Starting phenix.real_space_refine on Wed Mar 20 17:44:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbu_6483/03_2024/3jbu_6483_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbu_6483/03_2024/3jbu_6483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbu_6483/03_2024/3jbu_6483.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbu_6483/03_2024/3jbu_6483.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbu_6483/03_2024/3jbu_6483_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbu_6483/03_2024/3jbu_6483_neut.pdb" } resolution = 3.64 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: 5 Type Number sf(0) Gaussians P 4637 5.49 5 S 138 5.16 5 C 71828 2.51 5 N 26713 2.21 5 O 40018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I ASP 106": "OD1" <-> "OD2" 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 "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 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "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 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 TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "j ARG 13": "NH1" <-> "NH2" 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 110": "OE1" <-> "OE2" Residue "k GLU 121": "OE1" <-> "OE2" Residue "l GLU 10": "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 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 ARG 33": "NH1" <-> "NH2" Residue "q PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 76": "OD1" <-> "OD2" 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 3": "OE1" <-> "OE2" Residue "z PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 143334 Number of models: 1 Model: "" Number of chains: 54 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: "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: "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: "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: {'CIS': 1, 'PCIS': 1, 'PTRANS': 2, 'TRANS': 144} 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: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 203 Classifications: {'peptide': 26} Link IDs: {'CIS': 4, 'PTRANS': 1, 'TRANS': 20} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 32831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1530, 32831 Classifications: {'RNA': 1530} Modifications used: {'rna2p_pur': 120, 'rna2p_pyr': 89, 'rna3p_pur': 752, 'rna3p_pyr': 569} Link IDs: {'rna2p': 209, 'rna3p': 1320} Chain: "X" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 232 Classifications: {'RNA': 11} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "a" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2528 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 56, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 104} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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': 246, 'rna2p_pyr': 139, 'rna3p_pur': 1428, 'rna3p_pyr': 1090} Link IDs: {'rna2p': 385, 'rna3p': 2517} Chain: "v" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Classifications: {'RNA': 76} Modifications used: {'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 31, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 64} Time building chain proxies: 55.39, per 1000 atoms: 0.39 Number of scatterers: 143334 At special positions: 0 Unit cell: (271.92, 291.72, 228.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 138 16.00 P 4637 15.00 O 40018 8.00 N 26713 7.00 C 71828 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 51757 O5' U A 375 .*. O " rejected from bonding due to valence issues. Atom "ATOM 51780 O4' G A 376 .*. O " rejected from bonding due to valence issues. Atom "ATOM 51757 O5' U A 375 .*. O " rejected from bonding due to valence issues. Atom "ATOM 72631 O5' U A1348 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 66.77 Conformation dependent library (CDL) restraints added in 6.6 seconds 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10280 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 69 sheets defined 34.1% alpha, 15.8% beta 1001 base pairs and 1615 stacking pairs defined. Time for finding SS restraints: 46.52 Creating SS restraints... Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 32 through 36 removed outlier: 3.975A pdb=" N ASN B 35 " --> pdb=" O GLY B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.566A pdb=" N MET B 48 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA B 54 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE B 59 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 removed outlier: 4.112A pdb=" N ASP B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 121 removed outlier: 3.598A pdb=" N VAL B 106 " --> pdb=" O ASN B 102 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLN B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 145 removed outlier: 4.142A pdb=" N ALA B 133 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASN B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 4.230A pdb=" N ASP B 152 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 177 removed outlier: 3.741A pdb=" N ILE B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.943A pdb=" N TYR B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 224 removed outlier: 4.412A pdb=" N VAL B 220 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ARG B 221 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG B 224 " --> pdb=" O ARG B 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 45 removed outlier: 3.916A pdb=" N ASN C 31 " --> pdb=" O GLU C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 removed outlier: 3.884A pdb=" N VAL C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 Processing helix chain 'C' and resid 83 through 94 removed outlier: 3.910A pdb=" N LYS C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL C 89 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.873A pdb=" N ILE C 119 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN C 122 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 143 removed outlier: 4.265A pdb=" N MET C 133 " --> pdb=" O PHE C 129 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN C 139 " --> pdb=" O ARG C 135 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'D' and resid 7 through 15 removed outlier: 3.973A pdb=" N SER D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 43 removed outlier: 3.719A pdb=" N ALA D 42 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG D 43 " --> pdb=" O HIS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 62 removed outlier: 3.810A pdb=" N VAL D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 79 Processing helix chain 'D' and resid 84 through 96 removed outlier: 3.627A pdb=" N ASN D 88 " --> pdb=" O ASN D 84 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU D 89 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU D 90 " --> pdb=" O GLY D 86 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 103 Processing helix chain 'D' and resid 109 through 119 removed outlier: 3.516A pdb=" N ALA D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 149 Processing helix chain 'D' and resid 151 through 160 removed outlier: 3.578A pdb=" N LYS D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU D 159 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU D 160 " --> pdb=" O ALA D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 190 Processing helix chain 'D' and resid 196 through 204 removed outlier: 4.064A pdb=" N VAL D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 69 removed outlier: 4.006A pdb=" N ALA E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 114 removed outlier: 3.934A pdb=" N VAL E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 136 Processing helix chain 'E' and resid 137 through 142 removed outlier: 3.823A pdb=" N GLY E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 157 Processing helix chain 'F' and resid 14 through 16 No H-bonds generated for 'chain 'F' and resid 14 through 16' Processing helix chain 'F' and resid 17 through 31 removed outlier: 3.633A pdb=" N MET F 21 " --> pdb=" O GLN F 17 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE F 29 " --> pdb=" O TYR F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 removed outlier: 3.834A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP F 72 " --> pdb=" O GLN F 68 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE F 80 " --> pdb=" O THR F 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 30 removed outlier: 3.666A pdb=" N LYS G 24 " --> pdb=" O GLU G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 53 removed outlier: 3.726A pdb=" N TYR G 43 " --> pdb=" O GLU G 39 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR G 48 " --> pdb=" O SER G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 66 Processing helix chain 'G' and resid 67 through 69 No H-bonds generated for 'chain 'G' and resid 67 through 69' Processing helix chain 'G' and resid 91 through 108 removed outlier: 3.831A pdb=" N ARG G 95 " --> pdb=" O ARG G 91 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASN G 96 " --> pdb=" O PRO G 92 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA G 99 " --> pdb=" O ARG G 95 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG G 108 " --> pdb=" O VAL G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 125 removed outlier: 4.126A pdb=" N LEU G 117 " --> pdb=" O LYS G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 140 removed outlier: 3.987A pdb=" N LYS G 136 " --> pdb=" O THR G 132 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG G 137 " --> pdb=" O ALA G 133 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP G 139 " --> pdb=" O LYS G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 147 Processing helix chain 'H' and resid 4 through 19 Processing helix chain 'H' and resid 29 through 42 removed outlier: 3.512A pdb=" N GLU H 42 " --> pdb=" O VAL H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 118 removed outlier: 4.574A pdb=" N GLN H 117 " --> pdb=" O ARG H 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 38 Processing helix chain 'I' and resid 43 through 48 removed outlier: 3.905A pdb=" N ARG I 48 " --> pdb=" O ARG I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 54 removed outlier: 3.950A pdb=" N VAL I 54 " --> pdb=" O PRO I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 87 removed outlier: 3.815A pdb=" N THR I 83 " --> pdb=" O ARG I 79 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG I 84 " --> pdb=" O HIS I 80 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA I 85 " --> pdb=" O GLY I 81 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET I 87 " --> pdb=" O THR I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 101 removed outlier: 3.772A pdb=" N ARG I 94 " --> pdb=" O ASP I 90 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU I 96 " --> pdb=" O SER I 92 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYS I 99 " --> pdb=" O SER I 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 32 removed outlier: 5.948A pdb=" N GLN J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR J 28 " --> pdb=" O GLU J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 87 removed outlier: 4.264A pdb=" N ASP J 85 " --> pdb=" O LYS J 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 57 removed outlier: 3.527A pdb=" N SER K 57 " --> pdb=" O SER K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 73 removed outlier: 3.794A pdb=" N ASP K 71 " --> pdb=" O GLU K 67 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL K 73 " --> pdb=" O CYS K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 77 Processing helix chain 'K' and resid 91 through 102 removed outlier: 4.301A pdb=" N ILE K 96 " --> pdb=" O ARG K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 7 removed outlier: 3.783A pdb=" N VAL L 7 " --> pdb=" O VAL L 3 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 18 Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 43 through 47 removed outlier: 3.650A pdb=" N LEU M 47 " --> pdb=" O ILE M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 61 Processing helix chain 'M' and resid 64 through 81 removed outlier: 4.074A pdb=" N LEU M 68 " --> pdb=" O VAL M 64 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER M 75 " --> pdb=" O GLU M 71 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE M 76 " --> pdb=" O ILE M 72 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS M 77 " --> pdb=" O SER M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 91 Processing helix chain 'N' and resid 2 through 19 removed outlier: 3.827A pdb=" N LYS N 6 " --> pdb=" O LYS N 2 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP N 17 " --> pdb=" O VAL N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 27 Processing helix chain 'N' and resid 41 through 43 No H-bonds generated for 'chain 'N' and resid 41 through 43' Processing helix chain 'N' and resid 44 through 49 Processing helix chain 'N' and resid 73 through 77 Processing helix chain 'N' and resid 81 through 88 removed outlier: 3.679A pdb=" N GLU N 85 " --> pdb=" O ILE N 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 13 Processing helix chain 'O' and resid 23 through 42 removed outlier: 3.632A pdb=" N GLN O 27 " --> pdb=" O SER O 23 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL O 28 " --> pdb=" O THR O 24 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA O 29 " --> pdb=" O GLU O 25 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS O 37 " --> pdb=" O ALA O 33 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN O 39 " --> pdb=" O ILE O 35 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLY O 40 " --> pdb=" O ASN O 36 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N HIS O 41 " --> pdb=" O HIS O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 73 removed outlier: 3.723A pdb=" N GLY O 54 " --> pdb=" O HIS O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 85 removed outlier: 4.093A pdb=" N LEU O 80 " --> pdb=" O ARG O 76 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE O 81 " --> pdb=" O TYR O 77 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG O 83 " --> pdb=" O ARG O 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 61 Processing helix chain 'P' and resid 70 through 76 removed outlier: 4.023A pdb=" N LEU P 74 " --> pdb=" O ARG P 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 30 Processing helix chain 'R' and resid 40 through 45 removed outlier: 3.527A pdb=" N THR R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 62 Processing helix chain 'S' and resid 11 through 19 removed outlier: 3.690A pdb=" N LYS S 17 " --> pdb=" O HIS S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 44 removed outlier: 3.866A pdb=" N MET S 43 " --> pdb=" O PHE S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 66 removed outlier: 3.594A pdb=" N VAL S 66 " --> pdb=" O ASP S 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 73 Processing helix chain 'T' and resid 6 through 39 removed outlier: 3.572A pdb=" N ILE T 11 " --> pdb=" O LYS T 7 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU T 14 " --> pdb=" O ALA T 10 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N HIS T 19 " --> pdb=" O LYS T 15 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER T 22 " --> pdb=" O LYS T 18 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET T 27 " --> pdb=" O ARG T 23 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS T 32 " --> pdb=" O ARG T 28 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS T 33 " --> pdb=" O THR T 29 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL T 34 " --> pdb=" O PHE T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 61 Proline residue: T 55 - end of helix Processing helix chain 'T' and resid 66 through 84 removed outlier: 4.474A pdb=" N LYS T 70 " --> pdb=" O ILE T 66 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA T 71 " --> pdb=" O HIS T 67 " (cutoff:3.500A) Processing helix chain 'U' and resid 15 through 22 removed outlier: 3.713A pdb=" N SER U 21 " --> pdb=" O PHE U 18 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS U 22 " --> pdb=" O LYS U 19 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 53 removed outlier: 4.334A pdb=" N LYS U 48 " --> pdb=" O ARG U 44 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA U 49 " --> pdb=" O LYS U 45 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL U 52 " --> pdb=" O LYS U 48 " (cutoff:3.500A) Processing helix chain '0' and resid 41 through 44 Processing helix chain '0' and resid 53 through 63 Processing helix chain '0' and resid 63 through 74 Processing helix chain '1' and resid 3 through 8 removed outlier: 3.834A pdb=" N ARG 1 7 " --> pdb=" O ALA 1 3 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU 1 8 " --> pdb=" O LYS 1 4 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 3 through 8' Processing helix chain '1' and resid 10 through 34 Processing helix chain '1' and resid 39 through 42 Processing helix chain '1' and resid 43 through 61 removed outlier: 4.094A pdb=" N ARG 1 47 " --> pdb=" O LEU 1 43 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG 1 48 " --> pdb=" O LYS 1 44 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ASP 1 49 " --> pdb=" O GLN 1 45 " (cutoff:3.500A) removed outlier: 3.697A 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 51 removed outlier: 3.517A pdb=" N MET 2 47 " --> pdb=" O ALA 2 43 " (cutoff:3.500A) Processing helix chain '3' and resid 9 through 17 Processing helix chain '3' and resid 18 through 20 No H-bonds generated for 'chain '3' and resid 18 through 20' Processing helix chain '6' and resid 8 through 17 Processing helix chain '6' and resid 17 through 23 Processing helix chain '6' and resid 24 through 38 Processing helix chain '7' and resid 37 through 43 Processing helix chain '7' and resid 51 through 53 No H-bonds generated for 'chain '7' and resid 51 through 53' Processing helix chain '7' and resid 54 through 62 Processing helix chain '8' and resid 30 through 33 Processing helix chain 'c' and resid 30 through 32 No H-bonds generated for 'chain 'c' and resid 30 through 32' Processing helix chain 'c' and resid 133 through 135 No H-bonds generated for 'chain 'c' and resid 133 through 135' Processing helix chain 'c' and resid 197 through 203 removed outlier: 3.559A pdb=" N MET c 201 " --> pdb=" O ALA c 198 " (cutoff:3.500A) Processing helix chain 'c' and resid 207 through 213 removed outlier: 3.970A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 225 Processing helix chain 'c' and resid 263 through 265 No H-bonds generated for 'chain 'c' and resid 263 through 265' Processing helix chain 'd' and resid 39 through 44 Processing helix chain 'd' and resid 56 through 60 Processing helix chain 'd' and resid 61 through 72 removed outlier: 3.756A pdb=" N ALA d 71 " --> pdb=" O HIS d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 102 Processing helix chain 'd' and resid 120 through 126 Processing helix chain 'd' and resid 182 through 184 No H-bonds generated for 'chain 'd' and resid 182 through 184' Processing helix chain 'e' and resid 15 through 20 Processing helix chain 'e' and resid 24 through 38 Processing helix chain 'e' and resid 97 through 115 Processing helix chain 'e' and resid 130 through 141 Processing helix chain 'e' and resid 154 through 161 Processing helix chain 'e' and resid 173 through 175 No H-bonds generated for 'chain 'e' and resid 173 through 175' Processing helix chain 'e' and resid 176 through 183 removed outlier: 3.684A pdb=" N LEU e 180 " --> pdb=" O ASP e 176 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE e 181 " --> pdb=" O PRO e 177 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE e 183 " --> pdb=" O SER e 179 " (cutoff:3.500A) Processing helix chain 'e' and resid 190 through 201 Processing