000 chunk 194 optimal weight: 20.0000 chunk 191 optimal weight: 10.0000 chunk 629 optimal weight: 0.0040 chunk 674 optimal weight: 3.9990 chunk 489 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 778 optimal weight: 9.9990 overall best weight: 5.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 36 ASN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 29 ASN ** f 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 136 GLN q 58 GLN ** t 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN F 13 ASN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 ASN G 88 GLN ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 HIS H 31 ASN ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 111 GLN S 42 ASN ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 39 GLN X 68 HIS ** Y 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 ASN Y 81 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 160967 Z= 0.218 Angle : 0.608 12.022 241169 Z= 0.311 Chirality : 0.033 0.359 30857 Planarity : 0.005 0.072 12688 Dihedral : 23.387 179.253 81483 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.73 % Favored : 89.09 % Rotamer: Outliers : 5.79 % Allowed : 35.37 % Favored : 58.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.15 (0.11), residues: 5620 helix: -0.12 (0.13), residues: 1707 sheet: -1.53 (0.16), residues: 1027 loop : -2.25 (0.11), residues: 2886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP H 21 HIS 0.007 0.001 HIS d 165 PHE 0.042 0.002 PHE H 129 TYR 0.031 0.002 TYR p 98 ARG 0.015 0.001 ARG U 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1491 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 1220 time to evaluate : 6.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8388 (tt0) cc_final: 0.8132 (mt0) REVERT: c 139 SER cc_start: 0.8427 (m) cc_final: 0.8173 (t) REVERT: e 25 MET cc_start: 0.9044 (mmm) cc_final: 0.8628 (tpp) REVERT: f 29 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.8153 (m-40) REVERT: f 35 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8508 (m) REVERT: i 135 MET cc_start: 0.1945 (mmt) cc_final: 0.1135 (mtm) REVERT: j 98 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8048 (pm20) REVERT: l 10 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7692 (tm-30) REVERT: m 110 GLU cc_start: 0.7758 (pp20) cc_final: 0.7381 (pp20) REVERT: m 129 THR cc_start: 0.8452 (p) cc_final: 0.8232 (t) REVERT: n 43 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7466 (mt-10) REVERT: n 78 LYS cc_start: 0.9265 (tppp) cc_final: 0.8986 (tppp) REVERT: o 55 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8006 (mp0) REVERT: o 68 LYS cc_start: 0.9116 (mttt) cc_final: 0.8914 (mttp) REVERT: q 48 ASP cc_start: 0.7345 (m-30) cc_final: 0.7078 (m-30) REVERT: q 58 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8306 (tp-100) REVERT: q 70 GLN cc_start: 0.9068 (tt0) cc_final: 0.8728 (tp-100) REVERT: s 33 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.8984 (mm) REVERT: s 35 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.9013 (mt) REVERT: t 4 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8536 (tm-30) REVERT: u 21 ARG cc_start: 0.8579 (ptm160) cc_final: 0.8263 (ttp80) REVERT: u 45 GLN cc_start: 0.8546 (tm-30) cc_final: 0.7702 (tm-30) REVERT: u 80 ASP cc_start: 0.7467 (m-30) cc_final: 0.7222 (t0) REVERT: v 30 ILE cc_start: 0.9482 (pt) cc_final: 0.9268 (pp) REVERT: x 34 SER cc_start: 0.9044 (m) cc_final: 0.8604 (p) REVERT: y 45 GLN cc_start: 0.8816 (pt0) cc_final: 0.8375 (tm-30) REVERT: y 49 ASP cc_start: 0.8284 (p0) cc_final: 0.7892 (p0) REVERT: C 19 PHE cc_start: 0.8816 (p90) cc_final: 0.8318 (p90) REVERT: D 1 MET cc_start: 0.7516 (tpp) cc_final: 0.7213 (tpp) REVERT: G 29 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.7839 (p90) REVERT: G 36 LYS cc_start: 0.9245 (mtmt) cc_final: 0.8969 (tttm) REVERT: G 190 SER cc_start: 0.8844 (t) cc_final: 0.8411 (m) REVERT: G 198 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8696 (m) REVERT: G 212 TYR cc_start: 0.8163 (m-80) cc_final: 0.7720 (m-80) REVERT: H 138 GLN cc_start: 0.8843 (mt0) cc_final: 0.8560 (mp10) REVERT: H 167 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.7107 (m-80) REVERT: I 3 TYR cc_start: 0.7179 (t80) cc_final: 0.6935 (t80) REVERT: I 50 TYR cc_start: 0.8315 (t80) cc_final: 0.7652 (t80) REVERT: I 82 LYS cc_start: 0.7485 (mptt) cc_final: 0.7236 (mptt) REVERT: I 84 ASN cc_start: 0.8821 (t0) cc_final: 0.8532 (p0) REVERT: I 127 ARG cc_start: 0.8290 (mpp80) cc_final: 0.7970 (mpp80) REVERT: I 131 ILE cc_start: 0.6816 (OUTLIER) cc_final: 0.6353 (pt) REVERT: I 181 PHE cc_start: 0.8573 (t80) cc_final: 0.7730 (t80) REVERT: I 190 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8437 (mm) REVERT: I 199 ILE cc_start: 0.9401 (mm) cc_final: 0.9201 (mp) REVERT: J 11 GLN cc_start: 0.8278 (tt0) cc_final: 0.7614 (tm-30) REVERT: J 14 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8577 (tm) REVERT: J 54 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7035 (tt0) REVERT: J 61 LYS cc_start: 0.9072 (tttt) cc_final: 0.8534 (tttm) REVERT: J 64 GLU cc_start: 0.8497 (tp30) cc_final: 0.7441 (tp30) REVERT: J 65 LYS cc_start: 0.8921 (ptpp) cc_final: 0.8425 (ptpp) REVERT: J 68 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7616 (pmm-80) REVERT: J 115 GLU cc_start: 0.8680 (tt0) cc_final: 0.8434 (pp20) REVERT: K 1 MET cc_start: 0.7406 (ptp) cc_final: 0.7146 (ptp) REVERT: K 9 MET cc_start: 0.8524 (mpt) cc_final: 0.7952 (mmm) REVERT: K 14 GLN cc_start: 0.8656 (mp10) cc_final: 0.8278 (mp10) REVERT: K 23 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8804 (mm-30) REVERT: K 65 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7945 (pp20) REVERT: L 17 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.7112 (p90) REVERT: L 85 GLN cc_start: 0.7577 (mp10) cc_final: 0.6958 (mm-40) REVERT: L 124 SER cc_start: 0.9006 (p) cc_final: 0.8754 (m) REVERT: L 143 MET cc_start: 0.9246 (tpp) cc_final: 0.8514 (tpp) REVERT: M 4 ASP cc_start: 0.7786 (t0) cc_final: 0.7178 (m-30) REVERT: M 17 GLN cc_start: 0.8513 (mm110) cc_final: 0.8173 (mm-40) REVERT: M 42 GLU cc_start: 0.8889 (tp30) cc_final: 0.8648 (tp30) REVERT: M 110 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8291 (ptp) REVERT: M 123 GLU cc_start: 0.7912 (tt0) cc_final: 0.7530 (pt0) REVERT: N 119 LYS cc_start: 0.8673 (ttmm) cc_final: 0.8436 (ttmm) REVERT: N 122 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8170 (tmt-80) REVERT: O 46 LYS cc_start: 0.9162 (mtmm) cc_final: 0.8860 (mtmm) REVERT: O 60 ASP cc_start: 0.8066 (m-30) cc_final: 0.7819 (t70) REVERT: O 64 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7941 (mm-40) REVERT: O 71 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9169 (mm) REVERT: P 76 TYR cc_start: 0.8913 (m-80) cc_final: 0.8690 (m-80) REVERT: Q 4 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8499 (t0) REVERT: Q 65 TYR cc_start: 0.7915 (t80) cc_final: 0.7686 (t80) REVERT: Q 102 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7181 (m-30) REVERT: R 30 LYS cc_start: 0.9384 (mtmm) cc_final: 0.9156 (mtmm) REVERT: R 43 LYS cc_start: 0.8336 (mtmt) cc_final: 0.8002 (mtmt) REVERT: R 77 LYS cc_start: 0.9659 (tttm) cc_final: 0.9300 (tmmt) REVERT: S 15 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9054 (tp) REVERT: S 45 LEU cc_start: 0.9227 (tt) cc_final: 0.9003 (tm) REVERT: T 9 LYS cc_start: 0.9249 (mtpp) cc_final: 0.9027 (mmmt) REVERT: T 46 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8469 (pttm) REVERT: T 70 LYS cc_start: 0.9169 (ttmm) cc_final: 0.8910 (ttmm) REVERT: U 13 LYS cc_start: 0.8449 (mttt) cc_final: 0.8155 (mmtp) REVERT: V 61 ARG cc_start: 0.8608 (pmm-80) cc_final: 0.7896 (pmm-80) REVERT: V 74 LEU cc_start: 0.8339 (pt) cc_final: 0.7064 (pp) REVERT: W 23 LYS cc_start: 0.8554 (mppt) cc_final: 0.8204 (mppt) REVERT: W 37 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8291 (mtpt) REVERT: W 56 ARG cc_start: 0.8615 (ttm-80) cc_final: 0.8013 (ptm160) REVERT: X 72 GLU cc_start: 0.8619 (tt0) cc_final: 0.7124 (tm-30) REVERT: Y 26 MET cc_start: 0.9264 (ttp) cc_final: 0.8857 (tmt) REVERT: Y 47 GLN cc_start: 0.8868 (tp-100) cc_final: 0.8583 (tp-100) outliers start: 271 outliers final: 181 residues processed: 1355 average time/residue: 1.8613 time to fit residues: 3815.8345 Evaluate side-chains 1368 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1162 time to evaluate : 6.