Starting phenix.real_space_refine on Fri Mar 22 14:48:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbv_6486/03_2024/3jbv_6486_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbv_6486/03_2024/3jbv_6486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbv_6486/03_2024/3jbv_6486.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbv_6486/03_2024/3jbv_6486.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbv_6486/03_2024/3jbv_6486_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbv_6486/03_2024/3jbv_6486_neut_updated.pdb" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4710 5.49 5 S 144 5.16 5 Cl 2 4.86 5 C 73162 2.51 5 N 27167 2.21 5 O 40726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "P GLU 45": "OE1" <-> "OE2" Residue "P GLU 48": "OE1" <-> "OE2" Residue "P ASP 55": "OD1" <-> "OD2" Residue "U GLU 30": "OE1" <-> "OE2" Residue "0 ARG 3": "NH1" <-> "NH2" Residue "0 ARG 11": "NH1" <-> "NH2" Residue "0 ARG 18": "NH1" <-> "NH2" Residue "0 ARG 37": "NH1" <-> "NH2" Residue "0 GLU 43": "OE1" <-> "OE2" Residue "0 ARG 50": "NH1" <-> "NH2" Residue "0 ARG 57": "NH1" <-> "NH2" Residue "0 ARG 74": "NH1" <-> "NH2" Residue "1 GLU 12": "OE1" <-> "OE2" Residue "1 ARG 29": "NH1" <-> "NH2" Residue "1 ARG 47": "NH1" <-> "NH2" Residue "1 ARG 52": "NH1" <-> "NH2" Residue "1 GLU 59": "OE1" <-> "OE2" Residue "2 ARG 11": "NH1" <-> "NH2" Residue "2 ARG 30": "NH1" <-> "NH2" Residue "2 GLU 37": "OE1" <-> "OE2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "2 GLU 59": "OE1" <-> "OE2" Residue "3 ARG 10": "NH1" <-> "NH2" Residue "3 ARG 16": "NH1" <-> "NH2" Residue "3 ARG 52": "NH1" <-> "NH2" Residue "4 GLU 32": "OE1" <-> "OE2" Residue "4 GLU 35": "OE1" <-> "OE2" Residue "4 ARG 44": "NH1" <-> "NH2" Residue "6 ARG 3": "NH1" <-> "NH2" Residue "6 ARG 12": "NH1" <-> "NH2" Residue "6 ARG 14": "NH1" <-> "NH2" Residue "6 ARG 19": "NH1" <-> "NH2" Residue "6 ARG 21": "NH1" <-> "NH2" Residue "6 ARG 33": "NH1" <-> "NH2" Residue "6 ARG 41": "NH1" <-> "NH2" Residue "7 ARG 13": "NH1" <-> "NH2" Residue "7 ARG 30": "NH1" <-> "NH2" Residue "7 ARG 40": "NH1" <-> "NH2" Residue "7 ARG 42": "NH1" <-> "NH2" Residue "8 ARG 24": "NH1" <-> "NH2" Residue "c GLU 35": "OE1" <-> "OE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ARG 63": "NH1" <-> "NH2" Residue "c ARG 80": "NH1" <-> "NH2" Residue "c TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 133": "NH1" <-> "NH2" Residue "c GLU 145": "OE1" <-> "OE2" Residue "c ARG 167": "NH1" <-> "NH2" Residue "c ARG 177": "NH1" <-> "NH2" Residue "c ARG 182": "NH1" <-> "NH2" Residue "c ARG 189": "NH1" <-> "NH2" Residue "c GLU 194": "OE1" <-> "OE2" Residue "c GLU 199": "OE1" <-> "OE2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c ARG 212": "NH1" <-> "NH2" Residue "i ASP 46": "OD1" <-> "OD2" Residue "i TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 141": "OD1" <-> "OD2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d GLU 17": "OE1" <-> "OE2" Residue "d GLU 28": "OE1" <-> "OE2" Residue "d GLU 30": "OE1" <-> "OE2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 59": "NH1" <-> "NH2" Residue "d GLU 64": "OE1" <-> "OE2" Residue "d GLU 74": "OE1" <-> "OE2" Residue "d ARG 77": "NH1" <-> "NH2" Residue "d GLU 81": "OE1" <-> "OE2" Residue "d ARG 83": "NH1" <-> "NH2" Residue "d GLU 88": "OE1" <-> "OE2" Residue "d PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 168": "OE1" <-> "OE2" Residue "d ARG 169": "NH1" <-> "NH2" Residue "d GLU 183": "OE1" <-> "OE2" Residue "d ARG 184": "NH1" <-> "NH2" Residue "e ARG 21": "NH1" <-> "NH2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e ARG 61": "NH1" <-> "NH2" Residue "e ARG 88": "NH1" <-> "NH2" Residue "e ARG 102": "NH1" <-> "NH2" Residue "e GLU 152": "OE1" <-> "OE2" Residue "e ARG 162": "NH1" <-> "NH2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "e ASP 191": "OD1" <-> "OD2" Residue "f GLU 32": "OE1" <-> "OE2" Residue "f GLU 42": "OE1" <-> "OE2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f GLU 94": "OE1" <-> "OE2" Residue "f GLU 98": "OE1" <-> "OE2" Residue "f ARG 102": "NH1" <-> "NH2" Residue "f ARG 110": "NH1" <-> "NH2" Residue "f ARG 112": "NH1" <-> "NH2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f ASP 123": "OD1" <-> "OD2" Residue "f ARG 133": "NH1" <-> "NH2" Residue "f GLU 134": "OE1" <-> "OE2" Residue "f GLU 140": "OE1" <-> "OE2" Residue "f ASP 142": "OD1" <-> "OD2" Residue "f GLU 164": "OE1" <-> "OE2" Residue "g ARG 3": "NH1" <-> "NH2" Residue "g ASP 16": "OD1" <-> "OD2" Residue "g GLU 32": "OE1" <-> "OE2" Residue "g PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 81": "OE1" <-> "OE2" Residue "g ASP 114": "OD1" <-> "OD2" Residue "g GLU 130": "OE1" <-> "OE2" Residue "g ARG 153": "NH1" <-> "NH2" Residue "g ARG 163": "NH1" <-> "NH2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "g GLU 173": "OE1" <-> "OE2" Residue "h ARG 27": "NH1" <-> "NH2" Residue "h PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ASP 14": "OD1" <-> "OD2" Residue "j GLU 31": "OE1" <-> "OE2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j GLU 91": "OE1" <-> "OE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "k GLU 92": "OE1" <-> "OE2" Residue "k GLU 121": "OE1" <-> "OE2" 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 PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 76": "OE1" <-> "OE2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m 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 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 104": "OE1" <-> "OE2" Residue "m ASP 106": "OD1" <-> "OD2" 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 ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n GLU 82": "OE1" <-> "OE2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 114": "OE1" <-> "OE2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "n GLU 120": "OE1" <-> "OE2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o GLU 46": "OE1" <-> "OE2" 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 11": "OE1" <-> "OE2" Residue "p ARG 21": "NH1" <-> "NH2" Residue "p ARG 39": "NH1" <-> "NH2" Residue "p GLU 44": "OE1" <-> "OE2" Residue "p ARG 62": "NH1" <-> "NH2" Residue "p GLU 68": "OE1" <-> "OE2" Residue "p GLU 71": "OE1" <-> "OE2" Residue "p ARG 89": "NH1" <-> "NH2" Residue "p TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 101": "NH1" <-> "NH2" Residue "p ARG 109": "NH1" <-> "NH2" Residue "q ARG 3": "NH1" <-> "NH2" Residue "q ARG 6": "NH1" <-> "NH2" Residue "q ARG 13": "NH1" <-> "NH2" Residue "q TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 33": "NH1" <-> "NH2" Residue "q ARG 48": "NH1" <-> "NH2" Residue "q ARG 70": "NH1" <-> "NH2" Residue "q GLU 111": "OE1" <-> "OE2" Residue "r GLU 16": "OE1" <-> "OE2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 23": "OE1" <-> "OE2" Residue "r GLU 31": "OE1" <-> "OE2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r GLU 70": "OE1" <-> "OE2" 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 "s GLU 2": "OE1" <-> "OE2" Residue "s GLU 59": "OE1" <-> "OE2" Residue "s GLU 78": "OE1" <-> "OE2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "t GLU 4": "OE1" <-> "OE2" Residue "t GLU 52": "OE1" <-> "OE2" Residue "t GLU 54": "OE1" <-> "OE2" Residue "t GLU 56": "OE1" <-> "OE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ARG 7": "NH1" <-> "NH2" Residue "u GLU 10": "OE1" <-> "OE2" Residue "u ARG 82": "NH1" <-> "NH2" Residue "u PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 86": "NH1" <-> "NH2" Residue "u GLU 88": "OE1" <-> "OE2" Residue "u ARG 94": "NH1" <-> "NH2" Residue "u PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 101": "OE1" <-> "OE2" Residue "w ASP 45": "OD1" <-> "OD2" Residue "w GLU 55": "OE1" <-> "OE2" Residue "w TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 69": "OE1" <-> "OE2" Residue "w TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 17": "OE1" <-> "OE2" Residue "y PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 83": "OE1" <-> "OE2" Residue "z GLU 10": "OE1" <-> "OE2" Residue "z PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 145911 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 32831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1530, 32831 Classifications: {'RNA': 1530} Modifications used: {'rna2p_pur': 121, 'rna2p_pyr': 89, 'rna3p_pur': 751, 'rna3p_pyr': 569} Link IDs: {'rna2p': 210, 'rna3p': 1319} Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D" 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: "E" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1105 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "G" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1174 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "H" 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: "I" 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: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" 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: "M" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 876 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "N" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "O" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 716 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" 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: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "S" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "T" 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: "U" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "V" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1620 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 33, 'rna3p_pyr': 30} Link IDs: {'rna2p': 13, 'rna3p': 62} Chain: "W" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1599 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 6, 'rna3p_pur': 27, 'rna3p_pyr': 31} Link IDs: {'rna2p': 16, 'rna3p': 58} Chain: "X" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 231 Classifications: {'RNA': 11} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "0" 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: "1" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "2" 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: "3" 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: "4" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "6" 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: "7" 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: "8" 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: "a" Number of atoms: 2506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2506 Classifications: {'RNA': 117} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 4, 'rna3p_pur': 53, 'rna3p_pyr': 50} Link IDs: {'rna2p': 14, 'rna3p': 102} Chain: "b" Number of atoms: 62321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62321 Classifications: {'RNA': 2903} Modifications used: {'p5*END': 1, 'rna2p_pur': 249, 'rna2p_pyr': 144, 'rna3p_pur': 1425, 'rna3p_pyr': 1085} Link IDs: {'rna2p': 393, 'rna3p': 2509} Chain: "c" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "i" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 976 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "d" 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: "e" 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: "f" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "g" 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: "h" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 145} 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: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "l" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "m" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1063 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain breaks: 1 Chain: "n" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} 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: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "u" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "w" 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: "y" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 569 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "z" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 211 Classifications: {'peptide': 27} Link IDs: {'CIS': 4, 'PTRANS': 2, 'TRANS': 20} Chain: "b" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'CLM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 56.40, per 1000 atoms: 0.39 Number of scatterers: 145911 At special positions: 0 Unit cell: (265.32, 287.76, 224.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 144 16.00 P 4710 15.00 O 40726 8.00 N 27167 7.00 C 73162 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 Atom "ATOM 83655 O4' U b1058 .*. O " rejected from bonding due to valence issues. Atom "ATOM 84080 O5' U b1078 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83698 O4' U b1060 .*. O " rejected from bonding due to valence issues. Atom "ATOM 84021 O4' C b1075 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83735 O5' G b1062 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83695 O5' U b1060 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83715 O5' U b1061 .*. O " rejected from bonding due to valence issues. Atom "ATOM 84080 O5' U b1078 .*. O " rejected from bonding due to valence issues. Atom "ATOM 84021 O4' C b1075 .*. O " rejected from bonding due to valence issues. Atom "ATOM 84061 O4' A b1077 .*. O " rejected from bonding due to valence issues. Atom "ATOM 84165 O4' U b1082 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83715 O5' U b1061 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83698 O4' U b1060 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83698 O4' U b1060 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83761 O4' G b1063 .*. O " rejected from bonding due to valence issues. Atom "ATOM 84021 O4' C b1075 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83761 O4' G b1063 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83784 O4' C b1064 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83655 O4' U b1058 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83695 O5' U b1060 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83761 O4' G b1063 .*. O " rejected from bonding due to valence issues. Atom "ATOM 84080 O5' U b1078 .*. O " rejected from bonding due to valence issues. Atom "ATOM 84145 O4' U b1081 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83738 O4' G b1062 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83695 O5' U b1060 .*. O " rejected from bonding due to valence issues. Atom "ATOM 7958 O5' U A 375 .*. O " rejected from bonding due to valence issues. Atom "ATOM 28832 O5' U A1348 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83781 O5' C b1064 .*. O " rejected from bonding due to valence issues. Atom "ATOM 84061 O4' A b1077 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83863 O5' G b1068 .*. O " rejected from bonding due to valence issues. Atom "ATOM 84165 O4' U b1082 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 68.76 Conformation dependent library (CDL) restraints added in 7.2 seconds 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10528 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 171 helices and 64 sheets defined 37.6% alpha, 18.2% beta 1129 base pairs and 1774 stacking pairs defined. Time for finding SS restraints: 70.49 Creating SS restraints... Processing helix chain 'B' and resid 23 through 28 removed outlier: 4.372A pdb=" N LYS B 27 " --> pdb=" O ASN B 23 " (cutoff:3.500A) Proline residue: B 28 - end of helix No H-bonds generated for 'chain 'B' and resid 23 through 28' Processing helix chain 'B' and resid 42 through 63 removed outlier: 3.746A pdb=" N VAL B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Proline residue: B 47 - end of helix removed outlier: 3.583A pdb=" N ARG B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 63 " --> pdb=" O ILE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 83 removed outlier: 3.500A pdb=" N VAL B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 127 removed outlier: 4.678A pdb=" N GLN B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLN B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N THR B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N PHE B 125 " --> pdb=" O GLN B 121 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASP B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS B 127 " --> pdb=" O GLY B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 146 removed outlier: 4.195A pdb=" N ALA B 133 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASN B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 154 removed outlier: 4.847A pdb=" N MET B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLY B 154 " --> pdb=" O ILE B 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 149 through 154' Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.887A pdb=" N GLU B 168 " --> pdb=" O ASP B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 179 removed outlier: 3.861A pdb=" N ASN B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 224 removed outlier: 4.010A pdb=" N VAL B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N THR B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N GLY B 223 " --> pdb=" O THR B 219 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG B 224 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 11 removed outlier: 6.379A pdb=" N ARG C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU C 11 " --> pdb=" O ASN C 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 6 through 11' Processing helix chain 'C' and resid 27 through 47 removed outlier: 3.665A pdb=" N ASN C 31 " --> pdb=" O GLU C 27 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 removed outlier: 4.040A pdb=" N VAL C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 94 removed outlier: 3.743A pdb=" N ARG C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL C 89 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.569A pdb=" N VAL C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 144 removed outlier: 3.708A pdb=" N MET C 133 " --> pdb=" O PHE C 129 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY C 144 " --> pdb=" O ALA C 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 15 removed outlier: 4.878A pdb=" N LEU D 10 " --> pdb=" O PRO D 6 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 65 removed outlier: 3.647A pdb=" N VAL D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.710A pdb=" N ARG D 80 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LYS D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 96 removed outlier: 4.021A pdb=" N LEU D 89 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU D 90 " --> pdb=" O GLY D 86 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 109 through 120 removed outlier: 4.005A pdb=" N HIS D 119 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 164 removed outlier: 4.348A pdb=" N LYS D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLN D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ARG D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 191 removed outlier: 3.845A pdb=" N LEU D 190 " --> pdb=" O GLU D 186 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N SER D 191 " --> pdb=" O ARG D 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 186 through 191' Processing helix chain 'D' and resid 196 through 205 removed outlier: 3.751A pdb=" N VAL D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 43 removed outlier: 4.321A pdb=" N ALA D 42 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG D 43 " --> pdb=" O HIS D 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 70 removed outlier: 3.588A pdb=" N ASN E 69 " --> pdb=" O LYS E 65 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N MET E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 removed outlier: 4.685A pdb=" N ALA E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 146 removed outlier: 3.901A pdb=" N ARG E 137 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA E 138 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N THR E 139 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ILE E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLU E 144 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ASN E 145 " --> pdb=" O ASP E 141 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET E 146 " --> pdb=" O GLY E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 158 removed outlier: 3.805A pdb=" N LYS E 155 " --> pdb=" O MET E 151 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG E 156 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 33 removed outlier: 4.429A pdb=" N VAL F 18 " --> pdb=" O GLN F 14 " (cutoff:3.500A) Proline residue: F 19 - end of helix removed outlier: 3.661A pdb=" N ILE F 22 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU F 23 " --> pdb=" O PRO F 19 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG F 24 " --> pdb=" O GLY F 20 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ALA F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 removed outlier: 3.811A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP F 72 " --> pdb=" O GLN F 68 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 30 Processing helix chain 'G' and resid 34 through 53 removed outlier: 5.550A pdb=" N ALA G 38 " --> pdb=" O LYS G 34 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR G 43 " --> pdb=" O GLU G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 69 removed outlier: 4.126A pdb=" N GLU G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN G 67 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 110 removed outlier: 3.856A pdb=" N ARG G 95 " --> pdb=" O ARG G 91 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN G 96 " --> pdb=" O PRO G 92 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 129 removed outlier: 3.738A pdb=" N GLU G 128 " --> pdb=" O SER G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 148 removed outlier: 3.627A pdb=" N ASP G 139 " --> pdb=" O LYS G 135 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL G 140 " --> pdb=" O LYS G 136 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA G 144 " --> pdb=" O VAL G 140 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU G 145 " --> pdb=" O HIS G 141 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASN G 147 " --> pdb=" O MET G 143 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 20 removed outlier: 3.806A pdb=" N ASN H 20 " --> pdb=" O GLY H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 43 Processing helix chain 'H' and resid 111 through 119 removed outlier: 3.675A pdb=" N GLN H 117 " --> pdb=" O ARG H 113 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA H 118 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 38 Processing helix chain 'I' and resid 41 through 55 removed outlier: 3.945A pdb=" N MET I 45 " --> pdb=" O GLU I 41 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG I 48 " --> pdb=" O ARG I 44 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN I 49 " --> pdb=" O MET I 45 " (cutoff:3.500A) Proline residue: I 50 - end of helix removed outlier: 3.730A pdb=" N LEU I 53 " --> pdb=" O GLN I 49 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL I 54 " --> pdb=" O PRO I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 90 removed outlier: 4.027A pdb=" N ALA I 85 " --> pdb=" O GLY I 81 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET I 87 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU I 88 " --> pdb=" O ARG I 84 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR I 89 " --> pdb=" O ALA I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 101 removed outlier: 3.871A pdb=" N GLU I 96 " --> pdb=" O SER I 92 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS I 99 " --> pdb=" O SER I 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 30 removed outlier: 3.950A pdb=" N ILE J 18 " --> pdb=" O ASP J 14 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR J 28 " --> pdb=" O GLU J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 89 removed outlier: 4.982A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N MET J 88 " --> pdb=" O VAL J 84 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG J 89 " --> pdb=" O ASP J 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 50 removed outlier: 3.773A pdb=" N GLY K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 59 removed outlier: 4.113A pdb=" N SER K 57 " --> pdb=" O GLY K 53 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 59 - end of helix No H-bonds generated for 'chain 'K' and resid 53 through 59' Processing helix chain 'K' and resid 60 through 75 removed outlier: 3.512A pdb=" N VAL K 73 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLU K 75 " --> pdb=" O ASP K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 103 removed outlier: 4.726A pdb=" N ILE K 96 " --> pdb=" O ARG K 92 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY K 103 " --> pdb=" O LEU K 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 10 Proline residue: L 10 - end of helix Processing helix chain 'L' and resid 112 through 117 removed outlier: 4.788A pdb=" N TYR L 116 " --> pdb=" O ALA L 112 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLY L 117 " --> pdb=" O ARG L 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 112 through 117' Processing helix chain 'M' and resid 13 through 21 removed outlier: 4.095A pdb=" N THR M 19 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER M 20 " --> pdb=" O ILE M 16 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 37 removed outlier: 3.519A pdb=" N ALA M 36 " --> pdb=" O ILE M 32 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY M 37 " --> pdb=" O LEU M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 63 removed outlier: 4.644A pdb=" N ASP M 53 " --> pdb=" O GLU M 49 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS M 61 " --> pdb=" O ASP M 57 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N VAL M 63 " --> pdb=" O VAL M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 82 Processing helix chain 'M' and resid 84 through 93 Processing helix chain 'M' and resid 105 through 110 removed outlier: 3.580A pdb=" N LYS M 109 " --> pdb=" O ALA M 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 21 removed outlier: 3.940A pdb=" N LYS N 6 " --> pdb=" O LYS N 2 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR N 19 " --> pdb=" O LEU N 15 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA N 21 " --> pdb=" O ASP N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 28 removed outlier: 4.661A pdb=" N LYS N 27 " --> pdb=" O ARG N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 49 removed outlier: 4.149A pdb=" N LEU N 45 " --> pdb=" O TRP N 41 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU N 47 " --> pdb=" O ALA N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 90 removed outlier: 3.771A pdb=" N ARG N 84 " --> pdb=" O ARG N 80 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU N 85 " --> pdb=" O ILE N 81 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG N 89 " --> pdb=" O GLU N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 15 removed outlier: 5.095A pdb=" N GLY O 15 " --> pdb=" O VAL O 11 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 46 removed outlier: 3.671A pdb=" N VAL O 28 " --> pdb=" O THR O 24 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA O 29 " --> pdb=" O GLU O 25 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N HIS O 37 " --> pdb=" O ALA O 33 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN O 39 " --> pdb=" O ILE O 35 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLY O 40 " --> pdb=" O ASN O 36 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA O 43 " --> pdb=" O GLN O 39 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLU O 44 " --> pdb=" O GLY O 40 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS O 45 " --> pdb=" O HIS O 41 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LYS O 46 " --> pdb=" O PHE O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 73 removed outlier: 4.783A pdb=" N ARG O 52 " --> pdb=" O ASP O 48 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG O 53 " --> pdb=" O HIS O 49 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLY O 54 " --> pdb=" O HIS O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 85 removed outlier: 3.500A pdb=" N LEU O 80 " --> pdb=" O ARG O 76 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 64 Processing helix chain 'P' and resid 68 through 79 removed outlier: 3.826A pdb=" N ALA P 73 " --> pdb=" O ASP P 69 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU P 74 " --> pdb=" O ARG P 70 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN P 79 " --> pdb=" O ILE P 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 32 removed outlier: 4.300A pdb=" N ASN R 30 " --> pdb=" O ALA R 26 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TYR R 31 " --> pdb=" O THR R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 removed outlier: 3.695A pdb=" N THR R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 65 removed outlier: 4.226A pdb=" N TYR R 63 " --> pdb=" O LYS R 59 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU R 64 " --> pdb=" O ARG R 60 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 24 removed outlier: 3.942A pdb=" N LYS S 16 " --> pdb=" O LEU S 12 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LYS S 17 " --> pdb=" O HIS S 13 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU S 19 " --> pdb=" O LEU S 15 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LYS S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ALA S 21 " --> pdb=" O LYS S 17 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL S 22 " --> pdb=" O VAL S 18 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU S 23 " --> pdb=" O GLU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 75 removed outlier: 4.061A pdb=" N PHE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA S 74 " --> pdb=" O LEU S 70 " (cutoff:3.500A) Proline residue: S 75 - end of helix No H-bonds generated for 'chain 'S' and resid 69 through 75' Processing helix chain 'T' and resid 7 through 41 removed outlier: 3.701A pdb=" N ILE T 11 " --> pdb=" O LYS T 7 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU T 14 " --> pdb=" O ALA T 10 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER T 22 " --> pdb=" O LYS T 18 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG T 23 " --> pdb=" O HIS T 19 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET T 27 " --> pdb=" O ARG T 23 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS T 32 " --> pdb=" O ARG T 28 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 64 removed outlier: 4.179A pdb=" N ALA T 46 " --> pdb=" O