helix chain 'f' and resid 3 through 20 removed outlier: 4.099A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR f 18 " --> pdb=" O LYS f 14 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU f 19 " --> pdb=" O LYS f 15 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE f 20 " --> pdb=" O LEU f 16 " (cutoff:3.500A) Processing helix chain 'f' and resid 24 through 28 Processing helix chain 'f' and resid 41 through 46 removed outlier: 4.237A pdb=" N ILE f 44 " --> pdb=" O GLY f 41 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP f 46 " --> pdb=" O ALA f 43 " (cutoff:3.500A) Processing helix chain 'f' and resid 47 through 61 removed outlier: 3.888A pdb=" N ASP f 51 " --> pdb=" O LYS f 47 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 106 removed outlier: 3.512A pdb=" N ILE f 106 " --> pdb=" O ARG f 102 " (cutoff:3.500A) Processing helix chain 'f' and resid 107 through 111 Processing helix chain 'f' and resid 134 through 138 removed outlier: 3.540A pdb=" N ILE f 137 " --> pdb=" O GLU f 134 " (cutoff:3.500A) Processing helix chain 'f' and resid 162 through 172 Processing helix chain 'g' and resid 3 through 7 Processing helix chain 'g' and resid 61 through 79 removed outlier: 3.664A pdb=" N SER g 74 " --> pdb=" O ALA g 70 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 152 removed outlier: 4.472A pdb=" N ARG g 152 " --> pdb=" O LEU g 148 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 34 removed outlier: 3.903A pdb=" N GLN h 33 " --> pdb=" O PHE h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 43 through 49 removed outlier: 4.354A pdb=" N ALA h 49 " --> pdb=" O GLU h 45 " (cutoff:3.500A) Processing helix chain 'h' and resid 49 through 58 removed outlier: 3.736A pdb=" N GLU h 53 " --> pdb=" O ALA h 49 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA h 56 " --> pdb=" O ALA h 52 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS h 57 " --> pdb=" O GLU h 53 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 67 Processing helix chain 'h' and resid 68 through 73 Processing helix chain 'j' and resid 24 through 37 removed outlier: 4.595A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 58 through 62 removed outlier: 3.606A pdb=" N VAL j 62 " --> pdb=" O ALA j 59 " (cutoff:3.500A) Processing helix chain 'j' and resid 67 through 72 Processing helix chain 'j' and resid 89 through 96 Processing helix chain 'j' and resid 97 through 109 removed outlier: 4.248A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 120 removed outlier: 3.559A pdb=" N PHE j 119 " --> pdb=" O GLY j 115 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG j 120 " --> pdb=" O ARG j 116 " (cutoff:3.500A) Processing helix chain 'j' and resid 131 through 136 removed outlier: 4.585A pdb=" N ALA j 134 " --> pdb=" O ASN j 131 " (cutoff:3.500A) Processing helix chain 'k' and resid 104 through 108 Processing helix chain 'k' and resid 112 through 119 Processing helix chain 'l' and resid 37 through 41 Processing helix chain 'l' and resid 56 through 61 Processing helix chain 'l' and resid 70 through 72 No H-bonds generated for 'chain 'l' and resid 70 through 72' Processing helix chain 'l' and resid 81 through 86 removed outlier: 3.963A pdb=" N VAL l 85 " --> pdb=" O LEU l 82 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU l 86 " --> pdb=" O ALA l 83 " (cutoff:3.500A) Processing helix chain 'l' and resid 91 through 98 removed outlier: 3.667A pdb=" N LEU l 95 " --> pdb=" O ASP l 91 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS l 96 " --> pdb=" O LEU l 92 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 138 removed outlier: 3.550A pdb=" N ALA l 133 " --> pdb=" O LYS l 129 " (cutoff:3.500A) Processing helix chain 'm' and resid 43 through 57 removed outlier: 3.507A pdb=" N MET m 53 " --> pdb=" O ALA m 49 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 122 Processing helix chain 'n' and resid 13 through 32 Processing helix chain 'n' and resid 38 through 55 removed outlier: 3.581A pdb=" N ARG n 45 " --> pdb=" O ALA n 41 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) Proline residue: n 50 - end of helix Processing helix chain 'n' and resid 59 through 69 Processing helix chain 'n' and resid 72 through 82 Processing helix chain 'n' and resid 82 through 87 Processing helix chain 'o' and resid 3 through 22 removed outlier: 3.687A pdb=" N ARG o 7 " --> pdb=" O LYS o 3 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG o 9 " --> pdb=" O SER o 5 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG o 15 " --> pdb=" O ALA o 11 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 85 Processing helix chain 'o' and resid 101 through 113 Processing helix chain 'p' and resid 3 through 11 removed outlier: 3.714A pdb=" N GLU p 11 " --> pdb=" O GLN p 7 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 56 Processing helix chain 'p' and resid 97 through 103 Processing helix chain 'p' and resid 104 through 109 removed outlier: 4.000A pdb=" N ARG p 109 " --> pdb=" O LYS p 106 " (cutoff:3.500A) Processing helix chain 'q' and resid 6 through 21 removed outlier: 3.512A pdb=" N ALA q 12 " --> pdb=" O VAL q 8 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE q 17 " --> pdb=" O ARG q 13 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 30 Processing helix chain 'q' and resid 31 through 72 removed outlier: 3.868A pdb=" N GLN q 37 " --> pdb=" O ARG q 33 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG q 51 " --> pdb=" O TYR q 47 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS q 54 " --> pdb=" O ARG q 50 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG q 55 " --> pdb=" O ARG q 51 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG q 58 " --> pdb=" O LYS q 54 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA q 67 " --> pdb=" O ALA q 63 " (cutoff:3.500A) Processing helix chain 'q' and resid 75 through 86 Processing helix chain 'q' and resid 91 through 102 Processing helix chain 'q' and resid 102 through 118 removed outlier: 3.594A pdb=" N ALA q 116 " --> pdb=" O LYS q 112 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 25 removed outlier: 3.641A pdb=" N LEU s 19 " --> pdb=" O GLN s 15 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 38 removed outlier: 3.697A pdb=" N ASP s 34 " --> pdb=" O SER s 30 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 62 removed outlier: 3.697A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL s 47 " --> pdb=" O ALA s 43 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS s 49 " --> pdb=" O VAL s 45 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP s 62 " --> pdb=" O ALA s 58 " (cutoff:3.500A) Processing helix chain 's' and resid 65 through 69 removed outlier: 3.710A pdb=" N LEU s 69 " --> pdb=" O ILE s 66 " (cutoff:3.500A) Processing helix chain 's' and resid 89 through 91 No H-bonds generated for 'chain 's' and resid 89 through 91' Processing helix chain 't' and resid 3 through 10 Processing helix chain 't' and resid 18 through 28 removed outlier: 3.540A pdb=" N GLU t 25 " --> pdb=" O SER t 21 " (cutoff:3.500A) Processing helix chain 't' and resid 39 through 51 Processing helix chain 'w' and resid 13 through 23 Processing helix chain 'w' and resid 44 through 51 Processing helix chain 'w' and resid 52 through 58 removed outlier: 7.036A pdb=" N GLU w 55 " --> pdb=" O ALA w 52 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 160 through 162 removed outlier: 7.880A pdb=" N LEU B 160 " --> pdb=" O PHE B 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 165 through 170 removed outlier: 4.333A pdb=" N GLY C 147 " --> pdb=" O PHE C 202 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 127 through 128 Processing sheet with id= D, first strand: chain 'E' and resid 12 through 13 removed outlier: 3.761A pdb=" N VAL E 37 " --> pdb=" O LYS E 13 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 17 through 24 removed outlier: 3.580A pdb=" N VAL E 24 " --> pdb=" O GLY E 27 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 85 through 88 removed outlier: 3.743A pdb=" N GLN E 96 " --> pdb=" O LEU E 123 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 41 through 46 removed outlier: 5.482A pdb=" N ASP F 41 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU F 61 " --> pdb=" O ASP F 41 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL F 60 " --> pdb=" O PHE F 8 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE F 8 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N MET F 90 " --> pdb=" O GLU F 5 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 72 through 75 Processing sheet with id= I, first strand: chain 'H' and resid 23 through 26 Processing sheet with id= J, first strand: chain 'H' and resid 110 through 111 removed outlier: 6.497A pdb=" N VAL H 102 " --> pdb=" O ILE H 125 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'I' and resid 28 through 29 Processing sheet with id= L, first strand: chain 'J' and resid 10 through 11 Processing sheet with id= M, first strand: chain 'J' and resid 48 through 52 Processing sheet with id= N, first strand: chain 'K' and resid 20 through 22 Processing sheet with id= O, first strand: chain 'K' and resid 83 through 85 Processing sheet with id= P, first strand: chain 'L' and resid 59 through 65 removed outlier: 4.915A pdb=" N PHE L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU L 56 " --> pdb=" O PHE L 60 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL L 51 " --> pdb=" O VAL L 36 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL L 36 " --> pdb=" O VAL L 51 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ARG L 53 " --> pdb=" O THR L 34 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR L 34 " --> pdb=" O ARG L 53 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL L 32 " --> pdb=" O ARG L 55 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'P' and resid 34 through 35 removed outlier: 7.192A pdb=" N VAL P 2 " --> pdb=" O THR P 66 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'P' and resid 37 through 39 Processing sheet with id= S, first strand: chain 'Q' and resid 11 through 13 removed outlier: 7.157A pdb=" N VAL Q 21 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'Q' and resid 58 through 62 removed outlier: 7.298A pdb=" N GLU Q 59 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'S' and resid 50 through 51 Processing sheet with id= V, first strand: chain '0' and resid 13 through 18 Processing sheet with id= W, first strand: chain '0' and resid 33 through 40 removed outlier: 3.569A pdb=" N ARG 0 45 " --> pdb=" O VAL 0 40 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '2' and resid 35 through 38 Processing sheet with id= Y, first strand: chain '3' and resid 28 through 30 Processing sheet with id= Z, first strand: chain '3' and resid 48 through 49 Processing sheet with id= AA, first strand: chain '4' and resid 20 through 25 removed outlier: 3.547A pdb=" N GLN 4 45 " --> pdb=" O ASP 4 40 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain '7' and resid 15 through 16 Processing sheet with id= AC, first strand: chain '8' and resid 2 through 4 removed outlier: 6.410A pdb=" N LYS 8 2 " --> pdb=" O ARG 8 36 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ILE 8 23 " --> pdb=" O GLN 8 37 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'c' and resid 4 through 5 Processing sheet with id= AE, first strand: chain 'c' and resid 34 through 35 Processing sheet with id= AF, first strand: chain 'c' and resid 101 through 105 removed outlier: 6.755A pdb=" N ILE c 91 " --> pdb=" O LEU c 81 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU c 81 " --> pdb=" O ILE c 91 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU c 93 " --> pdb=" O GLU c 79 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'c' and resid 129 through 131 removed outlier: 5.892A pdb=" N ILE c 164 " --> pdb=" O ARG c 175 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG c 175 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA c 166 " --> pdb=" O THR c 173 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS c 183 " --> pdb=" O ILE c 267 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE c 267 " --> pdb=" O LYS c 183 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'c' and resid 144 through 145 removed outlier: 6.174A pdb=" N VAL c 144 " --> pdb=" O GLN c 153 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'd' and resid 4 through 15 removed outlier: 5.680A pdb=" N LYS d 8 " --> pdb=" O GLU d 28 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU d 28 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY d 10 " --> pdb=" O VAL d 26 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU d 186 " --> pdb=" O VAL d 180 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL d 180 " --> pdb=" O LEU d 186 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU d 188 " --> pdb=" O VAL d 178 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP d 176 " --> pdb=" O LYS d 190 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL d 107 " --> pdb=" O SER d 174 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'd' and resid 80 through 83 removed outlier: 3.507A pdb=" N GLN d 36 " --> pdb=" O GLN d 49 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR d 51 " --> pdb=" O VAL d 34 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL d 34 " --> pdb=" O THR d 51 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'd' and resid 115 through 119 removed outlier: 6.043A pdb=" N MET d 165 " --> pdb=" O LYS d 116 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE d 118 " --> pdb=" O GLY d 163 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY d 163 " --> pdb=" O PHE d 118 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'e' and resid 2 through 3 Processing sheet with id= AM, first strand: chain 'e' and resid 118 through 121 removed outlier: 6.536A pdb=" N LEU e 147 " --> pdb=" O VAL e 187 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N THR e 189 " --> pdb=" O LEU e 147 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ILE e 149 " --> pdb=" O THR e 189 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'f' and resid 66 through 69 Processing sheet with id= AO, first strand: chain 'g' and resid 9 through 10 removed outlier: 3.741A pdb=" N THR g 51 " --> pdb=" O LYS g 44 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'g' and resid 18 through 20 Processing sheet with id= AQ, first strand: chain 'g' and resid 122 through 124 Processing sheet with id= AR, first strand: chain 'g' and resid 95 through 99 removed outlier: 3.733A pdb=" N SER g 106 " --> pdb=" O ARG g 95 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'h' and resid 18 through 19 removed outlier: 3.604A pdb=" N VAL h 19 " --> pdb=" O VAL h 3 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'h' and resid 131 through 132 Processing sheet with id= AU, first strand: chain 'j' and resid 122 through 124 removed outlier: 6.867A pdb=" N ILE j 54 " --> pdb=" O LYS j 123 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TYR j 16 " --> pdb=" O ILE j 55 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU j 57 " --> pdb=" O TYR j 16 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL j 18 " --> pdb=" O LEU j 57 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP j 15 " --> pdb=" O GLN j 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain 'j' and resid 73 through 76 Processing sheet with id= AW, first strand: chain 'k' and resid 92 through 94 removed outlier: 4.989A pdb=" N GLN k 93 " --> pdb=" O ASN k 88 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA k 83 " --> pdb=" O VAL k 63 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS k 59 " --> pdb=" O LEU k 87 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE k 39 " --> pdb=" O LYS k 23 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS k 23 " --> pdb=" O ILE k 39 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE k 41 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N CYS k 21 " --> pdb=" O ILE k 41 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE k 43 " --> pdb=" O VAL k 19 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL k 19 " --> pdb=" O ILE k 43 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLU k 45 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL k 10 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N CYS k 84 " --> pdb=" O MET k 7 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASN k 9 " --> pdb=" O CYS k 84 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU k 86 " --> pdb=" O ASN k 9 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'k' and resid 69 through 70 removed outlier: 3.657A pdb=" N VAL k 76 " --> pdb=" O VAL p 73 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA p 49 " --> pdb=" O THR p 60 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG p 62 " --> pdb=" O VAL p 47 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VAL p 47 " --> pdb=" O ARG p 62 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N ILE p 64 " --> pdb=" O GLY p 45 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N GLY p 45 " --> pdb=" O ILE p 64 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N THR p 25 " --> pdb=" O VAL p 86 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL p 86 " --> pdb=" O THR p 25 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU p 27 " --> pdb=" O ILE p 84 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE p 84 " --> pdb=" O GLU p 27 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS p 29 " --> pdb=" O ASP p 82 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'l' and resid 74 through 76 removed outlier: 3.614A pdb=" N LYS l 109 " --> pdb=" O ALA l 75 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'l' and resid 89 through 90 removed outlier: 3.583A pdb=" N GLU l 143 " --> pdb=" O VAL l 122 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'm' and resid 62 through 65 removed outlier: 6.716A pdb=" N LEU m 33 " --> pdb=" O LEU m 102 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU m 104 " --> pdb=" O PHE m 31 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N PHE m 31 " --> pdb=" O GLU m 104 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'm' and resid 39 through 42 removed outlier: 5.745A pdb=" N VAL m 89 " --> pdb=" O GLU m 75 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU m 75 " --> pdb=" O VAL m 89 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR m 91 " --> pdb=" O ILE m 73 " (cutoff:3.500A) Processing sheet with id= BC, 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) Processing sheet with id= BD, first strand: chain 'o' and resid 47 through 52 Processing sheet with id= BE, first strand: chain 'r' and resid 11 through 15 removed outlier: 3.554A pdb=" N MET r 40 " --> pdb=" O VAL r 4 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLN r 6 " --> pdb=" O VAL r 38 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL r 38 " --> pdb=" O GLN r 6 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'r' and resid 19 through 22 removed outlier: 6.994A pdb=" N PHE r 93 " --> pdb=" O HIS r 66 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N HIS r 66 " --> pdb=" O PHE r 93 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE r 101 " --> pdb=" O VAL r 58 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL r 58 " --> pdb=" O ILE r 101 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'r' and resid 72 through 78 removed outlier: 3.882A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 's' and resid 3 through 10 removed outlier: 5.361A pdb=" N SER s 101 " --> pdb=" O HIS s 9 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS s 73 " --> pdb=" O VAL s 106 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N SER s 108 " --> pdb=" O VAL s 71 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL s 71 " --> pdb=" O SER s 108 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 's' and resid 82 through 87 Processing sheet with id= BJ, first strand: chain 't' and resid 11 through 14 removed outlier: 4.422A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL t 57 " --> pdb=" O THR t 86 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 't' and resid 67 through 70 removed outlier: 3.833A pdb=" N ARG t 73 " --> pdb=" O HIS t 70 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'u' and resid 65 through 66 removed outlier: 3.545A pdb=" N LYS u 33 " --> pdb=" O LEU u 29 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLU u 10 " --> pdb=" O PHE u 73 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE u 72 " --> pdb=" O ASP u 81 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'u' and resid 41 through 45 Processing sheet with id= BN, first strand: chain 'u' and resid 83 through 88 removed outlier: 3.644A pdb=" N ARG u 86 " --> pdb=" O VAL u 93 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'w' and resid 3 through 8 removed outlier: 7.975A pdb=" N ASN w 5 " --> pdb=" O ASP w 43 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASP w 43 " --> pdb=" O ASN w 5 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N LYS w 25 " --> pdb=" O GLN w 87 " (cutoff:3.500A) removed outlier: 10.163A pdb=" N ILE w 89 " --> pdb=" O LYS w 25 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N PHE w 91 " --> pdb=" O PRO w 27 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE w 29 " --> pdb=" O PHE w 91 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP w 76 " --> pdb=" O ASP w 90 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N VAL w 92 " --> pdb=" O ALA w 74 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ALA w 74 " --> pdb=" O VAL w 92 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE w 4 " --> pdb=" O VAL w 64 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'y' and resid 22 through 23 removed outlier: 6.716A pdb=" N LEU y 59 " --> pdb=" O ILE y 37 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'y' and resid 30 through 31 1497 hydrogen bonds defined for protein. 