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 193 GLU Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain c residue 13 ARG Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 37 VAL Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain d residue 196 VAL Chi-restraints excluded: chain e residue 9 ASP Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 29 ASN Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 112 VAL Chi-restraints excluded: chain f residue 136 ASP Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 15 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain i residue 7 TYR Chi-restraints excluded: chain i residue 131 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 80 ASP Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 53 MET Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 96 ILE Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 43 GLU Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain n residue 110 MET Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 45 SER Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 55 GLU Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 83 ILE Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 58 GLN Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 35 ILE Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain t residue 42 GLU Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain z residue 11 SER Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 167 TYR Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 182 ASP Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 153 ARG Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 54 GLU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain J residue 77 ASN Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 65 GLU Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 122 ARG Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain Q residue 114 SER Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 17 ASP Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 19 ASN Chi-restraints excluded: chain T residue 46 LYS Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 32 PHE Chi-restraints excluded: chain U residue 60 TRP Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 37 LYS Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 69 ASN Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 52 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 900 optimal weight: 20.0000 chunk 948 optimal weight: 7.9990 chunk 865 optimal weight: 9.9990 chunk 922 optimal weight: 0.9990 chunk 555 optimal weight: 40.0000 chunk 401 optimal weight: 10.0000 chunk 724 optimal weight: 20.0000 chunk 283 optimal weight: 20.0000 chunk 833 optimal weight: 0.9980 chunk 872 optimal weight: 5.9990 chunk 919 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 36 ASN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 29 ASN ** f 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 128 ASN j 136 GLN ** t 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN B 4 GLN F 13 ASN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 HIS ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 ASN ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN X 68 HIS ** Y 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 81 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 160967 Z= 0.195 Angle : 0.605 13.826 241169 Z= 0.309 Chirality : 0.033 0.383 30857 Planarity : 0.005 0.097 12688 Dihedral : 23.373 179.110 81483 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.32 % Favored : 89.50 % Rotamer: Outliers : 5.39 % Allowed : 36.38 % Favored : 58.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.14 (0.11), residues: 5620 helix: -0.17 (0.13), residues: 1705 sheet: -1.46 (0.16), residues: 1001 loop : -2.21 (0.11), residues: 2914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP H 21 HIS 0.006 0.001 HIS d 165 PHE 0.042 0.002 PHE H 129 TYR 0.032 0.002 TYR p 98 ARG 0.017 0.001 ARG f 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1465 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1213 time to evaluate : 6.