ASP T 42 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLN T 47 " --> pdb=" O LYS T 43 " (cutoff:3.500A) Proline residue: T 55 - end of helix removed outlier: 4.250A pdb=" N ALA T 61 " --> pdb=" O VAL T 57 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA T 62 " --> pdb=" O ASP T 58 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS T 63 " --> pdb=" O ARG T 59 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY T 64 " --> pdb=" O GLN T 60 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 86 removed outlier: 3.711A pdb=" N ALA T 71 " --> pdb=" O HIS T 67 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS T 84 " --> pdb=" O ALA T 80 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA T 86 " --> pdb=" O ILE T 82 " (cutoff:3.500A) Processing helix chain 'U' and resid 15 through 23 removed outlier: 3.710A pdb=" N LYS U 19 " --> pdb=" O LEU U 15 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG U 20 " --> pdb=" O ARG U 16 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER U 21 " --> pdb=" O ARG U 17 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N CYS U 22 " --> pdb=" O PHE U 18 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU U 23 " --> pdb=" O LYS U 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 15 through 23' Processing helix chain 'U' and resid 26 through 31 removed outlier: 7.291A pdb=" N GLU U 30 " --> pdb=" O GLY U 26 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL U 31 " --> pdb=" O VAL U 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 26 through 31' Processing helix chain 'U' and resid 36 through 44 Proline residue: U 40 - end of helix removed outlier: 3.952A pdb=" N GLU U 43 " --> pdb=" O LYS U 39 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ARG U 44 " --> pdb=" O PRO U 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 36 through 44' Processing helix chain 'U' and resid 46 through 53 removed outlier: 3.970A pdb=" N VAL U 52 " --> pdb=" O LYS U 48 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS U 53 " --> pdb=" O ALA U 49 " (cutoff:3.500A) Processing helix chain '0' and resid 52 through 63 Processing helix chain '0' and resid 64 through 75 Processing helix chain '1' and resid 2 through 9 removed outlier: 6.070A pdb=" N LEU 1 6 " --> pdb=" O LYS 1 2 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG 1 7 " --> pdb=" O ALA 1 3 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU 1 8 " --> pdb=" O LYS 1 4 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LYS 1 9 " --> pdb=" O GLU 1 5 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 2 through 9' Processing helix chain '1' and resid 10 through 35 removed outlier: 3.601A pdb=" N GLY 1 35 " --> pdb=" O GLN 1 31 " (cutoff:3.500A) Processing helix chain '1' and resid 39 through 61 removed outlier: 4.733A pdb=" N LEU 1 43 " --> pdb=" O GLN 1 39 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LYS 1 44 " --> pdb=" O SER 1 40 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN 1 45 " --> pdb=" O HIS 1 41 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL 1 46 " --> pdb=" O LEU 1 42 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG 1 47 " --> pdb=" O LEU 1 43 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG 1 48 " --> pdb=" O LYS 1 44 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ASP 1 49 " --> pdb=" O GLN 1 45 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU 1 59 " --> pdb=" O THR 1 55 " (cutoff:3.500A) Processing helix chain '2' and resid 17 through 28 Processing helix chain '2' and resid 41 through 52 Processing helix chain '3' and resid 9 through 19 removed outlier: 4.871A pdb=" N HIS 3 19 " --> pdb=" O MET 3 15 " (cutoff:3.500A) Processing helix chain '6' and resid 8 through 16 Processing helix chain '6' and resid 17 through 25 removed outlier: 4.222A pdb=" N THR 6 24 " --> pdb=" O ALA 6 20 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LYS 6 25 " --> pdb=" O ARG 6 21 " (cutoff:3.500A) Processing helix chain '6' and resid 26 through 38 Processing helix chain '7' and resid 7 through 14 removed outlier: 3.545A pdb=" N LYS 7 12 " --> pdb=" O ARG 7 8 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG 7 13 " --> pdb=" O GLY 7 9 " (cutoff:3.500A) Processing helix chain '7' and resid 32 through 37 removed outlier: 4.390A pdb=" N LYS 7 36 " --> pdb=" O ILE 7 32 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ALA 7 37 " --> pdb=" O LEU 7 33 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 32 through 37' Processing helix chain '7' and resid 38 through 46 Proline residue: 7 46 - end of helix Processing helix chain '7' and resid 51 through 63 removed outlier: 4.883A pdb=" N GLY 7 56 " --> pdb=" O LYS 7 52 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU 7 57 " --> pdb=" O GLY 7 53 " (cutoff:3.500A) Proline residue: 7 63 - end of helix Processing helix chain 'c' and resid 10 through 16 removed outlier: 7.432A pdb=" N HIS c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL c 16 " --> pdb=" O GLY c 12 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 35 removed outlier: 4.004A pdb=" N LEU c 34 " --> pdb=" O PHE c 30 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLU c 35 " --> pdb=" O ALA c 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 30 through 35' Processing helix chain 'c' and resid 131 through 136 removed outlier: 3.718A pdb=" N ILE c 135 " --> pdb=" O PRO c 131 " (cutoff:3.500A) Proline residue: c 136 - end of helix No H-bonds generated for 'chain 'c' and resid 131 through 136' Processing helix chain 'c' and resid 207 through 215 removed outlier: 3.924A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG c 214 " --> pdb=" O ALA c 210 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 226 removed outlier: 3.736A pdb=" N MET c 225 " --> pdb=" O ARG c 221 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ASN c 226 " --> pdb=" O GLY c 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 221 through 226' Processing helix chain 'c' and resid 260 through 268 removed outlier: 5.907A pdb=" N ASP c 264 " --> pdb=" O ASN c 260 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LYS c 265 " --> pdb=" O LYS c 261 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N PHE c 266 " --> pdb=" O ARG c 262 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE c 267 " --> pdb=" O THR c 263 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL c 268 " --> pdb=" O ASP c 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 260 through 268' Processing helix chain 'c' and resid 197 through 202 removed outlier: 3.621A pdb=" N MET c 201 " --> pdb=" O ALA c 198 " (cutoff:3.500A) Processing helix chain 'i' and resid 24 through 29 removed outlier: 4.212A pdb=" N GLY i 28 " --> pdb=" O GLY i 24 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN i 29 " --> pdb=" O PRO i 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 24 through 29' Processing helix chain 'i' and resid 33 through 46 removed outlier: 5.564A pdb=" N CYS i 38 " --> pdb=" O ILE i 34 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LYS i 39 " --> pdb=" O MET i 35 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA i 40 " --> pdb=" O GLU i 36 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N PHE i 41 " --> pdb=" O PHE i 37 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASN i 42 " --> pdb=" O CYS i 38 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS i 44 " --> pdb=" O ALA i 40 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP i 46 " --> pdb=" O ASN i 42 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 82 removed outlier: 4.132A pdb=" N LEU i 78 " --> pdb=" O PRO i 74 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU i 79 " --> pdb=" O ALA i 75 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LYS i 80 " --> pdb=" O ALA i 76 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS i 81 " --> pdb=" O VAL i 77 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA i 82 " --> pdb=" O LEU i 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 74 through 82' Processing helix chain 'i' and resid 101 through 113 removed outlier: 4.808A pdb=" N LEU i 105 " --> pdb=" O SER i 101 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLN i 106 " --> pdb=" O ARG i 102 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLU i 107 " --> pdb=" O ALA i 103 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE i 108 " --> pdb=" O GLN i 104 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS i 112 " --> pdb=" O ILE i 108 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ALA i 113 " --> pdb=" O ALA i 109 " (cutoff:3.500A) Processing helix chain 'i' and resid 120 through 134 removed outlier: 3.573A pdb=" N MET i 124 " --> pdb=" O ASP i 120 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N THR i 125 " --> pdb=" O ILE i 121 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ARG i 126 " --> pdb=" O GLU i 122 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER i 127 " --> pdb=" O ALA i 123 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE i 128 " --> pdb=" O MET i 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 56 through 61 removed outlier: 5.448A pdb=" N THR d 61 " --> pdb=" O ALA d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 72 removed outlier: 3.735A pdb=" N ALA d 71 " --> pdb=" O HIS d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 103 removed outlier: 4.482A pdb=" N ALA d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASP d 103 " --> pdb=" O GLU d 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 98 through 103' Processing helix chain 'd' and resid 120 through 125 Processing helix chain 'e' and resid 15 through 20 Processing helix chain 'e' and resid 24 through 40 removed outlier: 3.924A pdb=" N ARG e 40 " --> pdb=" O ALA e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 97 through 116 Processing helix chain 'e' and resid 130 through 142 Processing helix chain 'e' and resid 154 through 163 removed outlier: 3.711A pdb=" N ARG e 162 " --> pdb=" O PHE e 158 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ASN e 163 " --> pdb=" O LEU e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 183 removed outlier: 3.671A pdb=" N LEU e 180 " --> pdb=" O ASP e 176 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE e 181 " --> pdb=" O PRO e 177 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE e 183 " --> pdb=" O SER e 179 " (cutoff:3.500A) Processing helix chain 'e' and resid 189 through 201 Processing helix chain 'f' and resid 2 through 21 removed outlier: 3.537A pdb=" N ASP f 6 " --> pdb=" O ALA f 2 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS f 9 " --> pdb=" O HIS f 5 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR f 18 " --> pdb=" O LYS f 14 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE f 20 " --> pdb=" O LEU f 16 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 47 removed outlier: 3.625A pdb=" N ASP f 46 " --> pdb=" O GLU f 42 " (cutoff:3.500A) Processing helix chain 'f' and resid 48 through 62 Processing helix chain 'f' and resid 93 through 111 removed outlier: 3.519A pdb=" N ILE f 106 " --> pdb=" O ARG f 102 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL f 108 " --> pdb=" O ILE f 104 " (cutoff:3.500A) Proline residue: f 109 - end of helix Processing helix chain 'f' and resid 162 through 174 removed outlier: 3.712A pdb=" N PHE f 173 " --> pdb=" O LEU f 169 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP f 174 " --> pdb=" O LEU f 170 " (cutoff:3.500A) Processing helix chain 'f' and resid 134 through 139 removed outlier: 3.550A pdb=" N ILE f 137 " --> pdb=" O GLU f 134 " (cutoff:3.500A) Proline residue: f 139 - end of helix Processing helix chain 'g' and resid 2 through 8 Proline residue: g 8 - end of helix Processing helix chain 'g' and resid 60 through 81 removed outlier: 5.056A pdb=" N GLN g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER g 74 " --> pdb=" O ALA g 70 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR g 80 " --> pdb=" O VAL g 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 153 removed outlier: 4.446A pdb=" N ARG g 152 " --> pdb=" O LEU g 148 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG g 153 " --> pdb=" O ARG g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 22 through 34 removed outlier: 3.755A pdb=" N ALA h 26 " --> pdb=" O LYS h 22 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ARG h 27 " --> pdb=" O ALA h 23 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN h 28 " --> pdb=" O GLY h 24 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE h 29 " --> pdb=" O TYR h 25 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LEU h 30 " --> pdb=" O ALA h 26 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL h 31 " --> pdb=" O ARG h 27 " (cutoff:3.500A) Proline residue: h 32 - end of helix No H-bonds generated for 'chain 'h' and resid 22 through 34' Processing helix chain 'h' and resid 43 through 54 removed outlier: 3.585A pdb=" N ALA h 49 " --> pdb=" O GLU h 45 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA h 52 " --> pdb=" O GLU h 48 " (cutoff:3.500A) Processing helix chain 'h' and resid 55 through 66 removed outlier: 6.396A pdb=" N ALA h 59 " --> pdb=" O GLU h 55 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU h 60 " --> pdb=" O ALA h 56 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL h 61 " --> pdb=" O LYS h 57 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU h 62 " --> pdb=" O LEU h 58 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA h 63 " --> pdb=" O ALA h 59 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA h 64 " --> pdb=" O GLU h 60 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ALA h 65 " --> pdb=" O VAL h 61 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN h 66 " --> pdb=" O LEU h 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 55 through 66' Processing helix chain 'h' and resid 67 through 75 removed outlier: 4.076A pdb=" N LYS h 71 " --> pdb=" O ALA h 67 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ALA h 74 " --> pdb=" O GLU h 70 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU h 75 " --> pdb=" O LYS h 71 " (cutoff:3.500A) Processing helix chain 'h' and resid 95 through 100 removed outlier: 4.377A pdb=" N ILE h 99 " --> pdb=" O GLY h 95 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 removed outlier: 4.969A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 88 through 96 Processing helix chain 'j' and resid 97 through 110 removed outlier: 4.175A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET j 108 " --> pdb=" O ALA j 104 " (cutoff:3.500A) Proline residue: j 110 - end of helix Processing helix chain 'j' and resid 112 through 123 removed outlier: 3.769A pdb=" N ARG j 120 " --> pdb=" O ARG j 116 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS j 121 " --> pdb=" O ALA j 117 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU j 122 " --> pdb=" O MET j 118 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LYS j 123 " --> pdb=" O PHE j 119 " (cutoff:3.500A) Processing helix chain 'k' and resid 109 through 119 removed outlier: 5.707A pdb=" N MET k 113 " --> pdb=" O SER k 109 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LYS k 114 " --> pdb=" O GLU k 110 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE k 115 " --> pdb=" O LYS k 111 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 62 Proline residue: l 62 - end of helix Processing helix chain 'l' and resid 68 through 75 removed outlier: 7.261A pdb=" N ALA l 72 " --> pdb=" O SER l 68 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE l 73 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ALA l 75 " --> pdb=" O ALA l 71 " (cutoff:3.500A) Processing helix chain 'l' and resid 78 through 83 removed outlier: 3.643A pdb=" N LEU l 82 " --> pdb=" O ARG l 78 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA l 83 " --> pdb=" O LEU l 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 78 through 83' Processing helix chain 'l' and resid 91 through 99 removed outlier: 3.707A pdb=" N LEU l 95 " --> pdb=" O ASP l 91 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS l 96 " --> pdb=" O LEU l 92 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 139 removed outlier: 3.776A pdb=" N GLY l 139 " --> pdb=" O ILE l 135 " (cutoff:3.500A) Processing helix chain 'm' and resid 42 through 58 Processing helix chain 'm' and resid 109 through 125 removed outlier: 3.544A pdb=" N ALA m 122 " --> pdb=" O LYS m 118 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS m 123 " --> pdb=" O LEU m 119 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU m 124 " --> pdb=" O ALA m 120 " (cutoff:3.500A) Proline residue: m 125 - end of helix Processing helix chain 'n' and resid 13 through 32 Processing helix chain 'n' and resid 38 through 57 removed outlier: 3.604A pdb=" N ARG n 45 " --> pdb=" O ALA n 41 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) Proline residue: n 50 - end of helix removed outlier: 4.392A pdb=" N THR n 57 " --> pdb=" O THR n 53 " (cutoff:3.500A) Processing helix chain 'n' and resid 59 through 71 removed outlier: 4.017A pdb=" N THR n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 88 removed outlier: 5.103A pdb=" N GLY n 84 " --> pdb=" O PHE n 80 " (cutoff:3.500A) Proline residue: n 85 - end of helix Processing helix chain 'o' and resid 2 through 22 removed outlier: 3.668A pdb=" N ARG o 7 " --> pdb=" O LYS o 3 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG o 9 " --> pdb=" O SER o 5 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG o 15 " --> pdb=" O ALA o 11 " (cutoff:3.500A) Processing helix chain 'o' and resid 56 through 63 removed outlier: 4.581A pdb=" N GLN o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU o 62 " --> pdb=" O ILE o 58 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LYS o 63 " --> pdb=" O ALA o 59 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 86 Processing helix chain 'o' and resid 101 through 114 removed outlier: 3.842A pdb=" N GLY o 114 " --> pdb=" O ALA o 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 14 removed outlier: 3.733A pdb=" N GLU p 11 " --> pdb=" O GLN p 7 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN p 12 " --> pdb=" O LEU p 8 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LYS p 14 " --> pdb=" O GLN p 10 " (cutoff:3.500A) Processing helix chain 'p' and resid 97 through 104 removed outlier: 4.611A pdb=" N ARG p 101 " --> pdb=" O LEU p 97 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU p 102 " --> pdb=" O TYR p 98 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG p 103 " --> pdb=" O TYR p 99 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N THR p 104 " --> pdb=" O LEU p 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 97 through 104' Processing helix chain 'q' and resid 7 through 22 removed outlier: 3.547A pdb=" N ARG q 11 " --> pdb=" O GLY q 7 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE q 17 " --> pdb=" O ARG q 13 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS q 22 " --> pdb=" O LEU q 18 " (cutoff:3.500A) Processing helix chain 'q' and resid 26 through 31 removed outlier: 3.885A pdb=" N ARG q 30 " --> pdb=" O GLY q 26 " (cutoff:3.500A) Processing helix chain 'q' and resid 32 through 37 removed outlier: 3.910A pdb=" N GLN q 37 " --> pdb=" O ARG q 33 " (cutoff:3.500A) Processing helix chain 'q' and resid 39 through 73 removed outlier: 3.825A pdb=" N ARG q 51 " --> pdb=" O TYR q 47 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS q 54 " --> pdb=" O ARG q 50 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG q 55 " --> pdb=" O ARG q 51 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG q 58 " --> pdb=" O LYS q 54 " (cutoff:3.500A) Processing helix chain 'q' and resid 75 through 87 Processing helix chain 'q' and resid 91 through 102 Processing helix chain 'q' and resid 103 through 118 removed outlier: 3.568A pdb=" N ALA q 116 " --> pdb=" O LYS q 112 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 25 removed outlier: 3.667A pdb=" N LEU s 19 " --> pdb=" O GLN s 15 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 39 removed outlier: 3.702A pdb=" N ASP s 34 " --> pdb=" O SER s 30 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 removed outlier: 3.604A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS s 49 " --> pdb=" O VAL s 45 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) Processing helix chain 't' and resid 3 through 11 removed outlier: 3.508A pdb=" N LEU t 7 " --> pdb=" O ARG t 3 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU t 11 " --> pdb=" O LEU t 7 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 27 removed outlier: 5.559A pdb=" N SER t 21 " --> pdb=" O SER t 17 " (cutoff:3.500A) Processing helix chain 't' and resid 39 through 51 Processing helix chain 'u' and resid 66 through 71 removed outlier: 4.032A pdb=" N VAL u 70 " --> pdb=" O GLN u 66 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ALA u 71 " --> pdb=" O VAL u 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 66 through 71' Processing helix chain 'w' and resid 13 through 24 Processing helix chain 'w' and resid 43 through 53 removed outlier: 3.535A pdb=" N VAL w 47 " --> pdb=" O ASP w 43 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET w 50 " --> pdb=" O LYS w 46 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA w 52 " --> pdb=" O MET w 48 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS w 53 " --> pdb=" O ASN w 49 " (cutoff:3.500A) Processing helix chain 'w' and resid 54 through 59 removed outlier: 3.790A pdb=" N SER w 58 " --> pdb=" O ALA w 54 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 29 through 32 removed outlier: 7.049A pdb=" N PHE B 29 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASN B 41 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 88 through 91 removed outlier: 4.484A pdb=" N GLY B 70 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 161 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 69 " --> pdb=" O PHE B 161 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL B 162 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA B 184 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE B 199 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL B 186 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 53 through 58 removed outlier: 4.339A pdb=" N VAL C 55 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C 66 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 63 " --> pdb=" O PRO C 97 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN C 99 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 67 " --> pdb=" O ASN C 101 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 163 through 168 removed outlier: 5.896A pdb=" N ARG C 163 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLY C 154 " --> pdb=" O ARG C 163 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY C 147 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY C 196 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS C 203 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ASP C 180 " --> pdb=" O LYS C 203 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 139 through 143 removed outlier: 4.704A pdb=" N ASP D 140 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE D 181 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU D 178 " --> pdb=" O ASP D 173 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 11 through 15 removed outlier: 4.449A pdb=" N GLN E 11 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU E 35 " --> pdb=" O ILE E 15 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 83 through 87 removed outlier: 3.872A pdb=" N GLN E 96 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN E 121 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 32 through 39 removed outlier: 4.130A pdb=" N ALA E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY E 50 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR E 36 " --> pdb=" O GLY E 48 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY E 48 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY E 46 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F' and resid 38 through 43 removed outlier: 4.272A pdb=" N ARG F 38 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN F 63 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU F 40 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TRP F 42 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE F 8 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE F 6 " --> pdb=" O MET F 62 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET F 90 " --> pdb=" O GLU F 5 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'G' and resid 72 through 77 removed outlier: 4.146A pdb=" N ARG G 77 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR G 84 " --> pdb=" O ARG G 77 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'H' and resid 22 through 28 removed outlier: 5.702A pdb=" N ALA H 22 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER H 28 " --> pdb=" O PRO H 56 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU H 51 " --> pdb=" O GLU H 57 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASP H 47 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'H' and resid 102 through 105 removed outlier: 7.007A pdb=" N VAL H 102 " --> pdb=" O ILE H 125 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'I' and resid 4 through 10 removed outlier: 4.013A pdb=" N LYS I 67 " --> pdb=" O ALA I 15 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR I 63 " --> pdb=" O PHE I 19 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS I 26 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL I 28 " --> pdb=" O LEU I 62 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE I 64 " --> pdb=" O VAL I 28 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'J' and resid 45 through 52 removed outlier: 3.893A pdb=" N ARG J 45 " --> pdb=" O THR J 69 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR J 69 " --> pdb=" O ARG J 45 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU J 47 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N HIS J 70 " --> pdb=" O ALA J 12 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA J 12 " --> pdb=" O HIS J 70 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL J 74 " --> pdb=" O ILE J 8 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE J 8 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE J 76 " --> pdb=" O ILE J 6 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE J 6 " --> pdb=" O ILE J 76 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG J 7 " --> pdb=" O SER J 101 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN J 99 " --> pdb=" O ARG J 9 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS J 11 " --> pdb=" O ASP J 97 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP J 97 " --> pdb=" O LYS J 11 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'K' and resid 29 through 35 removed outlier: 3.849A pdb=" N ILE K 30 " --> pdb=" O HIS K 23 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU K 82 " --> pdb=" O GLY K 18 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL K 83 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'K' and resid 82 through 87 removed outlier: 5.098A pdb=" N GLY K 87 " --> pdb=" O VAL K 112 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'L' and resid 28 through 32 removed outlier: 4.831A pdb=" N LEU L 80 " --> pdb=" O VAL L 97 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG L 82 " --> pdb=" O HIS L 95 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'L' and resid 35 through 40 removed outlier: 3.778A pdb=" N ARG L 35 " --> pdb=" O ARG L 53 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL L 51 " --> pdb=" O TYR L 37 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LYS L 50 " --> pdb=" O ILE L 66 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU L 56 " --> pdb=" O PHE L 60 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N PHE L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'P' and resid 4 through 9 removed outlier: 5.336A pdb=" N PHE P 16 " --> pdb=" O HIS P 9 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY P 49 " --> pdb=" O ASN P 40 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'Q' and resid 6 through 10 Processing sheet with id= 21, first strand: chain 'Q' and resid 18 through 30 No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 'S' and resid 47 through 51 Processing sheet with id= 23, first strand: chain '0' and resid 12 through 19 removed outlier: 4.724A pdb=" N ASN 0 23 " --> pdb=" O SER 0 19 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain '0' and resid 34 through 41 removed outlier: 6.689A pdb=" N SER 0 35 " --> pdb=" O ARG 0 50 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ARG 0 50 " --> pdb=" O SER 0 35 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG 0 37 " --> pdb=" O THR 0 48 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR 0 48 " --> pdb=" O ARG 0 37 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TRP 0 39 " --> pdb=" O PHE 0 46 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N PHE 0 46 " --> pdb=" O TRP 0 39 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLU 0 41 " --> pdb=" O LYS 0 44 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain '2' and resid 34 through 39 removed outlier: 4.497A pdb=" N HIS 2 34 " --> pdb=" O GLN 2 9 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N MET 2 54 " --> pdb=" O THR 2 10 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain '4' and resid 19 through 26 removed outlier: 6.090A pdb=" N HIS 4 19 " --> pdb=" O SER 4 13 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS 4 10 " --> pdb=" O ALA 4 52 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA 4 52 " --> pdb=" O LYS 4 10 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE 4 48 " --> pdb=" O SER 4 14 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU 4 51 " --> pdb=" O LEU 4 34 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU 4 34 " --> pdb=" O GLU 4 51 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain '7' and resid 22 through 25 No H-bonds generated for sheet with id= 27 Processing sheet with id= 28, first strand: chain '8' and resid 1 through 5 removed outlier: 5.485A pdb=" N ILE 8 23 " --> pdb=" O GLN 8 37 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'c' and resid 2 through 5 removed outlier: 3.626A pdb=" N VAL c 20 " --> pdb=" O ALA c 2 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'c' and resid 80 through 83 removed outlier: 3.580A pdb=" N ARG c 80 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU c 93 " --> pdb=" O GLU c 79 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ILE c 74 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N SER c 118 " --> pdb=" O ILE c 74 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASP c 114 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLY c 127 " --> pdb=" O GLN c 115 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN c 117 " --> pdb=" O GLY c 127 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'c' and resid 138 through 142 removed outlier: 4.386A pdb=" N SER c 139 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR c 173 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU c 180 " --> pdb=" O LEU c 176 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'i' and resid 56 through 60 removed outlier: 4.369A pdb=" N VAL i 57 " --> pdb=" O VAL i 69 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL i 69 " --> pdb=" O VAL i 57 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR i 67 " --> pdb=" O THR i 59 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'd' and resid 3 through 9 removed outlier: 4.166A pdb=" N SER d 199 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 13.565A pdb=" N GLY d 198 " --> pdb=" O LYS d 114 " (cutoff:3.500A) removed outlier: 12.262A pdb=" N LYS d 114 " --> pdb=" O GLY d 198 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU d 168 " --> pdb=" O SER d 113 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'd' and resid 11 through 16 removed outlier: 4.310A pdb=" N VAL d 20 " --> pdb=" O THR d 16 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'd' and resid 36 through 40 removed outlier: 3.562A pdb=" N GLN d 36 " --> pdb=" O GLN d 49 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU d 40 " --> pdb=" O TYR d 45 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR d 45 " --> pdb=" O LEU d 40 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN d 94 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'd' and resid 46 through 51 removed outlier: 5.598A pdb=" N ARG d 46 " --> pdb=" O LEU d 84 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'd' and resid 105 through 108 removed outlier: 6.066A pdb=" N LYS d 105 " --> pdb=" O VAL d 177 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'e' and resid 2 through 5 removed outlier: 4.343A pdb=" N LEU e 5 " --> pdb=" O SER e 10 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER e 10 " --> pdb=" O LEU e 5 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'e' and resid 117 through 120 removed outlier: 5.568A pdb=" N ARG e 117 " --> pdb=" O ASP e 184 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'f' and resid 65 through 69 removed outlier: 8.050A pdb=" N ILE f 85 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL f 40 " --> pdb=" O ILE f 85 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLY f 39 " --> pdb=" O GLY f 151 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLY f 151 " --> pdb=" O GLY f 39 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'g' and resid 16 through 19 removed outlier: 3.534A pdb=" N LYS g 27 " --> pdb=" O ASP g 16 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU g 33 " --> pdb=" O ILE g 26 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'g' and resid 41 through 45 removed outlier: 3.736A pdb=" N THR g 51 " --> pdb=" O LYS g 44 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'g' and resid 82 through 89 removed outlier: 3.759A pdb=" N LYS g 85 " --> pdb=" O LEU g 133 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU g 133 " --> pdb=" O LYS g 85 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR g 129 " --> pdb=" O LEU g 89 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU g 130 " --> pdb=" O PRO g 126 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'g' and resid 94 through 98 removed outlier: 3.691A pdb=" N SER g 106 " --> pdb=" O ARG g 95 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'h' and resid 16 through 20 removed outlier: 4.575A pdb=" N ASP h 17 " --> pdb=" O LEU h 5 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLN h 2 " --> pdb=" O ALA h 39 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LYS h 35 " --> pdb=" O LEU h 6 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'j' and resid 52 through 56 Processing sheet with id= 47, first strand: chain 'k' and resid 17 through 21 removed outlier: 6.755A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL k 10 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR k 6 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASN k 82 " --> pdb=" O MET k 7 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'm' and resid 37 through 40 No H-bonds generated for sheet with id= 48 Processing sheet with id= 49, first strand: chain 'm' and resid 62 through 65 removed outlier: 7.489A pdb=" N SER m 30 " --> pdb=" O LYS m 133 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS m 127 " --> pdb=" O VAL m 36 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'n' and resid 33 through 37 removed outlier: 6.228A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N TYR n 94 " --> pdb=" O VAL n 116 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'o' and resid 49 through 52 Processing sheet with id= 52, first strand: chain 'p' and resid 38 through 45 removed outlier: 6.684A pdb=" N THR p 25 " --> pdb=" O LYS p 87 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER p 83 " --> pdb=" O LYS p 29 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'p' and resid 49 through 52 removed outlier: 3.618A pdb=" N ALA p 49 " --> pdb=" O THR p 60 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N SER p 57 " --> pdb=" O THR p 76 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'r' and resid 11 through 15 removed outlier: 3.581A pdb=" N MET r 40 " --> pdb=" O VAL r 4 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'r' and resid 18 through 23 removed outlier: 4.263A pdb=" N GLN r 18 " --> pdb=" O ILE r 98 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'r' and resid 57 through 60 Processing sheet with id= 57, first strand: chain 'r' and resid 71 through 78 removed outlier: 3.962A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 's' and resid 2 through 8 Processing sheet with id= 59, first strand: chain 't' and resid 28 through 33 removed outlier: 6.487A pdb=" N ASN t 28 " --> pdb=" O LEU t 87 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG t 73 " --> pdb=" O HIS t 70 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LYS t 66 " --> pdb=" O ARG t 77 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ASP t 79 " --> pdb=" O LYS t 64 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LYS t 64 " --> pdb=" O ASP t 79 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS t 81 " --> pdb=" O VAL t 62 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL t 62 " --> pdb=" O LYS t 81 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA t 83 " --> pdb=" O THR t 60 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR t 60 " --> pdb=" O ALA t 83 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL t 85 " --> pdb=" O VAL t 58 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL t 58 " --> pdb=" O VAL t 85 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'u' and resid 40 through 45 No H-bonds generated for sheet with id= 60 Processing sheet with id= 61, first strand: chain 'u' and resid 82 through 87 removed outlier: 4.969A pdb=" N ARG u 82 " --> pdb=" O LYS u 97 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG u 86 " --> pdb=" O VAL u 93 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'w' and resid 69 through 72 removed outlier: 6.657A pdb=" N ALA w 39 " --> pdb=" O ARG w 9 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE w 89 " --> pdb=" O PRO w 27 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'y' and resid 27 through 31 removed outlier: 7.341A pdb=" N GLY y 27 " --> pdb=" O PHE y 69 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE y 69 " --> pdb=" O GLY y 27 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU y 29 " --> pdb=" O VAL y 67 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'y' and resid 51 through 54 removed outlier: 4.176A pdb=" N THR y 58 " --> pdb=" O GLY y 54 " (cutoff:3.500A) 1532 hydrogen bonds defined for protein. 4533 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2840 hydrogen bonds 4662 hydrogen bond angles 0 basepair planarities 1129 basepair parallelities 1774 stacking parallelities Total time for adding SS restraints: 193.74 Time building geometry restraints manager: 73.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 11778 1.28 - 1.42: 62746 1.42 - 1.56: 74338 1.56 - 1.69: 9504 1.69 - 1.83: 271 Bond restraints: 158637 Sorted by residual: bond pdb=" O3' C b2610 " pdb=" P C b2611 " ideal model delta sigma weight residual 1.607 1.826 -0.219 1.50e-02 4.44e+03 2.14e+02 bond pdb=" O3' U b2504 " pdb=" P G b2505 " ideal model delta sigma weight residual 1.607 1.810 -0.203 1.50e-02 4.44e+03 1.84e+02 bond pdb=" O3' C b2248 " pdb=" P U b2249 " ideal model delta sigma weight residual 1.607 1.779 -0.172 1.50e-02 4.44e+03 1.31e+02 bond pdb=" C5' U b 399 " pdb=" C4' U b 399 " ideal model delta sigma weight residual 1.508 1.672 -0.164 1.50e-02 4.44e+03 1.20e+02 bond pdb=" O3' C b1323 " pdb=" P G b1324 " ideal model delta sigma weight residual 1.607 1.766 -0.159 1.50e-02 4.44e+03 1.12e+02 ... (remaining 158632 not shown) Histogram of bond angle deviations from ideal: 83.82 - 96.34: 17 96.34 - 108.87: 56895 108.87 - 121.39: 138213 121.39 - 133.91: 42386 133.91 - 146.43: 26 Bond angle restraints: 237537 Sorted by residual: angle pdb=" O3' C W 36 " pdb=" P G W 37 " pdb=" O5' G W 37 " ideal model delta sigma weight residual 104.00 146.43 -42.43 1.50e+00 4.44e-01 8.00e+02 angle pdb=" C2' G b 400 " pdb=" C1' G b 400 " pdb=" N9 G b 400 " ideal model delta sigma weight residual 112.00 132.89 -20.89 1.50e+00 4.44e-01 1.94e+02 angle pdb=" C2' G b2123 " pdb=" C1' G b2123 " pdb=" N9 G b2123 " ideal model delta sigma weight residual 112.00 131.78 -19.78 1.50e+00 4.44e-01 1.74e+02 angle pdb=" C2' A b1275 " pdb=" C1' A b1275 " pdb=" N9 A b1275 " ideal model delta sigma weight residual 114.00 133.61 -19.61 1.50e+00 4.44e-01 1.71e+02 angle pdb=" O3' G b1930 " pdb=" C3' G b1930 " pdb=" C2' G b1930 " ideal model delta sigma weight residual 109.50 128.57 -19.07 1.50e+00 4.44e-01 1.62e+02 ... (remaining 237532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 87825 35.98 - 71.96: 12405 71.96 - 107.93: 1360 107.93 - 143.91: 72 143.91 - 179.89: 64 Dihedral angle restraints: 101726 sinusoidal: 85407 harmonic: 16319 Sorted by residual: dihedral pdb=" CA THR d 151 " pdb=" C THR d 151 " pdb=" N PRO d 152 " pdb=" CA PRO d 152 " ideal model delta harmonic sigma weight residual 180.00 -98.45 -81.55 0 5.00e+00 4.00e-02 2.66e+02 dihedral pdb=" C4' C b1079 " pdb=" C3' C b1079 " pdb=" C2' C b1079 " pdb=" C1' C b1079 " ideal model delta sinusoidal sigma weight residual 36.00 -49.81 85.81 1 8.00e+00 1.56e-02 1.39e+02 dihedral pdb=" C5' C b1079 " pdb=" C4' C b1079 " pdb=" C3' C b1079 " pdb=" O3' C b1079 " ideal model delta sinusoidal sigma weight residual 82.00 166.46 -84.46 1 8.00e+00 1.56e-02 1.36e+02 ... (remaining 101723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.293: 29976 0.293 - 0.586: 388 0.586 - 0.879: 23 0.879 - 1.172: 6 1.172 - 1.465: 3 Chirality restraints: 30396 Sorted by residual: chirality pdb=" C4' U b1657 " pdb=" C5' U b1657 " pdb=" O4' U b1657 " pdb=" C3' U b1657 " both_signs ideal model delta sigma weight residual False -2.50 -1.03 -1.47 2.00e-01 2.50e+01 5.37e+01 chirality pdb=" C1' A b1275 " pdb=" O4' A b1275 " pdb=" C2' A b1275 " pdb=" N9 A b1275 " both_signs ideal model delta sigma weight residual False 2.44 1.09 1.35 2.00e-01 2.50e+01 4.54e+01 chirality pdb=" C3' C b2161 " pdb=" C4' C b2161 " pdb=" O3' C b2161 " pdb=" C2' C b2161 " both_signs ideal model delta sigma weight residual False -2.48 -1.14 -1.34 2.00e-01 2.50e+01 4.47e+01 ... (remaining 30393 not shown) Planarity restraints: 12579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G b1059 " 0.058 2.00e-02 2.50e+03 1.62e-01 7.83e+02 pdb=" N9 G b1059 " 0.030 2.00e-02 2.50e+03 pdb=" C8 G b1059 " -0.021 2.00e-02 2.50e+03 pdb=" N7 G b1059 " -0.030 2.00e-02 2.50e+03 pdb=" C5 G b1059 " -0.041 2.00e-02 2.50e+03 pdb=" C6 G b1059 " -0.124 2.00e-02 2.50e+03 pdb=" O6 G b1059 " 0.341 2.00e-02 2.50e+03 pdb=" N1 G b1059 " -0.361 2.00e-02 2.50e+03 pdb=" C2 G b1059 " -0.080 2.00e-02 2.50e+03 pdb=" N2 G b1059 " 0.186 2.00e-02 2.50e+03 pdb=" N3 G b1059 " 0.050 2.00e-02 2.50e+03 pdb=" C4 G b1059 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 CLM b9000 " -0.180 2.00e-02 2.50e+03 2.22e-01 6.18e+02 pdb=" C2 CLM b9000 " 0.071 2.00e-02 2.50e+03 pdb=" C3 CLM b9000 " -0.267 2.00e-02 2.50e+03 pdb=" N2 CLM b9000 " 0.372 2.00e-02 2.50e+03 pdb=" O2 CLM b9000 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G b1382 " -0.019 2.00e-02 2.50e+03 1.41e-01 5.95e+02 pdb=" N9 G b1382 " 0.022 2.00e-02 2.50e+03 pdb=" C8 G b1382 " 0.007 2.00e-02 2.50e+03 pdb=" N7 G b1382 " 0.023 2.00e-02 2.50e+03 pdb=" C5 G b1382 " -0.064 2.00e-02 2.50e+03 pdb=" C6 G b1382 " 0.109 2.00e-02 2.50e+03 pdb=" O6 G b1382 " -0.233 2.00e-02 2.50e+03 pdb=" N1 G b1382 " 0.358 2.00e-02 2.50e+03 pdb=" C2 G b1382 " 0.052 2.00e-02 2.50e+03 pdb=" N2 G b1382 " -0.178 2.00e-02 2.50e+03 pdb=" N3 G b1382 " -0.029 2.00e-02 2.50e+03 pdb=" C4 G b1382 " -0.049 2.00e-02 2.50e+03 ... (remaining 12576 not shown) Histogram of nonbonded interaction distances: 0.39 - 1.29: 125 1.29 - 2.19: 794 2.19 - 3.10: 108094 3.10 - 4.00: 452560 4.00 - 4.90: 746746 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1308319 Sorted by model distance: nonbonded pdb=" N3 G b1062 " pdb=" CD2 LEU i 79 " model vdw 0.389 3.540 nonbonded pdb=" N3 C b1076 " pdb=" CG MET i 135 " model vdw 0.395 3.520 nonbonded pdb=" C4' G b1062 " pdb=" CB LEU i 78 " model vdw 0.434 3.870 nonbonded pdb=" C3' G b1062 " pdb=" CA LEU i 78 " model vdw 0.445 3.900 nonbonded pdb=" C2 A b1077 " pdb=" C ARG i 133 " model vdw 0.479 3.570 ... (remaining 1308314 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.590 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: 0.120 Extract box with map and model: 12.980 Check model and map are aligned: 1.540 Set scattering table: 1.010 Process input model: 495.670 Find NCS groups from input model: 3.190 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 519.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.219 158637 Z= 0.442 Angle : 1.324 42.429 237537 Z= 0.889 Chirality : 0.099 1.465 30396 Planarity : 0.012 0.222 12579 Dihedral : 25.425 179.891 91198 Min Nonbonded Distance : 0.389 Molprobity Statistics. All-atom Clashscore : 31.39 Ramachandran Plot: Outliers : 3.00 % Allowed : 8.13 % Favored : 88.86 % Rotamer: Outliers : 3.04 % Allowed : 6.26 % Favored : 90.70 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.07 % Twisted Proline : 0.52 % Twisted General : 0.11 % 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: -2.71 (0.10), residues: 5630 helix: -2.65 (0.09), residues: 1647 sheet: -2.12 (0.15), residues: 941 loop : -1.07 (0.11), residues: 3042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP C 200 HIS 0.017 0.002 HIS d 134 PHE 0.049 0.003 PHE 6 18 TYR 0.036 0.003 TYR H 127 ARG 0.025 0.001 ARG f 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2068 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1926 time to evaluate : 6.155 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: symmetry clash revert: symmetry clash REVERT: B 29 PHE cc_start: 0.7393 (p90) cc_final: 0.7173 (p90) REVERT: B 41 ASN cc_start: 0.5679 (t0) cc_final: 0.4915 (m110) REVERT: B 51 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7628 (mt-10) REVERT: B 55 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7109 (mt-10) REVERT: B 57 ASN cc_start: 0.5184 (m-40) cc_final: 0.4978 (m-40) REVERT: B 58 LYS cc_start: 0.4612 (pttp) cc_final: 0.4294 (mtpp) REVERT: B 136 ARG cc_start: 0.5051 (ttp80) cc_final: 0.4308 (mtp-110) REVERT: B 142 LYS cc_start: 0.6042 (mmtm) cc_final: 0.5756 (pttt) REVERT: B 185 ILE cc_start: 0.5284 (pt) cc_final: 0.5027 (pt) REVERT: B 221 ARG cc_start: 0.6688 (mtt-85) cc_final: 0.5798 (mtm110) REVERT: C 3 LYS cc_start: 0.8639 (mttp) cc_final: 0.8431 (mmtp) REVERT: C 130 ARG cc_start: 0.6285 (tpp80) cc_final: 0.5882 (tpt90) REVERT: C 141 MET cc_start: 0.7151 (mmm) cc_final: 0.6561 (ptt) REVERT: D 89 LEU cc_start: 0.7886 (tp) cc_final: 0.7614 (mt) REVERT: D 155 LYS cc_start: 0.6533 (mtmm) cc_final: 0.6326 (mmmt) REVERT: D 178 GLU cc_start: 0.7199 (tt0) cc_final: 0.6482 (tm-30) REVERT: E 10 LEU cc_start: 0.5436 (pp) cc_final: 0.4802 (pp) REVERT: E 60 GLN cc_start: 0.7838 (tt0) cc_final: 0.7496 (mm-40) REVERT: E 68 ARG cc_start: 0.7842 (mmt-90) cc_final: 0.7587 (mtp-110) REVERT: E 94 PHE cc_start: 0.6538 (m-10) cc_final: 0.6226 (m-10) REVERT: E 95 MET cc_start: 0.6946 (ttp) cc_final: 0.6648 (ttm) REVERT: E 151 MET cc_start: 0.6925 (ttt) cc_final: 0.6628 (mmm) REVERT: F 52 ASN cc_start: 0.6814 (t0) cc_final: 0.6543 (t0) REVERT: G 28 ILE cc_start: 0.7853 (mm) cc_final: 0.7515 (pt) REVERT: G 39 GLU cc_start: 0.6824 (tp30) cc_final: 0.6106 (tt0) REVERT: G 48 THR cc_start: 0.6490 (m) cc_final: 0.6045 (p) REVERT: G 49 LEU cc_start: 0.6685 (mt) cc_final: 0.6377 (mm) REVERT: G 62 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7951 (tp30) REVERT: G 65 LEU cc_start: 0.8326 (tp) cc_final: 0.8060 (tt) REVERT: G 102 TRP cc_start: 0.6660 (m-10) cc_final: 0.6257 (m-10) REVERT: H 75 GLN cc_start: 0.7565 (tt0) cc_final: 0.7270 (mt0) REVERT: H 88 LYS cc_start: 0.7966 (tttt) cc_final: 0.7496 (tptp) REVERT: H 91 LEU cc_start: 0.7551 (tp) cc_final: 0.6877 (pt) REVERT: I 79 ARG cc_start: 0.8214 (ttp-170) cc_final: 0.8010 (mtp-110) REVERT: I 96 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6906 (mp0) REVERT: I 106 ASP cc_start: 0.7812 (t70) cc_final: 0.7517 (t0) REVERT: J 59 LYS cc_start: 0.8538 (mmmt) cc_final: 0.8219 (tppp) REVERT: J 87 LEU cc_start: 0.5314 (tp) cc_final: 0.5109 (mt) REVERT: K 71 ASP cc_start: 0.7528 (m-30) cc_final: 0.7201 (m-30) REVERT: K 127 ARG cc_start: 0.8127 (mtm180) cc_final: 0.7548 (mtm-85) REVERT: L 74 GLN cc_start: 0.8075 (mt0) cc_final: 0.7353 (mm-40) REVERT: L 85 ARG cc_start: 0.7769 (ptm160) cc_final: 0.7412 (ttp-110) REVERT: M 89 ARG cc_start: 0.7271 (mmt180) cc_final: 0.7010 (mmt-90) REVERT: Q 10 ARG cc_start: 0.6753 (ttp-110) cc_final: 0.6532 (tpp80) REVERT: Q 26 ARG cc_start: 0.8062 (ptm160) cc_final: 0.7248 (ptt90) REVERT: Q 52 CYS cc_start: 0.3694 (p) cc_final: 0.3368 (p) REVERT: Q 59 GLU cc_start: 0.7735 (tt0) cc_final: 0.7297 (tm-30) REVERT: Q 61 ARG cc_start: 0.6542 (ptt-90) cc_final: 0.6340 (ttp80) REVERT: R 56 ARG cc_start: 0.7655 (mtp85) cc_final: 0.7388 (mtt90) REVERT: R 73 HIS cc_start: 0.6222 (m-70) cc_final: 0.5521 (m90) REVERT: S 35 ARG cc_start: 0.8169 (mtp85) cc_final: 0.7927 (mtp-110) REVERT: S 69 LYS cc_start: 0.7573 (mttt) cc_final: 0.7325 (mttm) REVERT: T 4 LYS cc_start: 0.6613 (mmtp) cc_final: 0.6300 (pttp) REVERT: T 66 ILE cc_start: 0.6421 (mm) cc_final: 0.6218 (mm) REVERT: T 75 LYS cc_start: 0.7318 (tttt) cc_final: 0.6953 (pttp) REVERT: U 17 ARG cc_start: 0.8021 (mmt-90) cc_final: 0.7285 (ptp90) REVERT: U 18 PHE cc_start: 0.7036 (m-80) cc_final: 0.6591 (m-10) REVERT: 0 40 VAL cc_start: 0.8012 (t) cc_final: 0.7691 (p) REVERT: 0 59 ILE cc_start: 0.8628 (mt) cc_final: 0.8302 (mm) REVERT: 1 13 GLU cc_start: 0.6531 (mt-10) cc_final: 0.6032 (tp30) REVERT: 1 37 LEU cc_start: 0.7074 (tp) cc_final: 0.6775 (tp) REVERT: 1 44 LYS cc_start: 0.7737 (ttmt) cc_final: 0.7402 (tttm) REVERT: 1 60 LYS cc_start: 0.7437 (ttmt) cc_final: 0.7207 (tttm) REVERT: 2 11 ARG cc_start: 0.7566 (mtt-85) cc_final: 0.7133 (mtt180) REVERT: 2 36 VAL cc_start: 0.7476 (OUTLIER) cc_final: 0.7255 (p) REVERT: 2 37 GLU cc_start: 0.8021 (tt0) cc_final: 0.7584 (mp0) REVERT: 4 27 LYS cc_start: 0.6750 (tttp) cc_final: 0.6526 (tttp) REVERT: 4 33 LYS cc_start: 0.7732 (mmtt) cc_final: 0.7512 (pttm) REVERT: 4 37 LYS cc_start: 0.7917 (mttt) cc_final: 0.7357 (mmmt) REVERT: 7 34 THR cc_start: 0.8968 (t) cc_final: 0.8729 (m) REVERT: 7 35 LYS cc_start: 0.8194 (ptpt) cc_final: 0.7857 (ptpt) REVERT: 8 13 ASN cc_start: 0.7914 (m-40) cc_final: 0.7645 (m-40) REVERT: c 5 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7211 (mppt) REVERT: c 108 LYS cc_start: 0.8184 (tttt) cc_final: 0.7852 (tptt) REVERT: c 115 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7607 (mm110) REVERT: c 143 ASN cc_start: 0.8440 (t0) cc_final: 0.8232 (t0) REVERT: c 147 LYS cc_start: 0.7614 (mttm) cc_final: 0.6889 (mmtt) REVERT: c 181 MET cc_start: 0.7940 (mmt) cc_final: 0.7458 (mtp) REVERT: c 191 THR cc_start: 0.8665 (m) cc_final: 0.8193 (p) REVERT: c 265 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7158 (mttt) REVERT: i 10 LEU cc_start: -0.1062 (OUTLIER) cc_final: -0.1683 (tp) REVERT: i 11 GLN cc_start: -0.0513 (OUTLIER) cc_final: -0.1036 (pp30) REVERT: d 77 ARG cc_start: 0.8014 (ptp90) cc_final: 0.7570 (ptm-80) REVERT: d 86 GLU cc_start: 0.7522 (tt0) cc_final: 0.6959 (tm-30) REVERT: d 97 SER cc_start: 0.8220 (t) cc_final: 0.7865 (p) REVERT: d 101 PHE cc_start: 0.8373 (m-80) cc_final: 0.7981 (m-80) REVERT: d 103 ASP cc_start: 0.8161 (m-30) cc_final: 0.7783 (p0) REVERT: d 168 GLU cc_start: 0.8297 (pt0) cc_final: 0.7575 (pm20) REVERT: d 186 LEU cc_start: 0.7669 (mt) cc_final: 0.7428 (mp) REVERT: e 1 MET cc_start: 0.1322 (tpt) cc_final: 0.0960 (tpt) REVERT: e 15 SER cc_start: 0.7502 (m) cc_final: 0.6638 (t) REVERT: e 61 ARG cc_start: 0.6496 (ptp-170) cc_final: 0.5970 (ptm-80) REVERT: e 108 ILE cc_start: 0.8762 (pp) cc_final: 0.8477 (mt) REVERT: e 116 ASP cc_start: 0.7628 (m-30) cc_final: 0.7311 (t70) REVERT: e 131 THR cc_start: 0.8148 (p) cc_final: 0.7632 (t) REVERT: e 144 GLU cc_start: 0.7147 (tt0) cc_final: 0.6498 (mp0) REVERT: e 154 ASP cc_start: 0.5164 (t0) cc_final: 0.4468 (m-30) REVERT: e 195 GLN cc_start: 0.7942 (mt0) cc_final: 0.7605 (mt0) REVERT: f 7 TYR cc_start: 0.7681 (t80) cc_final: 0.7416 (t80) REVERT: f 37 ASN cc_start: 0.7132 (t0) cc_final: 0.6688 (t0) REVERT: f 47 LYS cc_start: 0.7096 (mmmt) cc_final: 0.6801 (mmmt) REVERT: f 51 ASP cc_start: 0.8165 (m-30) cc_final: 0.7489 (t0) REVERT: f 63 GLN cc_start: 0.7344 (mt0) cc_final: 0.6864 (mt0) REVERT: f 72 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.6507 (tmtt) REVERT: f 83 TYR cc_start: 0.6976 (m-80) cc_final: 0.5881 (m-10) REVERT: f 101 GLU cc_start: 0.7624 (tt0) cc_final: 0.7044 (tm-30) REVERT: f 120 LYS cc_start: 0.7738 (mttp) cc_final: 0.7411 (tppt) REVERT: f 130 MET cc_start: 0.6285 (ptm) cc_final: 0.5707 (ppp) REVERT: f 132 VAL cc_start: 0.7625 (OUTLIER) cc_final: 0.7333 (m) REVERT: f 137 ILE cc_start: 0.6479 (pt) cc_final: 0.6156 (pt) REVERT: g 3 ARG cc_start: 0.7072 (mtm-85) cc_final: 0.6751 (mtp-110) REVERT: g 6 LYS cc_start: 0.6589 (mtmm) cc_final: 0.6201 (ttpt) REVERT: g 33 LEU cc_start: 0.6802 (mt) cc_final: 0.5534 (tt) REVERT: g 39 ASP cc_start: 0.8247 (m-30) cc_final: 0.7738 (p0) REVERT: g 44 LYS cc_start: 0.8729 (mttt) cc_final: 0.8428 (mmtt) REVERT: g 64 GLN cc_start: 0.7466 (mm-40) cc_final: 0.7196 (mm-40) REVERT: g 83 PHE cc_start: 0.7725 (m-80) cc_final: 0.7498 (m-80) REVERT: h 2 GLN cc_start: 0.8773 (mt0) cc_final: 0.8477 (mm-40) REVERT: h 129 GLU cc_start: 0.4723 (tt0) cc_final: 0.4499 (mm-30) REVERT: j 23 LYS cc_start: 0.7509 (mmmt) cc_final: 0.7230 (mmtt) REVERT: j 60 ASP cc_start: 0.8497 (p0) cc_final: 0.8198 (p0) REVERT: j 61 LYS cc_start: 0.6909 (mttt) cc_final: 0.6428 (tppt) REVERT: j 106 LYS cc_start: 0.8064 (tttt) cc_final: 0.7812 (ttmm) REVERT: j 108 MET cc_start: 0.8466 (mtt) cc_final: 0.7828 (mtt) REVERT: j 138 GLN cc_start: 0.7367 (pt0) cc_final: 0.6773 (mm-40) REVERT: k 80 ASP cc_start: 0.7515 (m-30) cc_final: 0.7261 (m-30) REVERT: l 1 MET cc_start: 0.6472 (ttp) cc_final: 0.6186 (ppp) REVERT: l 13 LYS cc_start: 0.8505 (mmtp) cc_final: 0.7391 (tptm) REVERT: l 38 GLN cc_start: 0.8506 (tt0) cc_final: 0.8293 (tt0) REVERT: l 69 ARG cc_start: 0.8502 (mmm-85) cc_final: 0.8284 (mmm-85) REVERT: l 81 ASP cc_start: 0.7636 (m-30) cc_final: 0.7356 (m-30) REVERT: l 94 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7467 (t) REVERT: m 10 ARG cc_start: 0.7433 (mtp-110) cc_final: 0.7109 (mmm160) REVERT: m 12 MET cc_start: 0.7964 (ttm) cc_final: 0.7749 (ttm) REVERT: m 45 GLN cc_start: 0.8575 (mt0) cc_final: 0.8293 (mt0) REVERT: m 50 ARG cc_start: 0.8309 (ttp80) cc_final: 0.7923 (ttp-170) REVERT: m 57 VAL cc_start: 0.7947 (m) cc_final: 0.7622 (p) REVERT: m 59 ARG cc_start: 0.8101 (mtt180) cc_final: 0.7770 (tpt170) REVERT: m 73 ILE cc_start: 0.8931 (mm) cc_final: 0.8717 (mm) REVERT: o 9 ARG cc_start: 0.8862 (mtt180) cc_final: 0.8567 (ttp-110) REVERT: o 40 ILE cc_start: 0.8271 (mt) cc_final: 0.7973 (mm) REVERT: o 80 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7614 (pt0) REVERT: o 89 ASP cc_start: 0.8012 (t70) cc_final: 0.7451 (m-30) REVERT: p 38 LYS cc_start: 0.6739 (tttp) cc_final: 0.6474 (mmmt) REVERT: p 66 ASN cc_start: 0.7689 (m110) cc_final: 0.7382 (m110) REVERT: q 4 VAL cc_start: 0.8222 (t) cc_final: 0.7971 (p) REVERT: q 16 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.8023 (ptmm) REVERT: q 22 LYS cc_start: 0.7672 (mmpt) cc_final: 0.7447 (mttp) REVERT: q 44 GLN cc_start: 0.8303 (mt0) cc_final: 0.8021 (mt0) REVERT: q 101 PHE cc_start: 0.8150 (m-80) cc_final: 0.7380 (m-80) REVERT: r 16 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7488 (tp30) REVERT: r 38 VAL cc_start: 0.7315 (OUTLIER) cc_final: 0.6872 (m) REVERT: r 77 PHE cc_start: 0.8987 (t80) cc_final: 0.8779 (t80) REVERT: s 1 MET cc_start: 0.6118 (tpt) cc_final: 0.5804 (pmm) REVERT: s 92 ARG cc_start: 0.8304 (mtt90) cc_final: 0.8016 (mmp-170) REVERT: t 3 ARG cc_start: 0.7746 (mtt180) cc_final: 0.7312 (mpt90) REVERT: t 88 LYS cc_start: 0.8527 (mmtt) cc_final: 0.8318 (mtmt) REVERT: u 26 LYS cc_start: 0.7797 (mmmt) cc_final: 0.7524 (mtpt) REVERT: u 37 GLU cc_start: 0.6021 (OUTLIER) cc_final: 0.5665 (mt-10) REVERT: u 42 VAL cc_start: 0.7080 (m) cc_final: 0.6821 (p) REVERT: u 43 LYS cc_start: 0.6832 (mtmm) cc_final: 0.6190 (mmtt) REVERT: u 79 LYS cc_start: 0.8408 (mttm) cc_final: 0.8056 (mtmt) REVERT: w 2 PHE cc_start: 0.7361 (m-80) cc_final: 0.7107 (m-80) REVERT: w 43 ASP cc_start: 0.6525 (t0) cc_final: 0.6172 (m-30) REVERT: w 48 MET cc_start: 0.6400 (tpt) cc_final: 0.5826 (tpt) REVERT: w 59 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7305 (mp0) REVERT: w 65 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8229 (p) REVERT: w 66 ASP cc_start: 0.6340 (m-30) cc_final: 0.6049 (m-30) REVERT: w 71 LYS cc_start: 0.7849 (mtpt) cc_final: 0.7098 (pttm) REVERT: w 76 ASP cc_start: 0.7937 (t70) cc_final: 0.7651 (t0) REVERT: w 77 VAL cc_start: 0.8643 (p) cc_final: 0.8205 (t) REVERT: w 93 ARG cc_start: 0.7389 (mtt90) cc_final: 0.6606 (mtm180) REVERT: y 35 SER cc_start: 0.8779 (m) cc_final: 0.8495 (m) REVERT: y 82 ILE cc_start: 0.8677 (mt) cc_final: 0.8244 (mm) REVERT: z 4 GLN cc_start: 0.4847 (OUTLIER) cc_final: 0.3357 (tm-30) REVERT: z 5 LYS cc_start: 0.5994 (OUTLIER) cc_final: 0.4181 (ptpt) REVERT: z 9 GLU cc_start: 0.3831 (OUTLIER) cc_final: 0.2626 (mt-10) REVERT: z 26 ARG cc_start: 0.5034 (OUTLIER) cc_final: 0.4458 (mmm-85) outliers start: 142 outliers final: 26 residues processed: 2019 average time/residue: 1.4004 time to fit residues: 4701.8814 Evaluate side-chains 1376 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1333 time to evaluate : 6.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 6 residue 44 VAL Chi-restraints excluded: chain c residue 5 LYS Chi-restraints excluded: chain c residue 115 GLN Chi-restraints excluded: chain c residue 157 SER Chi-restraints excluded: chain c residue 265 LYS Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 11 GLN Chi-restraints excluded: chain i residue 81 LYS Chi-restraints excluded: chain i residue 85 ILE Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 93 SER Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 187 VAL Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain l residue 94 THR Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain q residue 9 ILE Chi-restraints excluded: chain q residue 16 LYS Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain u residue 37 GLU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain z residue 4 GLN Chi-restraints excluded: chain z residue 5 LYS Chi-restraints excluded: chain z residue 9 GLU Chi-restraints excluded: chain z residue 10 GLU Chi-restraints excluded: chain z residue 12 LEU Chi-restraints excluded: chain z residue 15 THR Chi-restraints excluded: chain z residue 18 TRP Chi-restraints excluded: chain z residue 20 SER Chi-restraints excluded: chain z residue 21 GLN Chi-restraints excluded: chain z residue 26 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 861 optimal weight: 20.0000 chunk 773 optimal weight: 9.9990 chunk 428 optimal weight: 6.9990 chunk 264 optimal weight: 8.9990 chunk 521 optimal weight: 10.0000 chunk 413 optimal weight: 0.9980 chunk 799 optimal weight: 3.9990 chunk 309 optimal weight: 10.0000 chunk 486 optimal weight: 3.9990 chunk 595 optimal weight: 9.9990 chunk 926 optimal weight: 9.