4053 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2552 hydrogen bonds 4258 hydrogen bond angles 0 basepair planarities 1001 basepair parallelities 1615 stacking parallelities Total time for adding SS restraints: 169.66 Time building geometry restraints manager: 71.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 14229 1.31 - 1.44: 67731 1.44 - 1.57: 64373 1.57 - 1.70: 9266 1.70 - 1.83: 259 Bond restraints: 155858 Sorted by residual: bond pdb=" C2 G A 230 " pdb=" N3 G A 230 " ideal model delta sigma weight residual 1.323 1.765 -0.442 2.00e-02 2.50e+03 4.87e+02 bond pdb=" N1 G A 230 " pdb=" C2 G A 230 " ideal model delta sigma weight residual 1.373 1.804 -0.431 2.00e-02 2.50e+03 4.64e+02 bond pdb=" C6 G A 230 " pdb=" N1 G A 230 " ideal model delta sigma weight residual 1.391 1.817 -0.426 2.00e-02 2.50e+03 4.53e+02 bond pdb=" N3 G A 230 " pdb=" C4 G A 230 " ideal model delta sigma weight residual 1.350 1.760 -0.410 2.00e-02 2.50e+03 4.20e+02 bond pdb=" C5 G A 230 " pdb=" C6 G A 230 " ideal model delta sigma weight residual 1.419 1.818 -0.399 2.00e-02 2.50e+03 3.97e+02 ... (remaining 155853 not shown) Histogram of bond angle deviations from ideal: 74.20 - 88.45: 1 88.45 - 102.69: 8874 102.69 - 116.94: 131689 116.94 - 131.19: 91527 131.19 - 145.43: 1324 Bond angle restraints: 233415 Sorted by residual: angle pdb=" O3' C v 74 " pdb=" P C v 75 " pdb=" O5' C v 75 " ideal model delta sigma weight residual 104.00 74.20 29.80 1.50e+00 4.44e-01 3.95e+02 angle pdb=" N LEU h 62 " pdb=" CA LEU h 62 " pdb=" C LEU h 62 " ideal model delta sigma weight residual 111.07 131.26 -20.19 1.07e+00 8.73e-01 3.56e+02 angle pdb=" N VAL h 61 " pdb=" CA VAL h 61 " pdb=" C VAL h 61 " ideal model delta sigma weight residual 110.72 129.45 -18.73 1.01e+00 9.80e-01 3.44e+02 angle pdb=" C2' C b1102 " pdb=" C1' C b1102 " pdb=" N1 C b1102 " ideal model delta sigma weight residual 112.00 135.47 -23.47 1.50e+00 4.44e-01 2.45e+02 angle pdb=" C2' A b1509 " pdb=" C1' A b1509 " pdb=" N9 A b1509 " ideal model delta sigma weight residual 114.00 137.32 -23.32 1.50e+00 4.44e-01 2.42e+02 ... (remaining 233410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 86309 35.83 - 71.66: 12162 71.66 - 107.50: 1337 107.50 - 143.33: 61 143.33 - 179.16: 49 Dihedral angle restraints: 99918 sinusoidal: 83982 harmonic: 15936 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 -96.19 -83.81 0 5.00e+00 4.00e-02 2.81e+02 dihedral pdb=" O4' U b2118 " pdb=" C2' U b2118 " pdb=" C1' U b2118 " pdb=" C3' U b2118 " ideal model delta sinusoidal sigma weight residual 25.00 -54.18 79.18 1 8.00e+00 1.56e-02 1.22e+02 dihedral pdb=" O4' G b 801 " pdb=" C4' G b 801 " pdb=" C3' G b 801 " pdb=" C2' G b 801 " ideal model delta sinusoidal sigma weight residual -35.00 43.90 -78.90 1 8.00e+00 1.56e-02 1.21e+02 ... (remaining 99915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.279: 29391 0.279 - 0.558: 435 0.558 - 0.837: 29 0.837 - 1.116: 5 1.116 - 1.395: 4 Chirality restraints: 29864 Sorted by residual: chirality pdb=" CG LEU d 4 " pdb=" CB LEU d 4 " pdb=" CD1 LEU d 4 " pdb=" CD2 LEU d 4 " both_signs ideal model delta sigma weight residual False -2.59 -1.19 -1.40 2.00e-01 2.50e+01 4.87e+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 1.06 1.38 2.00e-01 2.50e+01 4.76e+01 chirality pdb=" C1' A b1509 " pdb=" O4' A b1509 " pdb=" C2' A b1509 " pdb=" N9 A b1509 " both_signs ideal model delta sigma weight residual False 2.44 1.10 1.34 2.00e-01 2.50e+01 4.48e+01 ... (remaining 29861 not shown) Planarity restraints: 12326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U b1943 " 0.222 2.00e-02 2.50e+03 1.08e-01 2.65e+02 pdb=" N1 U b1943 " -0.212 2.00e-02 2.50e+03 pdb=" C2 U b1943 " -0.032 2.00e-02 2.50e+03 pdb=" O2 U b1943 " -0.031 2.00e-02 2.50e+03 pdb=" N3 U b1943 " 0.033 2.00e-02 2.50e+03 pdb=" C4 U b1943 " 0.024 2.00e-02 2.50e+03 pdb=" O4 U b1943 " 0.057 2.00e-02 2.50e+03 pdb=" C5 U b1943 " 0.006 2.00e-02 2.50e+03 pdb=" C6 U b1943 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A b1088 " -0.232 2.00e-02 2.50e+03 9.50e-02 2.48e+02 pdb=" N9 A b1088 " 0.172 2.00e-02 2.50e+03 pdb=" C8 A b1088 " 0.064 2.00e-02 2.50e+03 pdb=" N7 A b1088 " -0.009 2.00e-02 2.50e+03 pdb=" C5 A b1088 " 0.020 2.00e-02 2.50e+03 pdb=" C6 A b1088 " -0.023 2.00e-02 2.50e+03 pdb=" N6 A b1088 " -0.064 2.00e-02 2.50e+03 pdb=" N1 A b1088 " -0.039 2.00e-02 2.50e+03 pdb=" C2 A b1088 " 0.008 2.00e-02 2.50e+03 pdb=" N3 A b1088 " 0.061 2.00e-02 2.50e+03 pdb=" C4 A b1088 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A b1272 " -0.192 2.00e-02 2.50e+03 8.73e-02 2.10e+02 pdb=" N9 A b1272 " 0.200 2.00e-02 2.50e+03 pdb=" C8 A b1272 " 0.016 2.00e-02 2.50e+03 pdb=" N7 A b1272 " -0.029 2.00e-02 2.50e+03 pdb=" C5 A b1272 " -0.017 2.00e-02 2.50e+03 pdb=" C6 A b1272 " -0.025 2.00e-02 2.50e+03 pdb=" N6 A b1272 " -0.023 2.00e-02 2.50e+03 pdb=" N1 A b1272 " -0.024 2.00e-02 2.50e+03 pdb=" C2 A b1272 " 0.009 2.00e-02 2.50e+03 pdb=" N3 A b1272 " 0.040 2.00e-02 2.50e+03 pdb=" C4 A b1272 " 0.046 2.00e-02 2.50e+03 ... (remaining 12323 not shown) Histogram of nonbonded interaction distances: 0.23 - 1.17: 12 1.17 - 2.10: 233 2.10 - 3.03: 85548 3.03 - 3.97: 438074 3.97 - 4.90: 733349 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1257216 Sorted by model distance: nonbonded pdb=" O ARG P 28 " pdb=" N1 G A 376 " model vdw 0.232 2.520 nonbonded pdb=" O2 C b1349 " pdb=" O6 G b1382 " model vdw 0.610 3.040 nonbonded pdb=" CB ARG P 5 " pdb=" O2' G A 376 " model vdw 0.862 3.440 nonbonded pdb=" NH2 ARG I 108 " pdb=" O6 G A1347 " model vdw 0.871 2.520 nonbonded pdb=" C ARG P 28 " pdb=" N1 G A 376 " model vdw 1.025 3.350 ... (remaining 1257211 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 group one per residue 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 13.140 Check model and map are aligned: 1.570 Set scattering table: 1.000 Process input model: 443.290 Find NCS groups from input model: 2.840 Set up NCS constraints: 0.390 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 467.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.442 155858 Z= 0.480 Angle : 1.319 29.801 233415 Z= 0.888 Chirality : 0.100 1.395 29864 Planarity : 0.012 0.123 12326 Dihedral : 25.152 179.158 89638 Min Nonbonded Distance : 0.232 Molprobity Statistics. All-atom Clashscore : 33.71 Ramachandran Plot: Outliers : 2.89 % Allowed : 8.00 % Favored : 89.10 % Rotamer: Outliers : 2.84 % Allowed : 5.45 % Favored : 91.71 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.09 % Twisted Proline : 0.55 % 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: -2.66 (0.10), residues: 5497 helix: -2.58 (0.09), residues: 1550 sheet: -2.26 (0.16), residues: 865 loop : -1.06 (0.11), residues: 3082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP c 213 HIS 0.043 0.002 HIS s 7 PHE 0.028 0.003 PHE 6 18 TYR 0.021 0.003 TYR q 45 ARG 0.042 0.001 ARG c 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2109 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1979 time to evaluate : 6.161 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 156 LEU cc_start: 0.6550 (mt) cc_final: 0.5922 (tt) REVERT: B 158 ASP cc_start: 0.6351 (m-30) cc_final: 0.6075 (m-30) REVERT: B 193 ASP cc_start: 0.6224 (m-30) cc_final: 0.5635 (t0) REVERT: B 199 ILE cc_start: 0.7442 (mt) cc_final: 0.7161 (tp) REVERT: B 221 ARG cc_start: 0.4809 (mtt-85) cc_final: 0.4289 (mpt-90) REVERT: C 17 TRP cc_start: 0.6781 (m-90) cc_final: 0.6028 (m-10) REVERT: C 71 ARG cc_start: 0.5287 (mtm-85) cc_final: 0.4903 (mmp80) REVERT: C 93 ILE cc_start: 0.5669 (mm) cc_final: 0.5446 (mm) REVERT: D 53 GLN cc_start: 0.7419 (mt0) cc_final: 0.6818 (mt0) REVERT: D 99 ASN cc_start: 0.6063 (t0) cc_final: 0.5770 (p0) REVERT: D 136 VAL cc_start: 0.3739 (m) cc_final: 0.3473 (p) REVERT: D 150 LYS cc_start: 0.8312 (mmtp) cc_final: 0.7728 (pptt) REVERT: D 155 LYS cc_start: 0.8136 (mtmm) cc_final: 0.7104 (tptt) REVERT: D 172 VAL cc_start: 0.6111 (t) cc_final: 0.5557 (m) REVERT: D 182 LYS cc_start: 0.5691 (pttp) cc_final: 0.5313 (tmtt) REVERT: E 102 THR cc_start: 0.5293 (p) cc_final: 0.5003 (p) REVERT: E 116 VAL cc_start: 0.7263 (m) cc_final: 0.6964 (m) REVERT: E 131 ASN cc_start: 0.6551 (t0) cc_final: 0.5694 (p0) REVERT: E 147 ASN cc_start: 0.3753 (t0) cc_final: 0.3476 (t0) REVERT: F 4 TYR cc_start: 0.7663 (m-80) cc_final: 0.7043 (m-80) REVERT: F 9 MET cc_start: 0.6963 (mtp) cc_final: 0.6557 (mtt) REVERT: F 41 ASP cc_start: 0.6905 (t70) cc_final: 0.6218 (m-30) REVERT: F 63 ASN cc_start: 0.8022 (m-40) cc_final: 0.7544 (m110) REVERT: G 21 LEU cc_start: 0.8719 (mt) cc_final: 0.8175 (tt) REVERT: G 30 MET cc_start: 0.6247 (ttm) cc_final: 0.5852 (tpp) REVERT: G 41 ILE cc_start: 0.6249 (mt) cc_final: 0.6019 (tt) REVERT: G 56 SER cc_start: 0.6457 (m) cc_final: 0.6146 (t) REVERT: G 150 PHE cc_start: 0.5593 (m-80) cc_final: 0.4220 (t80) REVERT: H 2 MET cc_start: 0.6088 (mmt) cc_final: 0.5855 (mpp) REVERT: H 30 LYS cc_start: 0.8359 (tttt) cc_final: 0.7647 (pttt) REVERT: H 127 TYR cc_start: 0.6935 (p90) cc_final: 0.6572 (p90) REVERT: I 45 MET cc_start: 0.6546 (mtt) cc_final: 0.6237 (mmt) REVERT: I 72 SER cc_start: 0.5878 (m) cc_final: 0.5116 (t) REVERT: I 113 LYS cc_start: 0.5301 (mtpp) cc_final: 0.5016 (mtpp) REVERT: J 5 ARG cc_start: 0.4451 (ptp90) cc_final: 0.3360 (ptt-90) REVERT: J 7 ARG cc_start: 0.3595 (mtt180) cc_final: 0.2729 (mmt90) REVERT: K 49 SER cc_start: 0.5566 (m) cc_final: 0.5310 (p) REVERT: K 121 ARG cc_start: 0.6428 (mmm160) cc_final: 0.5936 (tpt170) REVERT: M 52 ILE cc_start: 0.7642 (tt) cc_final: 0.7295 (tt) REVERT: M 69 ARG cc_start: 0.6586 (mmt-90) cc_final: 0.6338 (mmt180) REVERT: M 82 LEU cc_start: 0.7536 (mt) cc_final: 0.7199 (mt) REVERT: M 109 LYS cc_start: 0.5715 (mttt) cc_final: 0.4574 (tttm) REVERT: O 11 VAL cc_start: 0.8212 (t) cc_final: 0.7995 (m) REVERT: O 79 ARG cc_start: 0.8093 (tpt170) cc_final: 0.7653 (ttm170) REVERT: P 29 ASN cc_start: 0.3929 (OUTLIER) cc_final: 0.3173 (t0) REVERT: P 46 LYS cc_start: 0.2227 (OUTLIER) cc_final: 0.0879 (ttpp) REVERT: Q 18 LYS cc_start: 0.7617 (mtmm) cc_final: 0.7382 (ttmm) REVERT: Q 26 ARG cc_start: 0.7544 (ptm160) cc_final: 0.7236 (mtm180) REVERT: Q 48 GLU cc_start: 0.6342 (tp30) cc_final: 0.5914 (tp30) REVERT: Q 80 LYS cc_start: 0.8274 (ptmt) cc_final: 0.8001 (tptt) REVERT: S 10 ILE cc_start: 0.8347 (mm) cc_final: 0.8145 (mt) REVERT: S 12 LEU cc_start: 0.6685 (tp) cc_final: 0.5575 (pp) REVERT: S 43 MET cc_start: 0.6802 (mtp) cc_final: 0.6362 (mtp) REVERT: S 75 PRO cc_start: 0.7356 (Cg_exo) cc_final: 0.7139 (Cg_endo) REVERT: S 77 ARG cc_start: 0.6787 (ptp90) cc_final: 0.6327 (mtp180) REVERT: T 8 LYS cc_start: 0.7997 (pttm) cc_final: 0.7684 (pttt) REVERT: T 15 LYS cc_start: 0.8169 (mttt) cc_final: 0.7639 (tptp) REVERT: T 20 ASN cc_start: 0.8147 (m110) cc_final: 0.7700 (t0) REVERT: T 50 PHE cc_start: 0.6586 (t80) cc_final: 0.5564 (t80) REVERT: T 54 GLN cc_start: 0.8079 (tt0) cc_final: 0.7549 (mt0) REVERT: U 15 LEU cc_start: 0.6490 (mt) cc_final: 0.5969 (pt) REVERT: U 17 ARG cc_start: 0.6142 (mmt-90) cc_final: 0.5741 (mtm180) REVERT: U 32 ARG cc_start: 0.6645 (ttt180) cc_final: 0.6394 (ppt170) REVERT: U 38 GLU cc_start: 0.7139 (tt0) cc_final: 0.6872 (pt0) REVERT: 0 40 VAL cc_start: 0.8498 (t) cc_final: 0.8212 (p) REVERT: 0 70 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8365 (tt0) REVERT: 0 74 ARG cc_start: 0.6650 (ttm170) cc_final: 0.5231 (mtt90) REVERT: 0 76 GLU cc_start: 0.4960 (OUTLIER) cc_final: 0.4726 (mt-10) REVERT: 1 4 LYS cc_start: 0.8203 (tttp) cc_final: 0.7588 (tmtt) REVERT: 1 17 GLU cc_start: 0.6951 (tp30) cc_final: 0.6390 (tp30) REVERT: 1 20 ASN cc_start: 0.7569 (m-40) cc_final: 0.6879 (t0) REVERT: 1 25 GLN cc_start: 0.8445 (tt0) cc_final: 0.7807 (tp40) REVERT: 1 40 SER cc_start: 0.7990 (m) cc_final: 0.7682 (t) REVERT: 1 56 LEU cc_start: 0.8359 (mt) cc_final: 0.7581 (tt) REVERT: 2 7 ILE cc_start: 0.6720 (mt) cc_final: 0.6491 (mm) REVERT: 2 8 THR cc_start: 0.8170 (m) cc_final: 0.7942 (m) REVERT: 3 31 ASP cc_start: 0.7284 (t70) cc_final: 0.7028 (t70) REVERT: 3 37 LYS cc_start: 0.8235 (mtmt) cc_final: 0.7730 (mmmt) REVERT: 3 52 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.7021 (ttm110) REVERT: 6 22 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8226 (tpt) REVERT: 6 25 LYS cc_start: 0.8166 (tptt) cc_final: 0.7307 (ttpp) REVERT: 6 41 ARG cc_start: 0.7950 (mtt90) cc_final: 0.7017 (ptm160) REVERT: 7 32 ILE cc_start: 0.8458 (mt) cc_final: 0.7800 (tt) REVERT: 7 50 VAL cc_start: 0.8542 (t) cc_final: 0.8305 (m) REVERT: 7 55 LEU cc_start: 0.8729 (mt) cc_final: 0.8417 (tp) REVERT: 8 1 MET cc_start: 0.6728 (ppp) cc_final: 0.6076 (ptm) REVERT: 8 9 LYS cc_start: 0.8398 (mtpt) cc_final: 0.8118 (mtpt) REVERT: c 24 LEU cc_start: 0.7927 (mt) cc_final: 0.7306 (mt) REVERT: c 83 TYR cc_start: 0.8760 (t80) cc_final: 0.8554 (t80) REVERT: c 115 GLN cc_start: 0.7753 (mt0) cc_final: 0.7529 (mm-40) REVERT: c 225 MET cc_start: 0.8556 (mtt) cc_final: 0.8316 (mtt) REVERT: c 267 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7400 (pt) REVERT: c 269 ARG cc_start: 0.6042 (OUTLIER) cc_final: 0.5648 (ttm170) REVERT: d 82 PHE cc_start: 0.7088 (m-80) cc_final: 0.6875 (m-80) REVERT: d 84 LEU cc_start: 0.8283 (mt) cc_final: 0.7969 (mt) REVERT: d 103 ASP cc_start: 0.7378 (m-30) cc_final: 0.6578 (t0) REVERT: d 167 ASN cc_start: 0.7159 (t0) cc_final: 0.6910 (t0) REVERT: e 78 TRP cc_start: 0.8292 (m-90) cc_final: 0.8025 (m100) REVERT: e 111 GLU cc_start: 0.7575 (mm-30) cc_final: 0.6750 (tp30) REVERT: e 114 ARG cc_start: 0.7890 (mtm180) cc_final: 0.7590 (tpp-160) REVERT: e 117 ARG cc_start: 0.5129 (mtp180) cc_final: 0.4902 (mtm110) REVERT: e 159 LEU cc_start: 0.7874 (mt) cc_final: 0.7244 (tt) REVERT: e 181 ILE cc_start: 0.6942 (mt) cc_final: 0.6620 (mt) REVERT: e 187 VAL cc_start: 0.7199 (OUTLIER) cc_final: 0.6430 (t) REVERT: f 22 TYR cc_start: 0.6985 (m-80) cc_final: 0.6605 (m-80) REVERT: f 83 TYR cc_start: 0.7934 (m-80) cc_final: 0.7368 (m-10) REVERT: g 45 HIS cc_start: 0.6634 (t-170) cc_final: 0.6417 (t70) REVERT: g 153 ARG cc_start: 0.7879 (ttm170) cc_final: 0.7545 (mtt90) REVERT: h 50 ARG cc_start: 0.4045 (mtm180) cc_final: 0.3575 (mtt90) REVERT: h 70 GLU cc_start: 0.6747 (tt0) cc_final: 0.6321 (tp30) REVERT: j 11 VAL cc_start: 0.7714 (t) cc_final: 0.7505 (t) REVERT: j 43 GLU cc_start: 0.7710 (pm20) cc_final: 0.7496 (pm20) REVERT: j 108 MET cc_start: 0.7833 (mtt) cc_final: 0.7586 (mtp) REVERT: j 131 ASN cc_start: 0.5243 (OUTLIER) cc_final: 0.4978 (t0) REVERT: k 17 ARG cc_start: 0.8897 (mmt90) cc_final: 0.7680 (mtm180) REVERT: k 18 ARG cc_start: 0.7877 (mmm160) cc_final: 0.7554 (mmm160) REVERT: k 47 ILE cc_start: 0.8373 (pt) cc_final: 0.8117 (pt) REVERT: k 58 LEU cc_start: 0.8007 (pt) cc_final: 0.7079 (mt) REVERT: k 59 LYS cc_start: 0.7303 (mttt) cc_final: 0.7087 (mtmm) REVERT: k 80 ASP cc_start: 0.6224 (m-30) cc_final: 0.6013 (m-30) REVERT: k 106 GLU cc_start: 0.6775 (mp0) cc_final: 0.6564 (mp0) REVERT: l 12 SER cc_start: 0.8612 (t) cc_final: 0.8314 (t) REVERT: l 19 LEU cc_start: 0.8172 (mp) cc_final: 0.7878 (mp) REVERT: l 67 THR cc_start: 0.8353 (m) cc_final: 0.7966 (p) REVERT: l 77 ILE cc_start: 0.7893 (mt) cc_final: 0.7689 (mt) REVERT: m 1 MET cc_start: 0.5621 (ttp) cc_final: 0.5278 (pmm) REVERT: m 28 PHE cc_start: 0.6417 (m-80) cc_final: 0.6136 (m-10) REVERT: m 59 ARG cc_start: 0.6662 (mtt180) cc_final: 0.6348 (ptt180) REVERT: n 43 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7761 (tp30) REVERT: o 8 ILE cc_start: 0.8461 (mt) cc_final: 0.8151 (pt) REVERT: o 12 THR cc_start: 0.8826 (m) cc_final: 0.8496 (p) REVERT: o 89 ASP cc_start: 0.8613 (t70) cc_final: 0.8279 (t0) REVERT: p 51 ARG cc_start: 0.7509 (ttp80) cc_final: 0.7192 (ttt90) REVERT: p 98 TYR cc_start: 0.7551 (m-80) cc_final: 0.7299 (m-10) REVERT: q 61 TRP cc_start: 0.7786 (m-10) cc_final: 0.7322 (m-10) REVERT: q 84 LYS cc_start: 0.7585 (ttpt) cc_final: 0.7240 (mtmt) REVERT: q 102 ASP cc_start: 0.7397 (t0) cc_final: 0.6435 (t0) REVERT: r 47 VAL cc_start: 0.6373 (OUTLIER) cc_final: 0.5728 (t) REVERT: r 94 THR cc_start: 0.8724 (m) cc_final: 0.8520 (m) REVERT: s 40 ASN cc_start: 0.7073 (m110) cc_final: 0.6725 (p0) REVERT: s 61 ASN cc_start: 0.6090 (m-40) cc_final: 0.5625 (m-40) REVERT: s 81 SER cc_start: 0.8853 (m) cc_final: 0.8394 (p) REVERT: t 3 ARG cc_start: 0.8037 (mtt180) cc_final: 0.7577 (mpt180) REVERT: t 9 LYS cc_start: 0.8082 (mttt) cc_final: 0.7611 (mmtm) REVERT: t 17 SER cc_start: 0.7404 (p) cc_final: 0.6988 (t) REVERT: u 22 ARG cc_start: 0.5558 (mtp180) cc_final: 0.5264 (mtp-110) REVERT: u 41 LEU cc_start: 0.6056 (OUTLIER) cc_final: 0.5444 (pt) REVERT: u 43 LYS cc_start: 0.5103 (mtmm) cc_final: 0.4792 (mttp) REVERT: u 46 GLN cc_start: 0.7529 (tm-30) cc_final: 0.7156 (tm-30) REVERT: u 101 GLU cc_start: 0.7824 (tp30) cc_final: 0.7177 (mm-30) REVERT: w 2 PHE cc_start: 0.6519 (m-80) cc_final: 0.5690 (m-80) REVERT: w 7 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.5734 (tm-30) REVERT: w 10 LYS cc_start: 0.8149 (mttt) cc_final: 0.7795 (mmtm) REVERT: w 11 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7151 (mm-30) REVERT: w 55 GLU cc_start: 0.7433 (mp0) cc_final: 0.7108 (pm20) REVERT: y 35 SER cc_start: 0.9241 (m) cc_final: 0.8999 (p) REVERT: y 70 GLU cc_start: 0.7217 (pt0) cc_final: 0.6921 (mm-30) REVERT: z 21 GLN cc_start: 0.3608 (OUTLIER) cc_final: 0.2878 (pp30) outliers start: 130 outliers final: 23 residues processed: 2063 average time/residue: 1.4175 time to fit residues: 4907.9797 Evaluate side-chains 1169 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1133 time to evaluate : 6.