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8414 (tt0) cc_final: 0.8172 (mt0) REVERT: c 139 SER cc_start: 0.8425 (m) cc_final: 0.8185 (t) REVERT: e 25 MET cc_start: 0.8977 (mmm) cc_final: 0.8605 (tpp) REVERT: f 29 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.8325 (m-40) REVERT: f 35 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8417 (m) REVERT: i 116 MET cc_start: -0.1295 (mmt) cc_final: -0.1499 (mmm) REVERT: i 135 MET cc_start: 0.1887 (mmt) cc_final: 0.1068 (mtm) REVERT: j 98 GLU cc_start: 0.8267 (mm-30) cc_final: 0.8009 (pm20) REVERT: l 10 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7726 (tm-30) REVERT: m 129 THR cc_start: 0.8415 (p) cc_final: 0.8208 (t) REVERT: o 55 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8141 (mp0) REVERT: o 56 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8481 (mtmm) REVERT: p 10 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8243 (mt-10) REVERT: q 48 ASP cc_start: 0.7292 (m-30) cc_final: 0.7015 (m-30) REVERT: q 70 GLN cc_start: 0.9057 (tt0) cc_final: 0.8719 (tp-100) REVERT: s 33 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.8975 (mm) REVERT: s 35 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.9025 (mt) REVERT: t 4 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8489 (tm-30) REVERT: u 21 ARG cc_start: 0.8581 (ptm160) cc_final: 0.8267 (ttp80) REVERT: u 45 GLN cc_start: 0.8532 (tm-30) cc_final: 0.7680 (tm-30) REVERT: u 80 ASP cc_start: 0.7471 (m-30) cc_final: 0.7217 (t0) REVERT: v 7 GLU cc_start: 0.8994 (pm20) cc_final: 0.8724 (pm20) REVERT: x 34 SER cc_start: 0.9037 (m) cc_final: 0.8595 (p) REVERT: y 45 GLN cc_start: 0.8809 (pt0) cc_final: 0.8353 (tm-30) REVERT: y 49 ASP cc_start: 0.8283 (p0) cc_final: 0.7900 (p0) REVERT: A 23 LYS cc_start: 0.9222 (pmmt) cc_final: 0.8857 (pptt) REVERT: C 19 PHE cc_start: 0.8798 (p90) cc_final: 0.8331 (p90) REVERT: D 1 MET cc_start: 0.7551 (tpp) cc_final: 0.7233 (tpp) REVERT: G 29 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.7812 (p90) REVERT: G 36 LYS cc_start: 0.9232 (mtmt) cc_final: 0.8975 (tttm) REVERT: G 153 MET cc_start: 0.7811 (ttm) cc_final: 0.6877 (mtp) REVERT: G 190 SER cc_start: 0.8831 (t) cc_final: 0.8454 (m) REVERT: G 198 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8686 (m) REVERT: G 212 TYR cc_start: 0.8187 (m-80) cc_final: 0.7766 (m-80) REVERT: H 138 GLN cc_start: 0.8830 (mt0) cc_final: 0.8599 (mt0) REVERT: H 167 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.7094 (m-80) REVERT: I 3 TYR cc_start: 0.7207 (t80) cc_final: 0.6957 (t80) REVERT: I 50 TYR cc_start: 0.8309 (t80) cc_final: 0.7664 (t80) REVERT: I 82 LYS cc_start: 0.7454 (mptt) cc_final: 0.7184 (mptt) REVERT: I 84 ASN cc_start: 0.8768 (t0) cc_final: 0.8523 (p0) REVERT: I 123 MET cc_start: 0.7602 (tpp) cc_final: 0.7108 (tpp) REVERT: I 127 ARG cc_start: 0.8307 (mpp80) cc_final: 0.8105 (mpp80) REVERT: I 131 ILE cc_start: 0.6664 (OUTLIER) cc_final: 0.6266 (pt) REVERT: I 181 PHE cc_start: 0.8571 (t80) cc_final: 0.7748 (t80) REVERT: I 190 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8452 (mm) REVERT: J 11 GLN cc_start: 0.8200 (tt0) cc_final: 0.7608 (tm-30) REVERT: J 14 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8540 (tm) REVERT: J 54 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6991 (tt0) REVERT: J 61 LYS cc_start: 0.9070 (tttt) cc_final: 0.8538 (tttm) REVERT: J 115 GLU cc_start: 0.8680 (tt0) cc_final: 0.8438 (pp20) REVERT: K 14 GLN cc_start: 0.8590 (mp10) cc_final: 0.8262 (mp10) REVERT: K 65 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7956 (pp20) REVERT: K 90 MET cc_start: 0.7750 (mmm) cc_final: 0.7511 (tpp) REVERT: K 97 THR cc_start: 0.8447 (p) cc_final: 0.8242 (t) REVERT: L 17 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7109 (p90) REVERT: L 85 GLN cc_start: 0.7555 (mp10) cc_final: 0.6939 (mm-40) REVERT: L 124 SER cc_start: 0.9016 (p) cc_final: 0.8767 (m) REVERT: L 143 MET cc_start: 0.9258 (tpp) cc_final: 0.8491 (tpp) REVERT: M 4 ASP cc_start: 0.7733 (t0) cc_final: 0.7197 (m-30) REVERT: M 17 GLN cc_start: 0.8499 (mm110) cc_final: 0.8285 (mm-40) REVERT: M 42 GLU