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN B 176 ASN ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN D 119 HIS ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN D 135 GLN D 139 ASN ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN E 77 ASN E 82 HIS E 88 HIS E 147 ASN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN I 80 HIS K 23 HIS K 39 ASN K 80 ASN L 19 ASN L 58 ASN ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 HIS ** O 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 HIS O 50 HIS ** P 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN P 59 HIS Q 30 HIS Q 50 ASN ** S 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 56 HIS T 12 GLN T 74 HIS 1 25 GLN 1 58 ASN 7 28 ASN ** c 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 260 ASN i 11 GLN ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 106 GLN i 110 GLN ** d 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN f 5 HIS ** f 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 63 GLN g 30 ASN g 38 ASN g 45 HIS g 115 HIS h 28 ASN ** h 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 119 ASN h 128 HIS k 3 GLN n 18 GLN ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 100 HIS q 20 GLN q 52 GLN r 82 HIS s 7 HIS s 61 ASN t 59 ASN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 78 GLN z 4 GLN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.221 158637 Z= 0.307 Angle : 0.916 24.911 237537 Z= 0.462 Chirality : 0.050 2.506 30396 Planarity : 0.007 0.116 12579 Dihedral : 25.105 179.783 80024 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 1.15 % Allowed : 7.02 % Favored : 91.83 % Rotamer: Outliers : 5.79 % Allowed : 15.80 % Favored : 78.41 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.07 % Twisted Proline : 2.08 % 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: -1.89 (0.11), residues: 5630 helix: -0.82 (0.12), residues: 1708 sheet: -1.64 (0.15), residues: 1004 loop : -1.30 (0.11), residues: 2918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP c 213 HIS 0.014 0.002 HIS K 117 PHE 0.030 0.002 PHE i 68 TYR 0.032 0.003 TYR H 127 ARG 0.020 0.001 ARG P 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1672 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 1401 time to evaluate : 6.319 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: B 41 ASN cc_start: 0.5395 (t0) cc_final: 0.4635 (m110) REVERT: B 55 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7027 (mt-10) REVERT: B 117 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8217 (mm-30) REVERT: B 221 ARG cc_start: 0.6562 (mtt-85) cc_final: 0.5788 (mtm110) REVERT: C 69 THR cc_start: 0.7054 (p) cc_final: 0.6682 (p) REVERT: C 113 LYS cc_start: 0.6806 (ttmt) cc_final: 0.6603 (tppt) REVERT: C 128 MET cc_start: 0.5272 (ttt) cc_final: 0.4924 (ttt) REVERT: C 134 LYS cc_start: 0.6455 (OUTLIER) cc_final: 0.6004 (mptt) REVERT: C 141 MET cc_start: 0.6734 (mmm) cc_final: 0.6413 (ptt) REVERT: D 46 ARG cc_start: 0.6674 (ttm170) cc_final: 0.5686 (mpp80) REVERT: D 103 ARG cc_start: 0.7069 (mmt90) cc_final: 0.6010 (ptm160) REVERT: D 162 GLU cc_start: 0.6864 (mm-30) cc_final: 0.6340 (mp0) REVERT: D 178 GLU cc_start: 0.6740 (tt0) cc_final: 0.6507 (tt0) REVERT: E 44 ARG cc_start: 0.6793 (tpp-160) cc_final: 0.6232 (tpp80) REVERT: E 60 GLN cc_start: 0.8286 (tt0) cc_final: 0.8038 (mm-40) REVERT: E 68 ARG cc_start: 0.7909 (mmt-90) cc_final: 0.7654 (mtp-110) REVERT: E 94 PHE cc_start: 0.6493 (m-10) cc_final: 0.5909 (m-10) REVERT: E 121 ASN cc_start: 0.7767 (OUTLIER) cc_final: 0.7542 (m110) REVERT: E 122 VAL cc_start: 0.8710 (t) cc_final: 0.8182 (p) REVERT: F 65 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6481 (mm-30) REVERT: G 39 GLU cc_start: 0.6682 (tp30) cc_final: 0.5958 (tt0) REVERT: G 62 GLU cc_start: 0.8541 (mt-10) cc_final: 0.7701 (tp30) REVERT: G 100 MET cc_start: 0.6413 (OUTLIER) cc_final: 0.6086 (mtm) REVERT: G 109 LYS cc_start: 0.6392 (mmmt) cc_final: 0.6108 (mmmt) REVERT: G 121 ASN cc_start: 0.8336 (t0) cc_final: 0.8103 (t0) REVERT: G 143 MET cc_start: 0.7112 (tpp) cc_final: 0.6847 (tpp) REVERT: H 35 ILE cc_start: 0.8826 (mm) cc_final: 0.8534 (tp) REVERT: H 40 LYS cc_start: 0.8596 (tptt) cc_final: 0.8248 (tptm) REVERT: H 86 LYS cc_start: 0.7448 (mmtm) cc_final: 0.7152 (pttp) REVERT: H 87 ARG cc_start: 0.7929 (mmm-85) cc_final: 0.7296 (mtp-110) REVERT: H 88 LYS cc_start: 0.8062 (tttt) cc_final: 0.7503 (tptp) REVERT: H 91 LEU cc_start: 0.7529 (tp) cc_final: 0.7112 (pt) REVERT: I 11 ARG cc_start: 0.6861 (tpt-90) cc_final: 0.6642 (tpt-90) REVERT: I 87 MET cc_start: 0.5744 (ppp) cc_final: 0.5208 (ttt) REVERT: I 114 LYS cc_start: 0.7167 (mtmt) cc_final: 0.6964 (mtmt) REVERT: J 45 ARG cc_start: 0.6259 (tpp-160) cc_final: 0.5942 (tpp-160) REVERT: K 21 HIS cc_start: 0.7261 (OUTLIER) cc_final: 0.6961 (m-70) REVERT: K 82 GLU cc_start: 0.6066 (mp0) cc_final: 0.5822 (mp0) REVERT: K 127 ARG cc_start: 0.8457 (mtm180) cc_final: 0.7985 (mtm-85) REVERT: L 37 TYR cc_start: 0.5995 (m-10) cc_final: 0.5536 (m-10) REVERT: L 74 GLN cc_start: 0.7859 (mt0) cc_final: 0.7034 (mm-40) REVERT: L 75 GLU cc_start: 0.6623 (tm-30) cc_final: 0.6422 (tm-30) REVERT: L 94 TYR cc_start: 0.8744 (m-80) cc_final: 0.8481 (m-80) REVERT: M 69 ARG cc_start: 0.4621 (OUTLIER) cc_final: 0.4391 (mmt180) REVERT: M 102 LYS cc_start: 0.7642 (tttt) cc_final: 0.7366 (mttt) REVERT: N 6 LYS cc_start: 0.8016 (tttt) cc_final: 0.7794 (mtmt) REVERT: O 61 GLN cc_start: 0.8299 (mm-40) cc_final: 0.8004 (tt0) REVERT: Q 10 ARG cc_start: 0.6705 (ttp-110) cc_final: 0.6438 (tpp80) REVERT: Q 26 ARG cc_start: 0.8038 (ptm160) cc_final: 0.7254 (ptt90) REVERT: S 69 LYS cc_start: 0.7705 (mttt) cc_final: 0.7290 (mttm) REVERT: S 78 THR cc_start: 0.7576 (m) cc_final: 0.7256 (t) REVERT: T 4 LYS cc_start: 0.6752 (mmtp) cc_final: 0.6507 (pttp) REVERT: T 12 GLN cc_start: 0.8094 (mt0) cc_final: 0.7889 (tm-30) REVERT: T 75 LYS cc_start: 0.7618 (tttt) cc_final: 0.7015 (pttp) REVERT: U 13 VAL cc_start: 0.5421 (t) cc_final: 0.5199 (p) REVERT: U 17 ARG cc_start: 0.8049 (mmt-90) cc_final: 0.7335 (ptp90) REVERT: U 18 PHE cc_start: 0.7183 (m-80) cc_final: 0.6703 (m-10) REVERT: U 30 GLU cc_start: 0.7504 (pt0) cc_final: 0.6933 (mm-30) REVERT: U 32 ARG cc_start: 0.7054 (ptm-80) cc_final: 0.6853 (ptm160) REVERT: U 35 GLU cc_start: 0.5270 (pm20) cc_final: 0.4685 (pm20) REVERT: 1 13 GLU cc_start: 0.6692 (mt-10) cc_final: 0.6301 (tp30) REVERT: 1 44 LYS cc_start: 0.7992 (ttmt) cc_final: 0.7613 (tttm) REVERT: 1 54 LYS cc_start: 0.8258 (mttm) cc_final: 0.8040 (mttt) REVERT: 1 60 LYS cc_start: 0.7659 (ttmt) cc_final: 0.7275 (tttm) REVERT: 2 11 ARG cc_start: 0.7507 (mtt-85) cc_final: 0.6969 (mtt180) REVERT: 3 33 THR cc_start: 0.8302 (m) cc_final: 0.8093 (p) REVERT: 4 37 LYS cc_start: 0.7943 (mttt) cc_final: 0.7428 (mmmt) REVERT: 4 51 GLU cc_start: 0.5855 (OUTLIER) cc_final: 0.5536 (tm-30) REVERT: 8 9 LYS cc_start: 0.8086 (mtmm) cc_final: 0.7870 (mtpt) REVERT: 8 13 ASN cc_start: 0.8219 (m-40) cc_final: 0.7108 (t0) REVERT: c 5 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7171 (mppt) REVERT: c 108 LYS cc_start: 0.8241 (tttt) cc_final: 0.7940 (tptt) REVERT: c 115 GLN cc_start: 0.8144 (mm110) cc_final: 0.7869 (mm110) REVERT: c 147 LYS cc_start: 0.8065 (mttm) cc_final: 0.7548 (mmtt) REVERT: c 181 MET cc_start: 0.7871 (mmt) cc_final: 0.7576 (mtp) REVERT: c 265 LYS cc_start: 0.8112 (tmtt) cc_final: 0.7227 (mttt) REVERT: i 86 LYS cc_start: 0.1990 (OUTLIER) cc_final: 0.0914 (mmtp) REVERT: d 86 GLU cc_start: 0.7638 (tt0) cc_final: 0.7187 (tm-30) REVERT: d 139 SER cc_start: 0.9102 (m) cc_final: 0.8788 (t) REVERT: e 100 MET cc_start: 0.8649 (mtp) cc_final: 0.8139 (mtp) REVERT: e 111 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7945 (tp30) REVERT: e 116 ASP cc_start: 0.7735 (m-30) cc_final: 0.7434 (t70) REVERT: e 137 LYS cc_start: 0.7287 (tttt) cc_final: 0.7081 (tttt) REVERT: e 144 GLU cc_start: 0.7009 (tt0) cc_final: 0.6461 (mp0) REVERT: e 187 VAL cc_start: 0.7987 (OUTLIER) cc_final: 0.7755 (m) REVERT: e 188 MET cc_start: 0.8535 (mtm) cc_final: 0.8192 (mtm) REVERT: e 195 GLN cc_start: 0.8259 (mt0) cc_final: 0.8021 (mt0) REVERT: f 7 TYR cc_start: 0.7705 (t80) cc_final: 0.6962 (t80) REVERT: f 10 ASP cc_start: 0.7904 (t70) cc_final: 0.7013 (m-30) REVERT: f 11 GLU cc_start: 0.7767 (tp30) cc_final: 0.7309 (mm-30) REVERT: f 37 ASN cc_start: 0.7070 (t0) cc_final: 0.6702 (t0) REVERT: f 51 ASP cc_start: 0.8394 (m-30) cc_final: 0.7811 (t0) REVERT: f 64 LYS cc_start: 0.3412 (mttt) cc_final: 0.3135 (mttt) REVERT: f 83 TYR cc_start: 0.7623 (OUTLIER) cc_final: 0.6362 (m-10) REVERT: f 101 GLU cc_start: 0.7885 (tt0) cc_final: 0.7410 (tm-30) REVERT: f 130 MET cc_start: 0.5506 (ptm) cc_final: 0.5200 (ptp) REVERT: f 141 ILE cc_start: 0.6761 (OUTLIER) cc_final: 0.6505 (mp) REVERT: f 164 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7562 (tm-30) REVERT: f 170 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.7009 (mm) REVERT: g 30 ASN cc_start: 0.7432 (OUTLIER) cc_final: 0.7155 (t0) REVERT: g 39 ASP cc_start: 0.8201 (m-30) cc_final: 0.7748 (p0) REVERT: g 42 GLU cc_start: 0.7490 (tp30) cc_final: 0.7184 (tp30) REVERT: g 64 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7273 (mm-40) REVERT: g 81 GLU cc_start: 0.8149 (tt0) cc_final: 0.7826 (tt0) REVERT: g 83 PHE cc_start: 0.8070 (m-80) cc_final: 0.7540 (m-80) REVERT: g 99 LYS cc_start: 0.8069 (mptt) cc_final: 0.7768 (tmtt) REVERT: h 3 VAL cc_start: 0.7768 (OUTLIER) cc_final: 0.7523 (p) REVERT: h 43 ASN cc_start: 0.5088 (m-40) cc_final: 0.4549 (m-40) REVERT: h 48 GLU cc_start: 0.7177 (tp30) cc_final: 0.6890 (mt-10) REVERT: h 114 GLU cc_start: 0.4821 (OUTLIER) cc_final: 0.4496 (tm-30) REVERT: h 129 GLU cc_start: 0.5057 (tt0) cc_final: 0.4792 (mm-30) REVERT: j 60 ASP cc_start: 0.8635 (p0) cc_final: 0.8320 (p0) REVERT: j 108 MET cc_start: 0.8221 (mtt) cc_final: 0.7891 (mtt) REVERT: j 138 GLN cc_start: 0.7534 (pt0) cc_final: 0.7075 (tp40) REVERT: k 93 GLN cc_start: 0.8426 (mm-40) cc_final: 0.7912 (mt0) REVERT: l 13 LYS cc_start: 0.8168 (mmtp) cc_final: 0.6932 (tptm) REVERT: l 38 GLN cc_start: 0.8479 (tt0) cc_final: 0.8240 (tt0) REVERT: l 69 ARG cc_start: 0.8129 (mmm-85) cc_final: 0.7575 (mmm-85) REVERT: l 96 LYS cc_start: 0.8611 (ttmt) cc_final: 0.8347 (mtpt) REVERT: l 121 THR cc_start: 0.8139 (m) cc_final: 0.7860 (t) REVERT: m 12 MET cc_start: 0.8141 (ttm) cc_final: 0.7790 (ttm) REVERT: m 51 ARG cc_start: 0.8365 (mtt90) cc_final: 0.7561 (mmt180) REVERT: m 55 ARG cc_start: 0.7652 (mpt-90) cc_final: 0.7429 (mtt-85) REVERT: m 59 ARG cc_start: 0.8124 (mtt180) cc_final: 0.7779 (tpt170) REVERT: m 65 ILE cc_start: 0.8491 (mt) cc_final: 0.8282 (tt) REVERT: n 1 MET cc_start: 0.8574 (pmm) cc_final: 0.8304 (ptp) REVERT: o 80 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7391 (pp20) REVERT: o 89 ASP cc_start: 0.7971 (t70) cc_final: 0.7420 (m-30) REVERT: o 90 VAL cc_start: 0.7573 (m) cc_final: 0.7280 (m) REVERT: o 99 TYR cc_start: 0.8417 (t80) cc_final: 0.8194 (t80) REVERT: p 11 GLU cc_start: 0.8899 (pt0) cc_final: 0.8666 (pt0) REVERT: p 37 LYS cc_start: 0.6525 (ptpp) cc_final: 0.6109 (pttp) REVERT: p 38 LYS cc_start: 0.7050 (tttp) cc_final: 0.6639 (mmmt) REVERT: p 106 LYS cc_start: 0.7282 (mmtt) cc_final: 0.6953 (mtmt) REVERT: q 101 PHE cc_start: 0.8199 (m-80) cc_final: 0.7683 (m-80) REVERT: r 16 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7845 (tm-30) REVERT: r 101 ILE cc_start: 0.7783 (mm) cc_final: 0.7416 (tt) REVERT: s 1 MET cc_start: 0.6304 (tpt) cc_final: 0.5837 (pmm) REVERT: s 59 GLU cc_start: 0.7730 (tp30) cc_final: 0.7231 (mt-10) REVERT: t 3 ARG cc_start: 0.7674 (mtt180) cc_final: 0.7024 (mmt180) REVERT: t 26 LYS cc_start: 0.8046 (ttpt) cc_final: 0.7549 (tppt) REVERT: t 74 ILE cc_start: 0.6040 (OUTLIER) cc_final: 0.5495 (pp) REVERT: u 4 LYS cc_start: 0.6854 (mttp) cc_final: 0.6524 (mttp) REVERT: u 26 LYS cc_start: 0.7834 (mmmt) cc_final: 0.7541 (mtpt) REVERT: u 79 LYS cc_start: 0.8405 (mttm) cc_final: 0.8074 (mtmt) REVERT: w 4 ILE cc_start: 0.7797 (OUTLIER) cc_final: 0.7509 (pt) REVERT: w 43 ASP cc_start: 0.7029 (t0) cc_final: 0.6650 (m-30) REVERT: w 51 GLN cc_start: 0.8273 (pp30) cc_final: 0.7978 (pp30) REVERT: w 64 VAL cc_start: 0.7494 (t) cc_final: 0.7099 (m) REVERT: w 71 LYS cc_start: 0.7946 (mtpt) cc_final: 0.7426 (mtmm) REVERT: w 93 ARG cc_start: 0.7293 (mtt90) cc_final: 0.6960 (mtm180) REVERT: z 4 GLN cc_start: 0.5443 (OUTLIER) cc_final: 0.3507 (tm-30) REVERT: z 5 LYS cc_start: 0.5412 (OUTLIER) cc_final: 0.3821 (ptpt) REVERT: z 13 PHE cc_start: 0.6365 (OUTLIER) cc_final: 0.4847 (m-10) REVERT: z 26 ARG cc_start: 0.4767 (OUTLIER) cc_final: 0.4317 (mmm160) outliers start: 271 outliers final: 153 residues processed: 1554 average time/residue: 1.2956 time to fit residues: 3434.4666 Evaluate side-chains 1408 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1233 time to evaluate : 6.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 21 HIS Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain L residue 26 CYS Chi-restraints excluded: chain L residue 45 ASN Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 119 LYS Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 47 THR Chi-restraints excluded: chain S residue 65 MET Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 67 HIS Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain 0 residue 13 VAL Chi-restraints excluded: chain 3 residue 32 LYS Chi-restraints excluded: chain 4 residue 8 LYS Chi-restraints excluded: chain 4 residue 12 VAL Chi-restraints excluded: chain 4 residue 22 THR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 32 GLU Chi-restraints excluded: chain 4 residue 47 VAL Chi-restraints excluded: chain 4 residue 51 GLU Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 31 LEU Chi-restraints excluded: chain 6 residue 44 VAL Chi-restraints excluded: chain 8 residue 3 VAL Chi-restraints excluded: chain 8 residue 7 VAL Chi-restraints excluded: chain 8 residue 22 VAL Chi-restraints excluded: chain 8 residue 26 ILE Chi-restraints excluded: chain c residue 5 LYS Chi-restraints excluded: chain c residue 24 LEU Chi-restraints excluded: chain c residue 160 THR Chi-restraints excluded: chain c residue 201 MET Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 86 LYS Chi-restraints excluded: chain i residue 95 ASP Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 51 THR Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 105 LYS Chi-restraints excluded: chain d residue 113 SER Chi-restraints excluded: chain d residue 138 LEU Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 200 ASP Chi-restraints excluded: chain e residue 70 SER Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain e residue 187 VAL Chi-restraints excluded: chain f residue 6 ASP Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 134 GLU Chi-restraints excluded: chain f residue 141 ILE Chi-restraints excluded: chain f residue 170 LEU Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 30 ASN Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 121 ILE Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain h residue 114 GLU Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 124 VAL Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 7 SER Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain n residue 10 LEU Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain p residue 17 VAL Chi-restraints excluded: chain p residue 41 GLN Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain q residue 9 ILE Chi-restraints excluded: chain q residue 34 VAL Chi-restraints excluded: chain q residue 52 GLN Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 55 ASP Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain t residue 61 LEU Chi-restraints excluded: chain t residue 74 ILE Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain u residue 11 VAL Chi-restraints excluded: chain u residue 28 VAL Chi-restraints excluded: chain u residue 49 VAL Chi-restraints excluded: chain u residue 67 VAL Chi-restraints excluded: chain u residue 102 THR Chi-restraints excluded: chain w residue 4 ILE Chi-restraints excluded: chain w residue 77 VAL Chi-restraints excluded: chain y residue 51 VAL Chi-restraints excluded: chain y residue 71 VAL Chi-restraints excluded: chain y residue 81 SER Chi-restraints excluded: chain z residue 4 GLN Chi-restraints excluded: chain z residue 5 LYS Chi-restraints excluded: chain z residue 12 LEU Chi-restraints excluded: chain z residue 13 PHE Chi-restraints excluded: chain z residue 18 TRP Chi-restraints excluded: chain z residue 20 SER Chi-restraints excluded: chain z residue 26 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 514 optimal weight: 10.0000 chunk 287 optimal weight: 20.0000 chunk 770 optimal weight: 8.9990 chunk 630 optimal weight: 10.0000 chunk 255 optimal weight: 5.9990 chunk 927 optimal weight: 6.9990 chunk 1002 optimal weight: 8.9990 chunk 826 optimal weight: 7.9990 chunk 920 optimal weight: 2.9990 chunk 316 optimal weight: 7.9990 chunk 744 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN F 68 GLN ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 GLN O 27 GLN ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 41 HIS ** P 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 GLN T 69 ASN 0 6 GLN 1 58 ASN 8 35 GLN c 53 HIS c 153 GLN ** c 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 226 ASN ** i 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 106 GLN d 150 GLN e 115 GLN f 5 HIS f 27 GLN ** h 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 54 GLN l 99 ASN ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN q 37 GLN s 9 HIS s 31 GLN s 61 ASN u 27 ASN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 74 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.131 158637 Z= 0.315 Angle : 0.801 21.959 237537 Z= 0.410 Chirality : 0.045 0.669 30396 Planarity : 0.006 0.192 12579 Dihedral : 24.837 179.237 79971 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.65 % Favored : 90.48 % Rotamer: Outliers : 7.05 % Allowed : 19.03 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.07 % Twisted Proline : 2.08 % 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: -1.80 (0.11), residues: 5630 helix: -0.35 (0.12), residues: 1698 sheet: -1.67 (0.15), residues: 1079 loop : -1.47 (0.11), residues: 2853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 200 HIS 0.014 0.002 HIS T 19 PHE 0.031 0.003 PHE I 126 TYR 0.040 0.003 TYR M 22 ARG 0.020 0.001 ARG U 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1640 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 330 poor density : 1310 time to evaluate : 6.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 ILE cc_start: 0.6329 (mm) cc_final: 0.5771 (mm) REVERT: B 41 ASN cc_start: 0.5595 (t0) cc_final: 0.4893 (m110) REVERT: B 43 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7864 (pm20) REVERT: B 55 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6687 (mt-10) REVERT: B 99 MET cc_start: 0.7973 (mmm) cc_final: 0.7750 (mmm) REVERT: B 102 ASN cc_start: 0.7664 (t0) cc_final: 0.7435 (t0) REVERT: B 166 ASP cc_start: 0.4803 (m-30) cc_final: 0.4580 (m-30) REVERT: B 168 GLU cc_start: 0.7321 (mm-30) cc_final: 0.7002 (mm-30) REVERT: B 185 ILE cc_start: 0.5030 (pt) cc_final: 0.4728 (pt) REVERT: B 221 ARG cc_start: 0.6671 (mtt-85) cc_final: 0.6297 (mtt-85) REVERT: C 3 LYS cc_start: 0.8561 (mttp) cc_final: 0.8299 (tppt) REVERT: C 134 LYS cc_start: 0.6311 (OUTLIER) cc_final: 0.6024 (mptt) REVERT: C 169 GLU cc_start: 0.7086 (tt0) cc_final: 0.6494 (tt0) REVERT: C 198 LYS cc_start: 0.7770 (ttmt) cc_final: 0.7554 (ttmt) REVERT: D 46 ARG cc_start: 0.6693 (ttm170) cc_final: 0.5352 (mpp80) REVERT: D 71 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.6510 (m-80) REVERT: D 80 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7578 (ppt170) REVERT: D 92 LEU cc_start: 0.8163 (mt) cc_final: 0.7733 (mp) REVERT: D 93 LEU cc_start: 0.7939 (mt) cc_final: 0.7286 (pp) REVERT: D 98 ASP cc_start: 0.8010 (p0) cc_final: 0.7305 (m-30) REVERT: D 103 ARG cc_start: 0.7048 (mmt90) cc_final: 0.6052 (ptm160) REVERT: D 135 GLN cc_start: 0.5778 (mm110) cc_final: 0.5510 (pt0) REVERT: D 162 GLU cc_start: 0.6791 (mm-30) cc_final: 0.6282 (mp0) REVERT: E 49 TYR cc_start: 0.5856 (t80) cc_final: 0.5633 (t80) REVERT: E 63 MET cc_start: 0.7027 (mmm) cc_final: 0.6690 (mmm) REVERT: E 68 ARG cc_start: 0.8034 (mmt-90) cc_final: 0.7581 (mtp-110) REVERT: E 94 PHE cc_start: 0.6590 (m-10) cc_final: 0.6141 (m-10) REVERT: E 122 VAL cc_start: 0.8516 (OUTLIER) cc_final: 0.8248 (p) REVERT: F 65 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6312 (mm-30) REVERT: G 24 LYS cc_start: 0.7125 (OUTLIER) cc_final: 0.6901 (mtpt) REVERT: G 39 GLU cc_start: 0.6898 (tp30) cc_final: 0.6619 (mt-10) REVERT: G 62 GLU cc_start: 0.8600 (mt-10) cc_final: 0.7783 (tp30) REVERT: G 67 ASN cc_start: 0.4639 (m-40) cc_final: 0.4382 (m-40) REVERT: G 121 ASN cc_start: 0.8004 (t0) cc_final: 0.7789 (t0) REVERT: G 143 MET cc_start: 0.7413 (tpp) cc_final: 0.7058 (tpp) REVERT: H 26 MET cc_start: 0.7765 (ptp) cc_final: 0.7515 (ptp) REVERT: H 40 LYS cc_start: 0.8558 (tptt) cc_final: 0.8305 (tptm) REVERT: H 87 ARG cc_start: 0.8103 (mmm-85) cc_final: 0.7764 (mtp-110) REVERT: H 88 LYS cc_start: 0.7873 (tttt) cc_final: 0.7355 (tptp) REVERT: H 91 LEU cc_start: 0.7556 (tp) cc_final: 0.6819 (pt) REVERT: I 11 ARG cc_start: 0.6811 (tpt-90) cc_final: 0.5970 (tpt170) REVERT: I 87 MET cc_start: 0.6043 (ppp) cc_final: 0.5272 (ttt) REVERT: J 45 ARG cc_start: 0.6466 (tpp-160) cc_final: 0.6251 (tpp-160) REVERT: K 71 ASP cc_start: 0.6933 (m-30) cc_final: 0.6672 (m-30) REVERT: L 26 CYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7595 (p) REVERT: L 74 GLN cc_start: 0.8125 (mt0) cc_final: 0.7145 (mm-40) REVERT: M 69 ARG cc_start: 0.4820 (OUTLIER) cc_final: 0.4605 (mpt90) REVERT: O 61 GLN cc_start: 0.8405 (mm-40) cc_final: 0.8017 (tt0) REVERT: P 63 GLN cc_start: 0.6039 (mt0) cc_final: 0.5802 (mt0) REVERT: Q 10 ARG cc_start: 0.6576 (ttp-110) cc_final: 0.6331 (tpp80) REVERT: Q 26 ARG cc_start: 0.8143 (ptm160) cc_final: 0.7249 (ptt90) REVERT: Q 33 TYR cc_start: 0.5886 (m-80) cc_final: 0.5433 (m-80) REVERT: Q 38 LYS cc_start: 0.7321 (mmtm) cc_final: 0.7029 (mmtm) REVERT: R 47 ARG cc_start: 0.6831 (tpp-160) cc_final: 0.5581 (ptp-170) REVERT: R 56 ARG cc_start: 0.7911 (mtp85) cc_final: 0.7551 (mtt90) REVERT: S 78 THR cc_start: 0.7669 (m) cc_final: 0.7359 (t) REVERT: T 4 LYS cc_start: 0.6791 (mmtp) cc_final: 0.6555 (pttm) REVERT: T 12 GLN cc_start: 0.8375 (mt0) cc_final: 0.8077 (tm-30) REVERT: T 26 MET cc_start: 0.8021 (mtm) cc_final: 0.7521 (ttm) REVERT: T 59 ARG cc_start: 0.7634 (ttm170) cc_final: 0.6987 (ttm170) REVERT: T 75 LYS cc_start: 0.7412 (tttt) cc_final: 0.6874 (pttt) REVERT: U 17 ARG cc_start: 0.8157 (mmt-90) cc_final: 0.7366 (ptp90) REVERT: U 18 PHE cc_start: 0.7301 (m-80) cc_final: 0.6745 (m-10) REVERT: U 30 GLU cc_start: 0.8016 (pt0) cc_final: 0.6923 (mm-30) REVERT: U 35 GLU cc_start: 0.5299 (pm20) cc_final: 0.5012 (pm20) REVERT: 0 22 LEU cc_start: 0.9010 (mt) cc_final: 0.8790 (mp) REVERT: 1 13 GLU cc_start: 0.6967 (mt-10) cc_final: 0.6616 (tp30) REVERT: 1 17 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7521 (mm-30) REVERT: 1 39 GLN cc_start: 0.6440 (mm-40) cc_final: 0.6197 (mm-40) REVERT: 1 44 LYS cc_start: 0.7906 (ttmt) cc_final: 0.7506 (tttp) REVERT: 1 54 LYS cc_start: 0.8367 (mttm) cc_final: 0.8114 (mttt) REVERT: 1 60 LYS cc_start: 0.7733 (ttmt) cc_final: 0.7303 (tttm) REVERT: 2 11 ARG cc_start: 0.7515 (mtt-85) cc_final: 0.6882 (mtt180) REVERT: 2 36 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8122 (m) REVERT: 3 33 THR cc_start: 0.8351 (m) cc_final: 0.8124 (p) REVERT: 4 32 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: 4 37 LYS cc_start: 0.8013 (mttt) cc_final: 0.7387 (mmmt) REVERT: 4 51 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.5353 (tm-30) REVERT: 8 13 ASN cc_start: 0.8270 (m-40) cc_final: 0.7888 (m-40) REVERT: c 40 SER cc_start: 0.7829 (OUTLIER) cc_final: 0.7335 (p) REVERT: c 66 ASP cc_start: 0.8497 (t70) cc_final: 0.7826 (t0) REVERT: c 115 GLN cc_start: 0.8175 (mm110) cc_final: 0.7894 (mm110) REVERT: c 147 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8045 (mmtm) REVERT: c 181 MET cc_start: 0.7880 (mmt) cc_final: 0.7483 (mtp) REVERT: c 265 LYS cc_start: 0.8246 (tmtt) cc_final: 0.7285 (mttt) REVERT: i 37 PHE cc_start: 0.2628 (OUTLIER) cc_final: 0.1670 (t80) REVERT: i 86 LYS cc_start: -0.0348 (OUTLIER) cc_final: -0.0685 (pttt) REVERT: i 92 PRO cc_start: 0.2261 (OUTLIER) cc_final: 0.2053 (Cg_endo) REVERT: i 120 ASP cc_start: 0.1908 (t0) cc_final: 0.1022 (t0) REVERT: d 86 GLU cc_start: 0.7742 (tt0) cc_final: 0.7384 (tm-30) REVERT: d 139 SER cc_start: 0.9113 (m) cc_final: 0.8581 (t) REVERT: e 7 ASP cc_start: 0.3446 (OUTLIER) cc_final: 0.2732 (t0) REVERT: e 23 PHE cc_start: 0.7609 (t80) cc_final: 0.7378 (t80) REVERT: e 60 TRP cc_start: 0.7891 (m-90) cc_final: 0.7575 (m100) REVERT: e 61 ARG cc_start: 0.6793 (ptp-170) cc_final: 0.6457 (tmt-80) REVERT: e 100 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8429 (mtp) REVERT: e 116 ASP cc_start: 0.8007 (m-30) cc_final: 0.7465 (t70) REVERT: e 123 LYS cc_start: 0.6779 (tppt) cc_final: 0.6189 (ptpp) REVERT: e 144 GLU cc_start: 0.6998 (tt0) cc_final: 0.6301 (mp0) REVERT: e 155 GLU cc_start: 0.7947 (pm20) cc_final: 0.7519 (tp30) REVERT: f 10 ASP cc_start: 0.8066 (t70) cc_final: 0.7095 (m-30) REVERT: f 11 GLU cc_start: 0.7601 (tp30) cc_final: 0.7108 (mp0) REVERT: f 32 GLU cc_start: 0.8431 (tm-30) cc_final: 0.7877 (tm-30) REVERT: f 51 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7419 (t0) REVERT: f 64 LYS cc_start: 0.3386 (mttt) cc_final: 0.3130 (mttt) REVERT: f 73 SER cc_start: 0.6771 (m) cc_final: 0.6558 (p) REVERT: f 83 TYR cc_start: 0.7586 (OUTLIER) cc_final: 0.7104 (t80) REVERT: f 101 GLU cc_start: 0.7881 (tt0) cc_final: 0.7186 (tm-30) REVERT: g 30 ASN cc_start: 0.7434 (t0) cc_final: 0.7086 (m-40) REVERT: g 58 TYR cc_start: 0.6716 (m-80) cc_final: 0.6455 (m-80) REVERT: g 64 GLN cc_start: 0.7429 (mm-40) cc_final: 0.7020 (mm-40) REVERT: g 81 GLU cc_start: 0.7771 (tt0) cc_final: 0.7531 (tt0) REVERT: g 88 GLN cc_start: 0.6801 (pt0) cc_final: 0.5869 (pp30) REVERT: g 99 LYS cc_start: 0.8004 (mptt) cc_final: 0.7580 (tmtt) REVERT: h 2 GLN cc_start: 0.7454 (mm-40) cc_final: 0.7246 (mm-40) REVERT: h 3 VAL cc_start: 0.7711 (m) cc_final: 0.7509 (p) REVERT: h 114 GLU cc_start: 0.4049 (OUTLIER) cc_final: 0.3630 (tm-30) REVERT: h 127 GLU cc_start: 0.3455 (pt0) cc_final: 0.3146 (pt0) REVERT: h 129 GLU cc_start: 0.5078 (tt0) cc_final: 0.4874 (mm-30) REVERT: j 49 ASP cc_start: 0.8558 (p0) cc_final: 0.8247 (p0) REVERT: j 74 TYR cc_start: 0.8761 (m-80) cc_final: 0.8451 (m-80) REVERT: j 75 TYR cc_start: 0.8539 (m-80) cc_final: 0.8309 (m-80) REVERT: j 93 ILE cc_start: 0.8728 (mt) cc_final: 0.8513 (tp) REVERT: j 108 MET cc_start: 0.8330 (mtt) cc_final: 0.7864 (mtt) REVERT: j 138 GLN cc_start: 0.7800 (pt0) cc_final: 0.7224 (tp40) REVERT: k 18 ARG cc_start: 0.7631 (mmm-85) cc_final: 0.7420 (mmm-85) REVERT: k 89 ASN cc_start: 0.7196 (m-40) cc_final: 0.6831 (t0) REVERT: k 93 GLN cc_start: 0.8407 (mm-40) cc_final: 0.7900 (mt0) REVERT: m 1 MET cc_start: 0.6133 (ttm) cc_final: 0.5841 (ttm) REVERT: m 12 MET cc_start: 0.8258 (ttm) cc_final: 0.7945 (ttm) REVERT: m 51 ARG cc_start: 0.8300 (mtt90) cc_final: 0.7428 (mmt180) REVERT: m 59 ARG cc_start: 0.8476 (mtt180) cc_final: 0.8132 (tpt170) REVERT: m 65 ILE cc_start: 0.8520 (mt) cc_final: 0.8293 (tt) REVERT: m 104 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7904 (mt-10) REVERT: n 1 MET cc_start: 0.8785 (pmm) cc_final: 0.8400 (ptp) REVERT: n 62 ASN cc_start: 0.8727 (m-40) cc_final: 0.8438 (m-40) REVERT: o 80 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7361 (pp20) REVERT: o 89 ASP cc_start: 0.8143 (t70) cc_final: 0.7526 (m-30) REVERT: o 90 VAL cc_start: 0.7632 (m) cc_final: 0.7427 (m) REVERT: p 38 LYS cc_start: 0.6812 (tttp) cc_final: 0.6438 (mmmt) REVERT: p 71 GLU cc_start: 0.8689 (tp30) cc_final: 0.8411 (tp30) REVERT: q 37 GLN cc_start: 0.8462 (mt0) cc_final: 0.8231 (tt0) REVERT: q 97 ASP cc_start: 0.7409 (t0) cc_final: 0.6633 (t0) REVERT: q 101 PHE cc_start: 0.8283 (m-80) cc_final: 0.7811 (m-80) REVERT: r 13 ARG cc_start: 0.8603 (ttp-170) cc_final: 0.7804 (ttt-90) REVERT: r 16 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7971 (tm-30) REVERT: r 26 ASP cc_start: 0.8460 (m-30) cc_final: 0.8088 (m-30) REVERT: r 48 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7156 (ptmm) REVERT: r 80 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7896 (mtm-85) REVERT: r 101 ILE cc_start: 0.8256 (mm) cc_final: 0.7995 (tt) REVERT: s 39 THR cc_start: 0.8556 (m) cc_final: 0.8163 (p) REVERT: s 62 ASP cc_start: 0.6480 (p0) cc_final: 0.6277 (p0) REVERT: s 109 ASP cc_start: 0.7768 (m-30) cc_final: 0.7384 (p0) REVERT: t 3 ARG cc_start: 0.7579 (mtt180) cc_final: 0.6962 (mmt180) REVERT: t 26 LYS cc_start: 0.7837 (ttpt) cc_final: 0.7444 (tppt) REVERT: u 4 LYS cc_start: 0.7021 (mttp) cc_final: 0.6706 (mttp) REVERT: u 26 LYS cc_start: 0.7878 (mmmt) cc_final: 0.7259 (mtpt) REVERT: u 27 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7767 (p0) REVERT: u 79 LYS cc_start: 0.8321 (mttm) cc_final: 0.7795 (mtmt) REVERT: u 81 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.6901 (m-30) REVERT: w 19 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7450 (mtm180) REVERT: w 64 VAL cc_start: 0.7593 (t) cc_final: 0.7301 (m) REVERT: w 71 LYS cc_start: 0.7787 (mtpt) cc_final: 0.7358 (mmtt) REVERT: y 29 GLU cc_start: 0.7309 (tt0) cc_final: 0.6929 (tt0) REVERT: z 4 GLN cc_start: 0.5607 (OUTLIER) cc_final: 0.3731 (tm-30) REVERT: z 5 LYS cc_start: 0.4920 (OUTLIER) cc_final: 0.3495 (ptpt) REVERT: z 12 LEU cc_start: 0.2926 (OUTLIER) cc_final: 0.2719 (mp) outliers start: 330 outliers final: 201 residues processed: 1495 average time/residue: 1.2483 time to fit residues: 3209.4949 Evaluate side-chains 1428 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1199 time to evaluate : 6.