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain 0 residue 17 ASN Chi-restraints excluded: chain 0 residue 76 GLU Chi-restraints excluded: chain 1 residue 2 LYS Chi-restraints excluded: chain 2 residue 10 THR Chi-restraints excluded: chain 3 residue 52 ARG Chi-restraints excluded: chain 4 residue 47 VAL Chi-restraints excluded: chain 6 residue 22 MET Chi-restraints excluded: chain c residue 267 ILE Chi-restraints excluded: chain c residue 269 ARG Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain e residue 187 VAL Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain m residue 13 HIS Chi-restraints excluded: chain p residue 19 SER Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 41 LYS Chi-restraints excluded: chain u residue 41 LEU Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain w residue 7 GLU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain z residue 12 LEU Chi-restraints excluded: chain z residue 18 TRP Chi-restraints excluded: chain z residue 21 GLN Chi-restraints excluded: chain z residue 23 GLN Chi-restraints excluded: chain z residue 25 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 844 optimal weight: 20.0000 chunk 757 optimal weight: 20.0000 chunk 420 optimal weight: 5.9990 chunk 258 optimal weight: 9.9990 chunk 511 optimal weight: 5.9990 chunk 404 optimal weight: 0.0570 chunk 783 optimal weight: 8.9990 chunk 303 optimal weight: 6.9990 chunk 476 optimal weight: 3.9990 chunk 583 optimal weight: 40.0000 chunk 908 optimal weight: 10.0000 overall best weight: 4.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 ASN B 167 HIS ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 120 HIS E 134 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN G 121 ASN H 3 GLN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN K 39 ASN K 80 ASN ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 ASN ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 45 HIS O 50 HIS P 9 HIS Q 44 HIS Q 49 ASN R 51 GLN ** S 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 81 GLN 0 23 ASN 1 15 ASN 1 36 GLN ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 19 HIS 4 26 ASN 8 13 ASN c 226 ASN ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 136 GLN f 27 GLN f 52 ASN g 38 ASN g 88 GLN h 2 GLN ** h 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 88 ASN o 19 GLN o 100 HIS p 41 GLN p 52 ASN q 37 GLN q 56 GLN r 6 GLN s 7 HIS s 61 ASN t 59 ASN u 45 HIS ** w 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 78 GLN w 87 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.172 155858 Z= 0.286 Angle : 0.859 16.859 233415 Z= 0.431 Chirality : 0.045 0.363 29864 Planarity : 0.006 0.183 12326 Dihedral : 24.733 179.935 78692 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.75 % Allowed : 6.86 % Favored : 92.40 % Rotamer: Outliers : 5.45 % Allowed : 16.45 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.09 % Twisted Proline : 0.55 % Twisted General : 0.06 % 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: -1.91 (0.11), residues: 5497 helix: -0.87 (0.12), residues: 1596 sheet: -1.82 (0.15), residues: 949 loop : -1.23 (0.11), residues: 2952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 103 HIS 0.011 0.002 HIS f 5 PHE 0.029 0.003 PHE u 96 TYR 0.035 0.002 TYR R 63 ARG 0.059 0.001 ARG P 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1488 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 1239 time to evaluate : 6.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 ARG cc_start: 0.6762 (ttt180) cc_final: 0.6412 (ttt90) REVERT: B 67 LEU cc_start: 0.4786 (OUTLIER) cc_final: 0.4438 (tt) REVERT: B 93 HIS cc_start: 0.5199 (m90) cc_final: 0.4002 (t70) REVERT: B 199 ILE cc_start: 0.7498 (mt) cc_final: 0.7273 (tp) REVERT: C 26 LYS cc_start: 0.5607 (mtpp) cc_final: 0.5304 (mmtt) REVERT: C 71 ARG cc_start: 0.5636 (mtm-85) cc_final: 0.5191 (mmp80) REVERT: D 103 ARG cc_start: 0.6375 (mmt90) cc_final: 0.5343 (mmm-85) REVERT: D 150 LYS cc_start: 0.8183 (mmtp) cc_final: 0.7931 (pptt) REVERT: D 182 LYS cc_start: 0.5538 (pttp) cc_final: 0.5198 (tmtt) REVERT: E 131 ASN cc_start: 0.6636 (t0) cc_final: 0.5563 (m110) REVERT: E 134 ASN cc_start: 0.6447 (m-40) cc_final: 0.5740 (m110) REVERT: F 4 TYR cc_start: 0.7423 (m-80) cc_final: 0.7048 (m-80) REVERT: F 9 MET cc_start: 0.6534 (mtp) cc_final: 0.6270 (mtt) REVERT: F 40 GLU cc_start: 0.6992 (tp30) cc_final: 0.5363 (tm-30) REVERT: F 41 ASP cc_start: 0.6868 (t70) cc_final: 0.5987 (m-30) REVERT: F 63 ASN cc_start: 0.7833 (m-40) cc_final: 0.7624 (m-40) REVERT: G 21 LEU cc_start: 0.8635 (mt) cc_final: 0.8041 (tt) REVERT: G 30 MET cc_start: 0.6245 (ttm) cc_final: 0.5536 (mpp) REVERT: G 51 GLN cc_start: 0.6927 (tp40) cc_final: 0.6398 (mt0) REVERT: G 150 PHE cc_start: 0.5683 (m-80) cc_final: 0.4439 (t80) REVERT: H 2 MET cc_start: 0.6582 (mmt) cc_final: 0.6202 (mpp) REVERT: H 30 LYS cc_start: 0.8525 (tttt) cc_final: 0.7804 (pttt) REVERT: I 45 MET cc_start: 0.6595 (mtt) cc_final: 0.6236 (mmt) REVERT: I 47 VAL cc_start: 0.6356 (p) cc_final: 0.6129 (p) REVERT: I 72 SER cc_start: 0.5096 (m) cc_final: 0.4335 (t) REVERT: I 79 ARG cc_start: 0.7479 (ttp-170) cc_final: 0.6310 (mmm-85) REVERT: L 95 HIS cc_start: 0.6444 (m90) cc_final: 0.6070 (m90) REVERT: M 52 ILE cc_start: 0.6925 (tt) cc_final: 0.6623 (tp) REVERT: M 80 MET cc_start: 0.5818 (tpp) cc_final: 0.5371 (tpt) REVERT: N 12 ARG cc_start: 0.5323 (ttm110) cc_final: 0.4365 (mtm110) REVERT: P 14 ARG cc_start: 0.7152 (ptt180) cc_final: 0.5804 (tpp80) REVERT: P 46 LYS cc_start: 0.2987 (OUTLIER) cc_final: 0.1489 (ttmt) REVERT: Q 15 LYS cc_start: 0.7112 (mmtt) cc_final: 0.6754 (mmmt) REVERT: Q 26 ARG cc_start: 0.7377 (ptm160) cc_final: 0.7031 (ttp80) REVERT: Q 80 LYS cc_start: 0.8266 (ptmt) cc_final: 0.7875 (tptt) REVERT: R 20 ILE cc_start: 0.6599 (tt) cc_final: 0.6292 (mm) REVERT: S 12 LEU cc_start: 0.6421 (tp) cc_final: 0.6069 (pp) REVERT: S 73 PHE cc_start: 0.7525 (m-10) cc_final: 0.7251 (m-10) REVERT: S 75 PRO cc_start: 0.7275 (Cg_exo) cc_final: 0.7062 (Cg_endo) REVERT: T 17 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8192 (ttp80) REVERT: T 20 ASN cc_start: 0.8428 (m110) cc_final: 0.7981 (t0) REVERT: T 66 ILE cc_start: 0.6425 (mm) cc_final: 0.6171 (mm) REVERT: U 17 ARG cc_start: 0.6004 (mmt-90) cc_final: 0.5736 (mtm180) REVERT: U 38 GLU cc_start: 0.7296 (tt0) cc_final: 0.6938 (pt0) REVERT: U 53 LYS cc_start: 0.6849 (tppt) cc_final: 0.5965 (ptpt) REVERT: 0 40 VAL cc_start: 0.8287 (t) cc_final: 0.8072 (p) REVERT: 0 68 LEU cc_start: 0.7859 (mt) cc_final: 0.7485 (pp) REVERT: 1 4 LYS cc_start: 0.8001 (tttp) cc_final: 0.7607 (tmtt) REVERT: 1 20 ASN cc_start: 0.7539 (m-40) cc_final: 0.7248 (t0) REVERT: 1 25 GLN cc_start: 0.8420 (tt0) cc_final: 0.7795 (tp40) REVERT: 1 40 SER cc_start: 0.7963 (m) cc_final: 0.7672 (t) REVERT: 2 14 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7926 (mp) REVERT: 3 15 MET cc_start: 0.7720 (mtp) cc_final: 0.7474 (mtt) REVERT: 3 37 LYS cc_start: 0.8607 (mtmt) cc_final: 0.7722 (mmmt) REVERT: 3 55 ILE cc_start: 0.6923 (mm) cc_final: 0.6543 (mm) REVERT: 4 34 LEU cc_start: 0.6446 (tp) cc_final: 0.6218 (tt) REVERT: 6 41 ARG cc_start: 0.8452 (mtt90) cc_final: 0.7713 (mtp-110) REVERT: 8 1 MET cc_start: 0.7022 (ppp) cc_final: 0.6752 (ptm) REVERT: c 24 LEU cc_start: 0.8028 (mt) cc_final: 0.7814 (mt) REVERT: d 28 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7373 (tm-30) REVERT: d 84 LEU cc_start: 0.7864 (mt) cc_final: 0.7657 (mt) REVERT: d 103 ASP cc_start: 0.7386 (m-30) cc_final: 0.6438 (t0) REVERT: d 167 ASN cc_start: 0.7781 (t0) cc_final: 0.7566 (t0) REVERT: d 187 LEU cc_start: 0.8284 (tp) cc_final: 0.8018 (tp) REVERT: e 67 ARG cc_start: 0.8231 (mtm180) cc_final: 0.7897 (mtp85) REVERT: e 163 ASN cc_start: 0.8132 (t0) cc_final: 0.7679 (t0) REVERT: f 63 GLN cc_start: 0.6516 (mt0) cc_final: 0.6034 (mm-40) REVERT: f 67 ILE cc_start: 0.8559 (mt) cc_final: 0.8266 (pt) REVERT: f 83 TYR cc_start: 0.7908 (m-80) cc_final: 0.7405 (m-10) REVERT: f 115 ARG cc_start: 0.7864 (mmt180) cc_final: 0.7536 (mtt180) REVERT: g 153 ARG cc_start: 0.8149 (ttm170) cc_final: 0.7752 (mtt90) REVERT: g 155 GLU cc_start: 0.9571 (pt0) cc_final: 0.8863 (pp20) REVERT: h 47 PHE cc_start: 0.6041 (t80) cc_final: 0.5837 (t80) REVERT: h 50 ARG cc_start: 0.5040 (mtm180) cc_final: 0.4718 (mtt90) REVERT: h 149 GLU cc_start: 0.7675 (tp30) cc_final: 0.6934 (mp0) REVERT: j 2 LYS cc_start: 0.7972 (mttt) cc_final: 0.7720 (mttp) REVERT: j 14 ASP cc_start: 0.8072 (t0) cc_final: 0.7685 (t70) REVERT: j 106 LYS cc_start: 0.8822 (tttt) cc_final: 0.8605 (ttpt) REVERT: k 20 MET cc_start: 0.8242 (ttm) cc_final: 0.7727 (tpp) REVERT: k 87 LEU cc_start: 0.8531 (mp) cc_final: 0.8293 (mt) REVERT: k 92 GLU cc_start: 0.5785 (pp20) cc_final: 0.5554 (pp20) REVERT: l 7 SER cc_start: 0.8703 (p) cc_final: 0.8332 (t) REVERT: l 19 LEU cc_start: 0.8285 (mp) cc_final: 0.8064 (mp) REVERT: m 33 LEU cc_start: 0.8335 (tp) cc_final: 0.8134 (mt) REVERT: m 59 ARG cc_start: 0.6597 (mtt180) cc_final: 0.6315 (ptp-170) REVERT: m 119 LEU cc_start: 0.8423 (mm) cc_final: 0.7686 (mt) REVERT: n 72 ASP cc_start: 0.7473 (t0) cc_final: 0.7248 (t0) REVERT: o 35 ILE cc_start: 0.8432 (tt) cc_final: 0.8229 (tp) REVERT: o 62 LEU cc_start: 0.8048 (mm) cc_final: 0.7163 (tp) REVERT: o 64 TYR cc_start: 0.6896 (t80) cc_final: 0.6222 (t80) REVERT: o 89 ASP cc_start: 0.8646 (t70) cc_final: 0.8168 (t70) REVERT: p 109 ARG cc_start: 0.6655 (OUTLIER) cc_final: 0.6347 (ptp90) REVERT: q 84 LYS cc_start: 0.7553 (ttpt) cc_final: 0.7049 (mtmt) REVERT: q 102 ASP cc_start: 0.6911 (t0) cc_final: 0.6473 (t0) REVERT: q 110 VAL cc_start: 0.8125 (t) cc_final: 0.7848 (t) REVERT: r 31 GLU cc_start: 0.7513 (mp0) cc_final: 0.7310 (mp0) REVERT: s 53 SER cc_start: 0.9362 (m) cc_final: 0.9067 (m) REVERT: s 57 ASN cc_start: 0.8092 (m-40) cc_final: 0.7712 (m-40) REVERT: s 71 VAL cc_start: 0.8914 (t) cc_final: 0.8651 (m) REVERT: t 1 MET cc_start: 0.6448 (OUTLIER) cc_final: 0.5504 (mtp) REVERT: t 3 ARG cc_start: 0.7775 (mtt180) cc_final: 0.7446 (mpt180) REVERT: t 8 LEU cc_start: 0.8772 (mt) cc_final: 0.8342 (mt) REVERT: t 9 LYS cc_start: 0.8268 (mttt) cc_final: 0.8036 (mmpt) REVERT: t 42 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7702 (pt0) REVERT: t 59 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.8136 (m-40) REVERT: t 69 ARG cc_start: 0.4605 (ttm-80) cc_final: 0.4253 (ttt-90) REVERT: t 74 ILE cc_start: 0.7287 (mt) cc_final: 0.7065 (mm) REVERT: u 22 ARG cc_start: 0.6291 (mtp180) cc_final: 0.5902 (mtp-110) REVERT: u 101 GLU cc_start: 0.7762 (tp30) cc_final: 0.7234 (mm-30) REVERT: w 11 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7445 (mm-30) REVERT: w 48 MET cc_start: 0.7871 (tpp) cc_final: 0.7540 (tpp) REVERT: w 49 ASN cc_start: 0.6855 (p0) cc_final: 0.6105 (p0) REVERT: w 55 GLU cc_start: 0.7044 (mp0) cc_final: 0.6821 (pm20) REVERT: w 76 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.6752 (p0) REVERT: w 90 ASP cc_start: 0.8311 (m-30) cc_final: 0.7983 (m-30) REVERT: y 20 ARG cc_start: 0.8360 (mtt90) cc_final: 0.8007 (mtt-85) REVERT: y 70 GLU cc_start: 0.8055 (pt0) cc_final: 0.7719 (mm-30) outliers start: 249 outliers final: 133 residues processed: 1383 average time/residue: 1.2565 time to fit residues: 3003.8962 Evaluate side-chains 1140 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 999 time to evaluate : 6.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 HIS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 116 TYR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain P residue 6 LEU Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 51 GLN Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain T residue 38 ILE Chi-restraints excluded: chain 0 residue 39 TRP Chi-restraints excluded: chain 0 residue 52 SER Chi-restraints excluded: chain 1 residue 8 GLU Chi-restraints excluded: chain 1 residue 28 LEU Chi-restraints excluded: chain 2 residue 14 ILE Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 33 LYS Chi-restraints excluded: chain 4 residue 47 VAL Chi-restraints excluded: chain 4 residue 48 ILE Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 44 VAL Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 8 residue 20 ASP Chi-restraints excluded: chain 8 residue 22 VAL Chi-restraints excluded: chain 8 residue 24 ARG Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain d residue 28 GLU Chi-restraints excluded: chain d residue 35 THR Chi-restraints excluded: chain d residue 51 THR Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain d residue 145 SER Chi-restraints excluded: chain d residue 171 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain d residue 200 ASP Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain f residue 21 ASN Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 127 ASN Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 77 ILE Chi-restraints excluded: chain g residue 107 LEU Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 2 GLN Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 117 SER Chi-restraints excluded: chain l residue 27 LEU Chi-restraints excluded: chain l residue 94 THR Chi-restraints excluded: chain l residue 112 LEU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain l residue 141 LYS Chi-restraints excluded: chain m residue 13 HIS Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain p residue 8 LEU Chi-restraints excluded: chain p residue 64 ILE Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 78 SER Chi-restraints excluded: chain p residue 81 VAL Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 109 ARG Chi-restraints excluded: chain p residue 110 ILE Chi-restraints excluded: chain p residue 112 GLU Chi-restraints excluded: chain q residue 31 VAL Chi-restraints excluded: chain q residue 40 ILE Chi-restraints excluded: chain q residue 98 ILE Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 24 ILE Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain t residue 1 MET Chi-restraints excluded: chain t residue 59 ASN Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 28 VAL Chi-restraints excluded: chain w residue 45 ASP Chi-restraints excluded: chain w residue 53 LYS Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain w residue 76 ASP Chi-restraints excluded: chain y residue 51 VAL Chi-restraints excluded: chain y residue 53 CYS Chi-restraints excluded: chain y residue 71 VAL Chi-restraints excluded: chain z residue 10 GLU Chi-restraints excluded: chain z residue 12 LEU Chi-restraints excluded: chain z residue 25 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 504 optimal weight: 7.9990 chunk 281 optimal weight: 5.9990 chunk 755 optimal weight: 10.0000 chunk 618 optimal weight: 10.0000 chunk 250 optimal weight: 20.0000 chunk 909 optimal weight: 9.9990 chunk 982 optimal weight: 30.0000 chunk 810 optimal weight: 30.0000 chunk 902 optimal weight: 10.0000 chunk 310 optimal weight: 1.9990 chunk 729 optimal weight: 20.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 HIS ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 71 HIS ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 GLN Q 30 HIS Q 44 HIS R 51 GLN ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 67 HIS T 74 HIS 1 25 GLN ** 1 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 130 GLN d 150 GLN e 41 GLN f 37 ASN ** g 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 2 GLN h 28 ASN j 128 ASN n 9 GLN o 104 GLN p 52 ASN q 72 ASN r 6 GLN s 61 ASN ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 87 GLN z 4 GLN z 21 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.149 155858 Z= 0.335 Angle : 0.815 14.517 233415 Z= 0.413 Chirality : 0.044 0.323 29864 Planarity : 0.006 0.109 12326 Dihedral : 24.602 179.861 78641 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.00 % Favored : 91.43 % Rotamer: Outliers : 6.96 % Allowed : 19.31 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.09 % Twisted Proline : 0.55 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.11), residues: 5497 helix: -0.55 (0.12), residues: 1616 sheet: -1.63 (0.16), residues: 959 loop : -1.62 (0.11), residues: 2922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 103 HIS 0.025 0.002 HIS S 13 PHE 0.029 0.003 PHE K 60 TYR 0.026 0.003 TYR R 63 ARG 0.065 0.001 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1407 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 318 poor density : 1089 time to evaluate : 5.727 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 67 LEU cc_start: 0.4492 (OUTLIER) cc_final: 0.4156 (tt) REVERT: C 17 TRP cc_start: 0.7162 (m-90) cc_final: 0.6430 (m-10) REVERT: C 26 LYS cc_start: 0.5646 (mtpp) cc_final: 0.5166 (mmtt) REVERT: C 57 GLU cc_start: 0.5573 (tt0) cc_final: 0.5102 (tt0) REVERT: C 71 ARG cc_start: 0.5447 (mtm-85) cc_final: 0.5144 (mmp80) REVERT: C 203 LYS cc_start: 0.6483 (OUTLIER) cc_final: 0.4915 (ttpt) REVERT: D 103 ARG cc_start: 0.6588 (mmt90) cc_final: 0.5754 (ttm110) REVERT: D 150 LYS cc_start: 0.8550 (mmtp) cc_final: 0.8174 (pptt) REVERT: D 182 LYS cc_start: 0.5354 (pttp) cc_final: 0.4985 (tmtt) REVERT: E 65 LYS cc_start: 0.5716 (mtpt) cc_final: 0.5424 (mtpt) REVERT: F 9 MET cc_start: 0.6731 (mtp) cc_final: 0.6435 (mtt) REVERT: F 41 ASP cc_start: 0.7387 (t70) cc_final: 0.6444 (m-30) REVERT: G 30 MET cc_start: 0.6573 (ttm) cc_final: 0.6066 (tpp) REVERT: G 51 GLN cc_start: 0.6812 (tp40) cc_final: 0.6229 (mt0) REVERT: G 82 SER cc_start: 0.2662 (t) cc_final: 0.2441 (m) REVERT: G 150 PHE cc_start: 0.5538 (m-80) cc_final: 0.4347 (t80) REVERT: H 30 LYS cc_start: 0.8465 (tttt) cc_final: 0.7714 (pttt) REVERT: H 44 PHE cc_start: 0.6195 (m-80) cc_final: 0.5958 (m-80) REVERT: I 38 PHE cc_start: 0.6328 (OUTLIER) cc_final: 0.5873 (t80) REVERT: I 45 MET cc_start: 0.6646 (mtt) cc_final: 0.6207 (mmt) REVERT: I 56 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.6371 (pmm) REVERT: I 72 SER cc_start: 0.5548 (m) cc_final: 0.4824 (t) REVERT: I 113 LYS cc_start: 0.5753 (mtpp) cc_final: 0.5236 (tppt) REVERT: J 64 GLN cc_start: 0.7845 (pm20) cc_final: 0.7317 (pm20) REVERT: L 29 LYS cc_start: 0.7990 (mtpp) cc_final: 0.7613 (ttmm) REVERT: L 95 HIS cc_start: 0.6811 (m90) cc_final: 0.6131 (m90) REVERT: L 115 LYS cc_start: 0.4765 (mttt) cc_final: 0.4523 (mttm) REVERT: M 12 LYS cc_start: 0.7531 (tttp) cc_final: 0.6934 (ttpt) REVERT: M 21 ILE cc_start: 0.7434 (OUTLIER) cc_final: 0.6759 (mp) REVERT: M 26 LYS cc_start: 0.8067 (mmtp) cc_final: 0.7262 (mptt) REVERT: M 80 MET cc_start: 0.6050 (tpp) cc_final: 0.5692 (tpt) REVERT: N 5 MET cc_start: 0.6972 (mmt) cc_final: 0.6742 (mmp) REVERT: N 12 ARG cc_start: 0.5661 (ttm110) cc_final: 0.4671 (mtm-85) REVERT: Q 15 LYS cc_start: 0.7145 (mmtt) cc_final: 0.6728 (mmmt) REVERT: Q 66 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6629 (pp) REVERT: Q 80 LYS cc_start: 0.7755 (ptmt) cc_final: 0.7445 (tptt) REVERT: R 20 ILE cc_start: 0.5989 (tt) cc_final: 0.5693 (mm) REVERT: R 63 TYR cc_start: 0.5434 (m-80) cc_final: 0.5043 (m-80) REVERT: R 71 ASP cc_start: 0.7263 (t70) cc_final: 0.6894 (t0) REVERT: S 12 LEU cc_start: 0.6701 (tp) cc_final: 0.6199 (pp) REVERT: S 73 PHE cc_start: 0.7727 (m-10) cc_final: 0.7296 (m-10) REVERT: T 20 ASN cc_start: 0.8222 (m110) cc_final: 0.7690 (t0) REVERT: T 27 MET cc_start: 0.8407 (tmm) cc_final: 0.8073 (tmm) REVERT: T 38 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7504 (pt) REVERT: U 38 GLU cc_start: 0.7300 (tt0) cc_final: 0.7019 (pt0) REVERT: U 53 LYS cc_start: 0.6766 (tppt) cc_final: 0.5812 (ptpt) REVERT: 0 47 VAL cc_start: 0.8117 (t) cc_final: 0.7841 (p) REVERT: 1 4 LYS cc_start: 0.8035 (tttp) cc_final: 0.7446 (mptt) REVERT: 1 25 GLN cc_start: 0.8539 (tt0) cc_final: 0.7908 (tp40) REVERT: 2 9 GLN cc_start: 0.7445 (tp40) cc_final: 0.7155 (tp40) REVERT: 3 37 LYS cc_start: 0.8759 (mtmt) cc_final: 0.7875 (mmmt) REVERT: 4 40 ASP cc_start: 0.9012 (t0) cc_final: 0.8759 (t70) REVERT: 6 26 ASN cc_start: 0.8300 (m-40) cc_final: 0.8006 (m110) REVERT: 6 29 GLN cc_start: 0.8578 (mp10) cc_final: 0.8362 (mp10) REVERT: 7 15 LYS cc_start: 0.6904 (tttt) cc_final: 0.6172 (tptm) REVERT: 8 1 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7360 (ptm) REVERT: c 24 LEU cc_start: 0.8380 (mt) cc_final: 0.8121 (mt) REVERT: c 129 THR cc_start: 0.7754 (OUTLIER) cc_final: 0.7550 (m) REVERT: c 181 MET cc_start: 0.6807 (mtp) cc_final: 0.6459 (mmt) REVERT: c 188 CYS cc_start: 0.5425 (m) cc_final: 0.5036 (m) REVERT: c 212 ARG cc_start: 0.8509 (mmm-85) cc_final: 0.8260 (tpt-90) REVERT: c 221 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8319 (mtm-85) REVERT: d 28 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7467 (tm-30) REVERT: d 103 ASP cc_start: 0.7179 (m-30) cc_final: 0.5910 (t0) REVERT: f 38 MET cc_start: 0.7576 (mtp) cc_final: 0.7271 (mtt) REVERT: f 83 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.7619 (m-10) REVERT: f 115 ARG cc_start: 0.7994 (mmt180) cc_final: 0.7385 (mtt180) REVERT: f 150 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7715 (ptp-170) REVERT: g 109 PHE cc_start: 0.8457 (m-80) cc_final: 0.8166 (m-80) REVERT: g 153 ARG cc_start: 0.8166 (ttm170) cc_final: 0.7791 (mtt90) REVERT: g 155 GLU cc_start: 0.9517 (pt0) cc_final: 0.8864 (pp20) REVERT: g 175 LYS cc_start: 0.6571 (tttt) cc_final: 0.6152 (pttt) REVERT: h 33 GLN cc_start: 0.7434 (mp10) cc_final: 0.6926 (mt0) REVERT: h 42 LYS cc_start: 0.5547 (tptp) cc_final: 0.5306 (tptp) REVERT: h 50 ARG cc_start: 0.5253 (mtm180) cc_final: 0.5027 (mtt-85) REVERT: j 2 LYS cc_start: 0.8170 (mttt) cc_final: 0.7893 (mttm) REVERT: j 12 LYS cc_start: 0.8241 (ttpt) cc_final: 0.7982 (tptt) REVERT: j 129 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8218 (mm-30) REVERT: k 7 MET cc_start: 0.7724 (mmm) cc_final: 0.7518 (mmm) REVERT: k 12 ASP cc_start: 0.6667 (p0) cc_final: 0.6467 (p0) REVERT: k 58 LEU cc_start: 0.8691 (pt) cc_final: 0.8134 (mt) REVERT: l 4 ASN cc_start: 0.8975 (p0) cc_final: 0.8645 (p0) REVERT: l 7 SER cc_start: 0.8641 (p) cc_final: 0.8317 (t) REVERT: l 58 TYR cc_start: 0.8392 (p90) cc_final: 0.8155 (p90) REVERT: m 59 ARG cc_start: 0.7208 (mtt180) cc_final: 0.6387 (ptp-170) REVERT: n 9 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7729 (tt0) REVERT: n 65 LEU cc_start: 0.8918 (tp) cc_final: 0.8685 (mp) REVERT: n 72 ASP cc_start: 0.8396 (t0) cc_final: 0.7867 (t0) REVERT: n 75 ILE cc_start: 0.8248 (mm) cc_final: 0.7995 (mm) REVERT: o 62 LEU cc_start: 0.8362 (mm) cc_final: 0.7482 (tp) REVERT: o 84 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8411 (mm-30) REVERT: o 93 ASP cc_start: 0.7935 (t0) cc_final: 0.7712 (t0) REVERT: p 11 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8615 (tm-30) REVERT: p 102 GLU cc_start: 0.7121 (mp0) cc_final: 0.6323 (pp20) REVERT: p 109 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6507 (ptp90) REVERT: q 84 LYS cc_start: 0.7750 (ttpt) cc_final: 0.7413 (mtmt) REVERT: q 102 ASP cc_start: 0.6636 (t0) cc_final: 0.6387 (t0) REVERT: r 1 MET cc_start: 0.8241 (ppp) cc_final: 0.7964 (ppp) REVERT: r 31 GLU cc_start: 0.7708 (mp0) cc_final: 0.7498 (mp0) REVERT: t 3 ARG cc_start: 0.6993 (mtt180) cc_final: 0.6704 (mpt180) REVERT: t 8 LEU cc_start: 0.8608 (mt) cc_final: 0.8233 (tp) REVERT: t 9 LYS cc_start: 0.8413 (mttt) cc_final: 0.7848 (mmtt) REVERT: u 22 ARG cc_start: 0.6470 (mtp180) cc_final: 0.6232 (mtp-110) REVERT: u 58 ILE cc_start: 0.5893 (mt) cc_final: 0.5651 (mt) REVERT: u 101 GLU cc_start: 0.7385 (tp30) cc_final: 0.6875 (mm-30) REVERT: w 20 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6966 (mt) REVERT: w 29 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7764 (tt) REVERT: w 51 GLN cc_start: 0.8660 (pp30) cc_final: 0.8382 (pp30) REVERT: w 59 GLU cc_start: 0.5014 (mt-10) cc_final: 0.4802 (pt0) REVERT: w 76 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7603 (p0) REVERT: y 15 ASP cc_start: 0.7295 (t0) cc_final: 0.7019 (m-30) REVERT: y 29 GLU cc_start: 0.7767 (tt0) cc_final: 0.7244 (mt-10) REVERT: y 50 ASN cc_start: 0.9038 (m-40) cc_final: 0.8833 (m110) REVERT: z 4 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.6738 (tm-30) REVERT: z 10 GLU cc_start: 0.4667 (OUTLIER) cc_final: 0.4304 (mt-10) outliers start: 318 outliers final: 204 residues processed: 1279 average time/residue: 1.2300 time to fit residues: 2741.9161 Evaluate side-chains 1178 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 954 time to evaluate : 6.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 HIS Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 116 TYR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 112 ARG Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 68 SER Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 60 ILE Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain T residue 38 ILE Chi-restraints excluded: chain T residue 50 PHE Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain 0 residue 39 TRP Chi-restraints excluded: chain 0 residue 42 SER Chi-restraints excluded: chain 0 residue 52 SER Chi-restraints excluded: chain 1 residue 8 GLU Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 1 residue 28 LEU Chi-restraints excluded: chain 2 residue 6 LYS Chi-restraints excluded: chain 2 residue 10 THR Chi-restraints excluded: chain 2 residue 25 LEU Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 4 residue 5 ILE Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 29 THR Chi-restraints excluded: chain 4 residue 43 VAL Chi-restraints excluded: chain 4 residue 47 VAL Chi-restraints excluded: chain 4 residue 48 ILE Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 30 VAL Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 8 residue 1 MET Chi-restraints excluded: chain 8 residue 2 LYS Chi-restraints excluded: chain 8 residue 20 ASP Chi-restraints excluded: chain 8 residue 22 VAL Chi-restraints excluded: chain 8 residue 28 SER Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 140 THR Chi-restraints excluded: chain c residue 160 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 180 GLU Chi-restraints excluded: chain c residue 221 ARG Chi-restraints excluded: chain c residue 263 THR Chi-restraints excluded: chain d residue 5 VAL Chi-restraints excluded: chain d residue 28 GLU Chi-restraints excluded: chain d residue 51 THR Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 168 GLU Chi-restraints excluded: chain d residue 171 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain d residue 200 ASP Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 115 GLN Chi-restraints excluded: chain e residue 159 LEU Chi-restraints excluded: chain f residue 21 ASN Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 51 ASP Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 147 ASP Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain f residue 150 ARG Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 26 ILE Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 77 ILE Chi-restraints excluded: chain g residue 107 LEU Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain g residue 141 ILE Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 11 ASN Chi-restraints excluded: chain h residue 91 PHE Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 108 MET Chi-restraints excluded: chain j residue 138 GLN Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 117 SER Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 94 THR Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain m residue 13 HIS Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 9 GLN Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 4 LYS Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain p residue 8 LEU Chi-restraints excluded: chain p residue 20 PHE Chi-restraints excluded: chain p residue 48 ILE Chi-restraints excluded: chain p residue 64 ILE Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 78 SER Chi-restraints excluded: chain p residue 81 VAL Chi-restraints excluded: chain p residue 84 ILE Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 109 ARG Chi-restraints excluded: chain p residue 112 GLU Chi-restraints excluded: chain q residue 40 ILE Chi-restraints excluded: chain q residue 74 ILE Chi-restraints excluded: chain q residue 98 ILE Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 24 ILE Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 15 THR Chi-restraints excluded: chain u residue 28 VAL Chi-restraints excluded: chain u residue 74 ASN Chi-restraints excluded: chain u residue 82 ARG Chi-restraints excluded: chain w residue 7 GLU Chi-restraints excluded: chain w residue 17 SER Chi-restraints excluded: chain w residue 20 LEU Chi-restraints excluded: chain w residue 29 ILE Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 53 LYS Chi-restraints excluded: chain w residue 64 VAL Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain w residue 76 ASP Chi-restraints excluded: chain w residue 89 ILE Chi-restraints excluded: chain y residue 31 VAL Chi-restraints excluded: chain y residue 36 ILE Chi-restraints excluded: chain y residue 53 CYS Chi-restraints excluded: chain y residue 71 VAL Chi-restraints excluded: chain z residue 4 GLN Chi-restraints excluded: chain z residue 10 GLU Chi-restraints excluded: chain z residue 18 TRP Chi-restraints excluded: chain z residue 21 GLN Chi-restraints excluded: chain z residue 25 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 898 optimal weight: 9.9990 chunk 683 optimal weight: 20.0000 chunk 472 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 434 optimal weight: 8.9990 chunk 610 optimal weight: 20.0000 chunk 913 optimal weight: 30.0000 chunk 966 optimal weight: 10.0000 chunk 477 optimal weight: 7.9990 chunk 865 optimal weight: 10.0000 chunk 260 optimal weight: 3.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 HIS E 145 ASN E 147 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN T 77 ASN ** 1 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 53 HIS d 130 GLN d 150 GLN e 163 ASN ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 35 HIS p 52 ASN t 28 ASN t 70 HIS t 91 GLN z 21 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.5725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 155858 Z= 0.316 Angle : 0.773 14.548 233415 Z= 0.390 Chirality : 0.043 0.468 29864 Planarity : 0.006 0.112 12326 Dihedral : 24.550 179.839 78633 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.06 % Favored : 91.40 % Rotamer: Outliers : 7.90 % Allowed : 21.15 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.09 % Twisted Proline : 0.55 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.11), residues: 5497 helix: -0.39 (0.13), residues: 1612 sheet: -1.75 (0.15), residues: 957 loop : -1.76 (0.11), residues: 2928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.004 TRP S 33 HIS 0.033 0.002 HIS P 9 PHE 0.043 0.003 PHE J 49 TYR 0.030 0.003 TYR F 4 ARG 0.013 0.001 ARG H 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1377 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 361 poor density : 1016 time to evaluate : 6.272 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: B 67 LEU cc_start: 0.4595 (OUTLIER) cc_final: 0.4219 (tt) REVERT: C 17 TRP cc_start: 0.7409 (m-90) cc_final: 0.6719 (m-10) REVERT: C 26 LYS cc_start: 0.5367 (mtpp) cc_final: 0.4801 (mmtt) REVERT: C 71 ARG cc_start: 0.5454 (mtm-85) cc_final: 0.5189 (mmp80) REVERT: C 180 ASP cc_start: 0.5306 (OUTLIER) cc_final: 0.4425 (t70) REVERT: C 203 LYS cc_start: 0.6237 (OUTLIER) cc_final: 0.4773 (tptt) REVERT: D 25 ARG cc_start: 0.2662 (ptp90) cc_final: 0.1394 (mtm-85) REVERT: D 49 ASP cc_start: 0.7873 (t0) cc_final: 0.7636 (t0) REVERT: D 103 ARG cc_start: 0.6621 (mmt90) cc_final: 0.5675 (ttm110) REVERT: D 123 MET cc_start: 0.7146 (tpp) cc_final: 0.6939 (tmm) REVERT: D 136 VAL cc_start: 0.3084 (OUTLIER) cc_final: 0.2795 (t) REVERT: D 198 LEU cc_start: 0.7518 (tp) cc_final: 0.7095 (tp) REVERT: E 147 ASN cc_start: 0.4339 (OUTLIER) cc_final: 0.3771 (t0) REVERT: F 9 MET cc_start: 0.6858 (mtp) cc_final: 0.6549 (mtt) REVERT: F 41 ASP cc_start: 0.7428 (t70) cc_final: 0.6507 (m-30) REVERT: G 51 GLN cc_start: 0.6565 (tp40) cc_final: 0.5989 (mt0) REVERT: H 30 LYS cc_start: 0.8502 (tttt) cc_final: 0.7741 (pttt) REVERT: H 44 PHE cc_start: 0.5962 (m-80) cc_final: 0.5731 (m-80) REVERT: I 29 ILE cc_start: 0.5627 (OUTLIER) cc_final: 0.5356 (mt) REVERT: I 38 PHE cc_start: 0.6066 (OUTLIER) cc_final: 0.5726 (t80) REVERT: I 45 MET cc_start: 0.6656 (mtt) cc_final: 0.6159 (mmt) REVERT: I 72 SER cc_start: 0.5403 (m) cc_final: 0.5170 (t) REVERT: I 79 ARG cc_start: 0.7498 (ttp-170) cc_final: 0.6431 (mmm-85) REVERT: I 113 LYS cc_start: 0.5730 (mtpp) cc_final: 0.5210 (tppt) REVERT: L 35 ARG cc_start: 0.8687 (tpt-90) cc_final: 0.7144 (ttm170) REVERT: L 95 HIS cc_start: 0.6818 (m90) cc_final: 0.6123 (m90) REVERT: L 115 LYS cc_start: 0.4843 (mttt) cc_final: 0.4507 (mttm) REVERT: M 12 LYS cc_start: 0.7501 (tttp) cc_final: 0.7252 (tttp) REVERT: M 21 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.7166 (mp) REVERT: M 26 LYS cc_start: 0.8216 (mmtp) cc_final: 0.7445 (mptt) REVERT: M 69 ARG cc_start: 0.6984 (mmt180) cc_final: 0.6503 (ttp-110) REVERT: N 72 PHE cc_start: 0.7589 (t80) cc_final: 0.7368 (t80) REVERT: N 73 LEU cc_start: 0.8264 (mt) cc_final: 0.8013 (mp) REVERT: Q 15 LYS cc_start: 0.7179 (mmtt) cc_final: 0.6595 (mmmt) REVERT: Q 17 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7362 (mp0) REVERT: Q 48 GLU cc_start: 0.5989 (OUTLIER) cc_final: 0.5660 (pp20) REVERT: R 20 ILE cc_start: 0.5775 (tt) cc_final: 0.5451 (mm) REVERT: R 32 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8096 (mp) REVERT: R 56 ARG cc_start: 0.8414 (ttm170) cc_final: 0.8189 (ttm170) REVERT: S 12 LEU cc_start: 0.7147 (tp) cc_final: 0.6868 (pp) REVERT: S 73 PHE cc_start: 0.7744 (m-10) cc_final: 0.7269 (m-10) REVERT: U 38 GLU cc_start: 0.7297 (tt0) cc_final: 0.6982 (pt0) REVERT: U 53 LYS cc_start: 0.6278 (tppt) cc_final: 0.5749 (pttt) REVERT: 0 44 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.7969 (mptt) REVERT: 0 47 VAL cc_start: 0.8164 (t) cc_final: 0.7920 (p) REVERT: 1 4 LYS cc_start: 0.7721 (tttp) cc_final: 0.7152 (mptt) REVERT: 1 25 GLN cc_start: 0.8445 (tt0) cc_final: 0.7747 (tp40) REVERT: 2 9 GLN cc_start: 0.7744 (tp40) cc_final: 0.7475 (tp40) REVERT: 3 37 LYS cc_start: 0.8707 (mtmt) cc_final: 0.7739 (mmmt) REVERT: 6 41 ARG cc_start: 0.8417 (mtt90) cc_final: 0.7623 (ptm160) REVERT: 8 1 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7477 (ptm) REVERT: c 24 LEU cc_start: 0.8324 (mt) cc_final: 0.7978 (mt) REVERT: c 35 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7811 (tp30) REVERT: c 121 ASP cc_start: 0.7761 (p0) cc_final: 0.7467 (p0) REVERT: c 181 MET cc_start: 0.6888 (mtp) cc_final: 0.6505 (mmt) REVERT: c 188 CYS cc_start: 0.5799 (m) cc_final: 0.4946 (m) REVERT: c 212 ARG cc_start: 0.8436 (mmm-85) cc_final: 0.8156 (tpt-90) REVERT: d 28 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: d 103 ASP cc_start: 0.7052 (m-30) cc_final: 0.5969 (t0) REVERT: e 122 GLU cc_start: 0.7566 (tp30) cc_final: 0.6907 (tp30) REVERT: f 38 MET cc_start: 0.7577 (mtp) cc_final: 0.7260 (mtt) REVERT: f 83 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.7658 (m-10) REVERT: g 88 GLN cc_start: 0.5460 (pt0) cc_final: 0.5255 (mp10) REVERT: g 153 ARG cc_start: 0.8189 (ttm170) cc_final: 0.7826 (mtt90) REVERT: g 155 GLU cc_start: 0.9368 (pt0) cc_final: 0.8730 (pp20) REVERT: g 175 LYS cc_start: 0.6541 (tttt) cc_final: 0.6249 (pttt) REVERT: h 33 GLN cc_start: 0.7793 (mp10) cc_final: 0.7226 (mt0) REVERT: j 2 LYS cc_start: 0.8126 (mttt) cc_final: 0.7811 (mttm) REVERT: j 12 LYS cc_start: 0.8325 (ttpt) cc_final: 0.8045 (pptt) REVERT: j 23 LYS cc_start: 0.4532 (OUTLIER) cc_final: 0.4197 (mttm) REVERT: k 4 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7497 (tt0) REVERT: k 7 MET cc_start: 0.8099 (mmm) cc_final: 0.7815 (mmm) REVERT: k 58 LEU cc_start: 0.8738 (pt) cc_final: 0.8270 (mt) REVERT: k 92 GLU cc_start: 0.5981 (pp20) cc_final: 0.5764 (pp20) REVERT: m 59 ARG cc_start: 0.7481 (mtt180) cc_final: 0.6551 (ptp-170) REVERT: n 72 ASP cc_start: 0.8458 (t0) cc_final: 0.8180 (t0) REVERT: o 84 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8425 (mm-30) REVERT: o 93 ASP cc_start: 0.7849 (t0) cc_final: 0.7587 (t0) REVERT: p 10 GLN cc_start: 0.7001 (pt0) cc_final: 0.6698 (mp10) REVERT: p 11 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8636 (tm-30) REVERT: p 50 ILE cc_start: 0.8722 (mm) cc_final: 0.8377 (mm) REVERT: p 70 VAL cc_start: 0.8488 (t) cc_final: 0.8153 (p) REVERT: p 102 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6638 (pp20) REVERT: q 32 TYR cc_start: 0.7791 (t80) cc_final: 0.7588 (t80) REVERT: q 84 LYS cc_start: 0.7730 (ttpt) cc_final: 0.7354 (mtmt) REVERT: r 1 MET cc_start: 0.8343 (ppp) cc_final: 0.8100 (ppp) REVERT: r 10 LYS cc_start: 0.6397 (OUTLIER) cc_final: 0.5568 (mtmt) REVERT: r 40 MET cc_start: 0.7059 (tmm) cc_final: 0.6340 (tmm) REVERT: s 92 ARG cc_start: 0.8097 (mtp180) cc_final: 0.7808 (mtm180) REVERT: t 3 ARG cc_start: 0.6954 (mtt180) cc_final: 0.6724 (mpt180) REVERT: t 8 LEU cc_start: 0.8620 (mt) cc_final: 0.8234 (tp) REVERT: t 79 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7784 (m-30) REVERT: u 22 ARG cc_start: 0.6556 (mtp180) cc_final: 0.6342 (mtm110) REVERT: u 86 ARG cc_start: 0.6665 (ptt180) cc_final: 0.6429 (ptt180) REVERT: u 101 GLU cc_start: 0.7373 (tp30) cc_final: 0.6805 (mm-30) REVERT: w 20 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6916 (mt) REVERT: w 59 GLU cc_start: 0.5660 (mt-10) cc_final: 0.5410 (pt0) REVERT: y 15 ASP cc_start: 0.7159 (t0) cc_final: 0.6892 (m-30) REVERT: y 29 GLU cc_start: 0.7652 (tt0) cc_final: 0.7395 (mt-10) REVERT: z 4 GLN cc_start: 0.6110 (OUTLIER) cc_final: 0.5888 (tm-30) REVERT: z 10 GLU cc_start: 0.4958 (OUTLIER) cc_final: 0.3945 (mt-10) REVERT: z 25 ILE cc_start: 0.4214 (OUTLIER) cc_final: 0.3914 (pt) outliers start: 361 outliers final: 242 residues processed: 1238 average time/residue: 1.2065 time to fit residues: 2604.3883 Evaluate side-chains 1190 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 925 time to evaluate : 6.