cc_start: 0.8889 (tp30) cc_final: 0.8626 (tp30) REVERT: M 110 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8273 (ptp) REVERT: M 123 GLU cc_start: 0.7929 (tt0) cc_final: 0.7563 (pt0) REVERT: N 65 THR cc_start: 0.9442 (OUTLIER) cc_final: 0.9077 (p) REVERT: N 111 GLU cc_start: 0.8583 (tp30) cc_final: 0.8287 (mp0) REVERT: N 119 LYS cc_start: 0.8661 (ttmm) cc_final: 0.8429 (ttmm) REVERT: N 122 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8143 (tmt-80) REVERT: O 46 LYS cc_start: 0.9040 (mtmm) cc_final: 0.8651 (mtmm) REVERT: O 64 GLN cc_start: 0.8274 (mm-40) cc_final: 0.7943 (mm-40) REVERT: P 76 TYR cc_start: 0.8881 (m-80) cc_final: 0.8669 (m-80) REVERT: Q 4 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8517 (t0) REVERT: Q 46 SER cc_start: 0.8454 (m) cc_final: 0.8026 (t) REVERT: Q 65 TYR cc_start: 0.7866 (t80) cc_final: 0.7656 (t80) REVERT: Q 102 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7190 (m-30) REVERT: R 30 LYS cc_start: 0.9431 (mtmm) cc_final: 0.9213 (mtmm) REVERT: R 77 LYS cc_start: 0.9660 (tttm) cc_final: 0.9279 (tmmt) REVERT: S 15 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9043 (tp) REVERT: S 22 LYS cc_start: 0.8281 (mptt) cc_final: 0.7880 (mppt) REVERT: S 45 LEU cc_start: 0.9176 (tt) cc_final: 0.8960 (tm) REVERT: T 9 LYS cc_start: 0.9233 (mtpp) cc_final: 0.9000 (mmmt) REVERT: T 46 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8379 (pttm) REVERT: U 13 LYS cc_start: 0.8450 (mttt) cc_final: 0.8169 (mmtp) REVERT: V 10 ARG cc_start: 0.7922 (mtp85) cc_final: 0.7626 (mtp85) REVERT: V 74 LEU cc_start: 0.8364 (pt) cc_final: 0.7946 (pp) REVERT: W 23 LYS cc_start: 0.8539 (mppt) cc_final: 0.8242 (mppt) REVERT: W 37 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8280 (mtpt) REVERT: W 56 ARG cc_start: 0.8608 (ttm-80) cc_final: 0.7990 (ptm160) REVERT: X 64 GLU cc_start: 0.8246 (tp30) cc_final: 0.7781 (tm-30) REVERT: X 72 GLU cc_start: 0.8645 (tt0) cc_final: 0.7174 (tm-30) REVERT: Y 26 MET cc_start: 0.9275 (ttp) cc_final: 0.8885 (tmt) REVERT: Y 47 GLN cc_start: 0.8830 (tp-100) cc_final: 0.8536 (tp-100) outliers start: 252 outliers final: 170 residues processed: 1346 average time/residue: 1.8787 time to fit residues: 3831.2137 Evaluate side-chains 1362 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1169 time to evaluate : 6.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 187 CYS Chi-restraints excluded: chain b residue 193 GLU Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain c residue 13 ARG Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 37 VAL Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 196 VAL Chi-restraints excluded: chain e residue 9 ASP Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 100 GLU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 29 ASN Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 112 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 15 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain i residue 7 TYR Chi-restraints excluded: chain i residue 85 ILE Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 80 ASP Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain n residue 110 MET Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 45 SER Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 55 GLU Chi-restraints excluded: chain o residue 56 LYS Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 83 ILE Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 35 ILE Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain t residue 42 GLU Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 4 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 167 TYR Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 153 ARG Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 54 GLU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain J residue 77 ASN Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 65 GLU Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 122 ARG Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 29 LYS Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain Q residue 114 SER Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 17 