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 166 TRP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 80 ARG Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 124 LYS Chi-restraints excluded: chain L residue 26 CYS Chi-restraints excluded: chain L residue 45 ASN Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 119 LYS Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain Q residue 17 GLU Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 47 THR Chi-restraints excluded: chain S residue 65 MET Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 69 ASN Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain 0 residue 13 VAL Chi-restraints excluded: chain 0 residue 64 ILE Chi-restraints excluded: chain 1 residue 11 VAL Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 3 residue 29 SER Chi-restraints excluded: chain 3 residue 32 LYS Chi-restraints excluded: chain 4 residue 12 VAL Chi-restraints excluded: chain 4 residue 22 THR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 32 GLU Chi-restraints excluded: chain 4 residue 47 VAL Chi-restraints excluded: chain 4 residue 48 ILE Chi-restraints excluded: chain 4 residue 51 GLU Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 9 VAL Chi-restraints excluded: chain 8 residue 3 VAL Chi-restraints excluded: chain 8 residue 7 VAL Chi-restraints excluded: chain 8 residue 22 VAL Chi-restraints excluded: chain c residue 16 VAL Chi-restraints excluded: chain c residue 24 LEU Chi-restraints excluded: chain c residue 40 SER Chi-restraints excluded: chain c residue 77 VAL Chi-restraints excluded: chain c residue 147 LYS Chi-restraints excluded: chain c residue 201 MET Chi-restraints excluded: chain c residue 216 VAL Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain i residue 37 PHE Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 86 LYS Chi-restraints excluded: chain i residue 92 PRO Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 51 THR Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain e residue 7 ASP Chi-restraints excluded: chain e residue 70 SER Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 100 MET Chi-restraints excluded: chain e residue 131 THR Chi-restraints excluded: chain e residue 175 ILE Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 6 ASP Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 28 VAL Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 51 ASP Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 123 ASP Chi-restraints excluded: chain f residue 134 GLU Chi-restraints excluded: chain f residue 154 ILE Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 19 ILE Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 80 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 151 TYR Chi-restraints excluded: chain h residue 40 THR Chi-restraints excluded: chain h residue 114 GLU Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain j residue 31 GLU Chi-restraints excluded: chain j residue 43 GLU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 100 VAL Chi-restraints excluded: chain j residue 105 VAL Chi-restraints excluded: chain j residue 124 VAL Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 28 SER Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 95 LEU Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain m residue 101 VAL Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain p residue 8 LEU Chi-restraints excluded: chain p residue 17 VAL Chi-restraints excluded: chain p residue 41 GLN Chi-restraints excluded: chain p residue 85 SER Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 92 VAL Chi-restraints excluded: chain q residue 9 ILE Chi-restraints excluded: chain q residue 34 VAL Chi-restraints excluded: chain q residue 71 GLN Chi-restraints excluded: chain q residue 83 LEU Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 39 LEU Chi-restraints excluded: chain r residue 48 LYS Chi-restraints excluded: chain r residue 55 ASP Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 80 ARG Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain t residue 1 MET Chi-restraints excluded: chain t residue 61 LEU Chi-restraints excluded: chain t residue 74 ILE Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain u residue 12 ILE Chi-restraints excluded: chain u residue 27 ASN Chi-restraints excluded: chain u residue 67 VAL Chi-restraints excluded: chain u residue 81 ASP Chi-restraints excluded: chain u residue 102 THR Chi-restraints excluded: chain w residue 19 ARG Chi-restraints excluded: chain w residue 61 LEU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain w residue 77 VAL Chi-restraints excluded: chain y residue 51 VAL Chi-restraints excluded: chain y residue 81 SER Chi-restraints excluded: chain z residue 3 GLU Chi-restraints excluded: chain z residue 4 GLN Chi-restraints excluded: chain z residue 5 LYS Chi-restraints excluded: chain z residue 12 LEU Chi-restraints excluded: chain z residue 17 VAL Chi-restraints excluded: chain z residue 18 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 916 optimal weight: 10.0000 chunk 697 optimal weight: 10.0000 chunk 481 optimal weight: 30.0000 chunk 102 optimal weight: 50.0000 chunk 442 optimal weight: 10.0000 chunk 623 optimal weight: 10.0000 chunk 931 optimal weight: 7.9990 chunk 985 optimal weight: 0.0670 chunk 486 optimal weight: 8.9990 chunk 882 optimal weight: 8.9990 chunk 265 optimal weight: 0.0670 overall best weight: 5.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 ASN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 ASN ** G 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 ASN ** P 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 HIS 1 58 ASN ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 49 GLN d 150 GLN f 37 ASN g 104 ASN h 73 ASN h 135 HIS l 4 ASN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 16 HIS q 44 GLN r 6 GLN t 48 GLN u 27 ASN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 74 ASN ** w 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 158637 Z= 0.262 Angle : 0.719 14.916 237537 Z= 0.368 Chirality : 0.041 0.538 30396 Planarity : 0.006 0.150 12579 Dihedral : 24.681 179.745 79956 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.76 % Favored : 91.47 % Rotamer: Outliers : 6.50 % Allowed : 21.50 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.07 % Twisted Proline : 1.04 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.11), residues: 5630 helix: -0.13 (0.12), residues: 1702 sheet: -1.53 (0.15), residues: 1036 loop : -1.59 (0.11), residues: 2892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 200 HIS 0.011 0.002 HIS 1 41 PHE 0.030 0.002 PHE I 126 TYR 0.026 0.002 TYR H 127 ARG 0.024 0.001 ARG 0 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1578 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 1274 time to evaluate : 5.683 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: B 41 ASN cc_start: 0.5565 (t0) cc_final: 0.5007 (m110) REVERT: B 55 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6703 (mt-10) REVERT: B 102 ASN cc_start: 0.7590 (t0) cc_final: 0.7345 (t0) REVERT: B 112 ARG cc_start: 0.7839 (mmm160) cc_final: 0.7428 (mmm160) REVERT: B 168 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6891 (mm-30) REVERT: B 169 HIS cc_start: 0.6951 (p-80) cc_final: 0.5998 (m-70) REVERT: B 224 ARG cc_start: 0.5999 (ptp90) cc_final: 0.4903 (mmp-170) REVERT: C 3 LYS cc_start: 0.8553 (mttp) cc_final: 0.8241 (tppt) REVERT: C 58 ARG cc_start: 0.6948 (ttt180) cc_final: 0.6306 (ttp-170) REVERT: C 106 ARG cc_start: 0.7968 (mpt-90) cc_final: 0.7592 (mmt90) REVERT: C 134 LYS cc_start: 0.6450 (OUTLIER) cc_final: 0.6214 (mptt) REVERT: C 205 GLU cc_start: 0.6020 (pm20) cc_final: 0.5137 (tp30) REVERT: D 46 ARG cc_start: 0.6782 (ttm170) cc_final: 0.5364 (mpp80) REVERT: D 71 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.7095 (m-80) REVERT: D 92 LEU cc_start: 0.8209 (mt) cc_final: 0.7917 (mp) REVERT: D 103 ARG cc_start: 0.6957 (mmt90) cc_final: 0.5793 (mtp180) REVERT: D 123 MET cc_start: 0.8270 (mtt) cc_final: 0.7991 (mtp) REVERT: D 135 GLN cc_start: 0.5661 (mm110) cc_final: 0.5284 (pt0) REVERT: D 140 ASP cc_start: 0.4464 (t70) cc_final: 0.3895 (m-30) REVERT: D 158 LEU cc_start: 0.6739 (mp) cc_final: 0.6494 (mp) REVERT: D 162 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6439 (mp0) REVERT: E 63 MET cc_start: 0.7003 (mmm) cc_final: 0.6679 (mmm) REVERT: E 68 ARG cc_start: 0.7754 (mmt-90) cc_final: 0.7500 (mtp-110) REVERT: E 94 PHE cc_start: 0.6400 (m-10) cc_final: 0.6028 (m-10) REVERT: E 111 ARG cc_start: 0.7478 (ttm-80) cc_final: 0.7072 (ttm-80) REVERT: F 65 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6535 (mm-30) REVERT: G 24 LYS cc_start: 0.6876 (OUTLIER) cc_final: 0.6533 (mtpt) REVERT: G 49 LEU cc_start: 0.7020 (mt) cc_final: 0.6805 (mt) REVERT: G 62 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8044 (pt0) REVERT: G 92 PRO cc_start: 0.7662 (Cg_exo) cc_final: 0.7414 (Cg_endo) REVERT: G 121 ASN cc_start: 0.8052 (t0) cc_final: 0.7809 (t0) REVERT: G 143 MET cc_start: 0.7399 (tpp) cc_final: 0.7020 (tpp) REVERT: H 8 ASP cc_start: 0.8477 (t0) cc_final: 0.8203 (m-30) REVERT: H 29 SER cc_start: 0.6718 (t) cc_final: 0.6400 (t) REVERT: H 40 LYS cc_start: 0.8543 (tptt) cc_final: 0.8322 (tptm) REVERT: H 88 LYS cc_start: 0.7907 (tttt) cc_final: 0.7366 (tptp) REVERT: H 91 LEU cc_start: 0.7500 (tp) cc_final: 0.6802 (pt) REVERT: H 110 MET cc_start: 0.8222 (ptp) cc_final: 0.7955 (ptt) REVERT: I 11 ARG cc_start: 0.6930 (tpt-90) cc_final: 0.6549 (tpt-90) REVERT: I 87 MET cc_start: 0.6122 (ppp) cc_final: 0.5227 (ttt) REVERT: I 106 ASP cc_start: 0.7271 (t0) cc_final: 0.6707 (t0) REVERT: J 45 ARG cc_start: 0.6936 (tpp-160) cc_final: 0.6653 (tpp-160) REVERT: K 34 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7953 (t) REVERT: K 71 ASP cc_start: 0.6933 (m-30) cc_final: 0.6694 (m-30) REVERT: L 71 HIS cc_start: 0.7267 (m90) cc_final: 0.6975 (m90) REVERT: M 18 LEU cc_start: 0.8904 (mp) cc_final: 0.8693 (mt) REVERT: M 62 PHE cc_start: 0.6772 (m-80) cc_final: 0.6405 (m-10) REVERT: M 75 SER cc_start: 0.8212 (t) cc_final: 0.7833 (m) REVERT: P 47 GLU cc_start: 0.5177 (OUTLIER) cc_final: 0.4391 (tp30) REVERT: P 77 GLU cc_start: 0.4463 (OUTLIER) cc_final: 0.4263 (mm-30) REVERT: Q 10 ARG cc_start: 0.6775 (ttp-110) cc_final: 0.6444 (tpp80) REVERT: Q 26 ARG cc_start: 0.8010 (ptm160) cc_final: 0.6989 (ptt90) REVERT: Q 33 TYR cc_start: 0.6248 (m-80) cc_final: 0.5513 (m-80) REVERT: Q 61 ARG cc_start: 0.6369 (tmm160) cc_final: 0.6141 (tmm160) REVERT: R 47 ARG cc_start: 0.6822 (tpp-160) cc_final: 0.5757 (ptp-170) REVERT: R 56 ARG cc_start: 0.7946 (mtp85) cc_final: 0.7568 (mtt90) REVERT: S 43 MET cc_start: 0.5200 (mmp) cc_final: 0.4871 (mmm) REVERT: S 78 THR cc_start: 0.7683 (m) cc_final: 0.7383 (t) REVERT: T 4 LYS cc_start: 0.7017 (mmtp) cc_final: 0.6522 (pttm) REVERT: T 26 MET cc_start: 0.7891 (mtm) cc_final: 0.7541 (ttm) REVERT: T 59 ARG cc_start: 0.7667 (ttm170) cc_final: 0.7098 (ttm110) REVERT: T 74 HIS cc_start: 0.8051 (m-70) cc_final: 0.7688 (m-70) REVERT: T 75 LYS cc_start: 0.7476 (tttt) cc_final: 0.6831 (pttt) REVERT: U 17 ARG cc_start: 0.8163 (mmt-90) cc_final: 0.7473 (ptp90) REVERT: U 18 PHE cc_start: 0.7168 (m-80) cc_final: 0.6679 (m-10) REVERT: U 30 GLU cc_start: 0.7703 (pt0) cc_final: 0.6397 (mm-30) REVERT: 1 13 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6573 (tp30) REVERT: 1 17 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7529 (mm-30) REVERT: 1 39 GLN cc_start: 0.6551 (mm-40) cc_final: 0.6241 (mm-40) REVERT: 1 44 LYS cc_start: 0.7836 (ttmt) cc_final: 0.7459 (tttp) REVERT: 1 54 LYS cc_start: 0.8434 (mttm) cc_final: 0.8120 (mttt) REVERT: 1 60 LYS cc_start: 0.7938 (ttmt) cc_final: 0.7380 (tttm) REVERT: 2 11 ARG cc_start: 0.7372 (mtt-85) cc_final: 0.7070 (mtt-85) REVERT: 3 33 THR cc_start: 0.8443 (m) cc_final: 0.8215 (p) REVERT: 3 46 ASP cc_start: 0.8452 (m-30) cc_final: 0.7701 (t70) REVERT: 4 30 LYS cc_start: 0.7065 (mmtm) cc_final: 0.6672 (mtpm) REVERT: 4 32 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: 4 37 LYS cc_start: 0.8064 (mttt) cc_final: 0.7406 (mmmt) REVERT: 4 51 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.5984 (tm-30) REVERT: 8 13 ASN cc_start: 0.8236 (m-40) cc_final: 0.7386 (t0) REVERT: c 40 SER cc_start: 0.7571 (OUTLIER) cc_final: 0.7197 (p) REVERT: c 66 ASP cc_start: 0.8506 (t70) cc_final: 0.7873 (t0) REVERT: c 115 GLN cc_start: 0.8138 (mm110) cc_final: 0.7878 (mm110) REVERT: c 145 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7799 (mm-30) REVERT: c 147 LYS cc_start: 0.8261 (mttm) cc_final: 0.7470 (mmtt) REVERT: c 181 MET cc_start: 0.7999 (mmt) cc_final: 0.7556 (mtp) REVERT: c 183 LYS cc_start: 0.8491 (mttp) cc_final: 0.8161 (mttm) REVERT: c 265 LYS cc_start: 0.8292 (tmtt) cc_final: 0.7328 (mttp) REVERT: i 37 PHE cc_start: 0.2980 (OUTLIER) cc_final: 0.2705 (t80) REVERT: i 112 LYS cc_start: -0.0696 (OUTLIER) cc_final: -0.1200 (pttp) REVERT: d 49 GLN cc_start: 0.8287 (tt0) cc_final: 0.7974 (tt0) REVERT: d 86 GLU cc_start: 0.7735 (tt0) cc_final: 0.7347 (tm-30) REVERT: d 100 LEU cc_start: 0.8558 (tp) cc_final: 0.8208 (tt) REVERT: d 139 SER cc_start: 0.9073 (m) cc_final: 0.8638 (t) REVERT: e 7 ASP cc_start: 0.3854 (OUTLIER) cc_final: 0.2911 (t0) REVERT: e 23 PHE cc_start: 0.8425 (t80) cc_final: 0.8142 (t80) REVERT: e 61 ARG cc_start: 0.6857 (ptp-170) cc_final: 0.6512 (tmt-80) REVERT: e 116 ASP cc_start: 0.8057 (m-30) cc_final: 0.7503 (t70) REVERT: e 123 LYS cc_start: 0.6644 (tppt) cc_final: 0.5910 (ptpp) REVERT: e 137 LYS cc_start: 0.7799 (tttt) cc_final: 0.7237 (tptp) REVERT: e 144 GLU cc_start: 0.6844 (tt0) cc_final: 0.6196 (mp0) REVERT: e 189 THR cc_start: 0.5256 (OUTLIER) cc_final: 0.5052 (m) REVERT: e 199 MET cc_start: 0.8015 (mtm) cc_final: 0.7753 (ttm) REVERT: f 10 ASP cc_start: 0.8164 (t70) cc_final: 0.7405 (t0) REVERT: f 51 ASP cc_start: 0.8336 (m-30) cc_final: 0.7626 (t0) REVERT: f 64 LYS cc_start: 0.3318 (mttt) cc_final: 0.3050 (mttt) REVERT: f 101 GLU cc_start: 0.7601 (tt0) cc_final: 0.7079 (tm-30) REVERT: g 30 ASN cc_start: 0.7045 (t0) cc_final: 0.6739 (m-40) REVERT: g 58 TYR cc_start: 0.7147 (m-80) cc_final: 0.6840 (m-80) REVERT: g 81 GLU cc_start: 0.7675 (tt0) cc_final: 0.7450 (tt0) REVERT: g 163 ARG cc_start: 0.8127 (ptm-80) cc_final: 0.7927 (ptm160) REVERT: h 2 GLN cc_start: 0.6990 (mm-40) cc_final: 0.6779 (mm-40) REVERT: h 17 ASP cc_start: 0.6368 (t0) cc_final: 0.5973 (t0) REVERT: j 74 TYR cc_start: 0.8781 (m-80) cc_final: 0.8451 (m-80) REVERT: j 108 MET cc_start: 0.8335 (mtt) cc_final: 0.8071 (mtt) REVERT: j 138 GLN cc_start: 0.7753 (pt0) cc_final: 0.7083 (tp-100) REVERT: k 14 SER cc_start: 0.8458 (p) cc_final: 0.8173 (p) REVERT: k 17 ARG cc_start: 0.8659 (mmt-90) cc_final: 0.8423 (mtt-85) REVERT: k 88 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8399 (m-40) REVERT: k 93 GLN cc_start: 0.8270 (mm-40) cc_final: 0.7621 (mt0) REVERT: l 2 ARG cc_start: 0.6289 (mpt180) cc_final: 0.5681 (mmm160) REVERT: l 13 LYS cc_start: 0.8108 (mmtp) cc_final: 0.6607 (tptm) REVERT: m 1 MET cc_start: 0.6126 (ttm) cc_final: 0.5609 (ttm) REVERT: m 12 MET cc_start: 0.8309 (ttm) cc_final: 0.7973 (ttm) REVERT: m 51 ARG cc_start: 0.8318 (mtt90) cc_final: 0.7507 (mmt180) REVERT: m 59 ARG cc_start: 0.8510 (mtt180) cc_final: 0.8208 (tpt170) REVERT: n 53 THR cc_start: 0.8874 (m) cc_final: 0.8562 (p) REVERT: n 103 ARG cc_start: 0.8340 (ttp-170) cc_final: 0.7989 (ttm-80) REVERT: o 61 GLN cc_start: 0.7295 (mt0) cc_final: 0.6782 (mp10) REVERT: o 80 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7295 (pp20) REVERT: o 89 ASP cc_start: 0.8165 (t70) cc_final: 0.7478 (m-30) REVERT: o 90 VAL cc_start: 0.7637 (m) cc_final: 0.7348 (m) REVERT: o 91 SER cc_start: 0.7339 (m) cc_final: 0.6963 (m) REVERT: q 22 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7259 (mmtm) REVERT: q 97 ASP cc_start: 0.7440 (t0) cc_final: 0.6927 (t0) REVERT: r 13 ARG cc_start: 0.8584 (ttp-170) cc_final: 0.7738 (ttt-90) REVERT: r 16 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7933 (tm-30) REVERT: r 26 ASP cc_start: 0.8429 (m-30) cc_final: 0.8081 (m-30) REVERT: r 48 LYS cc_start: 0.7752 (ptmm) cc_final: 0.7392 (ptmm) REVERT: s 39 THR cc_start: 0.8555 (m) cc_final: 0.8143 (p) REVERT: s 59 GLU cc_start: 0.7957 (tp30) cc_final: 0.7446 (mt-10) REVERT: s 62 ASP cc_start: 0.7312 (p0) cc_final: 0.6711 (p0) REVERT: t 3 ARG cc_start: 0.7222 (mtt180) cc_final: 0.6523 (mmt180) REVERT: t 26 LYS cc_start: 0.7943 (ttpt) cc_final: 0.7573 (tppt) REVERT: t 37 ASP cc_start: 0.6315 (OUTLIER) cc_final: 0.5879 (t0) REVERT: u 27 ASN cc_start: 0.7649 (OUTLIER) cc_final: 0.7359 (p0) REVERT: u 62 GLU cc_start: 0.7720 (pm20) cc_final: 0.7240 (pp20) REVERT: u 79 LYS cc_start: 0.8228 (mttm) cc_final: 0.7913 (mtmt) REVERT: u 82 ARG cc_start: 0.7239 (mtp85) cc_final: 0.6546 (mtm-85) REVERT: w 4 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7122 (mm) REVERT: w 71 LYS cc_start: 0.7738 (mtpt) cc_final: 0.7316 (mmtt) REVERT: w 93 ARG cc_start: 0.7309 (mtt90) cc_final: 0.6561 (mtm180) REVERT: y 29 GLU cc_start: 0.7354 (tt0) cc_final: 0.6976 (tt0) REVERT: y 39 ARG cc_start: 0.7308 (mmm-85) cc_final: 0.7048 (mmm-85) REVERT: z 4 GLN cc_start: 0.5540 (OUTLIER) cc_final: 0.3513 (tm-30) REVERT: z 5 LYS cc_start: 0.5028 (OUTLIER) cc_final: 0.3531 (ptpt) REVERT: z 12 LEU cc_start: 0.3493 (OUTLIER) cc_final: 0.3176 (mt) outliers start: 304 outliers final: 200 residues processed: 1442 average time/residue: 1.2628 time to fit residues: 3142.2379 Evaluate side-chains 1404 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1183 time to evaluate : 6.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 166 TRP Chi-restraints excluded: chain C residue 200 TRP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 45 MET Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 45 ASN Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 119 LYS Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 32 ILE Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 17 GLU Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain 0 residue 13 VAL Chi-restraints excluded: chain 0 residue 67 VAL Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 3 residue 43 ILE Chi-restraints excluded: chain 4 residue 12 VAL Chi-restraints excluded: chain 4 residue 22 THR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 32 GLU Chi-restraints excluded: chain 4 residue 47 VAL Chi-restraints excluded: chain 4 residue 51 GLU Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 7 residue 34 THR Chi-restraints excluded: chain 8 residue 3 VAL Chi-restraints excluded: chain 8 residue 16 ILE Chi-restraints excluded: chain 8 residue 18 LYS Chi-restraints excluded: chain c residue 24 LEU Chi-restraints excluded: chain c residue 35 GLU Chi-restraints excluded: chain c residue 40 SER Chi-restraints excluded: chain c residue 146 MET Chi-restraints excluded: chain c residue 154 LEU Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain c residue 201 MET Chi-restraints excluded: chain c residue 225 MET Chi-restraints excluded: chain i residue 37 PHE Chi-restraints excluded: chain i residue 69 VAL Chi-restraints excluded: chain i residue 89 SER Chi-restraints excluded: chain i residue 95 ASP Chi-restraints excluded: chain i residue 112 LYS Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 11 MET Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 51 THR Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 105 LYS Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 7 ASP Chi-restraints excluded: chain e residue 70 SER Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 120 VAL Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain e residue 189 THR Chi-restraints excluded: chain f residue 6 ASP Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain f residue 28 VAL Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 123 ASP Chi-restraints excluded: chain f residue 134 GLU Chi-restraints excluded: chain f residue 154 ILE Chi-restraints excluded: chain g residue 19 ILE Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 151 TYR Chi-restraints excluded: chain h residue 40 THR Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 43 GLU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 80 HIS Chi-restraints excluded: chain j residue 105 VAL Chi-restraints excluded: chain j residue 124 VAL Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 54 LYS Chi-restraints excluded: chain k residue 88 ASN Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 95 LEU Chi-restraints excluded: chain l residue 96 LYS Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain m residue 101 VAL Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain n residue 10 LEU Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 5 SER Chi-restraints excluded: chain o residue 20 GLU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 45 SER Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 108 ASP Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 8 LEU Chi-restraints excluded: chain p residue 17 VAL Chi-restraints excluded: chain p residue 41 GLN Chi-restraints excluded: chain p residue 85 SER Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 92 VAL Chi-restraints excluded: chain q residue 9 ILE Chi-restraints excluded: chain q residue 22 LYS Chi-restraints excluded: chain q residue 34 VAL Chi-restraints excluded: chain q residue 40 ILE Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 55 ASP Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 85 LYS Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 61 LEU Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain u residue 11 VAL Chi-restraints excluded: chain u residue 18 ASP Chi-restraints excluded: chain u residue 27 ASN Chi-restraints excluded: chain u residue 49 VAL Chi-restraints excluded: chain u residue 58 ILE Chi-restraints excluded: chain u residue 67 VAL Chi-restraints excluded: chain u residue 100 SER Chi-restraints excluded: chain u residue 102 THR Chi-restraints excluded: chain w residue 4 ILE Chi-restraints excluded: chain w residue 61 LEU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 51 VAL Chi-restraints excluded: chain z residue 3 GLU Chi-restraints excluded: chain z residue 4 GLN Chi-restraints excluded: chain z residue 5 LYS Chi-restraints excluded: chain z residue 12 LEU Chi-restraints excluded: chain z residue 17 VAL Chi-restraints excluded: chain z residue 18 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 821 optimal weight: 5.9990 chunk 559 optimal weight: 10.0000 chunk 14 optimal weight: 40.0000 chunk 734 optimal weight: 10.0000 chunk 406 optimal weight: 9.9990 chunk 841 optimal weight: 10.0000 chunk 681 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 503 optimal weight: 10.0000 chunk 884 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 overall best weight: 8.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 ASN C 184 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 48 GLN ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 HIS T 69 ASN 1 58 ASN ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 29 GLN ** c 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 93 ASN ** d 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 22 GLN g 104 ASN j 131 ASN l 4 ASN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 18 GLN n 107 ASN p 3 ASN p 77 HIS q 37 GLN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 158637 Z= 0.375 Angle : 0.830 14.498 237537 Z= 0.419 Chirality : 0.046 0.487 30396 Planarity : 0.006 0.151 12579 Dihedral : 24.777 179.981 79955 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.82 % Allowed : 9.45 % Favored : 89.73 % Rotamer: Outliers : 8.08 % Allowed : 22.32 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.07 % Twisted Proline : 1.04 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.11), residues: 5630 helix: -0.32 (0.12), residues: 1689 sheet: -1.67 (0.15), residues: 1062 loop : -1.85 (0.11), residues: 2879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 200 HIS 0.013 0.002 HIS 7 26 PHE 0.040 0.003 PHE r 53 TYR 0.032 0.003 TYR H 127 ARG 0.010 0.001 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1609 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 378 poor density : 1231 time to evaluate : 6.255 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: B 35 ASN cc_start: 0.7261 (m-40) cc_final: 0.5512 (p0) REVERT: B 55 GLU cc_start: 0.6594 (mt-10) cc_final: 0.6270 (mt-10) REVERT: B 102 ASN cc_start: 0.7703 (t0) cc_final: 0.7473 (t0) REVERT: B 112 ARG cc_start: 0.7811 (mmm160) cc_final: 0.7367 (mmm160) REVERT: B 117 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8156 (mm-30) REVERT: B 168 GLU cc_start: 0.7284 (mm-30) cc_final: 0.7053 (mm-30) REVERT: B 169 HIS cc_start: 0.6986 (p-80) cc_final: 0.5967 (m-70) REVERT: B 185 ILE cc_start: 0.5060 (pt) cc_final: 0.4667 (pt) REVERT: C 27 GLU cc_start: 0.6572 (pm20) cc_final: 0.6366 (pm20) REVERT: C 40 GLN cc_start: 0.7117 (pt0) cc_final: 0.5935 (tp40) REVERT: C 128 MET cc_start: 0.4601 (ttt) cc_final: 0.4277 (ttt) REVERT: C 134 LYS cc_start: 0.6292 (OUTLIER) cc_final: 0.5935 (mptt) REVERT: C 169 GLU cc_start: 0.6804 (tm-30) cc_final: 0.6083 (tt0) REVERT: D 46 ARG cc_start: 0.6895 (ttm170) cc_final: 0.5504 (mpp80) REVERT: D 71 PHE cc_start: 0.7606 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: D 92 LEU cc_start: 0.8265 (mt) cc_final: 0.7950 (mp) REVERT: D 103 ARG cc_start: 0.7158 (mmt90) cc_final: 0.5953 (mtp180) REVERT: D 140 ASP cc_start: 0.4429 (t70) cc_final: 0.3671 (m-30) REVERT: D 201 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7540 (pt0) REVERT: E 49 TYR cc_start: 0.6141 (t80) cc_final: 0.5703 (t80) REVERT: E 63 MET cc_start: 0.6784 (mmm) cc_final: 0.6534 (mmm) REVERT: E 68 ARG cc_start: 0.8059 (mmt-90) cc_final: 0.7584 (mtp-110) REVERT: E 94 PHE cc_start: 0.6589 (m-10) cc_final: 0.6141 (m-10) REVERT: E 111 ARG cc_start: 0.7284 (ttm-80) cc_final: 0.7023 (ttm-80) REVERT: E 121 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7559 (m110) REVERT: F 47 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7287 (pp) REVERT: F 65 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7077 (mm-30) REVERT: G 24 LYS cc_start: 0.7147 (OUTLIER) cc_final: 0.6854 (mtpt) REVERT: G 49 LEU cc_start: 0.6769 (mt) cc_final: 0.6540 (mt) REVERT: G 121 ASN cc_start: 0.8085 (t0) cc_final: 0.7834 (t0) REVERT: G 143 MET cc_start: 0.7618 (tpp) cc_final: 0.7208 (tpp) REVERT: H 8 ASP cc_start: 0.8497 (t70) cc_final: 0.8264 (m-30) REVERT: H 26 MET cc_start: 0.7815 (ptp) cc_final: 0.7610 (ptp) REVERT: H 29 SER cc_start: 0.6844 (t) cc_final: 0.6540 (t) REVERT: H 40 LYS cc_start: 0.8567 (tptt) cc_final: 0.8340 (tptm) REVERT: H 87 ARG cc_start: 0.8211 (mmm-85) cc_final: 0.8000 (mtp-110) REVERT: H 91 LEU cc_start: 0.7582 (tp) cc_final: 0.6882 (pt) REVERT: H 117 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6955 (mm-40) REVERT: H 124 ILE cc_start: 0.6999 (tt) cc_final: 0.6508 (tt) REVERT: I 87 MET cc_start: 0.6281 (ppp) cc_final: 0.5878 (ppp) REVERT: J 45 ARG cc_start: 0.7198 (tpp-160) cc_final: 0.6994 (tpp-160) REVERT: K 34 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8119 (t) REVERT: L 24 GLU cc_start: 0.6343 (tt0) cc_final: 0.5605 (tp30) REVERT: M 62 PHE cc_start: 0.6920 (m-80) cc_final: 0.6485 (m-10) REVERT: M 75 SER cc_start: 0.8203 (t) cc_final: 0.7898 (m) REVERT: O 27 GLN cc_start: 0.7077 (mt0) cc_final: 0.6865 (mt0) REVERT: O 58 MET cc_start: 0.8025 (mmp) cc_final: 0.6990 (mtp) REVERT: Q 26 ARG cc_start: 0.7888 (ptm160) cc_final: 0.6833 (ptt90) REVERT: Q 33 TYR cc_start: 0.6864 (m-80) cc_final: 0.5951 (m-80) REVERT: Q 56 ASP cc_start: 0.6434 (m-30) cc_final: 0.6161 (m-30) REVERT: R 47 ARG cc_start: 0.7080 (tpp-160) cc_final: 0.5879 (ptp-170) REVERT: S 43 MET cc_start: 0.5359 (mmp) cc_final: 0.4968 (mmm) REVERT: T 4 LYS cc_start: 0.7370 (mmtp) cc_final: 0.6780 (pttm) REVERT: T 26 MET cc_start: 0.7996 (mtm) cc_final: 0.7611 (ttm) REVERT: T 75 LYS cc_start: 0.7307 (tttt) cc_final: 0.6512 (pttt) REVERT: U 17 ARG cc_start: 0.8158 (mmt-90) cc_final: 0.7535 (ptp90) REVERT: U 18 PHE cc_start: 0.6763 (m-80) cc_final: 0.6285 (m-10) REVERT: 0 22 LEU cc_start: 0.9026 (mt) cc_final: 0.8763 (mp) REVERT: 0 39 TRP cc_start: 0.7660 (t-100) cc_final: 0.6797 (t-100) REVERT: 0 40 VAL cc_start: 0.7498 (t) cc_final: 0.6849 (m) REVERT: 1 2 LYS cc_start: 0.7068 (mttt) cc_final: 0.6447 (ttpp) REVERT: 1 17 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7723 (mm-30) REVERT: 1 39 GLN cc_start: 0.6219 (mm-40) cc_final: 0.6000 (mm-40) REVERT: 1 44 LYS cc_start: 0.7854 (ttmt) cc_final: 0.7356 (tttp) REVERT: 1 60 LYS cc_start: 0.8041 (ttmt) cc_final: 0.7475 (tttm) REVERT: 2 3 LYS cc_start: 0.7124 (mttt) cc_final: 0.6663 (mmmt) REVERT: 2 11 ARG cc_start: 0.7432 (mtt-85) cc_final: 0.7106 (mtt-85) REVERT: 3 33 THR cc_start: 0.8509 (m) cc_final: 0.8285 (p) REVERT: 3 46 ASP cc_start: 0.8259 (m-30) cc_final: 0.7432 (t70) REVERT: 4 30 LYS cc_start: 0.6978 (mmtm) cc_final: 0.6717 (mttm) REVERT: 4 32 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: 4 50 LYS cc_start: 0.7320 (mtmt) cc_final: 0.6933 (mtmm) REVERT: 4 51 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6103 (tm-30) REVERT: 7 26 HIS cc_start: 0.7985 (OUTLIER) cc_final: 0.7469 (m170) REVERT: 8 13 ASN cc_start: 0.8291 (m-40) cc_final: 0.7564 (t0) REVERT: c 40 SER cc_start: 0.7616 (OUTLIER) cc_final: 0.7272 (p) REVERT: c 66 ASP cc_start: 0.8765 (t70) cc_final: 0.8196 (t0) REVERT: c 115 GLN cc_start: 0.8485 (mm110) cc_final: 0.8065 (mm110) REVERT: c 147 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7258 (mmtt) REVERT: c 181 MET cc_start: 0.8059 (mmt) cc_final: 0.7540 (mtp) REVERT: c 183 LYS cc_start: 0.8567 (mttp) cc_final: 0.8189 (mttm) REVERT: c 265 LYS cc_start: 0.8282 (tmtt) cc_final: 0.7390 (mttt) REVERT: i 37 PHE cc_start: 0.3704 (OUTLIER) cc_final: 0.3227 (t80) REVERT: i 93 ASN cc_start: 0.3997 (OUTLIER) cc_final: 0.3434 (t0) REVERT: i 112 LYS cc_start: -0.0710 (OUTLIER) cc_final: -0.1168 (pttp) REVERT: d 4 LEU cc_start: 0.8669 (mt) cc_final: 0.8458 (mt) REVERT: d 11 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7351 (ttp) REVERT: d 100 LEU cc_start: 0.8529 (tp) cc_final: 0.8263 (tt) REVERT: e 9 GLN cc_start: 0.5232 (mm-40) cc_final: 0.5017 (mm110) REVERT: e 23 PHE cc_start: 0.8858 (t80) cc_final: 0.8139 (t80) REVERT: e 61 ARG cc_start: 0.6888 (ptp-170) cc_final: 0.6630 (tmt-80) REVERT: e 116 ASP cc_start: 0.7936 (m-30) cc_final: 0.7404 (t70) REVERT: e 123 LYS cc_start: 0.6811 (tppt) cc_final: 0.5947 (ptpp) REVERT: e 137 LYS cc_start: 0.8006 (tttt) cc_final: 0.7472 (tptp) REVERT: e 144 GLU cc_start: 0.6767 (tt0) cc_final: 0.6123 (mp0) REVERT: e 149 ILE cc_start: 0.8369 (mt) cc_final: 0.8024 (tt) REVERT: e 199 MET cc_start: 0.8029 (mtm) cc_final: 0.7782 (ttm) REVERT: f 37 ASN cc_start: 0.6619 (t0) cc_final: 0.6410 (t0) REVERT: f 51 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.7606 (t0) REVERT: g 58 TYR cc_start: 0.7438 (m-80) cc_final: 0.7210 (m-80) REVERT: g 69 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6735 (tmt-80) REVERT: h 2 GLN cc_start: 0.7081 (mm-40) cc_final: 0.6773 (mm-40) REVERT: h 3 VAL cc_start: 0.7665 (m) cc_final: 0.7459 (p) REVERT: h 17 ASP cc_start: 0.6175 (t0) cc_final: 0.5601 (t0) REVERT: h 47 PHE cc_start: 0.7896 (t80) cc_final: 0.6980 (m-80) REVERT: j 74 TYR cc_start: 0.8805 (m-80) cc_final: 0.8445 (m-80) REVERT: j 80 HIS cc_start: 0.8075 (OUTLIER) cc_final: 0.7277 (t-90) REVERT: j 108 MET cc_start: 0.8273 (mtt) cc_final: 0.8024 (mtt) REVERT: j 138 GLN cc_start: 0.7863 (pt0) cc_final: 0.6984 (tp-100) REVERT: k 14 SER cc_start: 0.8477 (p) cc_final: 0.8074 (p) REVERT: k 93 GLN cc_start: 0.8430 (mm-40) cc_final: 0.7740 (mt0) REVERT: l 2 ARG cc_start: 0.6769 (mpt180) cc_final: 0.6097 (mmm160) REVERT: m 1 MET cc_start: 0.6046 (ttm) cc_final: 0.5585 (ttm) REVERT: m 12 MET cc_start: 0.8393 (ttm) cc_final: 0.8080 (ttm) REVERT: m 40 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7706 (mtp180) REVERT: m 51 ARG cc_start: 0.8370 (mtt90) cc_final: 0.7424 (mmt180) REVERT: m 59 ARG cc_start: 0.8500 (mtt180) cc_final: 0.8194 (tpt170) REVERT: n 1 MET cc_start: 0.8801 (pmm) cc_final: 0.8434 (ptp) REVERT: n 94 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.7676 (m-80) REVERT: n 103 ARG cc_start: 0.8440 (ttp-170) cc_final: 0.8058 (ttm-80) REVERT: o 80 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7260 (pp20) REVERT: o 89 ASP cc_start: 0.7622 (t70) cc_final: 0.7246 (m-30) REVERT: o 91 SER cc_start: 0.7401 (m) cc_final: 0.7037 (m) REVERT: q 22 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7413 (mmtm) REVERT: q 28 ARG cc_start: 0.8235 (mtp85) cc_final: 0.7869 (mtp-110) REVERT: q 97 ASP cc_start: 0.7453 (t0) cc_final: 0.6790 (t0) REVERT: r 4 VAL cc_start: 0.9156 (OUTLIER) cc_final: 0.8892 (p) REVERT: r 13 ARG cc_start: 0.8618 (ttp-170) cc_final: 0.7900 (ttt-90) REVERT: r 25 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7637 (mm) REVERT: r 26 ASP cc_start: 0.8411 (m-30) cc_final: 0.8026 (m-30) REVERT: r 48 LYS cc_start: 0.7672 (ptmm) cc_final: 0.7381 (ptmm) REVERT: r 80 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7519 (mtt90) REVERT: s 39 THR cc_start: 0.8686 (m) cc_final: 0.8249 (p) REVERT: s 59 GLU cc_start: 0.7898 (tp30) cc_final: 0.7412 (mt-10) REVERT: t 3 ARG cc_start: 0.7203 (mtt180) cc_final: 0.6479 (mmt180) REVERT: t 26 LYS cc_start: 0.8055 (ttpt) cc_final: 0.7708 (tppt) REVERT: t 37 ASP cc_start: 0.6388 (OUTLIER) cc_final: 0.5891 (t0) REVERT: t 52 GLU cc_start: 0.6331 (mt-10) cc_final: 0.6004 (tt0) REVERT: u 27 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.7338 (p0) REVERT: u 62 GLU cc_start: 0.7722 (pm20) cc_final: 0.7219 (pp20) REVERT: u 79 LYS cc_start: 0.8216 (mttm) cc_final: 0.7932 (mtpp) REVERT: u 81 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.7207 (m-30) REVERT: u 82 ARG cc_start: 0.7254 (mtp85) cc_final: 0.6597 (mtm-85) REVERT: w 4 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7122 (mm) REVERT: w 5 ASN cc_start: 0.7993 (m-40) cc_final: 0.7526 (t0) REVERT: w 19 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7436 (mtm180) REVERT: w 48 MET cc_start: 0.6830 (tpt) cc_final: 0.6588 (tpt) REVERT: w 55 GLU cc_start: 0.7917 (mp0) cc_final: 0.6930 (mt-10) REVERT: w 59 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7452 (mp0) REVERT: w 71 LYS cc_start: 0.7740 (mtpt) cc_final: 0.7320 (mmtt) REVERT: z 4 GLN cc_start: 0.5813 (OUTLIER) cc_final: 0.4187 (tm-30) REVERT: z 5 LYS cc_start: 0.5513 (OUTLIER) cc_final: 0.3855 (ptpt) REVERT: z 12 LEU cc_start: 0.4473 (OUTLIER) cc_final: 0.3686 (mt) outliers start: 378 outliers final: 265 residues processed: 1452 average time/residue: 1.2412 time to fit residues: 3124.2640 Evaluate side-chains 1488 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 1190 time to evaluate : 5.