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 HIS Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 168 ARG Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 91 ARG Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 5 TYR Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain K residue 30 ILE 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 110 THR Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 116 TYR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 112 ARG Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain O residue 44 GLU Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 68 SER Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 17 GLU Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 48 GLU Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain T residue 50 PHE Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain 0 residue 44 LYS Chi-restraints excluded: chain 0 residue 52 SER Chi-restraints excluded: chain 0 residue 60 ASP Chi-restraints excluded: chain 1 residue 8 GLU Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 2 residue 10 THR Chi-restraints excluded: chain 2 residue 25 LEU Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 2 residue 57 VAL Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 4 residue 5 ILE Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 47 VAL Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 16 HIS Chi-restraints excluded: chain 6 residue 30 VAL Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 8 residue 1 MET Chi-restraints excluded: chain 8 residue 2 LYS Chi-restraints excluded: chain 8 residue 20 ASP Chi-restraints excluded: chain 8 residue 22 VAL Chi-restraints excluded: chain 8 residue 28 SER Chi-restraints excluded: chain c residue 6 CYS Chi-restraints excluded: chain c residue 63 ARG Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 140 THR Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 180 GLU Chi-restraints excluded: chain c residue 245 VAL Chi-restraints excluded: chain d residue 5 VAL Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 28 GLU Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 51 THR Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 168 GLU Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain d residue 171 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain d residue 200 ASP Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 55 SER Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 105 LEU Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 175 ILE Chi-restraints excluded: chain e residue 189 THR Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 51 ASP Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 127 ASN Chi-restraints excluded: chain f residue 147 ASP Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 56 ASP Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain g residue 107 LEU Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 11 ASN Chi-restraints excluded: chain h residue 61 VAL Chi-restraints excluded: chain h residue 91 PHE Chi-restraints excluded: chain h residue 147 VAL Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 23 LYS Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 44 TYR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 69 ARG Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 108 MET Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 117 SER Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 94 THR Chi-restraints excluded: chain l residue 112 LEU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain m residue 13 HIS Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 57 VAL 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 24 MET Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 4 LYS Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 56 LYS Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 8 LEU Chi-restraints excluded: chain p residue 17 VAL Chi-restraints excluded: chain p residue 20 PHE Chi-restraints excluded: chain p residue 30 VAL Chi-restraints excluded: chain p residue 48 ILE Chi-restraints excluded: chain p residue 64 ILE Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 81 VAL Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 102 GLU Chi-restraints excluded: chain p residue 112 GLU Chi-restraints excluded: chain q residue 40 ILE Chi-restraints excluded: chain q residue 98 ILE Chi-restraints excluded: chain r residue 10 LYS Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 24 ILE Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 61 LEU Chi-restraints excluded: chain t residue 70 HIS Chi-restraints excluded: chain t residue 78 SER Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 15 THR Chi-restraints excluded: chain u residue 28 VAL Chi-restraints excluded: chain u residue 82 ARG Chi-restraints excluded: chain w residue 7 GLU Chi-restraints excluded: chain w residue 17 SER Chi-restraints excluded: chain w residue 20 LEU Chi-restraints excluded: chain w residue 29 ILE Chi-restraints excluded: chain w residue 45 ASP Chi-restraints excluded: chain w residue 53 LYS Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain y residue 30 SER Chi-restraints excluded: chain y residue 36 ILE Chi-restraints excluded: chain y residue 71 VAL Chi-restraints excluded: chain z residue 4 GLN Chi-restraints excluded: chain z residue 10 GLU Chi-restraints excluded: chain z residue 25 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 805 optimal weight: 10.0000 chunk 548 optimal weight: 20.0000 chunk 14 optimal weight: 0.0980 chunk 719 optimal weight: 20.0000 chunk 398 optimal weight: 0.7980 chunk 824 optimal weight: 10.0000 chunk 668 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 493 optimal weight: 5.9990 chunk 867 optimal weight: 10.0000 chunk 243 optimal weight: 0.4980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN D 130 ASN D 151 GLN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN S 13 HIS ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 60 GLN 1 31 GLN 1 36 GLN ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 58 HIS c 115 GLN d 130 GLN ** e 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 115 HIS p 52 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.5937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 155858 Z= 0.153 Angle : 0.610 13.800 233415 Z= 0.315 Chirality : 0.035 0.331 29864 Planarity : 0.005 0.104 12326 Dihedral : 24.331 179.895 78633 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.19 % Favored : 92.27 % Rotamer: Outliers : 5.49 % Allowed : 24.32 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.09 % Twisted Proline : 0.55 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.11), residues: 5497 helix: 0.01 (0.13), residues: 1612 sheet: -1.44 (0.16), residues: 944 loop : -1.61 (0.11), residues: 2941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 103 HIS 0.027 0.001 HIS t 70 PHE 0.021 0.002 PHE h 47 TYR 0.018 0.002 TYR R 63 ARG 0.026 0.001 ARG S 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1281 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1030 time to evaluate : 6.244 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 10 LYS cc_start: 0.4990 (tmtt) cc_final: 0.4489 (mttt) REVERT: B 203 ASP cc_start: 0.3690 (p0) cc_final: 0.2419 (t0) REVERT: B 204 ASP cc_start: 0.5533 (m-30) cc_final: 0.5106 (m-30) REVERT: C 17 TRP cc_start: 0.7426 (m-90) cc_final: 0.6816 (m-10) REVERT: C 26 LYS cc_start: 0.5524 (mtpp) cc_final: 0.5043 (mmtt) REVERT: C 71 ARG cc_start: 0.5487 (mtm-85) cc_final: 0.5188 (mmp80) REVERT: C 127 VAL cc_start: 0.5701 (m) cc_final: 0.5496 (p) REVERT: C 128 MET cc_start: 0.3061 (ttt) cc_final: 0.2329 (tpt) REVERT: C 180 ASP cc_start: 0.4923 (OUTLIER) cc_final: 0.4422 (t70) REVERT: D 25 ARG cc_start: 0.3227 (ptp90) cc_final: 0.2186 (mtm-85) REVERT: D 103 ARG cc_start: 0.6635 (mmt90) cc_final: 0.5673 (ttm110) REVERT: D 104 MET cc_start: 0.7680 (tpp) cc_final: 0.7390 (tpp) REVERT: D 122 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7920 (mp) REVERT: D 123 MET cc_start: 0.6829 (tpp) cc_final: 0.6577 (tmm) REVERT: D 136 VAL cc_start: 0.3183 (OUTLIER) cc_final: 0.2898 (t) REVERT: D 198 LEU cc_start: 0.7297 (tp) cc_final: 0.7068 (tp) REVERT: F 9 MET cc_start: 0.6769 (mtp) cc_final: 0.6474 (mtt) REVERT: F 41 ASP cc_start: 0.6526 (t70) cc_final: 0.5613 (m-30) REVERT: F 88 MET cc_start: 0.3633 (tmm) cc_final: 0.3409 (tmm) REVERT: G 21 LEU cc_start: 0.8570 (mt) cc_final: 0.7963 (tt) REVERT: G 30 MET cc_start: 0.6387 (ttp) cc_final: 0.5200 (mpp) REVERT: G 51 GLN cc_start: 0.6594 (tp40) cc_final: 0.6039 (mt0) REVERT: H 14 ARG cc_start: 0.7215 (ptm160) cc_final: 0.6877 (ttp80) REVERT: H 30 LYS cc_start: 0.8455 (tttt) cc_final: 0.7710 (pttt) REVERT: H 127 TYR cc_start: 0.6483 (p90) cc_final: 0.5561 (p90) REVERT: I 12 LYS cc_start: 0.5895 (ptpt) cc_final: 0.5285 (ptmm) REVERT: I 29 ILE cc_start: 0.5548 (OUTLIER) cc_final: 0.5302 (mt) REVERT: I 38 PHE cc_start: 0.6153 (OUTLIER) cc_final: 0.5930 (t80) REVERT: I 45 MET cc_start: 0.6531 (mtt) cc_final: 0.6182 (mmt) REVERT: I 72 SER cc_start: 0.5130 (m) cc_final: 0.4447 (t) REVERT: I 79 ARG cc_start: 0.7446 (ttp-170) cc_final: 0.6354 (mmm-85) REVERT: J 47 GLU cc_start: 0.5816 (mt-10) cc_final: 0.5576 (mt-10) REVERT: L 95 HIS cc_start: 0.6525 (m90) cc_final: 0.6033 (m90) REVERT: L 110 LYS cc_start: 0.5053 (mtmm) cc_final: 0.4761 (mtmt) REVERT: L 115 LYS cc_start: 0.4981 (mttt) cc_final: 0.4756 (mttm) REVERT: M 21 ILE cc_start: 0.7224 (OUTLIER) cc_final: 0.6787 (mp) REVERT: M 26 LYS cc_start: 0.8038 (mmtp) cc_final: 0.7171 (mptt) REVERT: M 57 ASP cc_start: 0.7519 (p0) cc_final: 0.6976 (p0) REVERT: M 65 GLU cc_start: 0.6437 (mm-30) cc_final: 0.6226 (mm-30) REVERT: M 69 ARG cc_start: 0.6949 (mmt180) cc_final: 0.6532 (ttp-110) REVERT: M 103 THR cc_start: 0.7407 (m) cc_final: 0.7075 (t) REVERT: N 41 TRP cc_start: 0.5136 (p90) cc_final: 0.4795 (p90) REVERT: N 73 LEU cc_start: 0.8158 (mt) cc_final: 0.7875 (mp) REVERT: Q 16 MET cc_start: 0.4596 (mtm) cc_final: 0.4239 (mtm) REVERT: Q 18 LYS cc_start: 0.8029 (mmmt) cc_final: 0.7709 (mmtt) REVERT: Q 29 LYS cc_start: 0.8187 (mmmm) cc_final: 0.7914 (mmmt) REVERT: Q 66 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.5557 (tp) REVERT: R 20 ILE cc_start: 0.5613 (tt) cc_final: 0.5403 (mm) REVERT: S 12 LEU cc_start: 0.6992 (tp) cc_final: 0.6453 (pp) REVERT: S 73 PHE cc_start: 0.7576 (m-10) cc_final: 0.7066 (m-10) REVERT: T 27 MET cc_start: 0.8244 (tmm) cc_final: 0.8029 (tmm) REVERT: U 53 LYS cc_start: 0.6405 (tppt) cc_final: 0.5935 (pttt) REVERT: 0 17 ASN cc_start: 0.8564 (t0) cc_final: 0.8275 (t0) REVERT: 0 54 LYS cc_start: 0.8640 (tppt) cc_final: 0.8256 (tmtt) REVERT: 1 4 LYS cc_start: 0.7737 (tttp) cc_final: 0.7178 (mptt) REVERT: 1 25 GLN cc_start: 0.8376 (tt0) cc_final: 0.7675 (tp40) REVERT: 2 9 GLN cc_start: 0.7516 (tp40) cc_final: 0.7213 (tp40) REVERT: 3 15 MET cc_start: 0.7960 (mtp) cc_final: 0.7531 (mtt) REVERT: 3 37 LYS cc_start: 0.8572 (mtmt) cc_final: 0.7806 (tptt) REVERT: 6 41 ARG cc_start: 0.8369 (mtt90) cc_final: 0.7640 (ptm160) REVERT: 8 1 MET cc_start: 0.7869 (ppp) cc_final: 0.7387 (ptm) REVERT: 8 36 ARG cc_start: 0.8020 (ttm-80) cc_final: 0.7684 (ttm170) REVERT: c 24 LEU cc_start: 0.8481 (mt) cc_final: 0.8247 (mt) REVERT: c 35 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7868 (tp30) REVERT: c 64 ILE cc_start: 0.8733 (mt) cc_final: 0.8369 (mp) REVERT: c 121 ASP cc_start: 0.7743 (p0) cc_final: 0.7472 (p0) REVERT: c 167 ARG cc_start: 0.8082 (ttm170) cc_final: 0.7643 (ttm170) REVERT: c 181 MET cc_start: 0.6723 (mtp) cc_final: 0.6286 (mmt) REVERT: c 188 CYS cc_start: 0.5844 (m) cc_final: 0.5010 (m) REVERT: d 28 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: d 103 ASP cc_start: 0.7014 (OUTLIER) cc_final: 0.5923 (t0) REVERT: e 67 ARG cc_start: 0.8340 (mtm-85) cc_final: 0.7973 (mtp85) REVERT: e 122 GLU cc_start: 0.7470 (tp30) cc_final: 0.6891 (tp30) REVERT: f 83 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.7740 (m-10) REVERT: f 150 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7337 (mtt180) REVERT: f 175 PHE cc_start: 0.4677 (OUTLIER) cc_final: 0.4151 (t80) REVERT: g 81 GLU cc_start: 0.7229 (tt0) cc_final: 0.6845 (tm-30) REVERT: g 88 GLN cc_start: 0.5418 (pt0) cc_final: 0.5137 (mp10) REVERT: g 153 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7642 (mtt90) REVERT: g 155 GLU cc_start: 0.9219 (pt0) cc_final: 0.8582 (pp20) REVERT: g 175 LYS cc_start: 0.6458 (tttt) cc_final: 0.6173 (pttt) REVERT: h 4 ILE cc_start: 0.4534 (OUTLIER) cc_final: 0.3747 (tp) REVERT: h 33 GLN cc_start: 0.7671 (mp10) cc_final: 0.7248 (mt0) REVERT: h 47 PHE cc_start: 0.5990 (t80) cc_final: 0.5768 (t80) REVERT: h 50 ARG cc_start: 0.5299 (mtm180) cc_final: 0.4638 (mtt-85) REVERT: j 2 LYS cc_start: 0.8103 (mttt) cc_final: 0.7784 (mttm) REVERT: j 12 LYS cc_start: 0.8247 (ttpt) cc_final: 0.8030 (pptt) REVERT: j 90 GLU cc_start: 0.6469 (tp30) cc_final: 0.6173 (tp30) REVERT: k 4 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7291 (tt0) REVERT: k 7 MET cc_start: 0.8080 (mmm) cc_final: 0.7844 (mmm) REVERT: k 39 ILE cc_start: 0.8851 (pt) cc_final: 0.8375 (mt) REVERT: k 44 LYS cc_start: 0.8420 (mmmm) cc_final: 0.7962 (mmtm) REVERT: k 58 LEU cc_start: 0.8619 (pt) cc_final: 0.8205 (mt) REVERT: k 98 ARG cc_start: 0.7664 (ttm110) cc_final: 0.7359 (ttm110) REVERT: m 59 ARG cc_start: 0.7508 (mtt180) cc_final: 0.6518 (ptp-170) REVERT: m 119 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7574 (mt) REVERT: n 72 ASP cc_start: 0.8472 (t0) cc_final: 0.8249 (t0) REVERT: n 75 ILE cc_start: 0.8273 (mm) cc_final: 0.8041 (mm) REVERT: n 114 GLU cc_start: 0.8171 (pt0) cc_final: 0.7870 (pt0) REVERT: o 17 LYS cc_start: 0.8213 (tptp) cc_final: 0.7992 (tptt) REVERT: o 84 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8409 (mm-30) REVERT: o 93 ASP cc_start: 0.7552 (t0) cc_final: 0.7346 (t0) REVERT: p 9 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6635 (mt-10) REVERT: p 11 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8791 (tm-30) REVERT: p 70 VAL cc_start: 0.8530 (t) cc_final: 0.8119 (p) REVERT: p 102 GLU cc_start: 0.7029 (mp0) cc_final: 0.6464 (pp20) REVERT: q 32 TYR cc_start: 0.7648 (t80) cc_final: 0.7419 (t80) REVERT: q 84 LYS cc_start: 0.7696 (ttpt) cc_final: 0.7389 (mtmt) REVERT: r 1 MET cc_start: 0.8384 (ppp) cc_final: 0.8168 (ppp) REVERT: r 40 MET cc_start: 0.6852 (tmm) cc_final: 0.6014 (tmm) REVERT: r 84 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8312 (ptt-90) REVERT: s 57 ASN cc_start: 0.8196 (m-40) cc_final: 0.7917 (m-40) REVERT: t 3 ARG cc_start: 0.6949 (mtt180) cc_final: 0.6679 (mpt180) REVERT: t 8 LEU cc_start: 0.8685 (mt) cc_final: 0.8418 (tp) REVERT: u 101 GLU cc_start: 0.7601 (tp30) cc_final: 0.6960 (mm-30) REVERT: w 7 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: w 20 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6832 (mt) REVERT: w 53 LYS cc_start: 0.5236 (OUTLIER) cc_final: 0.5019 (ptpp) REVERT: y 15 ASP cc_start: 0.7001 (t0) cc_final: 0.6790 (m-30) outliers start: 251 outliers final: 165 residues processed: 1171 average time/residue: 1.2161 time to fit residues: 2489.6415 Evaluate side-chains 1132 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 948 time to evaluate : 6.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 91 ARG Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 116 TYR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 112 ARG Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 44 GLU Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain P residue 6 LEU Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 68 SER Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain T residue 50 PHE Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain 0 residue 52 SER Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 2 residue 57 VAL Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 29 THR Chi-restraints excluded: chain 6 residue 30 VAL Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 8 residue 20 ASP Chi-restraints excluded: chain c residue 6 CYS Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 140 THR Chi-restraints excluded: chain c residue 263 THR Chi-restraints excluded: chain d residue 28 GLU Chi-restraints excluded: chain d residue 51 THR Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain d residue 103 ASP Chi-restraints excluded: chain d residue 168 GLU Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 189 THR Chi-restraints excluded: chain f residue 21 ASN Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 127 ASN Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain f residue 150 ARG Chi-restraints excluded: chain f residue 175 PHE Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 107 LEU Chi-restraints excluded: chain g residue 121 ILE Chi-restraints excluded: chain g residue 151 TYR Chi-restraints excluded: chain g residue 153 ARG Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 11 ASN Chi-restraints excluded: chain h residue 30 LEU Chi-restraints excluded: chain h residue 91 PHE Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 69 ARG Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 117 SER Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 112 LEU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 13 HIS Chi-restraints excluded: chain m residue 108 VAL Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 129 THR 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 4 LYS Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain p residue 8 LEU Chi-restraints excluded: chain p residue 20 PHE Chi-restraints excluded: chain p residue 30 VAL Chi-restraints excluded: chain p residue 64 ILE Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 112 GLU Chi-restraints excluded: chain q residue 80 ILE Chi-restraints excluded: chain q residue 98 ILE Chi-restraints excluded: chain q residue 103 LYS Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 84 ARG Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 24 ILE Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 78 SER Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 45 HIS Chi-restraints excluded: chain u residue 82 ARG Chi-restraints excluded: chain w residue 7 GLU Chi-restraints excluded: chain w residue 20 LEU Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 53 LYS Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 64 VAL Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 36 ILE Chi-restraints excluded: chain y residue 50 ASN Chi-restraints excluded: chain y residue 59 LEU Chi-restraints excluded: chain y residue 71 VAL Chi-restraints excluded: chain z residue 20 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 325 optimal weight: 20.0000 chunk 870 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 567 optimal weight: 20.0000 chunk 238 optimal weight: 20.0000 chunk 967 optimal weight: 10.0000 chunk 803 optimal weight: 10.0000 chunk 447 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 320 optimal weight: 1.9990 chunk 507 optimal weight: 7.9990 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN D 73 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 GLN ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 81 GLN ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 195 GLN ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 52 ASN q 14 HIS z 21 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.6259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 155858 Z= 0.268 Angle : 0.711 14.444 233415 Z= 0.359 Chirality : 0.040 0.324 29864 Planarity : 0.005 0.107 12326 Dihedral : 24.380 179.910 78630 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.68 % Favored : 90.76 % Rotamer: Outliers : 7.02 % Allowed : 24.06 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.09 % Twisted Proline : 0.55 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.11), residues: 5497 helix: -0.09 (0.13), residues: 1602 sheet: -1.40 (0.16), residues: 948 loop : -1.76 (0.11), residues: 2947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 103 HIS 0.012 0.001 HIS t 70 PHE 0.030 0.002 PHE K 60 TYR 0.025 0.002 TYR M 22 ARG 0.011 0.001 ARG H 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1287 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 966 time to evaluate : 5.619 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: B 15 PHE cc_start: 0.5498 (m-80) cc_final: 0.5202 (m-80) REVERT: B 166 ASP cc_start: 0.5727 (m-30) cc_final: 0.5514 (m-30) REVERT: B 203 ASP cc_start: 0.3596 (p0) cc_final: 0.2524 (t0) REVERT: B 204 ASP cc_start: 0.5536 (m-30) cc_final: 0.5124 (m-30) REVERT: B 211 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6990 (mt) REVERT: C 17 TRP cc_start: 0.7202 (m-90) cc_final: 0.6581 (m-10) REVERT: C 26 LYS cc_start: 0.5281 (mtpp) cc_final: 0.4749 (mmmt) REVERT: C 71 ARG cc_start: 0.5550 (mtm-85) cc_final: 0.5238 (mmp80) REVERT: C 180 ASP cc_start: 0.4639 (OUTLIER) cc_final: 0.3698 (t70) REVERT: C 203 LYS cc_start: 0.6400 (pttt) cc_final: 0.4980 (tptt) REVERT: D 25 ARG cc_start: 0.3020 (ptp90) cc_final: 0.1915 (mtm-85) REVERT: D 103 ARG cc_start: 0.6660 (mmt90) cc_final: 0.5736 (ttm110) REVERT: D 136 VAL cc_start: 0.2462 (OUTLIER) cc_final: 0.2226 (t) REVERT: D 198 LEU cc_start: 0.7539 (tp) cc_final: 0.7280 (tp) REVERT: F 9 MET cc_start: 0.7122 (mtp) cc_final: 0.6741 (mtt) REVERT: F 41 ASP cc_start: 0.6787 (t70) cc_final: 0.5945 (m-30) REVERT: F 49 TYR cc_start: 0.8372 (p90) cc_final: 0.7995 (p90) REVERT: G 51 GLN cc_start: 0.6623 (tp40) cc_final: 0.6026 (mt0) REVERT: H 30 LYS cc_start: 0.8475 (tttt) cc_final: 0.7735 (pttt) REVERT: I 12 LYS cc_start: 0.6059 (ptpt) cc_final: 0.5478 (ptmm) REVERT: I 29 ILE cc_start: 0.5606 (OUTLIER) cc_final: 0.5348 (mt) REVERT: I 38 PHE cc_start: 0.5932 (OUTLIER) cc_final: 0.5646 (t80) REVERT: I 45 MET cc_start: 0.6767 (mtt) cc_final: 0.6242 (mmt) REVERT: I 72 SER cc_start: 0.5839 (m) cc_final: 0.5232 (t) REVERT: I 79 ARG cc_start: 0.7505 (ttp-170) cc_final: 0.6439 (mmm-85) REVERT: K 22 ILE cc_start: 0.7308 (OUTLIER) cc_final: 0.6972 (pt) REVERT: L 35 ARG cc_start: 0.8610 (tpt-90) cc_final: 0.7004 (ttm170) REVERT: L 95 HIS cc_start: 0.6716 (m90) cc_final: 0.6120 (m90) REVERT: M 21 ILE cc_start: 0.6904 (OUTLIER) cc_final: 0.6182 (mp) REVERT: M 26 LYS cc_start: 0.8203 (mmtp) cc_final: 0.7435 (mptt) REVERT: M 65 GLU cc_start: 0.6809 (mm-30) cc_final: 0.6546 (mm-30) REVERT: M 103 THR cc_start: 0.8102 (m) cc_final: 0.7742 (t) REVERT: Q 17 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: Q 39 ARG cc_start: 0.5736 (mtp180) cc_final: 0.5421 (mtp180) REVERT: Q 47 ASP cc_start: 0.6710 (t0) cc_final: 0.6176 (t0) REVERT: Q 48 GLU cc_start: 0.5954 (pp20) cc_final: 0.5745 (pp20) REVERT: S 12 LEU cc_start: 0.7261 (tp) cc_final: 0.6755 (pp) REVERT: T 27 MET cc_start: 0.8256 (tmm) cc_final: 0.8025 (tmm) REVERT: U 38 GLU cc_start: 0.7490 (tt0) cc_final: 0.7069 (pt0) REVERT: U 53 LYS cc_start: 0.6356 (tppt) cc_final: 0.5827 (pttt) REVERT: 0 44 LYS cc_start: 0.8631 (tptt) cc_final: 0.7980 (mppt) REVERT: 0 54 LYS cc_start: 0.8667 (tppt) cc_final: 0.8327 (tmtt) REVERT: 0 68 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7314 (mp) REVERT: 1 4 LYS cc_start: 0.7659 (tttp) cc_final: 0.7093 (mptt) REVERT: 1 25 GLN cc_start: 0.8390 (tt0) cc_final: 0.7682 (tp40) REVERT: 2 9 GLN cc_start: 0.7793 (tp40) cc_final: 0.7592 (tp40) REVERT: 3 37 LYS cc_start: 0.8677 (mtmt) cc_final: 0.7865 (tptt) REVERT: 6 41 ARG cc_start: 0.8269 (mtt90) cc_final: 0.7633 (ptm160) REVERT: 8 1 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7512 (ptm) REVERT: c 24 LEU cc_start: 0.8398 (mt) cc_final: 0.8081 (mt) REVERT: c 35 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7865 (tp30) REVERT: c 167 ARG cc_start: 0.8160 (ttm170) cc_final: 0.7547 (ttm170) REVERT: c 181 MET cc_start: 0.6848 (mtp) cc_final: 0.6353 (mmt) REVERT: c 188 CYS cc_start: 0.5960 (m) cc_final: 0.5073 (m) REVERT: c 261 LYS cc_start: 0.6932 (mttt) cc_final: 0.6527 (mtpp) REVERT: d 28 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7829 (tm-30) REVERT: e 122 GLU cc_start: 0.7608 (tp30) cc_final: 0.7030 (tp30) REVERT: f 83 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7755 (m-10) REVERT: f 140 GLU cc_start: 0.5397 (mp0) cc_final: 0.4751 (tp30) REVERT: g 81 GLU cc_start: 0.7575 (tt0) cc_final: 0.7177 (tm-30) REVERT: g 88 GLN cc_start: 0.5718 (pt0) cc_final: 0.5447 (mp10) REVERT: g 153 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7841 (mtt90) REVERT: g 155 GLU cc_start: 0.9297 (pt0) cc_final: 0.8686 (pp20) REVERT: h 4 ILE cc_start: 0.4620 (OUTLIER) cc_final: 0.3816 (tp) REVERT: h 33 GLN cc_start: 0.7810 (mp10) cc_final: 0.7419 (mt0) REVERT: j 2 LYS cc_start: 0.8063 (mttt) cc_final: 0.7732 (mttm) REVERT: j 12 LYS cc_start: 0.8230 (ttpt) cc_final: 0.8029 (pptt) REVERT: j 90 GLU cc_start: 0.6611 (tp30) cc_final: 0.6305 (tp30) REVERT: k 7 MET cc_start: 0.8181 (mmm) cc_final: 0.7909 (mmm) REVERT: k 44 LYS cc_start: 0.8579 (mmmm) cc_final: 0.8164 (mmtm) REVERT: k 58 LEU cc_start: 0.8583 (pt) cc_final: 0.8013 (mt) REVERT: k 59 LYS cc_start: 0.7815 (mttt) cc_final: 0.7333 (mtpt) REVERT: k 98 ARG cc_start: 0.7914 (ttm110) cc_final: 0.7654 (ttm110) REVERT: m 59 ARG cc_start: 0.7577 (mtt180) cc_final: 0.6586 (ptp-170) REVERT: n 72 ASP cc_start: 0.8106 (t0) cc_final: 0.7899 (t0) REVERT: n 75 ILE cc_start: 0.8357 (mm) cc_final: 0.8089 (mm) REVERT: n 112 TYR cc_start: 0.8326 (m-80) cc_final: 0.8088 (m-80) REVERT: o 84 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8322 (mm-30) REVERT: p 11 GLU cc_start: 0.9081 (tm-30) cc_final: 0.8864 (tm-30) REVERT: p 12 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8145 (tt0) REVERT: p 50 ILE cc_start: 0.8732 (mm) cc_final: 0.8341 (mm) REVERT: p 70 VAL cc_start: 0.8474 (t) cc_final: 0.8147 (p) REVERT: p 102 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6383 (pp20) REVERT: q 84 LYS cc_start: 0.7638 (ttpt) cc_final: 0.7287 (mtmt) REVERT: r 1 MET cc_start: 0.8419 (ppp) cc_final: 0.8191 (ppp) REVERT: r 40 MET cc_start: 0.7007 (tmm) cc_final: 0.6468 (tmm) REVERT: r 84 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8288 (ptt-90) REVERT: s 57 ASN cc_start: 0.8204 (m-40) cc_final: 0.7956 (m-40) REVERT: s 92 ARG cc_start: 0.8016 (mtp180) cc_final: 0.7606 (mtm180) REVERT: t 3 ARG cc_start: 0.6939 (mtt180) cc_final: 0.6622 (mpt180) REVERT: t 8 LEU cc_start: 0.8652 (mt) cc_final: 0.8322 (tp) REVERT: t 79 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7878 (m-30) REVERT: u 101 GLU cc_start: 0.7562 (tp30) cc_final: 0.6896 (mm-30) REVERT: w 20 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6889 (mt) REVERT: w 53 LYS cc_start: 0.4885 (OUTLIER) cc_final: 0.4636 (ptpp) REVERT: y 29 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7574 (mt-10) REVERT: z 10 GLU cc_start: 0.4887 (OUTLIER) cc_final: 0.3742 (mt-10) outliers start: 321 outliers final: 246 residues processed: 1165 average time/residue: 1.2098 time to fit residues: 2463.7690 Evaluate side-chains 1192 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 925 time to evaluate : 5.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 91 ARG Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain I residue 5 TYR Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 116 TYR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 112 ARG Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 44 GLU Chi-restraints excluded: chain P residue 6 LEU Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 68 SER Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 17 GLU Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain T residue 50 PHE Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain 0 residue 14 THR Chi-restraints excluded: chain 0 residue 42 SER Chi-restraints excluded: chain 0 residue 52 SER Chi-restraints excluded: chain 0 residue 56 MET Chi-restraints excluded: chain 0 residue 68 LEU Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 2 residue 57 VAL Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 43 VAL Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 2 LYS Chi-restraints excluded: chain 6 residue 30 VAL Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 8 residue 1 MET Chi-restraints excluded: chain 8 residue 2 LYS Chi-restraints excluded: chain 8 residue 20 ASP Chi-restraints excluded: chain 8 residue 22 VAL Chi-restraints excluded: chain c residue 6 CYS Chi-restraints excluded: chain c residue 63 ARG Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 140 THR Chi-restraints excluded: chain c residue 180 GLU Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 28 GLU Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 51 THR Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain d residue 103 ASP Chi-restraints excluded: chain d residue 145 SER Chi-restraints excluded: chain d residue 168 GLU Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain d residue 171 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain d residue 200 ASP Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 33 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 55 SER Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 115 GLN Chi-restraints excluded: chain e residue 175 ILE Chi-restraints excluded: chain e residue 189 THR Chi-restraints excluded: chain f residue 21 ASN Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 127 ASN Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain f residue 175 PHE Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 56 ASP Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain g residue 107 LEU Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 121 ILE Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain g residue 153 ARG Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 11 ASN Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 40 THR Chi-restraints excluded: chain h residue 91 PHE Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain h residue 147 VAL Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 69 ARG Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 94 THR Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain m residue 13 HIS Chi-restraints excluded: chain m residue 25 ASP 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 m residue 129 THR Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 4 LYS Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain p residue 8 LEU Chi-restraints excluded: chain p residue 12 GLN Chi-restraints excluded: chain p residue 20 PHE Chi-restraints excluded: chain p residue 30 VAL Chi-restraints excluded: chain p residue 48 ILE Chi-restraints excluded: chain p residue 64 ILE Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 102 GLU Chi-restraints excluded: chain p residue 112 GLU Chi-restraints excluded: chain q residue 40 ILE Chi-restraints excluded: chain q residue 74 ILE Chi-restraints excluded: chain q residue 80 ILE Chi-restraints excluded: chain q residue 98 ILE Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 84 ARG Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 24 ILE Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 25 GLU Chi-restraints excluded: chain t residue 78 SER Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 15 THR Chi-restraints excluded: chain w residue 7 GLU Chi-restraints excluded: chain w residue 20 LEU Chi-restraints excluded: chain w residue 29 ILE Chi-restraints excluded: chain w residue 45 ASP Chi-restraints excluded: chain w residue 53 LYS Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 64 VAL Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 50 ASN Chi-restraints excluded: chain y residue 59 LEU Chi-restraints excluded: chain y residue 66 LYS Chi-restraints excluded: chain y residue 71 VAL Chi-restraints excluded: chain y residue 81 SER Chi-restraints excluded: chain z residue 10 GLU Chi-restraints excluded: chain z residue 21 GLN Chi-restraints excluded: chain z residue 25 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 932 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 551 optimal weight: 30.0000 chunk 706 optimal weight: 10.0000 chunk 547 optimal weight: 40.0000 chunk 814 optimal weight: 20.0000 chunk 540 optimal weight: 20.0000 chunk 963 optimal weight: 10.0000 chunk 603 optimal weight: 30.0000 chunk 587 optimal weight: 40.0000 chunk 444 optimal weight: 9.9990 overall best weight: 9.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN D 130 ASN E 145 ASN ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 ASN M 7 ASN ** P 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 HIS R 51 GLN S 13 HIS ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 81 GLN 0 23 ASN 1 41 HIS ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 90 ASN d 32 ASN d 49 GLN d 130 GLN d 150 GLN ** e 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 195 GLN ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 131 ASN p 52 ASN q 52 GLN t 70 HIS y 50 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.6740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 155858 Z= 0.385 Angle : 0.850 15.011 233415 Z= 0.424 Chirality : 0.045 0.303 29864 Planarity : 0.007 0.111 12326 Dihedral : 24.651 179.921 78630 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.82 % Favored : 89.59 % Rotamer: Outliers : 8.49 % Allowed : 23.56 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.09 % Twisted Proline : 0.55 % Twisted General : 0.06 % 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: -2.32 (0.11), residues: 5497 helix: -0.53 (0.13), residues: 1583 sheet: -1.77 (0.16), residues: 984 loop : -2.04 (0.11), residues: 2930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 103 HIS 0.015 0.002 HIS P 9 PHE 0.032 0.003 PHE K 60 TYR 0.039 0.003 TYR M 22 ARG 0.013 0.001 ARG M 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1330 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 388 poor density : 942 time to evaluate : 6.273 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 15 PHE cc_start: 0.5420 (m-80) cc_final: 0.5071 (m-80) REVERT: B 29 PHE cc_start: 0.4712 (OUTLIER) cc_final: 0.4430 (p90) REVERT: B 153 MET cc_start: 0.3310 (OUTLIER) cc_final: 0.3027 (ttp) REVERT: B 203 ASP cc_start: 0.4496 (p0) cc_final: 0.2941 (t0) REVERT: B 211 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6705 (mt) REVERT: C 17 TRP cc_start: 0.7366 (m-90) cc_final: 0.6649 (m-10) REVERT: C 26 LYS cc_start: 0.5116 (mtpp) cc_final: 0.4166 (mmmt) REVERT: C 71 ARG cc_start: 0.5634 (mtm-85) cc_final: 0.5325 (mmp80) REVERT: C 180 ASP cc_start: 0.3779 (OUTLIER) cc_final: 0.3295 (t70) REVERT: C 203 LYS cc_start: 0.6503 (OUTLIER) cc_final: 0.4951 (tptt) REVERT: D 25 ARG cc_start: 0.3271 (ptp90) cc_final: 0.2056 (mtm180) REVERT: D 104 MET cc_start: 0.7623 (tpp) cc_final: 0.7339 (tpp) REVERT: F 9 MET cc_start: 0.7288 (mtp) cc_final: 0.6821 (mtt) REVERT: F 41 ASP cc_start: 0.6987 (t70) cc_final: 0.6164 (m-30) REVERT: F 45 ARG cc_start: 0.6395 (tpp80) cc_final: 0.5860 (tpp80) REVERT: G 51 GLN cc_start: 0.6410 (tp40) cc_final: 0.5868 (mt0) REVERT: H 30 LYS cc_start: 0.8428 (tttt) cc_final: 0.7603 (pttt) REVERT: I 12 LYS cc_start: 0.5941 (ptpt) cc_final: 0.5403 (ptmm) REVERT: I 38 PHE cc_start: 0.6004 (OUTLIER) cc_final: 0.5722 (t80) REVERT: I 45 MET cc_start: 0.6856 (mtt) cc_final: 0.6447 (mmt) REVERT: J 60 ASP cc_start: 0.7733 (m-30) cc_final: 0.7394 (t0) REVERT: J 64 GLN cc_start: 0.7961 (pm20) cc_final: 0.7726 (pm20) REVERT: L 8 ARG cc_start: 0.6351 (OUTLIER) cc_final: 0.6009 (mmt90) REVERT: L 95 HIS cc_start: 0.6816 (m90) cc_final: 0.6232 (m90) REVERT: L 115 LYS cc_start: 0.4801 (mttm) cc_final: 0.4459 (pttt) REVERT: M 21 ILE cc_start: 0.7249 (OUTLIER) cc_final: 0.6740 (mp) REVERT: M 26 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7558 (mptt) REVERT: M 65 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6654 (mm-30) REVERT: M 103 THR cc_start: 0.8169 (m) cc_final: 0.7751 (t) REVERT: O 16 ARG cc_start: 0.5590 (mtt180) cc_final: 0.5135 (ptt-90) REVERT: Q 18 LYS cc_start: 0.8092 (mmmt) cc_final: 0.7867 (tppt) REVERT: Q 37 ILE cc_start: 0.6847 (OUTLIER) cc_final: 0.6497 (pt) REVERT: Q 47 ASP cc_start: 0.6800 (t0) cc_final: 0.6328 (t0) REVERT: Q 67 SER cc_start: 0.5835 (OUTLIER) cc_final: 0.5457 (p) REVERT: T 27 MET cc_start: 0.8276 (tmm) cc_final: 0.7937 (tmm) REVERT: T 81 GLN cc_start: 0.7399 (OUTLIER) cc_final: 0.7190 (tt0) REVERT: U 38 GLU cc_start: 0.7532 (tt0) cc_final: 0.7078 (pt0) REVERT: 0 44 LYS cc_start: 0.8896 (tptt) cc_final: 0.8455 (mptt) REVERT: 0 48 THR cc_start: 0.8305 (p) cc_final: 0.8090 (t) REVERT: 1 4 LYS cc_start: 0.7705 (tttp) cc_final: 0.7089 (mptt) REVERT: 1 25 GLN cc_start: 0.8201 (tt0) cc_final: 0.7329 (tp40) REVERT: 3 37 LYS cc_start: 0.8684 (mtmt) cc_final: 0.7689 (mmmt) REVERT: 4 33 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.7021 (mmtp) REVERT: 6 41 ARG cc_start: 0.8287 (mtt90) cc_final: 0.7664 (ptm160) REVERT: 7 15 LYS cc_start: 0.7251 (tttt) cc_final: 0.6755 (mmtt) REVERT: 8 1 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7562 (ptm) REVERT: c 35 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8089 (tp30) REVERT: c 117 GLN cc_start: 0.8235 (tt0) cc_final: 0.7725 (tt0) REVERT: c 167 ARG cc_start: 0.8193 (ttm170) cc_final: 0.7455 (ttm170) REVERT: c 181 MET cc_start: 0.6886 (mtp) cc_final: 0.6374 (mmt) REVERT: c 261 LYS cc_start: 0.7114 (mttt) cc_final: 0.6574 (mtpp) REVERT: d 28 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7942 (tm-30) REVERT: d 46 ARG cc_start: 0.6110 (mtp-110) cc_final: 0.4686 (ptp90) REVERT: e 122 GLU cc_start: 0.7852 (tp30) cc_final: 0.7344 (tp30) REVERT: e 148 ILE cc_start: 0.7887 (mm) cc_final: 0.7604 (mt) REVERT: f 83 TYR cc_start: 0.8397 (OUTLIER) cc_final: 0.7738 (m-10) REVERT: f 175 PHE cc_start: 0.5190 (OUTLIER) cc_final: 0.4684 (m-80) REVERT: g 81 GLU cc_start: 0.7599 (tt0) cc_final: 0.7200 (tm-30) REVERT: g 88 GLN cc_start: 0.5960 (pt0) cc_final: 0.5724 (mp10) REVERT: g 153 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7955 (mtt90) REVERT: g 155 GLU cc_start: 0.9324 (pt0) cc_final: 0.8724 (pp20) REVERT: g 157 TYR cc_start: 0.7591 (m-80) cc_final: 0.7359 (m-10) REVERT: h 33 GLN cc_start: 0.7879 (mp10) cc_final: 0.7423 (mt0) REVERT: j 2 LYS cc_start: 0.8083 (mttt) cc_final: 0.7806 (mttm) REVERT: j 12 LYS cc_start: 0.8124 (ttpt) cc_final: 0.7893 (pptt) REVERT: j 102 GLU cc_start: 0.7548 (mt-10) cc_final: 0.6983 (mt-10) REVERT: k 20 MET cc_start: 0.8488 (ttm) cc_final: 0.8164 (ttm) REVERT: k 58 LEU cc_start: 0.8676 (pt) cc_final: 0.8138 (mt) REVERT: k 98 ARG cc_start: 0.7938 (ttm110) cc_final: 0.7695 (ttm110) REVERT: l 7 SER cc_start: 0.8282 (p) cc_final: 0.7946 (t) REVERT: m 59 ARG cc_start: 0.7884 (mtt180) cc_final: 0.6685 (ptp-170) REVERT: n 75 ILE cc_start: 0.8431 (mm) cc_final: 0.8170 (mm) REVERT: o 80 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8044 (mt-10) REVERT: o 84 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8239 (mm-30) REVERT: o 93 ASP cc_start: 0.7761 (t0) cc_final: 0.7525 (t0) REVERT: p 11 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8662 (tm-30) REVERT: p 12 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.8006 (tt0) REVERT: p 70 VAL cc_start: 0.8582 (t) cc_final: 0.8257 (p) REVERT: p 110 ILE cc_start: 0.8507 (mt) cc_final: 0.8271 (mt) REVERT: p 111 LYS cc_start: 0.5853 (mmtt) cc_final: 0.4822 (ptmt) REVERT: q 75 SER cc_start: 0.8553 (m) cc_final: 0.8294 (m) REVERT: q 84 LYS cc_start: 0.7698 (ttpt) cc_final: 0.7421 (mtmt) REVERT: r 20 VAL cc_start: 0.7345 (OUTLIER) cc_final: 0.7116 (m) REVERT: r 37 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7780 (mm-30) REVERT: r 40 MET cc_start: 0.7505 (tmm) cc_final: 0.7186 (tmm) REVERT: r 84 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8300 (ptt-90) REVERT: s 57 ASN cc_start: 0.8254 (m-40) cc_final: 0.8017 (m-40) REVERT: s 92 ARG cc_start: 0.8094 (mtp180) cc_final: 0.7856 (mtm180) REVERT: t 8 LEU cc_start: 0.8675 (mt) cc_final: 0.8358 (tp) REVERT: t 42 GLU cc_start: 0.8429 (tp30) cc_final: 0.8192 (tp30) REVERT: t 79 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7891 (m-30) REVERT: t 88 LYS cc_start: 0.6409 (mmtt) cc_final: 0.6153 (tmtt) REVERT: u 101 GLU cc_start: 0.7472 (tp30) cc_final: 0.6971 (mm-30) REVERT: w 11 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6841 (mm-30) REVERT: w 20 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6920 (mt) REVERT: y 29 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7566 (mt-10) REVERT: y 68 LYS cc_start: 0.8781 (mmmm) cc_final: 0.7736 (pttt) REVERT: z 10 GLU cc_start: 0.4909 (OUTLIER) cc_final: 0.3648 (mt-10) outliers start: 388 outliers final: 284 residues processed: 1185 average time/residue: 1.2367 time to fit residues: 2549.5058 Evaluate side-chains 1216 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 308 poor density : 908 time to evaluate : 5.