ASP Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 19 ASN Chi-restraints excluded: chain T residue 46 LYS Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain U residue 32 PHE Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 61 ARG Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 37 LYS Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 605 optimal weight: 10.0000 chunk 975 optimal weight: 20.0000 chunk 595 optimal weight: 20.0000 chunk 462 optimal weight: 50.0000 chunk 678 optimal weight: 2.9990 chunk 1023 optimal weight: 6.9990 chunk 941 optimal weight: 20.0000 chunk 814 optimal weight: 20.0000 chunk 84 optimal weight: 40.0000 chunk 629 optimal weight: 7.9990 chunk 499 optimal weight: 20.0000 overall best weight: 9.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 36 ASN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 136 GLN ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN G 88 GLN ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 HIS ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN P 27 ASN ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 39 GLN V 49 ASN X 68 HIS Y 81 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.142 160967 Z= 0.351 Angle : 0.707 14.089 241169 Z= 0.359 Chirality : 0.038 0.417 30857 Planarity : 0.005 0.116 12688 Dihedral : 23.484 179.865 81483 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.10 % Favored : 87.72 % Rotamer: Outliers : 5.00 % Allowed : 37.10 % Favored : 57.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.30 (0.11), residues: 5620 helix: -0.33 (0.12), residues: 1698 sheet: -1.62 (0.16), residues: 1009 loop : -2.26 (0.11), residues: 2913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 21 HIS 0.007 0.001 HIS V 46 PHE 0.049 0.002 PHE H 129 TYR 0.031 0.002 TYR p 98 ARG 0.018 0.001 ARG U 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1411 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1177 time to evaluate : 6.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 102 TYR cc_start: 0.8514 (m-10) cc_final: 0.8311 (m-80) REVERT: b 224 MET cc_start: 0.8195 (tpp) cc_final: 0.7919 (mmt) REVERT: c 94 GLN cc_start: 0.8499 (tt0) cc_final: 0.8083 (mt0) REVERT: c 139 SER cc_start: 0.8473 (m) cc_final: 0.8199 (t) REVERT: e 25 MET cc_start: 0.9035 (mmm) cc_final: 0.8582 (tpp) REVERT: f 35 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8421 (m) REVERT: i 127 SER cc_start: 0.0868 (OUTLIER) cc_final: 0.0480 (m) REVERT: i 135 MET cc_start: 0.1635 (mmt) cc_final: 0.0953 (mtm) REVERT: l 10 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7779 (tm-30) REVERT: m 129 THR cc_start: 0.8567 (p) cc_final: 0.8318 (t) REVERT: o 55 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8132 (mp0) REVERT: o 56 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8629 (mtmm) REVERT: p 6 GLN cc_start: 0.8896 (mt0) cc_final: 0.8107 (mt0) REVERT: p 10 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8287 (mt-10) REVERT: q 48 ASP cc_start: 0.7460 (m-30) cc_final: 0.7080 (m-30) REVERT: q 70 GLN cc_start: 0.9095 (tt0) cc_final: 0.8712 (tp-100) REVERT: q 94 LEU cc_start: 0.9212 (mm) cc_final: 0.8967 (mp) REVERT: s 33 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.8955 (mm) REVERT: t 4 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8506 (tm-30) REVERT: u 5 ARG cc_start: 0.8861 (mtm180) cc_final: 0.8443 (mpp80) REVERT: u 7 ASP cc_start: 0.8067 (m-30) cc_final: 0.7845 (m-30) REVERT: u 21 ARG cc_start: 0.8533 (ptm160) cc_final: 0.8211 (ttp80) REVERT: u 45 GLN cc_start: 0.8478 (tm-30) cc_final: 0.7994 (tm-30) REVERT: u 80 ASP cc_start: 0.7558 (m-30) cc_final: 0.7353 (t0) REVERT: v 7 GLU cc_start: 0.8901 (pm20) cc_final: 0.8644 (pm20) REVERT: v 30 ILE cc_start: 0.9590 (mm) cc_final: 0.9286 (mt) REVERT: v 31 TYR cc_start: 0.7997 (p90) cc_final: 0.6702 (p90) REVERT: x 34 SER cc_start: 0.9039 (m) cc_final: 0.8618 (p) REVERT: y 45 GLN cc_start: 0.8816 (pt0) cc_final: 0.8583 (pt0) REVERT: A 23 LYS cc_start: 0.9208 (pmmt) cc_final: 0.8933 (pptt) REVERT: A 34 LEU cc_start: 0.9257 (pt) cc_final: 0.8833 (pp) REVERT: D 1 MET cc_start: 0.7575 (tpp) cc_final: 0.7340 (tpp) REVERT: G 29 