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 166 TRP Chi-restraints excluded: chain C residue 200 TRP Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 117 GLN Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 45 MET Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain K residue 124 LYS Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 45 ASN Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 119 LYS Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 32 ILE Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain Q residue 17 GLU Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 47 THR Chi-restraints excluded: chain T residue 3 ILE Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain 0 residue 13 VAL Chi-restraints excluded: chain 0 residue 64 ILE Chi-restraints excluded: chain 0 residue 67 VAL Chi-restraints excluded: chain 1 residue 11 VAL Chi-restraints excluded: chain 1 residue 40 SER Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 29 SER Chi-restraints excluded: chain 3 residue 32 LYS Chi-restraints excluded: chain 4 residue 12 VAL Chi-restraints excluded: chain 4 residue 22 THR Chi-restraints excluded: chain 4 residue 23 THR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 32 GLU Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 47 VAL Chi-restraints excluded: chain 4 residue 51 GLU Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 9 VAL Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 7 residue 26 HIS Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 8 residue 3 VAL Chi-restraints excluded: chain 8 residue 7 VAL Chi-restraints excluded: chain 8 residue 16 ILE Chi-restraints excluded: chain 8 residue 26 ILE Chi-restraints excluded: chain c residue 24 LEU Chi-restraints excluded: chain c residue 35 GLU Chi-restraints excluded: chain c residue 40 SER Chi-restraints excluded: chain c residue 77 VAL Chi-restraints excluded: chain c residue 147 LYS Chi-restraints excluded: chain c residue 154 LEU Chi-restraints excluded: chain c residue 160 THR Chi-restraints excluded: chain c residue 201 MET Chi-restraints excluded: chain c residue 216 VAL Chi-restraints excluded: chain c residue 225 MET Chi-restraints excluded: chain c residue 229 ASP Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain i residue 37 PHE Chi-restraints excluded: chain i residue 69 VAL Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 89 SER Chi-restraints excluded: chain i residue 93 ASN Chi-restraints excluded: chain i residue 112 LYS Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 11 MET Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 51 THR Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 105 LYS Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 7 ASP Chi-restraints excluded: chain e residue 31 VAL Chi-restraints excluded: chain e residue 70 SER Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 120 VAL Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 6 ASP Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 51 ASP Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 123 ASP Chi-restraints excluded: chain f residue 134 GLU Chi-restraints excluded: chain f residue 154 ILE Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain g residue 69 ARG Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 80 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 151 TYR Chi-restraints excluded: chain h residue 40 THR Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 43 GLU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 80 HIS Chi-restraints excluded: chain j residue 105 VAL Chi-restraints excluded: chain j residue 124 VAL Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 28 SER Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 80 SER Chi-restraints excluded: chain l residue 95 LEU Chi-restraints excluded: chain l residue 96 LYS Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 40 ARG Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain m residue 101 VAL Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 10 LEU Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain n residue 94 TYR Chi-restraints excluded: chain o residue 5 SER Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 20 GLU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 26 LEU Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 45 SER Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 108 ASP Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 8 LEU Chi-restraints excluded: chain p residue 17 VAL Chi-restraints excluded: chain p residue 41 GLN Chi-restraints excluded: chain p residue 85 SER Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain q residue 9 ILE Chi-restraints excluded: chain q residue 18 LEU Chi-restraints excluded: chain q residue 22 LYS Chi-restraints excluded: chain q residue 40 ILE Chi-restraints excluded: chain q residue 71 GLN Chi-restraints excluded: chain q residue 83 LEU Chi-restraints excluded: chain r residue 4 VAL Chi-restraints excluded: chain r residue 25 LEU Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 39 LEU Chi-restraints excluded: chain r residue 55 ASP Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 80 ARG Chi-restraints excluded: chain r residue 85 LYS Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 61 LEU Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 11 VAL Chi-restraints excluded: chain u residue 12 ILE Chi-restraints excluded: chain u residue 18 ASP Chi-restraints excluded: chain u residue 27 ASN Chi-restraints excluded: chain u residue 49 VAL Chi-restraints excluded: chain u residue 58 ILE Chi-restraints excluded: chain u residue 67 VAL Chi-restraints excluded: chain u residue 73 PHE Chi-restraints excluded: chain u residue 81 ASP Chi-restraints excluded: chain u residue 100 SER Chi-restraints excluded: chain u residue 102 THR Chi-restraints excluded: chain w residue 4 ILE Chi-restraints excluded: chain w residue 19 ARG Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 61 LEU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 51 VAL Chi-restraints excluded: chain z residue 3 GLU Chi-restraints excluded: chain z residue 4 GLN Chi-restraints excluded: chain z residue 5 LYS Chi-restraints excluded: chain z residue 12 LEU Chi-restraints excluded: chain z residue 17 VAL Chi-restraints excluded: chain z residue 18 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 331 optimal weight: 1.9990 chunk 887 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 578 optimal weight: 10.0000 chunk 243 optimal weight: 10.0000 chunk 986 optimal weight: 6.9990 chunk 819 optimal weight: 0.5980 chunk 456 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 326 optimal weight: 0.9980 chunk 518 optimal weight: 10.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 ASN D 39 GLN D 40 HIS ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 HIS P 18 GLN 1 58 ASN ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 29 GLN e 115 GLN g 104 ASN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 107 ASN p 77 HIS q 44 GLN r 6 GLN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 51 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.5298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 158637 Z= 0.178 Angle : 0.651 14.102 237537 Z= 0.334 Chirality : 0.037 0.436 30396 Planarity : 0.005 0.145 12579 Dihedral : 24.580 179.313 79955 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.21 % Favored : 92.13 % Rotamer: Outliers : 5.64 % Allowed : 25.29 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.07 % Twisted Proline : 1.04 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.11), residues: 5630 helix: 0.12 (0.13), residues: 1700 sheet: -1.46 (0.15), residues: 1037 loop : -1.72 (0.11), residues: 2893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 22 HIS 0.010 0.001 HIS 1 41 PHE 0.032 0.002 PHE r 53 TYR 0.017 0.002 TYR N 19 ARG 0.010 0.001 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1473 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 1209 time to evaluate : 6.307 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: B 55 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6736 (mt-10) REVERT: B 68 PHE cc_start: 0.6895 (m-80) cc_final: 0.6624 (m-80) REVERT: B 168 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7175 (mm-30) REVERT: B 169 HIS cc_start: 0.6851 (p-80) cc_final: 0.5595 (m-70) REVERT: B 222 GLU cc_start: 0.6429 (pp20) cc_final: 0.6175 (pm20) REVERT: B 224 ARG cc_start: 0.6369 (ptp90) cc_final: 0.5504 (tmm160) REVERT: C 27 GLU cc_start: 0.6503 (pm20) cc_final: 0.6256 (pm20) REVERT: C 128 MET cc_start: 0.4527 (ttt) cc_final: 0.4194 (ttt) REVERT: C 134 LYS cc_start: 0.6130 (OUTLIER) cc_final: 0.5821 (mptt) REVERT: C 169 GLU cc_start: 0.6794 (tm-30) cc_final: 0.6249 (tt0) REVERT: D 46 ARG cc_start: 0.6791 (ttm170) cc_final: 0.5388 (mpp80) REVERT: D 71 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.7034 (m-80) REVERT: D 103 ARG cc_start: 0.7149 (mmt90) cc_final: 0.5773 (mtp180) REVERT: D 123 MET cc_start: 0.7739 (mtp) cc_final: 0.7515 (mmt) REVERT: D 140 ASP cc_start: 0.4539 (t70) cc_final: 0.4030 (m-30) REVERT: E 44 ARG cc_start: 0.6767 (tpp80) cc_final: 0.6497 (tpp80) REVERT: E 49 TYR cc_start: 0.5647 (t80) cc_final: 0.5378 (t80) REVERT: E 56 PRO cc_start: 0.7591 (Cg_exo) cc_final: 0.7340 (Cg_endo) REVERT: E 60 GLN cc_start: 0.8115 (mm110) cc_final: 0.7696 (mm-40) REVERT: E 63 MET cc_start: 0.7441 (mmm) cc_final: 0.7036 (mmm) REVERT: E 68 ARG cc_start: 0.7826 (mmt-90) cc_final: 0.7545 (mtp-110) REVERT: E 94 PHE cc_start: 0.6457 (m-10) cc_final: 0.6007 (m-10) REVERT: F 47 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7122 (pp) REVERT: F 62 MET cc_start: 0.7852 (mmm) cc_final: 0.7460 (mtp) REVERT: F 65 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6842 (mm-30) REVERT: G 62 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8242 (pt0) REVERT: G 98 LEU cc_start: 0.6943 (tp) cc_final: 0.6723 (tt) REVERT: G 121 ASN cc_start: 0.8096 (t0) cc_final: 0.7843 (t0) REVERT: G 143 MET cc_start: 0.7524 (tpp) cc_final: 0.7084 (tpp) REVERT: H 29 SER cc_start: 0.6702 (t) cc_final: 0.6412 (t) REVERT: H 40 LYS cc_start: 0.8507 (tptt) cc_final: 0.8288 (tptm) REVERT: H 91 LEU cc_start: 0.7437 (tp) cc_final: 0.6828 (pt) REVERT: I 11 ARG cc_start: 0.6974 (tpt-90) cc_final: 0.6205 (tpt170) REVERT: I 87 MET cc_start: 0.6198 (ppp) cc_final: 0.5876 (ppp) REVERT: J 68 ARG cc_start: 0.6345 (ttm110) cc_final: 0.6134 (ttm110) REVERT: M 62 PHE cc_start: 0.6867 (m-80) cc_final: 0.6508 (m-10) REVERT: M 75 SER cc_start: 0.8001 (t) cc_final: 0.7525 (m) REVERT: O 61 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8039 (tt0) REVERT: P 25 ARG cc_start: 0.6500 (ttp-110) cc_final: 0.5910 (mtm110) REVERT: P 29 ASN cc_start: 0.6517 (p0) cc_final: 0.5891 (t0) REVERT: Q 8 GLN cc_start: 0.7156 (tm-30) cc_final: 0.6795 (mm110) REVERT: Q 26 ARG cc_start: 0.7838 (ptm160) cc_final: 0.6845 (ptt90) REVERT: Q 33 TYR cc_start: 0.6820 (m-80) cc_final: 0.6175 (m-80) REVERT: R 47 ARG cc_start: 0.7064 (tpp-160) cc_final: 0.5841 (ptp-170) REVERT: S 43 MET cc_start: 0.5338 (mmp) cc_final: 0.4965 (mmm) REVERT: S 55 GLN cc_start: 0.5490 (OUTLIER) cc_final: 0.4509 (pm20) REVERT: S 64 GLU cc_start: 0.7671 (mm-30) cc_final: 0.6855 (tt0) REVERT: S 78 THR cc_start: 0.7589 (m) cc_final: 0.7277 (t) REVERT: T 4 LYS cc_start: 0.7191 (mmtp) cc_final: 0.6632 (pttm) REVERT: T 26 MET cc_start: 0.7830 (mtm) cc_final: 0.7619 (ttm) REVERT: T 75 LYS cc_start: 0.7354 (tttt) cc_final: 0.6646 (pttt) REVERT: 0 39 TRP cc_start: 0.7737 (t-100) cc_final: 0.7080 (t-100) REVERT: 0 40 VAL cc_start: 0.7509 (t) cc_final: 0.7092 (m) REVERT: 1 13 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6676 (tp30) REVERT: 1 17 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7419 (mm-30) REVERT: 1 18 LEU cc_start: 0.8758 (tp) cc_final: 0.8405 (tt) REVERT: 1 39 GLN cc_start: 0.6154 (mm-40) cc_final: 0.5950 (mm-40) REVERT: 1 44 LYS cc_start: 0.7760 (ttmt) cc_final: 0.7263 (tptm) REVERT: 1 54 LYS cc_start: 0.8654 (mptt) cc_final: 0.8413 (mmtm) REVERT: 1 60 LYS cc_start: 0.7983 (ttmt) cc_final: 0.7569 (tmtt) REVERT: 2 3 LYS cc_start: 0.7203 (mttt) cc_final: 0.6777 (mmmt) REVERT: 3 33 THR cc_start: 0.8499 (m) cc_final: 0.8255 (p) REVERT: 3 46 ASP cc_start: 0.8199 (m-30) cc_final: 0.7412 (t70) REVERT: 4 30 LYS cc_start: 0.7028 (mmtm) cc_final: 0.6693 (mttm) REVERT: 4 32 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7701 (mp0) REVERT: 4 51 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6103 (tm-30) REVERT: 6 41 ARG cc_start: 0.8538 (mtt-85) cc_final: 0.8210 (mtp180) REVERT: 8 1 MET cc_start: 0.7582 (ptm) cc_final: 0.7325 (ptm) REVERT: 8 13 ASN cc_start: 0.8244 (m-40) cc_final: 0.7534 (t0) REVERT: c 66 ASP cc_start: 0.8562 (t70) cc_final: 0.7810 (t0) REVERT: c 115 GLN cc_start: 0.8227 (mm110) cc_final: 0.7810 (mm110) REVERT: c 147 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7503 (mmtt) REVERT: c 181 MET cc_start: 0.8083 (mmt) cc_final: 0.7683 (mtp) REVERT: c 183 LYS cc_start: 0.8575 (mttp) cc_final: 0.8210 (mtpp) REVERT: c 265 LYS cc_start: 0.8163 (tmtt) cc_final: 0.7346 (mttt) REVERT: i 93 ASN cc_start: 0.3756 (OUTLIER) cc_final: 0.3143 (t0) REVERT: i 112 LYS cc_start: -0.0679 (OUTLIER) cc_final: -0.1081 (pttp) REVERT: i 133 ARG cc_start: 0.2653 (tmm-80) cc_final: 0.2365 (ttp80) REVERT: d 4 LEU cc_start: 0.8612 (mt) cc_final: 0.8387 (mt) REVERT: d 58 ASN cc_start: 0.8861 (p0) cc_final: 0.8520 (m110) REVERT: d 86 GLU cc_start: 0.7651 (tt0) cc_final: 0.7377 (tm-30) REVERT: d 100 LEU cc_start: 0.8524 (tp) cc_final: 0.8239 (tt) REVERT: e 15 SER cc_start: 0.6955 (m) cc_final: 0.6400 (t) REVERT: e 23 PHE cc_start: 0.8722 (t80) cc_final: 0.8077 (t80) REVERT: e 61 ARG cc_start: 0.6790 (ptp-170) cc_final: 0.6531 (tmt-80) REVERT: e 116 ASP cc_start: 0.8043 (m-30) cc_final: 0.7532 (t70) REVERT: e 123 LYS cc_start: 0.6789 (tppt) cc_final: 0.6038 (ptpp) REVERT: e 137 LYS cc_start: 0.8040 (tttt) cc_final: 0.7599 (tptp) REVERT: e 144 GLU cc_start: 0.6765 (tt0) cc_final: 0.6147 (mp0) REVERT: f 64 LYS cc_start: 0.3356 (mttt) cc_final: 0.2996 (mttt) REVERT: f 77 PHE cc_start: 0.7917 (m-10) cc_final: 0.7549 (m-10) REVERT: f 170 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6976 (mm) REVERT: g 30 ASN cc_start: 0.6699 (t0) cc_final: 0.6295 (m-40) REVERT: g 58 TYR cc_start: 0.7674 (m-80) cc_final: 0.7455 (m-80) REVERT: h 2 GLN cc_start: 0.7029 (mm-40) cc_final: 0.6719 (mm-40) REVERT: h 3 VAL cc_start: 0.7720 (m) cc_final: 0.7513 (p) REVERT: h 17 ASP cc_start: 0.6051 (t0) cc_final: 0.5600 (t0) REVERT: j 44 TYR cc_start: 0.8952 (t80) cc_final: 0.8482 (t80) REVERT: j 52 ASP cc_start: 0.8085 (m-30) cc_final: 0.7594 (m-30) REVERT: j 74 TYR cc_start: 0.8751 (m-80) cc_final: 0.8348 (m-80) REVERT: j 80 HIS cc_start: 0.8037 (OUTLIER) cc_final: 0.7250 (t-90) REVERT: j 108 MET cc_start: 0.8388 (mtt) cc_final: 0.8032 (mtt) REVERT: j 138 GLN cc_start: 0.7695 (pt0) cc_final: 0.6834 (tp-100) REVERT: k 14 SER cc_start: 0.8392 (p) cc_final: 0.8139 (p) REVERT: k 17 ARG cc_start: 0.8769 (mmt-90) cc_final: 0.8499 (mtt-85) REVERT: k 93 GLN cc_start: 0.8285 (mm-40) cc_final: 0.7617 (mt0) REVERT: l 2 ARG cc_start: 0.6274 (mpt180) cc_final: 0.5730 (mmm160) REVERT: m 1 MET cc_start: 0.5989 (ttm) cc_final: 0.5620 (ttm) REVERT: m 51 ARG cc_start: 0.8457 (mtt90) cc_final: 0.7567 (mmt180) REVERT: m 59 ARG cc_start: 0.8562 (mtt180) cc_final: 0.8186 (tpt170) REVERT: n 94 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.6939 (m-80) REVERT: n 103 ARG cc_start: 0.8328 (ttp-170) cc_final: 0.8051 (ttm-80) REVERT: o 80 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7143 (pp20) REVERT: o 89 ASP cc_start: 0.8020 (t70) cc_final: 0.7413 (m-30) REVERT: o 91 SER cc_start: 0.7621 (m) cc_final: 0.7254 (m) REVERT: p 72 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7598 (ttp80) REVERT: p 73 VAL cc_start: 0.8496 (m) cc_final: 0.8166 (t) REVERT: q 28 ARG cc_start: 0.8087 (mtp85) cc_final: 0.7667 (mtp-110) REVERT: q 97 ASP cc_start: 0.7428 (t0) cc_final: 0.6934 (t0) REVERT: r 13 ARG cc_start: 0.8658 (ttp-170) cc_final: 0.7880 (ttt-90) REVERT: r 26 ASP cc_start: 0.8403 (m-30) cc_final: 0.8170 (m-30) REVERT: s 39 THR cc_start: 0.8590 (m) cc_final: 0.8180 (p) REVERT: s 59 GLU cc_start: 0.8024 (tp30) cc_final: 0.7556 (mt-10) REVERT: s 66 ILE cc_start: 0.8200 (mt) cc_final: 0.7992 (tt) REVERT: t 3 ARG cc_start: 0.7236 (mtt180) cc_final: 0.6421 (mmt180) REVERT: t 26 LYS cc_start: 0.8025 (ttpt) cc_final: 0.7675 (tppt) REVERT: t 52 GLU cc_start: 0.6275 (mt-10) cc_final: 0.6035 (tt0) REVERT: u 40 ASN cc_start: 0.7421 (OUTLIER) cc_final: 0.6789 (t0) REVERT: u 53 ASN cc_start: 0.7293 (OUTLIER) cc_final: 0.6934 (t0) REVERT: u 62 GLU cc_start: 0.7646 (pm20) cc_final: 0.7261 (pp20) REVERT: u 79 LYS cc_start: 0.8177 (mttm) cc_final: 0.7692 (mtmt) REVERT: u 81 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.7161 (m-30) REVERT: u 82 ARG cc_start: 0.7170 (mtp85) cc_final: 0.6674 (mtm-85) REVERT: w 4 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7091 (mm) REVERT: w 5 ASN cc_start: 0.7886 (m-40) cc_final: 0.7363 (t0) REVERT: w 55 GLU cc_start: 0.8135 (mp0) cc_final: 0.7254 (mt-10) REVERT: w 59 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7475 (mp0) REVERT: w 71 LYS cc_start: 0.7697 (mtpt) cc_final: 0.7274 (mmtt) REVERT: w 93 ARG cc_start: 0.7275 (mtt90) cc_final: 0.6655 (mtm180) REVERT: y 29 GLU cc_start: 0.7335 (tt0) cc_final: 0.6850 (tt0) REVERT: z 3 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.5495 (tt0) REVERT: z 4 GLN cc_start: 0.5486 (OUTLIER) cc_final: 0.3905 (tm-30) REVERT: z 5 LYS cc_start: 0.5445 (OUTLIER) cc_final: 0.3773 (ptpt) REVERT: z 12 LEU cc_start: 0.4253 (OUTLIER) cc_final: 0.3707 (mt) outliers start: 264 outliers final: 181 residues processed: 1354 average time/residue: 1.2646 time to fit residues: 2960.7638 Evaluate side-chains 1353 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1151 time to evaluate : 6.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 166 TRP Chi-restraints excluded: chain C residue 200 TRP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 45 MET Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 45 ASN Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 32 ILE Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 96 LYS Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 56 ARG Chi-restraints excluded: chain Q residue 17 GLU Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 55 GLN Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 67 HIS Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain 0 residue 13 VAL Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 3 residue 29 SER Chi-restraints excluded: chain 3 residue 43 ILE Chi-restraints excluded: chain 4 residue 22 THR Chi-restraints excluded: chain 4 residue 27 LYS Chi-restraints excluded: chain 4 residue 32 GLU Chi-restraints excluded: chain 4 residue 47 VAL Chi-restraints excluded: chain 4 residue 51 GLU Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 8 residue 3 VAL Chi-restraints excluded: chain 8 residue 16 ILE Chi-restraints excluded: chain 8 residue 18 LYS Chi-restraints excluded: chain c residue 24 LEU Chi-restraints excluded: chain c residue 35 GLU Chi-restraints excluded: chain c residue 40 SER Chi-restraints excluded: chain c residue 59 LYS Chi-restraints excluded: chain c residue 147 LYS Chi-restraints excluded: chain c residue 154 LEU Chi-restraints excluded: chain c residue 201 MET Chi-restraints excluded: chain c residue 216 VAL Chi-restraints excluded: chain c residue 225 MET Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 52 LEU Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 79 LEU Chi-restraints excluded: chain i residue 93 ASN Chi-restraints excluded: chain i residue 95 ASP Chi-restraints excluded: chain i residue 112 LYS Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 51 THR Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 200 ASP Chi-restraints excluded: chain e residue 7 ASP Chi-restraints excluded: chain e residue 70 SER Chi-restraints excluded: chain e residue 120 VAL Chi-restraints excluded: chain e residue 141 MET Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 6 ASP Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 73 SER Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 123 ASP Chi-restraints excluded: chain f residue 130 MET Chi-restraints excluded: chain f residue 134 GLU Chi-restraints excluded: chain f residue 154 ILE Chi-restraints excluded: chain f residue 170 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 114 ASP Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 151 TYR Chi-restraints excluded: chain h residue 40 THR Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 80 HIS Chi-restraints excluded: chain j residue 105 VAL Chi-restraints excluded: chain j residue 124 VAL Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 95 LEU Chi-restraints excluded: chain l residue 96 LYS Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 108 VAL Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain n residue 10 LEU Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain n residue 94 TYR Chi-restraints excluded: chain o residue 5 SER Chi-restraints excluded: chain o residue 20 GLU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 45 SER Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain p residue 17 VAL Chi-restraints excluded: chain p residue 41 GLN Chi-restraints excluded: chain p residue 72 ARG Chi-restraints excluded: chain p residue 85 SER Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain q residue 9 ILE Chi-restraints excluded: chain q residue 83 LEU Chi-restraints excluded: chain r residue 4 VAL Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 39 LEU Chi-restraints excluded: chain r residue 55 ASP Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 85 LYS Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain t residue 61 LEU Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain u residue 11 VAL Chi-restraints excluded: chain u residue 18 ASP Chi-restraints excluded: chain u residue 40 ASN Chi-restraints excluded: chain u residue 49 VAL Chi-restraints excluded: chain u residue 53 ASN Chi-restraints excluded: chain u residue 58 ILE Chi-restraints excluded: chain u residue 67 VAL Chi-restraints excluded: chain u residue 73 PHE Chi-restraints excluded: chain u residue 81 ASP Chi-restraints excluded: chain u residue 102 THR Chi-restraints excluded: chain w residue 4 ILE Chi-restraints excluded: chain w residue 51 GLN Chi-restraints excluded: chain z residue 3 GLU Chi-restraints excluded: chain z residue 4 GLN Chi-restraints excluded: chain z residue 5 LYS Chi-restraints excluded: chain z residue 12 LEU Chi-restraints excluded: chain z residue 17 VAL Chi-restraints excluded: chain z residue 18 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 951 optimal weight: 10.0000 chunk 111 optimal weight: 30.0000 chunk 562 optimal weight: 10.0000 chunk 720 optimal weight: 10.0000 chunk 558 optimal weight: 10.0000 chunk 830 optimal weight: 20.0000 chunk 551 optimal weight: 30.0000 chunk 983 optimal weight: 2.9990 chunk 615 optimal weight: 10.0000 chunk 599 optimal weight: 30.0000 chunk 453 optimal weight: 20.0000 overall best weight: 8.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN F 63 ASN ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 HIS ** S 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 36 GLN 1 58 ASN ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 29 GLN ** c 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 93 ASN e 115 GLN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 88 ASN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 74 ASN w 49 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 158637 Z= 0.392 Angle : 0.821 13.429 237537 Z= 0.411 Chirality : 0.045 0.403 30396 Planarity : 0.006 0.144 12579 Dihedral : 24.705 179.301 79951 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.69 % Allowed : 9.89 % Favored : 89.41 % Rotamer: Outliers : 7.27 % Allowed : 24.20 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.07 % Twisted Proline : 1.04 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.11), residues: 5630 helix: -0.24 (0.12), residues: 1696 sheet: -1.55 (0.15), residues: 1040 loop : -1.93 (0.11), residues: 2894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 200 HIS 0.011 0.002 HIS 1 41 PHE 0.039 0.003 PHE I 126 TYR 0.033 0.003 TYR H 127 ARG 0.021 0.001 ARG L 113 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1502 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 340 poor density : 1162 time to evaluate : 8.732 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: B 55 GLU cc_start: 0.6573 (mt-10) cc_final: 0.6244 (mt-10) REVERT: C 27 GLU cc_start: 0.6851 (pm20) cc_final: 0.6536 (pm20) REVERT: C 41 TYR cc_start: 0.7489 (m-80) cc_final: 0.7079 (m-80) REVERT: C 134 LYS cc_start: 0.6095 (OUTLIER) cc_final: 0.5818 (mptt) REVERT: C 169 GLU cc_start: 0.6614 (tm-30) cc_final: 0.6016 (tt0) REVERT: C 202 PHE cc_start: 0.7947 (t80) cc_final: 0.7580 (t80) REVERT: D 46 ARG cc_start: 0.6871 (ttm170) cc_final: 0.5470 (mpp80) REVERT: D 71 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7370 (m-80) REVERT: D 103 ARG cc_start: 0.7292 (mmt90) cc_final: 0.5851 (mtp180) REVERT: D 140 ASP cc_start: 0.4801 (t70) cc_final: 0.4253 (m-30) REVERT: E 44 ARG cc_start: 0.6906 (tpp80) cc_final: 0.6660 (tpp80) REVERT: E 49 TYR cc_start: 0.6255 (t80) cc_final: 0.5924 (t80) REVERT: E 60 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7727 (mm-40) REVERT: E 63 MET cc_start: 0.7150 (mmm) cc_final: 0.6724 (mmm) REVERT: E 68 ARG cc_start: 0.8096 (mmt-90) cc_final: 0.7616 (mtp-110) REVERT: E 94 PHE cc_start: 0.6575 (m-10) cc_final: 0.6138 (m-10) REVERT: E 111 ARG cc_start: 0.7361 (ttm-80) cc_final: 0.7085 (ttm-80) REVERT: F 47 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7219 (pp) REVERT: F 62 MET cc_start: 0.7925 (mmm) cc_final: 0.7448 (mtp) REVERT: F 65 GLU cc_start: 0.7483 (mm-30) cc_final: 0.6966 (mm-30) REVERT: G 121 ASN cc_start: 0.8143 (t0) cc_final: 0.7892 (t0) REVERT: G 143 MET cc_start: 0.7662 (tpp) cc_final: 0.7240 (tpp) REVERT: H 29 SER cc_start: 0.6813 (t) cc_final: 0.6539 (t) REVERT: H 40 LYS cc_start: 0.8541 (tptt) cc_final: 0.8321 (tptm) REVERT: H 91 LEU cc_start: 0.7592 (tp) cc_final: 0.6930 (pt) REVERT: H 123 GLU cc_start: 0.6341 (tm-30) cc_final: 0.6116 (tm-30) REVERT: H 124 ILE cc_start: 0.6895 (tt) cc_final: 0.6578 (tt) REVERT: I 11 ARG cc_start: 0.6858 (tpt-90) cc_final: 0.6120 (tpt170) REVERT: I 87 MET cc_start: 0.6249 (ppp) cc_final: 0.5815 (ppp) REVERT: L 24 GLU cc_start: 0.6119 (tt0) cc_final: 0.5483 (tp30) REVERT: M 75 SER cc_start: 0.8033 (t) cc_final: 0.7564 (m) REVERT: O 27 GLN cc_start: 0.7073 (mt0) cc_final: 0.6852 (mt0) REVERT: Q 8 GLN cc_start: 0.7272 (tm-30) cc_final: 0.6817 (mm-40) REVERT: Q 26 ARG cc_start: 0.7933 (ptm160) cc_final: 0.6828 (ptt90) REVERT: Q 33 TYR cc_start: 0.6851 (m-80) cc_final: 0.5978 (m-80) REVERT: R 47 ARG cc_start: 0.7113 (tpp-160) cc_final: 0.5843 (ptp-170) REVERT: S 27 LYS cc_start: 0.6521 (mptt) cc_final: 0.4886 (tttt) REVERT: S 43 MET cc_start: 0.5480 (mmp) cc_final: 0.5067 (mmm) REVERT: S 55 GLN cc_start: 0.5702 (OUTLIER) cc_final: 0.4746 (pm20) REVERT: S 64 GLU cc_start: 0.7567 (mm-30) cc_final: 0.6818 (tt0) REVERT: T 4 LYS cc_start: 0.7425 (mmtp) cc_final: 0.6821 (pttm) REVERT: T 26 MET cc_start: 0.7984 (mtm) cc_final: 0.7668 (ttm) REVERT: 0 39 TRP cc_start: 0.7800 (t-100) cc_final: 0.6935 (t-100) REVERT: 0 40 VAL cc_start: 0.7655 (t) cc_final: 0.7019 (m) REVERT: 1 17 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7590 (mm-30) REVERT: 1 44 LYS cc_start: 0.7927 (ttmt) cc_final: 0.7334 (tptm) REVERT: 1 60 LYS cc_start: 0.8098 (ttmt) cc_final: 0.7616 (tmtt) REVERT: 2 3 LYS cc_start: 0.7120 (mttt) cc_final: 0.6677 (mmmt) REVERT: 2 56 LYS cc_start: 0.7104 (pttt) cc_final: 0.6677 (mmmm) REVERT: 2 58 GLU cc_start: 0.5919 (mp0) cc_final: 0.5647 (mp0) REVERT: 3 33 THR cc_start: 0.8559 (m) cc_final: 0.8324 (p) REVERT: 4 30 LYS cc_start: 0.6949 (mmtm) cc_final: 0.6721 (mttm) REVERT: 4 32 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: 4 50 LYS cc_start: 0.7335 (mtmt) cc_final: 0.7040 (mtmm) REVERT: 4 51 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6130 (tm-30) REVERT: 7 26 HIS cc_start: 0.8002 (OUTLIER) cc_final: 0.7678 (m170) REVERT: 8 13 ASN cc_start: 0.8171 (m-40) cc_final: 0.7506 (t0) REVERT: c 40 SER cc_start: 0.7570 (m) cc_final: 0.7235 (p) REVERT: c 66 ASP cc_start: 0.8771 (t70) cc_final: 0.8058 (t0) REVERT: c 115 GLN cc_start: 0.8442 (mm110) cc_final: 0.8083 (mm110) REVERT: c 181 MET cc_start: 0.8065 (mmt) cc_final: 0.7560 (mtp) REVERT: c 183 LYS cc_start: 0.8578 (mttp) cc_final: 0.8292 (mttm) REVERT: c 242 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8510 (mmtt) REVERT: c 265 LYS cc_start: 0.8275 (tmtt) cc_final: 0.7374 (mttt) REVERT: i 93 ASN cc_start: 0.3651 (OUTLIER) cc_final: 0.3197 (t0) REVERT: i 112 LYS cc_start: -0.0600 (OUTLIER) cc_final: -0.0984 (pttp) REVERT: i 124 MET cc_start: 0.1707 (tpt) cc_final: 0.1374 (ttt) REVERT: i 133 ARG cc_start: 0.2507 (tmm-80) cc_final: 0.2221 (ttp80) REVERT: d 4 LEU cc_start: 0.8675 (mt) cc_final: 0.8436 (mt) REVERT: d 86 GLU cc_start: 0.7784 (tt0) cc_final: 0.7456 (tm-30) REVERT: d 100 LEU cc_start: 0.8602 (tp) cc_final: 0.8283 (tt) REVERT: e 15 SER cc_start: 0.6929 (m) cc_final: 0.6239 (t) REVERT: e 23 PHE cc_start: 0.8941 (t80) cc_final: 0.8244 (t80) REVERT: e 60 TRP cc_start: 0.7674 (OUTLIER) cc_final: 0.6885 (m-90) REVERT: e 115 GLN cc_start: 0.8605 (mt0) cc_final: 0.8404 (mt0) REVERT: e 116 ASP cc_start: 0.7925 (m-30) cc_final: 0.7338 (t70) REVERT: e 144 GLU cc_start: 0.6809 (tt0) cc_final: 0.6172 (mp0) REVERT: e 149 ILE cc_start: 0.8421 (mt) cc_final: 0.8138 (tt) REVERT: f 51 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.7670 (t0) REVERT: f 72 LYS cc_start: 0.6934 (tptt) cc_final: 0.6718 (mmtm) REVERT: f 77 PHE cc_start: 0.7976 (m-80) cc_final: 0.7160 (m-80) REVERT: f 134 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6950 (pm20) REVERT: f 170 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7180 (mm) REVERT: h 2 GLN cc_start: 0.6875 (mm-40) cc_final: 0.6569 (mm-40) REVERT: h 17 ASP cc_start: 0.5619 (t0) cc_final: 0.4909 (t70) REVERT: h 47 PHE cc_start: 0.7756 (t80) cc_final: 0.6850 (m-80) REVERT: j 44 TYR cc_start: 0.8920 (t80) cc_final: 0.8506 (t80) REVERT: j 74 TYR cc_start: 0.8842 (m-80) cc_final: 0.8422 (m-80) REVERT: j 80 HIS cc_start: 0.8124 (OUTLIER) cc_final: 0.7338 (t-90) REVERT: j 108 MET cc_start: 0.8249 (mtt) cc_final: 0.8026 (mtt) REVERT: j 138 GLN cc_start: 0.7787 (pt0) cc_final: 0.6921 (tp-100) REVERT: k 14 SER cc_start: 0.8381 (p) cc_final: 0.8023 (p) REVERT: k 93 GLN cc_start: 0.8474 (mm-40) cc_final: 0.7749 (mt0) REVERT: l 2 ARG cc_start: 0.6632 (mpt180) cc_final: 0.6009 (mmm160) REVERT: l 13 LYS cc_start: 0.8049 (mmtp) cc_final: 0.6512 (tptp) REVERT: m 1 MET cc_start: 0.6269 (ttm) cc_final: 0.5915 (ttm) REVERT: m 40 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7685 (mtp180) REVERT: m 51 ARG cc_start: 0.8377 (mtt90) cc_final: 0.7423 (mmt180) REVERT: m 59 ARG cc_start: 0.8474 (mtt180) cc_final: 0.8172 (tpt170) REVERT: n 103 ARG cc_start: 0.8410 (ttp-170) cc_final: 0.7609 (ttm-80) REVERT: o 2 ASP cc_start: 0.6373 (p0) cc_final: 0.6097 (p0) REVERT: o 80 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7240 (pp20) REVERT: o 89 ASP cc_start: 0.7641 (t70) cc_final: 0.7380 (m-30) REVERT: o 91 SER cc_start: 0.7599 (m) cc_final: 0.7245 (m) REVERT: q 28 ARG cc_start: 0.8230 (mtp85) cc_final: 0.7812 (mtp-110) REVERT: q 97 ASP cc_start: 0.7196 (t0) cc_final: 0.6842 (t0) REVERT: r 13 ARG cc_start: 0.8627 (ttp-170) cc_final: 0.7880 (ttt-90) REVERT: r 26 ASP cc_start: 0.8434 (m-30) cc_final: 0.8201 (m-30) REVERT: r 40 MET cc_start: 0.7925 (tpt) cc_final: 0.7628 (tpt) REVERT: s 39 THR cc_start: 0.8563 (m) cc_final: 0.8088 (p) REVERT: s 59 GLU cc_start: 0.7959 (tp30) cc_final: 0.7449 (mt-10) REVERT: t 3 ARG cc_start: 0.7134 (mtt180) cc_final: 0.6421 (mmt180) REVERT: t 26 LYS cc_start: 0.8006 (ttpt) cc_final: 0.7621 (tppt) REVERT: t 37 ASP cc_start: 0.6450 (OUTLIER) cc_final: 0.5934 (t0) REVERT: t 52 GLU cc_start: 0.6500 (mt-10) cc_final: 0.6138 (tt0) REVERT: t 91 GLN cc_start: 0.4237 (OUTLIER) cc_final: 0.3639 (pt0) REVERT: u 17 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7810 (ptpt) REVERT: u 62 GLU cc_start: 0.7754 (pm20) cc_final: 0.7235 (pp20) REVERT: u 81 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: u 82 ARG cc_start: 0.7216 (mtp85) cc_final: 0.6560 (mtm-85) REVERT: w 4 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7092 (mm) REVERT: w 5 ASN cc_start: 0.7931 (m-40) cc_final: 0.7385 (t0) REVERT: w 19 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7433 (mtm180) REVERT: w 51 GLN cc_start: 0.7753 (pp30) cc_final: 0.7357 (pp30) REVERT: w 55 GLU cc_start: 0.7930 (mp0) cc_final: 0.7052 (mt-10) REVERT: w 59 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7461 (mp0) REVERT: w 71 LYS cc_start: 0.7719 (mtpt) cc_final: 0.7264 (mtmm) REVERT: y 29 GLU cc_start: 0.7433 (tt0) cc_final: 0.6933 (tt0) REVERT: z 4 GLN cc_start: 0.5571 (OUTLIER) cc_final: 0.3999 (tm-30) REVERT: z 5 LYS cc_start: 0.5038 (OUTLIER) cc_final: 0.3685 (ptpt) outliers start: 340 outliers final: 261 residues processed: 1352 average time/residue: 1.2776 time to fit residues: 2992.8851 Evaluate side-chains 1411 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1126 time to evaluate : 5.