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.7826 (p90) REVERT: G 36 LYS cc_start: 0.9251 (mtmt) cc_final: 0.9001 (tttm) REVERT: G 153 MET cc_start: 0.7905 (ttm) cc_final: 0.6856 (mtp) REVERT: G 190 SER cc_start: 0.8805 (t) cc_final: 0.8343 (p) REVERT: G 198 VAL cc_start: 0.9040 (OUTLIER) cc_final: 0.8746 (m) REVERT: G 212 TYR cc_start: 0.8130 (m-80) cc_final: 0.7669 (m-80) REVERT: H 41 TYR cc_start: 0.9221 (t80) cc_final: 0.8972 (t80) REVERT: H 138 GLN cc_start: 0.8856 (mt0) cc_final: 0.8656 (mt0) REVERT: H 167 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.7044 (m-80) REVERT: I 50 TYR cc_start: 0.8387 (t80) cc_final: 0.7732 (t80) REVERT: I 123 MET cc_start: 0.7774 (tpp) cc_final: 0.7322 (tpp) REVERT: I 127 ARG cc_start: 0.8309 (mpp80) cc_final: 0.8088 (mpp80) REVERT: I 131 ILE cc_start: 0.6916 (OUTLIER) cc_final: 0.6501 (pt) REVERT: I 181 PHE cc_start: 0.8525 (t80) cc_final: 0.7707 (t80) REVERT: J 11 GLN cc_start: 0.8267 (tt0) cc_final: 0.7558 (tm-30) REVERT: J 14 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8536 (tm) REVERT: J 22 LYS cc_start: 0.8533 (pttt) cc_final: 0.8270 (ptpt) REVERT: J 54 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.6987 (tt0) REVERT: J 61 LYS cc_start: 0.9056 (tttt) cc_final: 0.8572 (ttmt) REVERT: J 115 GLU cc_start: 0.8743 (tt0) cc_final: 0.8427 (pp20) REVERT: K 14 GLN cc_start: 0.8741 (mp10) cc_final: 0.8344 (mp10) REVERT: K 90 MET cc_start: 0.7663 (mmm) cc_final: 0.7318 (tpp) REVERT: K 97 THR cc_start: 0.8518 (p) cc_final: 0.8274 (t) REVERT: L 17 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.6922 (p90) REVERT: L 85 GLN cc_start: 0.7675 (mp10) cc_final: 0.7283 (mp10) REVERT: L 105 GLU cc_start: 0.8505 (pt0) cc_final: 0.8297 (pp20) REVERT: L 115 MET cc_start: 0.8898 (tpp) cc_final: 0.8480 (ttm) REVERT: L 143 MET cc_start: 0.9274 (tpp) cc_final: 0.8527 (tpp) REVERT: M 4 ASP cc_start: 0.7898 (t0) cc_final: 0.7190 (m-30) REVERT: M 17 GLN cc_start: 0.8509 (mm110) cc_final: 0.8163 (mm-40) REVERT: M 72 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8307 (pp20) REVERT: M 110 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8257 (ptp) REVERT: N 65 THR cc_start: 0.9395 (OUTLIER) cc_final: 0.9040 (p) REVERT: N 111 GLU cc_start: 0.8639 (tp30) cc_final: 0.8295 (mp0) REVERT: N 119 LYS cc_start: 0.8634 (ttmm) cc_final: 0.8354 (ttmm) REVERT: N 122 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8212 (tmt-80) REVERT: O 46 LYS cc_start: 0.9164 (mtmm) cc_final: 0.8843 (mtmm) REVERT: O 64 GLN cc_start: 0.8276 (mm-40) cc_final: 0.7937 (mm-40) REVERT: Q 102 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7341 (m-30) REVERT: R 30 LYS cc_start: 0.9463 (mtmm) cc_final: 0.9225 (mtmm) REVERT: R 77 LYS cc_start: 0.9642 (tttm) cc_final: 0.9294 (tmmt) REVERT: S 15 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8755 (tp) REVERT: S 45 LEU cc_start: 0.9212 (tt) cc_final: 0.8816 (tm) REVERT: S 53 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8006 (p0) REVERT: T 9 LYS cc_start: 0.9260 (mtpp) cc_final: 0.9010 (mmmt) REVERT: T 46 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8484 (pttm) REVERT: U 13 LYS cc_start: 0.8320 (mttt) cc_final: 0.7999 (mmtp) REVERT: V 74 LEU cc_start: 0.8360 (pt) cc_final: 0.7955 (pp) REVERT: W 37 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8421 (mtpt) REVERT: W 56 ARG cc_start: 0.8672 (ttm-80) cc_final: 0.8102 (ptm160) REVERT: X 64 GLU cc_start: 0.8282 (tp30) cc_final: 0.7608 (tm-30) REVERT: X 72 GLU cc_start: 0.8664 (tt0) cc_final: 0.7165 (tm-30) REVERT: Y 26 MET cc_start: 0.9317 (ttp) cc_final: 0.8862 (tmt) REVERT: Y 47 GLN cc_start: 0.8868 (tp-100) cc_final: 0.8522 (tp-100) outliers start: 234 outliers final: 177 residues processed: 1306 average time/residue: 1.8958 time to fit residues: 3740.1360 Evaluate side-chains 1336 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1139 time to evaluate : 6.