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 166 TRP Chi-restraints excluded: chain C residue 200 TRP Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 45 MET Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 45 ASN Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 71 HIS Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 116 TYR Chi-restraints excluded: chain L residue 119 LYS Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 32 ILE Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 56 ARG Chi-restraints excluded: chain Q residue 17 GLU Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 47 THR Chi-restraints excluded: chain S residue 55 GLN Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 67 HIS Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 39 LYS Chi-restraints excluded: chain 0 residue 13 VAL Chi-restraints excluded: chain 0 residue 67 VAL Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 3 residue 29 SER Chi-restraints excluded: chain 4 residue 12 VAL Chi-restraints excluded: chain 4 residue 22 THR Chi-restraints excluded: chain 4 residue 23 THR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 32 GLU Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 36 LEU Chi-restraints excluded: chain 4 residue 47 VAL Chi-restraints excluded: chain 4 residue 51 GLU Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 9 VAL Chi-restraints excluded: chain 7 residue 26 HIS Chi-restraints excluded: chain 8 residue 3 VAL Chi-restraints excluded: chain 8 residue 7 VAL Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 8 residue 16 ILE Chi-restraints excluded: chain 8 residue 18 LYS Chi-restraints excluded: chain c residue 24 LEU Chi-restraints excluded: chain c residue 35 GLU Chi-restraints excluded: chain c residue 59 LYS Chi-restraints excluded: chain c residue 147 LYS Chi-restraints excluded: chain c residue 154 LEU Chi-restraints excluded: chain c residue 160 THR Chi-restraints excluded: chain c residue 201 MET Chi-restraints excluded: chain c residue 216 VAL Chi-restraints excluded: chain c residue 225 MET Chi-restraints excluded: chain c residue 242 LYS Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 52 LEU Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 79 LEU Chi-restraints excluded: chain i residue 93 ASN Chi-restraints excluded: chain i residue 112 LYS Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 45 TYR Chi-restraints excluded: chain d residue 51 THR Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 103 ASP Chi-restraints excluded: chain d residue 105 LYS Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 7 ASP Chi-restraints excluded: chain e residue 60 TRP Chi-restraints excluded: chain e residue 70 SER Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 120 VAL Chi-restraints excluded: chain e residue 141 MET Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 6 ASP Chi-restraints excluded: chain f residue 7 TYR Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 51 ASP Chi-restraints excluded: chain f residue 74 VAL Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 123 ASP Chi-restraints excluded: chain f residue 130 MET Chi-restraints excluded: chain f residue 134 GLU Chi-restraints excluded: chain f residue 154 ILE Chi-restraints excluded: chain f residue 170 LEU Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 80 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 114 ASP Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 151 TYR Chi-restraints excluded: chain h residue 40 THR Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain j residue 43 GLU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 80 HIS Chi-restraints excluded: chain j residue 105 VAL Chi-restraints excluded: chain j residue 124 VAL Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 28 SER Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 80 SER Chi-restraints excluded: chain l residue 95 LEU Chi-restraints excluded: chain l residue 96 LYS Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 40 ARG Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 108 VAL Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 10 LEU Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain n residue 94 TYR Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 5 SER Chi-restraints excluded: chain o residue 20 GLU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 45 SER Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 8 LEU Chi-restraints excluded: chain p residue 17 VAL Chi-restraints excluded: chain p residue 72 ARG Chi-restraints excluded: chain p residue 85 SER Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 92 VAL Chi-restraints excluded: chain q residue 9 ILE Chi-restraints excluded: chain q residue 18 LEU Chi-restraints excluded: chain q residue 71 GLN Chi-restraints excluded: chain q residue 83 LEU Chi-restraints excluded: chain r residue 4 VAL Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 39 LEU Chi-restraints excluded: chain r residue 55 ASP Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 85 LYS Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain s residue 105 VAL Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 61 LEU Chi-restraints excluded: chain t residue 74 ILE Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain t residue 91 GLN Chi-restraints excluded: chain u residue 11 VAL Chi-restraints excluded: chain u residue 12 ILE Chi-restraints excluded: chain u residue 17 LYS Chi-restraints excluded: chain u residue 18 ASP Chi-restraints excluded: chain u residue 58 ILE Chi-restraints excluded: chain u residue 65 ILE Chi-restraints excluded: chain u residue 67 VAL Chi-restraints excluded: chain u residue 73 PHE Chi-restraints excluded: chain u residue 81 ASP Chi-restraints excluded: chain u residue 100 SER Chi-restraints excluded: chain u residue 102 THR Chi-restraints excluded: chain w residue 4 ILE Chi-restraints excluded: chain w residue 19 ARG Chi-restraints excluded: chain w residue 49 ASN Chi-restraints excluded: chain w residue 61 LEU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 51 VAL Chi-restraints excluded: chain z residue 3 GLU Chi-restraints excluded: chain z residue 4 GLN Chi-restraints excluded: chain z residue 5 LYS Chi-restraints excluded: chain z residue 17 VAL Chi-restraints excluded: chain z residue 18 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 608 optimal weight: 10.0000 chunk 392 optimal weight: 20.0000 chunk 587 optimal weight: 30.0000 chunk 296 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 190 optimal weight: 3.9990 chunk 625 optimal weight: 8.9990 chunk 669 optimal weight: 10.0000 chunk 486 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 772 optimal weight: 9.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 58 ASN ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 133 GLN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 88 ASN q 44 GLN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 49 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 158637 Z= 0.379 Angle : 0.816 16.156 237537 Z= 0.411 Chirality : 0.045 0.467 30396 Planarity : 0.006 0.152 12579 Dihedral : 24.765 179.368 79949 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.66 % Allowed : 9.61 % Favored : 89.73 % Rotamer: Outliers : 7.80 % Allowed : 24.18 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.07 % Twisted Proline : 1.04 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.11), residues: 5630 helix: -0.44 (0.12), residues: 1692 sheet: -1.64 (0.15), residues: 1005 loop : -2.09 (0.11), residues: 2933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 200 HIS 0.012 0.002 HIS 7 26 PHE 0.062 0.003 PHE U 18 TYR 0.033 0.003 TYR H 127 ARG 0.014 0.001 ARG U 17 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1541 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 365 poor density : 1176 time to evaluate : 6.176 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: B 55 GLU cc_start: 0.6608 (mt-10) cc_final: 0.6289 (mt-10) REVERT: B 153 MET cc_start: 0.6503 (OUTLIER) cc_final: 0.5803 (ttp) REVERT: C 2 GLN cc_start: 0.6014 (mt0) cc_final: 0.5795 (mp10) REVERT: C 27 GLU cc_start: 0.6999 (pm20) cc_final: 0.6598 (pm20) REVERT: C 41 TYR cc_start: 0.7311 (m-80) cc_final: 0.6920 (m-80) REVERT: C 107 LYS cc_start: 0.8366 (mtmt) cc_final: 0.7675 (mmtm) REVERT: C 134 LYS cc_start: 0.6319 (OUTLIER) cc_final: 0.6115 (mptt) REVERT: C 169 GLU cc_start: 0.6639 (tm-30) cc_final: 0.6153 (tt0) REVERT: C 183 TYR cc_start: 0.8122 (t80) cc_final: 0.7890 (t80) REVERT: C 202 PHE cc_start: 0.7991 (t80) cc_final: 0.7648 (t80) REVERT: D 46 ARG cc_start: 0.6918 (ttm170) cc_final: 0.5649 (mpp80) REVERT: D 69 ARG cc_start: 0.6003 (ptt180) cc_final: 0.5461 (ptp-170) REVERT: D 123 MET cc_start: 0.7756 (mtp) cc_final: 0.7074 (tpp) REVERT: D 127 ARG cc_start: 0.5751 (OUTLIER) cc_final: 0.5459 (ttm-80) REVERT: D 140 ASP cc_start: 0.5329 (t70) cc_final: 0.4801 (m-30) REVERT: E 44 ARG cc_start: 0.6831 (tpp80) cc_final: 0.6583 (tpp80) REVERT: E 49 TYR cc_start: 0.6385 (OUTLIER) cc_final: 0.5950 (t80) REVERT: E 63 MET cc_start: 0.6926 (mmm) cc_final: 0.6574 (mmm) REVERT: E 68 ARG cc_start: 0.8052 (mmt-90) cc_final: 0.7553 (mtp-110) REVERT: E 72 ASN cc_start: 0.5342 (OUTLIER) cc_final: 0.5135 (m110) REVERT: E 94 PHE cc_start: 0.6604 (m-10) cc_final: 0.6205 (m-10) REVERT: E 111 ARG cc_start: 0.7363 (ttm-80) cc_final: 0.7092 (ttm-80) REVERT: F 47 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7300 (pp) REVERT: F 62 MET cc_start: 0.7790 (mmm) cc_final: 0.7349 (mtp) REVERT: F 65 GLU cc_start: 0.7493 (mm-30) cc_final: 0.6806 (mm-30) REVERT: F 69 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6617 (pm20) REVERT: G 121 ASN cc_start: 0.8140 (t0) cc_final: 0.7882 (t0) REVERT: G 143 MET cc_start: 0.7688 (tpp) cc_final: 0.7297 (tpp) REVERT: H 29 SER cc_start: 0.6718 (t) cc_final: 0.6471 (t) REVERT: H 40 LYS cc_start: 0.8549 (tptt) cc_final: 0.8323 (tptm) REVERT: H 91 LEU cc_start: 0.7574 (tp) cc_final: 0.6919 (pt) REVERT: H 124 ILE cc_start: 0.7047 (tt) cc_final: 0.6608 (tt) REVERT: I 11 ARG cc_start: 0.6917 (tpt-90) cc_final: 0.6170 (tpt170) REVERT: I 87 MET cc_start: 0.6222 (ppp) cc_final: 0.5913 (ppp) REVERT: L 24 GLU cc_start: 0.6007 (tt0) cc_final: 0.5254 (tp30) REVERT: M 75 SER cc_start: 0.8043 (t) cc_final: 0.7550 (m) REVERT: O 58 MET cc_start: 0.8152 (mmp) cc_final: 0.7325 (mtp) REVERT: Q 8 GLN cc_start: 0.7374 (tm-30) cc_final: 0.6840 (mm-40) REVERT: Q 26 ARG cc_start: 0.7936 (ptm160) cc_final: 0.6859 (ptt90) REVERT: Q 33 TYR cc_start: 0.6838 (m-80) cc_final: 0.6013 (m-80) REVERT: R 47 ARG cc_start: 0.6983 (tpp-160) cc_final: 0.5737 (ptp-170) REVERT: R 53 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.7046 (mm-40) REVERT: S 27 LYS cc_start: 0.6782 (mptt) cc_final: 0.5307 (tttt) REVERT: S 43 MET cc_start: 0.5671 (mmp) cc_final: 0.5281 (mmm) REVERT: S 55 GLN cc_start: 0.5665 (OUTLIER) cc_final: 0.4702 (pm20) REVERT: T 4 LYS cc_start: 0.7445 (mmtp) cc_final: 0.6839 (pttm) REVERT: T 26 MET cc_start: 0.7955 (mtm) cc_final: 0.7712 (ttm) REVERT: U 17 ARG cc_start: 0.7283 (ttp80) cc_final: 0.7031 (ttp80) REVERT: 0 39 TRP cc_start: 0.7713 (t-100) cc_final: 0.6868 (t-100) REVERT: 0 40 VAL cc_start: 0.7533 (t) cc_final: 0.6920 (m) REVERT: 1 5 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7630 (pt0) REVERT: 1 17 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7576 (mm-30) REVERT: 1 44 LYS cc_start: 0.7863 (ttmt) cc_final: 0.7259 (tptm) REVERT: 1 59 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7321 (mm-30) REVERT: 1 60 LYS cc_start: 0.8282 (ttmt) cc_final: 0.7566 (tmtt) REVERT: 2 3 LYS cc_start: 0.7064 (mttt) cc_final: 0.6640 (mmmt) REVERT: 2 11 ARG cc_start: 0.7434 (mtt-85) cc_final: 0.6837 (mtt180) REVERT: 2 36 VAL cc_start: 0.8522 (OUTLIER) cc_final: 0.8145 (m) REVERT: 2 56 LYS cc_start: 0.7170 (pttt) cc_final: 0.6942 (mmmm) REVERT: 3 33 THR cc_start: 0.8586 (m) cc_final: 0.8339 (p) REVERT: 4 30 LYS cc_start: 0.7014 (mmtm) cc_final: 0.6785 (mttm) REVERT: 4 32 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: 4 50 LYS cc_start: 0.7155 (mtmt) cc_final: 0.6828 (mtmm) REVERT: 4 51 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6397 (tm-30) REVERT: 7 26 HIS cc_start: 0.7976 (OUTLIER) cc_final: 0.7675 (m170) REVERT: 8 13 ASN cc_start: 0.8205 (m-40) cc_final: 0.7554 (t0) REVERT: c 40 SER cc_start: 0.7747 (m) cc_final: 0.7337 (p) REVERT: c 66 ASP cc_start: 0.8766 (t70) cc_final: 0.8013 (t0) REVERT: c 167 ARG cc_start: 0.7183 (ttp-110) cc_final: 0.6942 (ttp-110) REVERT: c 181 MET cc_start: 0.8127 (mmt) cc_final: 0.7649 (mtp) REVERT: c 183 LYS cc_start: 0.8507 (mttp) cc_final: 0.8186 (mtpp) REVERT: c 242 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8494 (mmtt) REVERT: c 265 LYS cc_start: 0.8276 (tmtt) cc_final: 0.7366 (mttt) REVERT: i 32 VAL cc_start: -0.2055 (OUTLIER) cc_final: -0.2470 (t) REVERT: i 112 LYS cc_start: -0.0787 (OUTLIER) cc_final: -0.1124 (pttp) REVERT: d 4 LEU cc_start: 0.8637 (mt) cc_final: 0.8377 (mt) REVERT: d 40 LEU cc_start: 0.8093 (mp) cc_final: 0.7884 (mt) REVERT: d 86 GLU cc_start: 0.7817 (tt0) cc_final: 0.7549 (tm-30) REVERT: d 100 LEU cc_start: 0.8524 (tp) cc_final: 0.8211 (tt) REVERT: d 185 ASN cc_start: 0.7775 (m-40) cc_final: 0.7284 (m-40) REVERT: e 15 SER cc_start: 0.6869 (m) cc_final: 0.6152 (t) REVERT: e 23 PHE cc_start: 0.9077 (t80) cc_final: 0.8287 (t80) REVERT: e 60 TRP cc_start: 0.7763 (OUTLIER) cc_final: 0.6810 (m-90) REVERT: e 100 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8344 (mtp) REVERT: e 115 GLN cc_start: 0.8613 (mt0) cc_final: 0.8313 (mt0) REVERT: e 116 ASP cc_start: 0.7889 (m-30) cc_final: 0.7223 (t70) REVERT: e 123 LYS cc_start: 0.6772 (tppt) cc_final: 0.5463 (ptmm) REVERT: e 144 GLU cc_start: 0.6638 (tt0) cc_final: 0.6178 (mp0) REVERT: e 149 ILE cc_start: 0.8460 (mt) cc_final: 0.8142 (tt) REVERT: e 165 HIS cc_start: 0.6763 (t-90) cc_final: 0.6393 (t-90) REVERT: f 51 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.7658 (t0) REVERT: f 77 PHE cc_start: 0.7988 (m-80) cc_final: 0.7165 (m-80) REVERT: f 170 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7197 (mm) REVERT: g 160 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7470 (ttpt) REVERT: h 2 GLN cc_start: 0.6882 (mm-40) cc_final: 0.6356 (mm-40) REVERT: h 17 ASP cc_start: 0.5623 (t0) cc_final: 0.5105 (t70) REVERT: h 47 PHE cc_start: 0.7896 (t80) cc_final: 0.6914 (m-80) REVERT: j 74 TYR cc_start: 0.8817 (m-80) cc_final: 0.8404 (m-80) REVERT: j 80 HIS cc_start: 0.8167 (OUTLIER) cc_final: 0.7350 (t-90) REVERT: j 108 MET cc_start: 0.8264 (mtt) cc_final: 0.8054 (mtt) REVERT: j 138 GLN cc_start: 0.7658 (pt0) cc_final: 0.6772 (tp-100) REVERT: k 14 SER cc_start: 0.8334 (p) cc_final: 0.7990 (p) REVERT: k 93 GLN cc_start: 0.8418 (mm-40) cc_final: 0.7776 (mt0) REVERT: k 121 GLU cc_start: 0.6473 (tt0) cc_final: 0.6271 (tp30) REVERT: m 40 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7689 (mtp180) REVERT: m 51 ARG cc_start: 0.8371 (mtt90) cc_final: 0.7416 (mmt180) REVERT: m 59 ARG cc_start: 0.8466 (mtt180) cc_final: 0.8169 (tpt170) REVERT: n 103 ARG cc_start: 0.8446 (ttp-170) cc_final: 0.8151 (ttm-80) REVERT: o 2 ASP cc_start: 0.6603 (p0) cc_final: 0.6400 (p0) REVERT: o 80 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7262 (pp20) REVERT: o 89 ASP cc_start: 0.7702 (t70) cc_final: 0.7409 (m-30) REVERT: o 91 SER cc_start: 0.7627 (m) cc_final: 0.7266 (m) REVERT: q 28 ARG cc_start: 0.8213 (mtp85) cc_final: 0.7787 (mtp-110) REVERT: q 97 ASP cc_start: 0.7202 (t0) cc_final: 0.6818 (t0) REVERT: r 13 ARG cc_start: 0.8609 (ttp-170) cc_final: 0.7771 (ttt-90) REVERT: r 25 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7622 (mm) REVERT: r 26 ASP cc_start: 0.8415 (m-30) cc_final: 0.8127 (m-30) REVERT: s 39 THR cc_start: 0.8664 (m) cc_final: 0.8152 (p) REVERT: s 59 GLU cc_start: 0.7940 (tp30) cc_final: 0.7443 (mt-10) REVERT: t 3 ARG cc_start: 0.7226 (mtt180) cc_final: 0.6288 (mmt180) REVERT: t 26 LYS cc_start: 0.8016 (ttpt) cc_final: 0.7633 (tppt) REVERT: t 37 ASP cc_start: 0.6464 (OUTLIER) cc_final: 0.5947 (t0) REVERT: t 52 GLU cc_start: 0.6507 (mt-10) cc_final: 0.6273 (mt-10) REVERT: t 91 GLN cc_start: 0.4199 (OUTLIER) cc_final: 0.3413 (pt0) REVERT: u 62 GLU cc_start: 0.7779 (pm20) cc_final: 0.7236 (pp20) REVERT: u 81 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7407 (m-30) REVERT: u 82 ARG cc_start: 0.7203 (mtp85) cc_final: 0.6715 (mtm-85) REVERT: w 4 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7121 (mm) REVERT: w 5 ASN cc_start: 0.7959 (m-40) cc_final: 0.7434 (t0) REVERT: w 55 GLU cc_start: 0.8142 (mp0) cc_final: 0.7406 (mt-10) REVERT: w 59 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7599 (mp0) REVERT: w 71 LYS cc_start: 0.7703 (mtpt) cc_final: 0.7243 (mtmm) REVERT: y 29 GLU cc_start: 0.7226 (tt0) cc_final: 0.6765 (tt0) REVERT: y 39 ARG cc_start: 0.7768 (mmm-85) cc_final: 0.7241 (mtm180) REVERT: z 4 GLN cc_start: 0.5587 (OUTLIER) cc_final: 0.4056 (tm-30) REVERT: z 5 LYS cc_start: 0.5234 (OUTLIER) cc_final: 0.3753 (ptpt) outliers start: 365 outliers final: 286 residues processed: 1389 average time/residue: 1.2985 time to fit residues: 3131.6834 Evaluate side-chains 1456 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 1140 time to evaluate : 6.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 166 TRP Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 200 TRP Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 127 ARG Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 45 MET Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 45 ASN Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 71 HIS Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 119 LYS Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 32 ILE Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain O residue 13 GLU Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 56 ARG Chi-restraints excluded: chain Q residue 17 GLU Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 47 THR Chi-restraints excluded: chain S residue 55 GLN Chi-restraints excluded: chain T residue 3 ILE Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 67 HIS Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 39 LYS Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 13 VAL Chi-restraints excluded: chain 0 residue 67 VAL Chi-restraints excluded: chain 1 residue 13 GLU Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 1 residue 40 SER Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 29 SER Chi-restraints excluded: chain 3 residue 32 LYS Chi-restraints excluded: chain 4 residue 12 VAL Chi-restraints excluded: chain 4 residue 22 THR Chi-restraints excluded: chain 4 residue 23 THR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 32 GLU Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 47 VAL Chi-restraints excluded: chain 4 residue 51 GLU Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 9 VAL Chi-restraints excluded: chain 7 residue 26 HIS Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 8 residue 3 VAL Chi-restraints excluded: chain 8 residue 7 VAL Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 8 residue 16 ILE Chi-restraints excluded: chain 8 residue 18 LYS Chi-restraints excluded: chain 8 residue 26 ILE Chi-restraints excluded: chain c residue 24 LEU Chi-restraints excluded: chain c residue 35 GLU Chi-restraints excluded: chain c residue 59 LYS Chi-restraints excluded: chain c residue 147 LYS Chi-restraints excluded: chain c residue 154 LEU Chi-restraints excluded: chain c residue 199 GLU Chi-restraints excluded: chain c residue 201 MET Chi-restraints excluded: chain c residue 216 VAL Chi-restraints excluded: chain c residue 225 MET Chi-restraints excluded: chain c residue 242 LYS Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 52 LEU Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 79 LEU Chi-restraints excluded: chain i residue 112 LYS Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 45 TYR Chi-restraints excluded: chain d residue 51 THR Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 103 ASP Chi-restraints excluded: chain d residue 105 LYS Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 7 ASP Chi-restraints excluded: chain e residue 31 VAL Chi-restraints excluded: chain e residue 60 TRP Chi-restraints excluded: chain e residue 70 SER Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 100 MET Chi-restraints excluded: chain e residue 120 VAL Chi-restraints excluded: chain e residue 141 MET Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 6 ASP Chi-restraints excluded: chain f residue 7 TYR Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 51 ASP Chi-restraints excluded: chain f residue 74 VAL Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 123 ASP Chi-restraints excluded: chain f residue 130 MET Chi-restraints excluded: chain f residue 134 GLU Chi-restraints excluded: chain f residue 154 ILE Chi-restraints excluded: chain f residue 170 LEU Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 103 ILE Chi-restraints excluded: chain g residue 114 ASP Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 151 TYR Chi-restraints excluded: chain g residue 160 LYS Chi-restraints excluded: chain h residue 40 THR Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 80 HIS Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 105 VAL Chi-restraints excluded: chain j residue 124 VAL Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 28 SER Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 80 SER Chi-restraints excluded: chain l residue 95 LEU Chi-restraints excluded: chain l residue 96 LYS Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 40 ARG Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 108 VAL Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 10 LEU Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain n residue 94 TYR Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 5 SER Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 20 GLU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 26 LEU Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 45 SER Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 108 ASP Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 8 LEU Chi-restraints excluded: chain p residue 17 VAL Chi-restraints excluded: chain p residue 72 ARG Chi-restraints excluded: chain p residue 85 SER Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain q residue 9 ILE Chi-restraints excluded: chain q residue 18 LEU Chi-restraints excluded: chain q residue 40 ILE Chi-restraints excluded: chain q residue 83 LEU Chi-restraints excluded: chain r residue 4 VAL Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 25 LEU Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 39 LEU Chi-restraints excluded: chain r residue 55 ASP Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 85 LYS Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain s residue 105 VAL Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 61 LEU Chi-restraints excluded: chain t residue 74 ILE Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain t residue 91 GLN Chi-restraints excluded: chain u residue 11 VAL Chi-restraints excluded: chain u residue 18 ASP Chi-restraints excluded: chain u residue 58 ILE Chi-restraints excluded: chain u residue 65 ILE Chi-restraints excluded: chain u residue 67 VAL Chi-restraints excluded: chain u residue 73 PHE Chi-restraints excluded: chain u residue 81 ASP Chi-restraints excluded: chain u residue 100 SER Chi-restraints excluded: chain u residue 102 THR Chi-restraints excluded: chain w residue 4 ILE Chi-restraints excluded: chain w residue 61 LEU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 50 ASN Chi-restraints excluded: chain y residue 51 VAL Chi-restraints excluded: chain z residue 3 GLU Chi-restraints excluded: chain z residue 4 GLN Chi-restraints excluded: chain z residue 5 LYS Chi-restraints excluded: chain z residue 17 VAL Chi-restraints excluded: chain z residue 18 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 894 optimal weight: 7.9990 chunk 941 optimal weight: 7.9990 chunk 859 optimal weight: 0.0470 chunk 916 optimal weight: 5.9990 chunk 551 optimal weight: 30.0000 chunk 399 optimal weight: 5.9990 chunk 719 optimal weight: 10.0000 chunk 281 optimal weight: 0.2980 chunk 827 optimal weight: 6.9990 chunk 866 optimal weight: 10.0000 chunk 912 optimal weight: 7.9990 overall best weight: 3.8684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 HIS ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 ASN O 27 GLN 1 36 GLN 1 58 ASN ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 153 GLN ** c 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN f 21 ASN ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 88 ASN n 107 ASN q 44 GLN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 49 ASN w 51 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.5842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 158637 Z= 0.206 Angle : 0.671 12.581 237537 Z= 0.343 Chirality : 0.038 0.388 30396 Planarity : 0.005 0.137 12579 Dihedral : 24.598 179.651 79949 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.61 % Favored : 90.76 % Rotamer: Outliers : 6.33 % Allowed : 26.10 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.07 % Twisted Proline : 1.04 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.11), residues: 5630 helix: -0.08 (0.12), residues: 1701 sheet: -1.47 (0.15), residues: 1033 loop : -1.97 (0.11), residues: 2896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 22 HIS 0.010 0.001 HIS 1 41 PHE 0.025 0.002 PHE I 126 TYR 0.023 0.002 TYR H 127 ARG 0.028 0.001 ARG P 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1471 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 1175 time to evaluate : 6.196 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: B 18 GLN cc_start: 0.6406 (tp-100) cc_final: 0.6179 (tm-30) REVERT: B 55 GLU cc_start: 0.6617 (mt-10) cc_final: 0.6312 (mt-10) REVERT: C 27 GLU cc_start: 0.6920 (pm20) cc_final: 0.6557 (pm20) REVERT: C 41 TYR cc_start: 0.7407 (m-80) cc_final: 0.7050 (m-80) REVERT: C 58 ARG cc_start: 0.7063 (ttt180) cc_final: 0.6718 (ttp-170) REVERT: C 169 GLU cc_start: 0.6836 (tm-30) cc_final: 0.6547 (tt0) REVERT: C 202 PHE cc_start: 0.7892 (t80) cc_final: 0.7614 (t80) REVERT: D 46 ARG cc_start: 0.6488 (ttm170) cc_final: 0.5183 (mpp80) REVERT: D 69 ARG cc_start: 0.5933 (ptt180) cc_final: 0.5440 (ptp-170) REVERT: D 123 MET cc_start: 0.7636 (mtp) cc_final: 0.7245 (mmm) REVERT: D 140 ASP cc_start: 0.5547 (t70) cc_final: 0.5156 (m-30) REVERT: E 44 ARG cc_start: 0.6812 (tpp80) cc_final: 0.6557 (tpp80) REVERT: E 49 TYR cc_start: 0.6109 (OUTLIER) cc_final: 0.5733 (t80) REVERT: E 63 MET cc_start: 0.7092 (mmm) cc_final: 0.6718 (mmm) REVERT: E 68 ARG cc_start: 0.7754 (mmt-90) cc_final: 0.7455 (mtp-110) REVERT: E 94 PHE cc_start: 0.6543 (m-10) cc_final: 0.6116 (m-10) REVERT: E 111 ARG cc_start: 0.6981 (ttm-80) cc_final: 0.6671 (ttm-80) REVERT: F 47 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7154 (pp) REVERT: F 62 MET cc_start: 0.7848 (mmm) cc_final: 0.7486 (mtp) REVERT: F 65 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6317 (mm-30) REVERT: G 121 ASN cc_start: 0.8268 (t0) cc_final: 0.8020 (t0) REVERT: G 143 MET cc_start: 0.7698 (tpp) cc_final: 0.7300 (tpp) REVERT: H 29 SER cc_start: 0.6519 (t) cc_final: 0.6271 (t) REVERT: H 40 LYS cc_start: 0.8414 (tptt) cc_final: 0.8140 (tptm) REVERT: H 91 LEU cc_start: 0.7326 (tp) cc_final: 0.6668 (pt) REVERT: I 11 ARG cc_start: 0.6910 (tpt-90) cc_final: 0.6408 (tpt-90) REVERT: I 87 MET cc_start: 0.6171 (ppp) cc_final: 0.5902 (ppp) REVERT: J 64 GLN cc_start: 0.8261 (pp30) cc_final: 0.7678 (pp30) REVERT: L 24 GLU cc_start: 0.5640 (tt0) cc_final: 0.5028 (tp30) REVERT: M 75 SER cc_start: 0.7990 (t) cc_final: 0.7506 (m) REVERT: O 58 MET cc_start: 0.8042 (mmp) cc_final: 0.7242 (mtp) REVERT: Q 8 GLN cc_start: 0.7317 (tm-30) cc_final: 0.6668 (mm110) REVERT: Q 26 ARG cc_start: 0.7887 (ptm160) cc_final: 0.6837 (ptt90) REVERT: Q 33 TYR cc_start: 0.6804 (m-80) cc_final: 0.6024 (m-80) REVERT: R 47 ARG cc_start: 0.7118 (tpp-160) cc_final: 0.5916 (ptp-170) REVERT: S 27 LYS cc_start: 0.6891 (mptt) cc_final: 0.5648 (tttt) REVERT: S 55 GLN cc_start: 0.5629 (OUTLIER) cc_final: 0.4683 (pm20) REVERT: T 4 LYS cc_start: 0.7360 (mmtp) cc_final: 0.6785 (pttm) REVERT: T 12 GLN cc_start: 0.8449 (mt0) cc_final: 0.8116 (tm-30) REVERT: 0 39 TRP cc_start: 0.7526 (t-100) cc_final: 0.6903 (t-100) REVERT: 0 40 VAL cc_start: 0.7530 (t) cc_final: 0.7060 (m) REVERT: 1 13 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6598 (tp30) REVERT: 1 17 GLU cc_start: 0.7731 (mm-30) cc_final: 0.6990 (mm-30) REVERT: 1 44 LYS cc_start: 0.7625 (ttmt) cc_final: 0.7126 (tptm) REVERT: 1 54 LYS cc_start: 0.8769 (mmtm) cc_final: 0.8492 (mmtm) REVERT: 1 59 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7316 (mm-30) REVERT: 1 60 LYS cc_start: 0.8290 (ttmt) cc_final: 0.7559 (tmtt) REVERT: 2 3 LYS cc_start: 0.7055 (mttt) cc_final: 0.6765 (mmtt) REVERT: 2 56 LYS cc_start: 0.7216 (pttt) cc_final: 0.6771 (mmmm) REVERT: 2 58 GLU cc_start: 0.6255 (mt-10) cc_final: 0.5526 (mp0) REVERT: 3 33 THR cc_start: 0.8595 (m) cc_final: 0.8338 (p) REVERT: 4 30 LYS cc_start: 0.6939 (mmtm) cc_final: 0.6700 (mttm) REVERT: 4 32 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: 4 50 LYS cc_start: 0.7311 (mtmt) cc_final: 0.7075 (mtmm) REVERT: 4 51 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6750 (tm-30) REVERT: 6 25 LYS cc_start: 0.7690 (tptt) cc_final: 0.7475 (pttm) REVERT: 6 41 ARG cc_start: 0.8554 (mtt-85) cc_final: 0.8215 (mtp180) REVERT: 8 13 ASN cc_start: 0.8185 (m-40) cc_final: 0.7531 (t0) REVERT: c 66 ASP cc_start: 0.8654 (t70) cc_final: 0.7959 (t0) REVERT: c 147 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7442 (mtpt) REVERT: c 181 MET cc_start: 0.7920 (mmt) cc_final: 0.7489 (mtp) REVERT: c 183 LYS cc_start: 0.8396 (mttp) cc_final: 0.8071 (mtpp) REVERT: c 265 LYS cc_start: 0.8241 (tmtt) cc_final: 0.7354 (mttt) REVERT: i 112 LYS cc_start: -0.0967 (OUTLIER) cc_final: -0.1292 (pttp) REVERT: i 124 MET cc_start: 0.2180 (OUTLIER) cc_final: 0.1969 (ttt) REVERT: i 133 ARG cc_start: 0.2154 (ttp80) cc_final: 0.1946 (ttp80) REVERT: i 135 MET cc_start: -0.0471 (OUTLIER) cc_final: -0.1262 (ptp) REVERT: d 4 LEU cc_start: 0.8680 (mt) cc_final: 0.8384 (mt) REVERT: d 40 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7943 (mt) REVERT: d 58 ASN cc_start: 0.8888 (p0) cc_final: 0.8485 (m110) REVERT: d 86 GLU cc_start: 0.7627 (tt0) cc_final: 0.7417 (tm-30) REVERT: d 100 LEU cc_start: 0.8518 (tp) cc_final: 0.8264 (tt) REVERT: d 185 ASN cc_start: 0.7939 (m-40) cc_final: 0.7543 (m-40) REVERT: e 15 SER cc_start: 0.6993 (m) cc_final: 0.6299 (t) REVERT: e 23 PHE cc_start: 0.8890 (t80) cc_final: 0.8206 (t80) REVERT: e 116 ASP cc_start: 0.7921 (m-30) cc_final: 0.7306 (t70) REVERT: e 123 LYS cc_start: 0.6782 (tppt) cc_final: 0.5530 (ptmm) REVERT: e 144 GLU cc_start: 0.6631 (tt0) cc_final: 0.6160 (mp0) REVERT: e 149 ILE cc_start: 0.8402 (mt) cc_final: 0.8128 (tt) REVERT: e 165 HIS cc_start: 0.6697 (t-90) cc_final: 0.6320 (t-90) REVERT: f 64 LYS cc_start: 0.3354 (mttt) cc_final: 0.2998 (mttt) REVERT: f 77 PHE cc_start: 0.8064 (m-80) cc_final: 0.7195 (m-80) REVERT: f 170 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7283 (mm) REVERT: g 160 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7366 (ttpt) REVERT: h 2 GLN cc_start: 0.7046 (mm-40) cc_final: 0.6636 (mm-40) REVERT: h 17 ASP cc_start: 0.5510 (t0) cc_final: 0.5104 (t70) REVERT: j 74 TYR cc_start: 0.8744 (m-80) cc_final: 0.8311 (m-80) REVERT: j 80 HIS cc_start: 0.8142 (OUTLIER) cc_final: 0.7329 (t-90) REVERT: j 108 MET cc_start: 0.8343 (mtt) cc_final: 0.7969 (mtt) REVERT: j 138 GLN cc_start: 0.7747 (pt0) cc_final: 0.6839 (tp-100) REVERT: k 14 SER cc_start: 0.8467 (p) cc_final: 0.8242 (p) REVERT: k 93 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7692 (mt0) REVERT: k 113 MET cc_start: 0.6800 (tpp) cc_final: 0.6419 (ptm) REVERT: l 2 ARG cc_start: 0.6418 (mmt180) cc_final: 0.5700 (mmm160) REVERT: m 51 ARG cc_start: 0.8480 (mtt90) cc_final: 0.7554 (mmt180) REVERT: m 59 ARG cc_start: 0.8487 (mtt180) cc_final: 0.8194 (tpt170) REVERT: n 94 TYR cc_start: 0.7924 (OUTLIER) cc_final: 0.7581 (m-80) REVERT: n 103 ARG cc_start: 0.8426 (ttp-170) cc_final: 0.8135 (ttm-80) REVERT: o 80 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7123 (pp20) REVERT: o 89 ASP cc_start: 0.7667 (t70) cc_final: 0.7379 (m-30) REVERT: o 91 SER cc_start: 0.7634 (m) cc_final: 0.7288 (m) REVERT: p 31 TRP cc_start: 0.7870 (m100) cc_final: 0.6676 (m100) REVERT: q 28 ARG cc_start: 0.8096 (mtp85) cc_final: 0.7697 (mtp-110) REVERT: q 97 ASP cc_start: 0.7446 (t0) cc_final: 0.7232 (t0) REVERT: r 26 ASP cc_start: 0.8437 (m-30) cc_final: 0.8164 (m-30) REVERT: r 40 MET cc_start: 0.7958 (tpt) cc_final: 0.7288 (tpt) REVERT: r 53 PHE cc_start: 0.7756 (m-10) cc_final: 0.7460 (m-10) REVERT: s 39 THR cc_start: 0.8592 (m) cc_final: 0.8126 (p) REVERT: s 59 GLU cc_start: 0.7834 (tp30) cc_final: 0.7489 (mt-10) REVERT: t 3 ARG cc_start: 0.7109 (mtt180) cc_final: 0.6214 (mmt180) REVERT: t 26 LYS cc_start: 0.8009 (ttpt) cc_final: 0.7619 (tppt) REVERT: t 37 ASP cc_start: 0.6294 (OUTLIER) cc_final: 0.5873 (t0) REVERT: u 62 GLU cc_start: 0.7692 (pm20) cc_final: 0.7215 (pp20) REVERT: u 81 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7356 (m-30) REVERT: u 82 ARG cc_start: 0.7207 (mtp85) cc_final: 0.6839 (mtm-85) REVERT: u 86 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.6960 (ptp90) REVERT: w 4 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.6982 (mm) REVERT: w 5 ASN cc_start: 0.7918 (m-40) cc_final: 0.7383 (t0) REVERT: w 55 GLU cc_start: 0.8139 (mp0) cc_final: 0.7345 (mt-10) REVERT: w 59 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7593 (mp0) REVERT: w 71 LYS cc_start: 0.7692 (mtpt) cc_final: 0.7316 (mmtt) REVERT: w 79 ARG cc_start: 0.8163 (mtp85) cc_final: 0.7301 (mtp85) REVERT: w 93 ARG cc_start: 0.7367 (mtt90) cc_final: 0.6701 (mtm180) REVERT: y 29 GLU cc_start: 0.7269 (tt0) cc_final: 0.6777 (tt0) REVERT: y 39 ARG cc_start: 0.7693 (mmm-85) cc_final: 0.7194 (mtm180) REVERT: y 83 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6614 (mp0) REVERT: z 4 GLN cc_start: 0.5333 (OUTLIER) cc_final: 0.3978 (tm-30) REVERT: z 5 LYS cc_start: 0.5173 (OUTLIER) cc_final: 0.3824 (ptpt) outliers start: 296 outliers final: 227 residues processed: 1338 average time/residue: 1.2793 time to fit residues: 2967.5691 Evaluate side-chains 1397 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1149 time to evaluate : 6.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 166 TRP Chi-restraints excluded: chain C residue 200 TRP Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 45 MET Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 71 HIS Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain O residue 13 GLU Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 56 ARG Chi-restraints excluded: chain Q residue 17 GLU Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 47 THR Chi-restraints excluded: chain S residue 55 GLN Chi-restraints excluded: chain T residue 3 ILE Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 67 HIS Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 39 LYS Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 13 VAL Chi-restraints excluded: chain 0 residue 67 VAL Chi-restraints excluded: chain 1 residue 13 GLU Chi-restraints excluded: chain 1 residue 40 SER Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 3 residue 29 SER Chi-restraints excluded: chain 3 residue 43 ILE Chi-restraints excluded: chain 4 residue 22 THR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 32 GLU Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 47 VAL Chi-restraints excluded: chain 4 residue 51 GLU Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 9 VAL Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 8 residue 3 VAL Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 8 residue 16 ILE Chi-restraints excluded: chain c residue 24 LEU Chi-restraints excluded: chain c residue 35 GLU Chi-restraints excluded: chain c residue 147 LYS Chi-restraints excluded: chain c residue 154 LEU Chi-restraints excluded: chain c residue 160 THR Chi-restraints excluded: chain c residue 201 MET Chi-restraints excluded: chain c residue 216 VAL Chi-restraints excluded: chain c residue 225 MET Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 52 LEU Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 79 LEU Chi-restraints excluded: chain i residue 112 LYS Chi-restraints excluded: chain i residue 124 MET Chi-restraints excluded: chain i residue 135 MET Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 51 THR Chi-restraints excluded: chain d residue 105 LYS Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 187 LEU Chi-restraints excluded: chain e residue 7 ASP Chi-restraints excluded: chain e residue 31 VAL Chi-restraints excluded: chain e residue 120 VAL Chi-restraints excluded: chain e residue 141 MET Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 6 ASP Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 21 ASN Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 123 ASP Chi-restraints excluded: chain f residue 130 MET Chi-restraints excluded: chain f residue 154 ILE Chi-restraints excluded: chain f residue 170 LEU Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 74 SER Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 114 ASP Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 151 TYR Chi-restraints excluded: chain g residue 160 LYS Chi-restraints excluded: chain h residue 40 THR Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 80 HIS Chi-restraints excluded: chain j residue 105 VAL Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 95 LEU Chi-restraints excluded: chain l residue 96 LYS Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 108 VAL Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 10 LEU Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain n residue 94 TYR Chi-restraints excluded: chain o residue 5 SER Chi-restraints excluded: chain o residue 20 GLU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 45 SER Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 17 VAL Chi-restraints excluded: chain p residue 85 SER Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 92 VAL Chi-restraints excluded: chain q residue 9 ILE Chi-restraints excluded: chain q residue 40 ILE Chi-restraints excluded: chain q residue 83 LEU Chi-restraints excluded: chain r residue 4 VAL Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 39 LEU Chi-restraints excluded: chain r residue 55 ASP Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 70 GLU Chi-restraints excluded: chain r residue 85 LYS Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 61 LEU Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 18 ASP Chi-restraints excluded: chain u residue 58 ILE Chi-restraints excluded: chain u residue 67 VAL Chi-restraints excluded: chain u residue 73 PHE Chi-restraints excluded: chain u residue 81 ASP Chi-restraints excluded: chain u residue 86 ARG Chi-restraints excluded: chain u residue 100 SER Chi-restraints excluded: chain u residue 102 THR Chi-restraints excluded: chain w residue 4 ILE Chi-restraints excluded: chain w residue 51 GLN Chi-restraints excluded: chain w residue 61 LEU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 50 ASN Chi-restraints excluded: chain y residue 51 VAL Chi-restraints excluded: chain z residue 3 GLU Chi-restraints excluded: chain z residue 4 GLN Chi-restraints excluded: chain z residue 5 LYS Chi-restraints excluded: chain z residue 18 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 601 optimal weight: 10.0000 chunk 968 optimal weight: 8.9990 chunk 591 optimal weight: 20.0000 chunk 459 optimal weight: 20.0000 chunk 673 optimal weight: 10.0000 chunk 1016 optimal weight: 5.9990 chunk 935 optimal weight: 0.3980 chunk 809 optimal weight: 8.9990 chunk 84 optimal weight: 30.0000 chunk 625 optimal weight: 10.0000 chunk 496 optimal weight: 10.0000 overall best weight: 6.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 HIS D 39 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 ASN ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 GLN ** T 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 58 ASN ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 134 ASN c 153 GLN ** c 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 21 ASN ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 88 ASN ** q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 49 ASN w 51 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.5846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.329 158637 Z= 0.290 Angle : 0.721 59.070 237537 Z= 0.376 Chirality : 0.040 0.586 30396 Planarity : 0.005 0.136 12579 Dihedral : 24.595 179.695 79949 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.61 % Favored : 90.78 % Rotamer: Outliers : 6.09 % Allowed : 26.46 % Favored : 67.44 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.07 % Twisted Proline : 1.04 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.11), residues: 5630 helix: -0.09 (0.12), residues: 1701 sheet: -1.46 (0.15), residues: 1033 loop : -1.96 (0.11), residues: 2896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 200 HIS 0.011 0.001 HIS T 74 PHE 0.027 0.002 PHE I 126 TYR 0.024 0.002 TYR H 127 ARG 0.039 0.001 ARG P 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1432 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1147 time to evaluate : 6.294 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: B 18 GLN cc_start: 0.6403 (tp-100) cc_final: 0.6172 (tm-30) REVERT: B 55 GLU cc_start: 0.6618 (mt-10) cc_final: 0.6301 (mt-10) REVERT: C 27 GLU cc_start: 0.6950 (pm20) cc_final: 0.6547 (pm20) REVERT: C 41 TYR cc_start: 0.7381 (m-80) cc_final: 0.6944 (m-80) REVERT: C 58 ARG cc_start: 0.7065 (ttt180) cc_final: 0.6723 (ttp-170) REVERT: C 169 GLU cc_start: 0.6838 (tm-30) cc_final: 0.6547 (tt0) REVERT: D 46 ARG cc_start: 0.6492 (ttm170) cc_final: 0.5214 (mpp80) REVERT: D 69 ARG cc_start: 0.5940 (ptt180) cc_final: 0.5443 (ptp-170) REVERT: D 123 MET cc_start: 0.7631 (mtp) cc_final: 0.7250 (mmm) REVERT: D 140 ASP cc_start: 0.5552 (t70) cc_final: 0.5160 (m-30) REVERT: E 49 TYR cc_start: 0.6113 (OUTLIER) cc_final: 0.5740 (t80) REVERT: E 63 MET cc_start: 0.7103 (mmm) cc_final: 0.6722 (mmm) REVERT: E 68 ARG cc_start: 0.7756 (mmt-90) cc_final: 0.7455 (mtp-110) REVERT: E 94 PHE cc_start: 0.6547 (m-10) cc_final: 0.6118 (m-10) REVERT: E 111 ARG cc_start: 0.7011 (ttm-80) cc_final: 0.6675 (ttm-80) REVERT: F 47 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7159 (pp) REVERT: F 62 MET cc_start: 0.7848 (mmm) cc_final: 0.7488 (mtp) REVERT: F 65 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6315 (mm-30) REVERT: G 121 ASN cc_start: 0.8270 (t0) cc_final: 0.8019 (t0) REVERT: G 143 MET cc_start: 0.7703 (tpp) cc_final: 0.7305 (tpp) REVERT: H 29 SER cc_start: 0.6528 (t) cc_final: 0.6283 (t) REVERT: H 40 LYS cc_start: 0.8410 (tptt) cc_final: 0.8139 (tptm) REVERT: H 91 LEU cc_start: 0.7243 (tp) cc_final: 0.6693 (pt) REVERT: I 11 ARG cc_start: 0.6908 (tpt-90) cc_final: 0.6416 (tpt-90) REVERT: I 87 MET cc_start: 0.6174 (ppp) cc_final: 0.5857 (ppp) REVERT: J 64 GLN cc_start: 0.8263 (pp30) cc_final: 0.7727 (pp30) REVERT: L 24 GLU cc_start: 0.5645 (tt0) cc_final: 0.5039 (tp30) REVERT: M 75 SER cc_start: 0.7986 (t) cc_final: 0.7503 (m) REVERT: O 58 MET cc_start: 0.8050 (mmp) cc_final: 0.7241 (mtp) REVERT: Q 8 GLN cc_start: 0.7318 (tm-30) cc_final: 0.6670 (mm110) REVERT: Q 26 ARG cc_start: 0.7889 (ptm160) cc_final: 0.6838 (ptt90) REVERT: Q 33 TYR cc_start: 0.6808 (m-80) cc_final: 0.6024 (m-80) REVERT: R 47 ARG cc_start: 0.7120 (tpp-160) cc_final: 0.5918 (ptp-170) REVERT: S 27 LYS cc_start: 0.6893 (mptt) cc_final: 0.5649 (tttt) REVERT: S 55 GLN cc_start: 0.5589 (OUTLIER) cc_final: 0.4660 (pm20) REVERT: T 4 LYS cc_start: 0.7361 (mmtp) cc_final: 0.6787 (pttm) REVERT: T 12 GLN cc_start: 0.8447 (mt0) cc_final: 0.8181 (tm-30) REVERT: 0 39 TRP cc_start: 0.7530 (t-100) cc_final: 0.6891 (t-100) REVERT: 0 40 VAL cc_start: 0.7519 (t) cc_final: 0.7053 (m) REVERT: 1 13 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6601 (tp30) REVERT: 1 17 GLU cc_start: 0.7735 (mm-30) cc_final: 0.6989 (mm-30) REVERT: 1 44 LYS cc_start: 0.7631 (ttmt) cc_final: 0.7184 (tptp) REVERT: 1 54 LYS cc_start: 0.8768 (mmtm) cc_final: 0.8484 (mmtm) REVERT: 1 59 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7317 (mm-30) REVERT: 1 60 LYS cc_start: 0.8289 (ttmt) cc_final: 0.7558 (tmtt) REVERT: 2 3 LYS cc_start: 0.7017 (mttt) cc_final: 0.6767 (mmtt) REVERT: 2 56 LYS cc_start: 0.7224 (pttt) cc_final: 0.6774 (mmmm) REVERT: 2 58 GLU cc_start: 0.6254 (mt-10) cc_final: 0.5540 (mp0) REVERT: 3 33 THR cc_start: 0.8594 (m) cc_final: 0.8339 (p) REVERT: 4 30 LYS cc_start: 0.6939 (mmtm) cc_final: 0.6700 (mttm) REVERT: 4 32 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: 4 50 LYS cc_start: 0.7311 (mtmt) cc_final: 0.7077 (mtmm) REVERT: 4 51 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6751 (tm-30) REVERT: 6 29 GLN cc_start: 0.7925 (mm110) cc_final: 0.7670 (mm-40) REVERT: 6 41 ARG cc_start: 0.8579 (mtt-85) cc_final: 0.8212 (mtp180) REVERT: 8 13 ASN cc_start: 0.8189 (m-40) cc_final: 0.7537 (t0) REVERT: c 66 ASP cc_start: 0.8662 (t70) cc_final: 0.7966 (t0) REVERT: c 147 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7446 (mtpt) REVERT: c 181 MET cc_start: 0.7927 (mmt) cc_final: 0.7495 (mtp) REVERT: c 183 LYS cc_start: 0.8405 (mttp) cc_final: 0.8080 (mtpp) REVERT: c 265 LYS cc_start: 0.8243 (tmtt) cc_final: 0.7339 (mttt) REVERT: i 112 LYS cc_start: -0.0964 (OUTLIER) cc_final: -0.1287 (pttp) REVERT: i 124 MET cc_start: 0.2185 (OUTLIER) cc_final: 0.1972 (ttt) REVERT: i 135 MET cc_start: -0.0484 (OUTLIER) cc_final: -0.1258 (ptp) REVERT: d 4 LEU cc_start: 0.8683 (mt) cc_final: 0.8384 (mt) REVERT: d 40 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7944 (mt) REVERT: d 58 ASN cc_start: 0.8889 (p0) cc_final: 0.8487 (m110) REVERT: d 89 GLU cc_start: 0.7401 (pm20) cc_final: 0.6706 (mp0) REVERT: d 100 LEU cc_start: 0.8516 (tp) cc_final: 0.8255 (tt) REVERT: d 185 ASN cc_start: 0.7979 (m-40) cc_final: 0.7542 (m-40) REVERT: e 15 SER cc_start: 0.6994 (m) cc_final: 0.6306 (t) REVERT: e 23 PHE cc_start: 0.8892 (t80) cc_final: 0.8211 (t80) REVERT: e 116 ASP cc_start: 0.7924 (m-30) cc_final: 0.7309 (t70) REVERT: e 123 LYS cc_start: 0.6781 (tppt) cc_final: 0.5527 (ptmm) REVERT: e 144 GLU cc_start: 0.6633 (tt0) cc_final: 0.6162 (mp0) REVERT: e 149 ILE cc_start: 0.8407 (mt) cc_final: 0.8133 (tt) REVERT: e 165 HIS cc_start: 0.6702 (t-90) cc_final: 0.6324 (t-90) REVERT: f 64 LYS cc_start: 0.3365 (mttt) cc_final: 0.3006 (mttt) REVERT: f 77 PHE cc_start: 0.8064 (m-80) cc_final: 0.7194 (m-80) REVERT: f 170 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7285 (mm) REVERT: g 160 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7369 (ttpt) REVERT: h 2 GLN cc_start: 0.7049 (mm-40) cc_final: 0.6639 (mm-40) REVERT: h 17 ASP cc_start: 0.5524 (t0) cc_final: 0.5107 (t70) REVERT: j 74 TYR cc_start: 0.8750 (m-80) cc_final: 0.8318 (m-80) REVERT: j 80 HIS cc_start: 0.8145 (OUTLIER) cc_final: 0.7333 (t-90) REVERT: j 108 MET cc_start: 0.8316 (mtt) cc_final: 0.7924 (mtt) REVERT: j 138 GLN cc_start: 0.7751 (pt0) cc_final: 0.6841 (tp-100) REVERT: k 14 SER cc_start: 0.8422 (p) cc_final: 0.8190 (p) REVERT: k 93 GLN cc_start: 0.8341 (mm-40) cc_final: 0.7697 (mt0) REVERT: l 2 ARG cc_start: 0.6419 (mmt180) cc_final: 0.5673 (mmm160) REVERT: m 40 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7649 (mtp180) REVERT: m 51 ARG cc_start: 0.8484 (mtt90) cc_final: 0.7556 (mmt180) REVERT: m 59 ARG cc_start: 0.8488 (mtt180) cc_final: 0.8196 (tpt170) REVERT: n 103 ARG cc_start: 0.8430 (ttp-170) cc_final: 0.8140 (ttm-80) REVERT: o 80 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7164 (pp20) REVERT: o 89 ASP cc_start: 0.7670 (t70) cc_final: 0.7382 (m-30) REVERT: o 91 SER cc_start: 0.7636 (m) cc_final: 0.7292 (m) REVERT: p 31 TRP cc_start: 0.7902 (m100) cc_final: 0.6678 (m100) REVERT: p 72 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7559 (ttp80) REVERT: q 28 ARG cc_start: 0.8140 (mtp85) cc_final: 0.7696 (mtp-110) REVERT: q 97 ASP cc_start: 0.7457 (t0) cc_final: 0.7237 (t0) REVERT: r 26 ASP cc_start: 0.8382 (m-30) cc_final: 0.8105 (m-30) REVERT: r 53 PHE cc_start: 0.7766 (m-10) cc_final: 0.7458 (m-10) REVERT: s 39 THR cc_start: 0.8594 (m) cc_final: 0.8129 (p) REVERT: s 59 GLU cc_start: 0.7905 (tp30) cc_final: 0.7490 (mt-10) REVERT: t 3 ARG cc_start: 0.7108 (mtt180) cc_final: 0.6216 (mmt180) REVERT: t 26 LYS cc_start: 0.8012 (ttpt) cc_final: 0.7622 (tppt) REVERT: t 37 ASP cc_start: 0.6299 (OUTLIER) cc_final: 0.5877 (t0) REVERT: u 62 GLU cc_start: 0.7698 (pm20) cc_final: 0.7220 (pp20) REVERT: u 81 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7362 (m-30) REVERT: u 82 ARG cc_start: 0.7211 (mtp85) cc_final: 0.6840 (mtm-85) REVERT: u 86 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6962 (ptp90) REVERT: w 4 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.6987 (mm) REVERT: w 5 ASN cc_start: 0.7920 (m-40) cc_final: 0.7385 (t0) REVERT: w 55 GLU cc_start: 0.8139 (mp0) cc_final: 0.7352 (mt-10) REVERT: w 59 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7594 (mp0) REVERT: w 71 LYS cc_start: 0.7693 (mtpt) cc_final: 0.7317 (mmtt) REVERT: w 79 ARG cc_start: 0.8245 (mtp85) cc_final: 0.7369 (mtp85) REVERT: w 93 ARG cc_start: 0.7372 (mtt90) cc_final: 0.6699 (mtm180) REVERT: y 29 GLU cc_start: 0.7275 (tt0) cc_final: 0.6782 (tt0) REVERT: y 39 ARG cc_start: 0.7704 (mmm-85) cc_final: 0.7206 (mtm180) REVERT: y 83 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6616 (mp0) REVERT: z 4 GLN cc_start: 0.5340 (OUTLIER) cc_final: 0.3983 (tm-30) REVERT: z 5 LYS cc_start: 0.5179 (OUTLIER) cc_final: 0.3826 (ptpt) outliers start: 285 outliers final: 250 residues processed: 1298 average time/residue: 1.2607 time to fit residues: 2832.4960 Evaluate side-chains 1410 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1138 time to evaluate : 6.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 166 TRP Chi-restraints excluded: chain C residue 200 TRP Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 45 MET Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 71 HIS Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 38 ILE Chi-restraints excluded: chain M residue 51 GLN Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 96 LYS Chi-restraints excluded: chain O residue 13 GLU Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 56 ARG Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 47 THR Chi-restraints excluded: chain S residue 55 GLN Chi-restraints excluded: chain T residue 3 ILE Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 67 HIS Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 39 LYS Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 13 VAL Chi-restraints excluded: chain 0 residue 22 LEU Chi-restraints excluded: chain 0 residue 67 VAL Chi-restraints excluded: chain 1 residue 13 GLU Chi-restraints excluded: chain 1 residue 40 SER Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 3 residue 29 SER Chi-restraints excluded: chain 3 residue 43 ILE Chi-restraints excluded: chain 3 residue 46 ASP Chi-restraints excluded: chain 4 residue 22 THR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 32 GLU Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 47 VAL Chi-restraints excluded: chain 4 residue 51 GLU Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 9 VAL Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 8 residue 3 VAL Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 8 residue 16 ILE Chi-restraints excluded: chain c residue 24 LEU Chi-restraints excluded: chain c residue 35 GLU Chi-restraints excluded: chain c residue 59 LYS Chi-restraints excluded: chain c residue 147 LYS Chi-restraints excluded: chain c residue 154 LEU Chi-restraints excluded: chain c residue 160 THR Chi-restraints excluded: chain c residue 201 MET Chi-restraints excluded: chain c residue 216 VAL Chi-restraints excluded: chain c residue 225 MET Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 52 LEU Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 79 LEU Chi-restraints excluded: chain i residue 112 LYS Chi-restraints excluded: chain i residue 124 MET Chi-restraints excluded: chain i residue 135 MET Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 51 THR Chi-restraints excluded: chain d residue 105 LYS Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 187 LEU Chi-restraints excluded: chain e residue 7 ASP Chi-restraints excluded: chain e residue 31 VAL Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 100 MET Chi-restraints excluded: chain e residue 120 VAL Chi-restraints excluded: chain e residue 141 MET Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 6 ASP Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 123 ASP Chi-restraints excluded: chain f residue 130 MET Chi-restraints excluded: chain f residue 154 ILE Chi-restraints excluded: chain f residue 170 LEU Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain g residue 74 SER Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 114 ASP Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 151 TYR Chi-restraints excluded: chain g residue 160 LYS Chi-restraints excluded: chain h residue 40 THR Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain j residue 31 GLU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 80 HIS Chi-restraints excluded: chain j residue 105 VAL Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 80 SER Chi-restraints excluded: chain l residue 95 LEU Chi-restraints excluded: chain l residue 96 LYS Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 40 ARG Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 108 VAL Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 10 LEU Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 5 SER Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 20 GLU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 45 SER Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain p residue 17 VAL Chi-restraints excluded: chain p residue 72 ARG Chi-restraints excluded: chain p residue 85 SER Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain q residue 9 ILE Chi-restraints excluded: chain q residue 31 VAL Chi-restraints excluded: chain q residue 40 ILE Chi-restraints excluded: chain q residue 83 LEU Chi-restraints excluded: chain r residue 4 VAL Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 39 LEU Chi-restraints excluded: chain r residue 55 ASP Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 85 LYS Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 61 LEU Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 18 ASP Chi-restraints excluded: chain u residue 29 LEU Chi-restraints excluded: chain u residue 58 ILE Chi-restraints excluded: chain u residue 67 VAL Chi-restraints excluded: chain u residue 73 PHE Chi-restraints excluded: chain u residue 81 ASP Chi-restraints excluded: chain u residue 86 ARG Chi-restraints excluded: chain u residue 100 SER Chi-restraints excluded: chain u residue 102 THR Chi-restraints excluded: chain w residue 4 ILE Chi-restraints excluded: chain w residue 51 GLN Chi-restraints excluded: chain w residue 61 LEU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 50 ASN Chi-restraints excluded: chain y residue 51 VAL Chi-restraints excluded: chain z residue 3 GLU Chi-restraints excluded: chain z residue 4 GLN Chi-restraints excluded: chain z residue 5 LYS Chi-restraints excluded: chain z residue 18 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 642 optimal weight: 10.0000 chunk 861 optimal weight: 0.0670 chunk 247 optimal weight: 30.0000 chunk 746 optimal weight: 2.9990 chunk 119 optimal weight: 20.0000 chunk 224 optimal weight: 10.0000 chunk 810 optimal weight: 7.9990 chunk 339 optimal weight: 20.0000 chunk 832 optimal weight: 0.4980 chunk 102 optimal weight: 50.0000 chunk 149 optimal weight: 10.0000 overall best weight: 4.3126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 HIS ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 GLN 1 58 ASN ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 88 ASN q 37 GLN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 49 ASN w 51 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.157535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.127708 restraints weight = 289130.674| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.28 r_work: 0.3538 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 158637 Z= 0.223 Angle : 0.676 14.210 237537 Z= 0.345 Chirality : 0.038 0.436 30396 Planarity : 0.005 0.132 12579 Dihedral : 24.554 179.904 79949 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.92 % Favored : 90.53 % Rotamer: Outliers : 5.96 % Allowed : 26.55 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.07 % Twisted Proline : 1.04 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.11), residues: 5630 helix: -0.04 (0.12), residues: 1705 sheet: -1.41 (0.15), residues: 1034 loop : -1.93 (0.11), residues: 2891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 200 HIS 0.014 0.001 HIS T 74 PHE 0.030 0.002 PHE h 47 TYR 0.024 0.002 TYR H 127 ARG 0.010 0.001 ARG L 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 45380.67 seconds wall clock time: 788 minutes 23.75 seconds (47303.75 seconds total)