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 36 ASN Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 144 GLU Chi-restraints excluded: chain b residue 167 ASP Chi-restraints excluded: chain b residue 187 CYS Chi-restraints excluded: chain b residue 193 GLU Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain c residue 13 ARG Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 37 VAL Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 196 VAL Chi-restraints excluded: chain e residue 9 ASP Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 112 VAL Chi-restraints excluded: chain f residue 136 ASP Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 15 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain i residue 7 TYR Chi-restraints excluded: chain i residue 85 ILE Chi-restraints excluded: chain i residue 127 SER Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 106 ASP Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain n residue 110 MET Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 45 SER Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 55 GLU Chi-restraints excluded: chain o residue 56 LYS Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 83 ILE Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain t residue 42 GLU Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain z residue 11 SER Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 167 TYR Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 153 ARG Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 54 GLU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 65 LYS Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain J residue 77 ASN Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 110 MET Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 122 ARG Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain Q residue 114 SER Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 51 GLN Chi-restraints excluded: chain R residue 80 MET Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 19 ASN Chi-restraints excluded: chain T residue 46 LYS Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain U residue 32 PHE Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 60 TRP Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 61 ARG Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 37 LYS Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 647 optimal weight: 5.9990 chunk 867 optimal weight: 9.9990 chunk 249 optimal weight: 10.0000 chunk 751 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 chunk 226 optimal weight: 10.0000 chunk 816 optimal weight: 30.0000 chunk 341 optimal weight: 20.0000 chunk 837 optimal weight: 9.9990 chunk 103 optimal weight: 50.0000 chunk 150 optimal weight: 10.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 36 ASN ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 29 ASN ** f 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 128 ASN j 136 GLN ** t 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN F 13 ASN G 88 GLN ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 HIS ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 ASN ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 GLN ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 ASN ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 HIS Y 81 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.060137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.044255 restraints weight = 751924.859| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.94 r_work: 0.2962 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 160967 Z= 0.337 Angle : 0.702 13.839 241169 Z= 0.357 Chirality : 0.038 0.421 30857 Planarity : 0.005 0.081 12688 Dihedral : 23.487 179.370 81483 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.14 % Favored : 87.69 % Rotamer: Outliers : 5.17 % Allowed : 37.27 % Favored : 57.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.20 % 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: -2.37 (0.11), residues: 5620 helix: -0.41 (0.12), residues: 1700 sheet: -1.70 (0.16), residues: 1003 loop : -2.27 (0.11), residues: 2917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 21 HIS 0.007 0.001 HIS d 165 PHE 0.074 0.002 PHE e 176 TYR 0.032 0.002 TYR p 98 ARG 0.015 0.001 ARG J 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 54444.92 seconds wall clock time: 942 minutes 27.56 seconds (56547.56 seconds total)