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 91 ARG Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 5 TYR Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 116 TYR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 26 LYS Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 112 ARG Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 44 GLU Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 60 ILE Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 51 GLN Chi-restraints excluded: chain S residue 13 HIS Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain T residue 20 ASN Chi-restraints excluded: chain T residue 50 PHE Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain T residue 81 GLN Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 23 GLU Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain 0 residue 14 THR Chi-restraints excluded: chain 0 residue 42 SER Chi-restraints excluded: chain 0 residue 52 SER Chi-restraints excluded: chain 0 residue 56 MET Chi-restraints excluded: chain 0 residue 58 VAL Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 2 residue 57 VAL Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 4 residue 5 ILE Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 33 LYS Chi-restraints excluded: chain 4 residue 43 VAL Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 2 LYS Chi-restraints excluded: chain 6 residue 30 VAL Chi-restraints excluded: chain 6 residue 44 VAL Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 8 residue 1 MET Chi-restraints excluded: chain 8 residue 2 LYS Chi-restraints excluded: chain 8 residue 20 ASP Chi-restraints excluded: chain 8 residue 22 VAL Chi-restraints excluded: chain c residue 6 CYS Chi-restraints excluded: chain c residue 63 ARG Chi-restraints excluded: chain c residue 116 ILE Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 140 THR Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 180 GLU Chi-restraints excluded: chain d residue 5 VAL Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 28 GLU Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 51 THR Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain d residue 168 GLU Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain d residue 171 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain d residue 193 VAL Chi-restraints excluded: chain d residue 200 ASP Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 33 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 55 SER Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 105 LEU Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 115 GLN Chi-restraints excluded: chain e residue 175 ILE Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 14 LYS Chi-restraints excluded: chain f residue 21 ASN Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 51 ASP Chi-restraints excluded: chain f residue 69 LYS Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 127 ASN Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain f residue 175 PHE Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 26 ILE Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 56 ASP Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 107 LEU Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 121 ILE Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain g residue 153 ARG Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 11 ASN Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 40 THR Chi-restraints excluded: chain h residue 91 PHE Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain h residue 147 VAL Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 31 GLU Chi-restraints excluded: chain j residue 44 TYR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 69 ARG Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 108 MET Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 117 SER Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 94 THR Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain m residue 13 HIS Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 106 ASP Chi-restraints excluded: chain m residue 108 VAL Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 47 VAL 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 o residue 4 LYS Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 8 LEU Chi-restraints excluded: chain p residue 12 GLN Chi-restraints excluded: chain p residue 20 PHE Chi-restraints excluded: chain p residue 30 VAL Chi-restraints excluded: chain p residue 48 ILE Chi-restraints excluded: chain p residue 64 ILE Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 112 GLU Chi-restraints excluded: chain p residue 115 ASN Chi-restraints excluded: chain q residue 6 ARG Chi-restraints excluded: chain q residue 40 ILE Chi-restraints excluded: chain q residue 52 GLN Chi-restraints excluded: chain q residue 74 ILE Chi-restraints excluded: chain q residue 80 ILE Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 70 GLU Chi-restraints excluded: chain r residue 84 ARG Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 24 ILE Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 25 GLU Chi-restraints excluded: chain t residue 70 HIS Chi-restraints excluded: chain t residue 78 SER Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain u residue 12 ILE Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 15 THR Chi-restraints excluded: chain u residue 45 HIS Chi-restraints excluded: chain u residue 82 ARG Chi-restraints excluded: chain w residue 7 GLU Chi-restraints excluded: chain w residue 20 LEU Chi-restraints excluded: chain w residue 29 ILE Chi-restraints excluded: chain w residue 45 ASP Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 53 LYS Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 64 VAL Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain y residue 30 SER Chi-restraints excluded: chain y residue 36 ILE Chi-restraints excluded: chain y residue 50 ASN Chi-restraints excluded: chain y residue 59 LEU Chi-restraints excluded: chain y residue 71 VAL Chi-restraints excluded: chain y residue 81 SER Chi-restraints excluded: chain z residue 10 GLU Chi-restraints excluded: chain z residue 18 TRP Chi-restraints excluded: chain z residue 25 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 596 optimal weight: 30.0000 chunk 384 optimal weight: 9.9990 chunk 575 optimal weight: 30.0000 chunk 290 optimal weight: 3.9990 chunk 189 optimal weight: 0.6980 chunk 186 optimal weight: 6.9990 chunk 612 optimal weight: 20.0000 chunk 656 optimal weight: 30.0000 chunk 476 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 757 optimal weight: 20.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 ASN ** N 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 HIS R 51 GLN S 13 HIS ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 74 HIS T 81 GLN ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 115 HIS p 52 ASN q 52 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.6856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 155858 Z= 0.206 Angle : 0.665 14.273 233415 Z= 0.340 Chirality : 0.038 0.289 29864 Planarity : 0.005 0.111 12326 Dihedral : 24.444 179.666 78630 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.99 % Favored : 91.49 % Rotamer: Outliers : 6.15 % Allowed : 26.40 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.09 % Twisted Proline : 0.55 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.11), residues: 5497 helix: -0.17 (0.13), residues: 1586 sheet: -1.56 (0.16), residues: 936 loop : -1.88 (0.11), residues: 2975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 103 HIS 0.032 0.001 HIS t 70 PHE 0.024 0.002 PHE B 31 TYR 0.027 0.002 TYR M 22 ARG 0.010 0.001 ARG t 73 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1247 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 966 time to evaluate : 6.201 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: B 10 LYS cc_start: 0.4912 (tmtt) cc_final: 0.4652 (mttt) REVERT: B 15 PHE cc_start: 0.5361 (m-80) cc_final: 0.5032 (m-80) REVERT: B 203 ASP cc_start: 0.4418 (p0) cc_final: 0.2905 (t0) REVERT: B 204 ASP cc_start: 0.5837 (m-30) cc_final: 0.5496 (m-30) REVERT: B 211 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6795 (mt) REVERT: C 17 TRP cc_start: 0.7364 (m-90) cc_final: 0.6707 (m-10) REVERT: C 27 GLU cc_start: 0.7456 (tp30) cc_final: 0.6533 (mp0) REVERT: C 71 ARG cc_start: 0.5590 (mtm-85) cc_final: 0.5295 (mmp80) REVERT: C 203 LYS cc_start: 0.6197 (pttt) cc_final: 0.4860 (tptt) REVERT: D 25 ARG cc_start: 0.3343 (ptp90) cc_final: 0.2274 (mtm180) REVERT: D 104 MET cc_start: 0.7760 (tpp) cc_final: 0.7435 (tpp) REVERT: D 198 LEU cc_start: 0.7646 (tp) cc_final: 0.7446 (tp) REVERT: F 9 MET cc_start: 0.7085 (mtp) cc_final: 0.6715 (mtt) REVERT: F 41 ASP cc_start: 0.6696 (t70) cc_final: 0.5851 (m-30) REVERT: F 45 ARG cc_start: 0.6304 (tpp80) cc_final: 0.5753 (tpp80) REVERT: G 30 MET cc_start: 0.6507 (ttp) cc_final: 0.5040 (mpp) REVERT: G 51 GLN cc_start: 0.6456 (tp40) cc_final: 0.5913 (mt0) REVERT: G 142 ARG cc_start: 0.6783 (ttp80) cc_final: 0.6506 (ttp80) REVERT: H 30 LYS cc_start: 0.8412 (tttt) cc_final: 0.7645 (pttt) REVERT: I 12 LYS cc_start: 0.6069 (ptpt) cc_final: 0.5676 (ptmm) REVERT: I 38 PHE cc_start: 0.6483 (OUTLIER) cc_final: 0.5897 (t80) REVERT: I 45 MET cc_start: 0.6698 (mtt) cc_final: 0.6298 (mmt) REVERT: I 59 LYS cc_start: 0.5125 (tmtt) cc_final: 0.4324 (mttt) REVERT: I 79 ARG cc_start: 0.7375 (ttp-170) cc_final: 0.6316 (mmm-85) REVERT: J 60 ASP cc_start: 0.7608 (m-30) cc_final: 0.7265 (t0) REVERT: J 64 GLN cc_start: 0.7923 (pm20) cc_final: 0.7719 (pm20) REVERT: K 15 VAL cc_start: 0.7002 (m) cc_final: 0.6732 (p) REVERT: L 8 ARG cc_start: 0.6377 (OUTLIER) cc_final: 0.5500 (mmt90) REVERT: L 95 HIS cc_start: 0.6614 (m90) cc_final: 0.6293 (m90) REVERT: L 115 LYS cc_start: 0.4872 (mttm) cc_final: 0.4454 (pttt) REVERT: M 21 ILE cc_start: 0.6888 (mp) cc_final: 0.6169 (mp) REVERT: M 26 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7453 (mptt) REVERT: M 103 THR cc_start: 0.8359 (m) cc_final: 0.7859 (t) REVERT: O 16 ARG cc_start: 0.5524 (mtt180) cc_final: 0.5216 (ptt-90) REVERT: Q 47 ASP cc_start: 0.6726 (t0) cc_final: 0.6222 (t0) REVERT: Q 56 ASP cc_start: 0.6359 (OUTLIER) cc_final: 0.6098 (p0) REVERT: Q 67 SER cc_start: 0.6706 (m) cc_final: 0.6152 (t) REVERT: T 27 MET cc_start: 0.8152 (tmm) cc_final: 0.7946 (tmm) REVERT: U 38 GLU cc_start: 0.7498 (tt0) cc_final: 0.7063 (pt0) REVERT: 0 44 LYS cc_start: 0.8832 (tptt) cc_final: 0.8356 (mptt) REVERT: 0 54 LYS cc_start: 0.8658 (tppt) cc_final: 0.8325 (tmtt) REVERT: 1 4 LYS cc_start: 0.7724 (tttp) cc_final: 0.7177 (mptt) REVERT: 1 25 GLN cc_start: 0.8090 (tt0) cc_final: 0.7480 (tp40) REVERT: 3 37 LYS cc_start: 0.8555 (mtmt) cc_final: 0.7823 (tptt) REVERT: 6 41 ARG cc_start: 0.8207 (mtt90) cc_final: 0.7602 (ptm160) REVERT: 8 1 MET cc_start: 0.7840 (ppp) cc_final: 0.7450 (ptm) REVERT: 8 36 ARG cc_start: 0.8149 (ttm-80) cc_final: 0.7789 (ttm170) REVERT: c 35 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8063 (tp30) REVERT: c 117 GLN cc_start: 0.8214 (tt0) cc_final: 0.7782 (tt0) REVERT: c 167 ARG cc_start: 0.8108 (ttm170) cc_final: 0.7462 (ttm170) REVERT: c 181 MET cc_start: 0.6731 (mtp) cc_final: 0.6247 (mmt) REVERT: c 261 LYS cc_start: 0.6935 (mttt) cc_final: 0.6467 (mtpp) REVERT: d 18 ASP cc_start: 0.8365 (m-30) cc_final: 0.7751 (p0) REVERT: d 28 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7903 (tm-30) REVERT: d 46 ARG cc_start: 0.6088 (mtp-110) cc_final: 0.4560 (ptp90) REVERT: d 187 LEU cc_start: 0.8838 (tp) cc_final: 0.8605 (tt) REVERT: e 23 PHE cc_start: 0.7277 (OUTLIER) cc_final: 0.6520 (m-80) REVERT: e 111 GLU cc_start: 0.6529 (mm-30) cc_final: 0.5845 (mm-30) REVERT: e 122 GLU cc_start: 0.7719 (tp30) cc_final: 0.7270 (tp30) REVERT: f 83 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.7710 (m-10) REVERT: f 140 GLU cc_start: 0.3145 (mm-30) cc_final: 0.2703 (tp30) REVERT: f 175 PHE cc_start: 0.5041 (OUTLIER) cc_final: 0.4517 (m-80) REVERT: g 32 GLU cc_start: 0.5575 (tm-30) cc_final: 0.5346 (tm-30) REVERT: g 77 ILE cc_start: 0.8026 (mm) cc_final: 0.7694 (tp) REVERT: g 81 GLU cc_start: 0.7644 (tt0) cc_final: 0.7269 (tm-30) REVERT: g 88 GLN cc_start: 0.6030 (pt0) cc_final: 0.5760 (mp10) REVERT: g 153 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7719 (mtt90) REVERT: g 155 GLU cc_start: 0.9197 (pt0) cc_final: 0.8597 (pp20) REVERT: g 157 TYR cc_start: 0.7410 (m-80) cc_final: 0.7196 (m-10) REVERT: g 160 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7516 (ttmm) REVERT: h 33 GLN cc_start: 0.7728 (mp10) cc_final: 0.7377 (mt0) REVERT: j 2 LYS cc_start: 0.7940 (mttt) cc_final: 0.7661 (mttm) REVERT: j 12 LYS cc_start: 0.8118 (ttpt) cc_final: 0.7895 (pptt) REVERT: j 90 GLU cc_start: 0.6676 (tp30) cc_final: 0.6367 (tp30) REVERT: k 7 MET cc_start: 0.7847 (mmm) cc_final: 0.7425 (mmt) REVERT: k 58 LEU cc_start: 0.8603 (pt) cc_final: 0.8042 (mt) REVERT: k 98 ARG cc_start: 0.7818 (ttm110) cc_final: 0.7485 (ttm110) REVERT: m 53 MET cc_start: 0.7942 (mtt) cc_final: 0.7402 (mtp) REVERT: m 59 ARG cc_start: 0.7829 (mtt180) cc_final: 0.6673 (ptp-170) REVERT: m 115 GLU cc_start: 0.8054 (tt0) cc_final: 0.7804 (tt0) REVERT: m 119 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.7743 (mt) REVERT: n 72 ASP cc_start: 0.8412 (t0) cc_final: 0.8201 (t0) REVERT: n 75 ILE cc_start: 0.8304 (mm) cc_final: 0.8092 (mm) REVERT: n 112 TYR cc_start: 0.8401 (m-80) cc_final: 0.8142 (m-80) REVERT: p 11 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8591 (tm-30) REVERT: p 12 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.6628 (mp10) REVERT: p 50 ILE cc_start: 0.8750 (mm) cc_final: 0.8248 (mm) REVERT: p 70 VAL cc_start: 0.8533 (t) cc_final: 0.8190 (p) REVERT: p 110 ILE cc_start: 0.8404 (mt) cc_final: 0.8159 (mt) REVERT: p 111 LYS cc_start: 0.5973 (mmtt) cc_final: 0.5036 (ptmt) REVERT: q 84 LYS cc_start: 0.7653 (ttpt) cc_final: 0.7291 (mtmt) REVERT: r 40 MET cc_start: 0.7234 (tmm) cc_final: 0.6923 (tmm) REVERT: r 84 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8315 (ptt-90) REVERT: s 57 ASN cc_start: 0.8071 (m-40) cc_final: 0.7854 (m-40) REVERT: t 8 LEU cc_start: 0.8718 (mt) cc_final: 0.8423 (tp) REVERT: t 79 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7740 (m-30) REVERT: u 101 GLU cc_start: 0.7466 (tp30) cc_final: 0.7067 (mm-30) REVERT: w 11 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6736 (mm-30) REVERT: w 20 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6928 (mt) REVERT: w 51 GLN cc_start: 0.8543 (pp30) cc_final: 0.8272 (tm-30) REVERT: y 29 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7670 (mt-10) REVERT: y 68 LYS cc_start: 0.8650 (mmmm) cc_final: 0.7609 (pttt) REVERT: z 10 GLU cc_start: 0.4704 (OUTLIER) cc_final: 0.3358 (mt-10) outliers start: 281 outliers final: 223 residues processed: 1137 average time/residue: 1.2384 time to fit residues: 2468.3559 Evaluate side-chains 1171 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 931 time to evaluate : 5.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 91 ARG Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 5 TYR Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 126 PHE Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 116 TYR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 26 LYS Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 112 ARG Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 44 GLU Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 30 HIS Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 51 GLN Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain T residue 50 PHE Chi-restraints excluded: chain T residue 67 HIS Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain 0 residue 14 THR Chi-restraints excluded: chain 0 residue 52 SER Chi-restraints excluded: chain 0 residue 56 MET Chi-restraints excluded: chain 0 residue 58 VAL Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 2 residue 10 THR Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 2 residue 57 VAL Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 6 residue 30 VAL Chi-restraints excluded: chain 6 residue 44 VAL Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 8 residue 20 ASP Chi-restraints excluded: chain 8 residue 28 SER Chi-restraints excluded: chain c residue 6 CYS Chi-restraints excluded: chain c residue 114 ASP Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 140 THR Chi-restraints excluded: chain c residue 180 GLU Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 28 GLU Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 51 THR Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain d residue 168 GLU Chi-restraints excluded: chain d residue 171 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain d residue 193 VAL Chi-restraints excluded: chain d residue 200 ASP Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 23 PHE Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 55 SER Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 115 GLN Chi-restraints excluded: chain e residue 175 ILE Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 127 ASN Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain f residue 175 PHE Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 56 ASP Chi-restraints excluded: chain g residue 107 LEU Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 121 ILE Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain g residue 153 ARG Chi-restraints excluded: chain g residue 160 LYS Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 11 ASN Chi-restraints excluded: chain h residue 30 LEU Chi-restraints excluded: chain h residue 40 THR Chi-restraints excluded: chain h residue 91 PHE Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain h residue 147 VAL Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 69 ARG Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 94 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 13 HIS 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 m residue 129 THR 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 o residue 4 LYS Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain p residue 8 LEU Chi-restraints excluded: chain p residue 12 GLN Chi-restraints excluded: chain p residue 20 PHE Chi-restraints excluded: chain p residue 30 VAL Chi-restraints excluded: chain p residue 48 ILE Chi-restraints excluded: chain p residue 64 ILE Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 112 GLU Chi-restraints excluded: chain p residue 115 ASN Chi-restraints excluded: chain q residue 52 GLN Chi-restraints excluded: chain q residue 74 ILE Chi-restraints excluded: chain q residue 80 ILE Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 84 ARG Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 24 ILE Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 25 GLU Chi-restraints excluded: chain t residue 78 SER Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain u residue 15 THR Chi-restraints excluded: chain u residue 82 ARG Chi-restraints excluded: chain w residue 7 GLU Chi-restraints excluded: chain w residue 17 SER Chi-restraints excluded: chain w residue 20 LEU Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 53 LYS Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 64 VAL Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 50 ASN Chi-restraints excluded: chain y residue 59 LEU Chi-restraints excluded: chain y residue 71 VAL Chi-restraints excluded: chain z residue 10 GLU Chi-restraints excluded: chain z residue 25 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 876 optimal weight: 30.0000 chunk 923 optimal weight: 20.0000 chunk 842 optimal weight: 10.0000 chunk 898 optimal weight: 10.0000 chunk 540 optimal weight: 30.0000 chunk 391 optimal weight: 6.9990 chunk 705 optimal weight: 10.0000 chunk 275 optimal weight: 1.9990 chunk 811 optimal weight: 30.0000 chunk 849 optimal weight: 20.0000 chunk 895 optimal weight: 10.0000 overall best weight: 7.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 HIS ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 HIS R 51 GLN ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 130 GLN ** d 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 195 GLN ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 87 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.7002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 155858 Z= 0.325 Angle : 0.766 14.793 233415 Z= 0.384 Chirality : 0.042 0.329 29864 Planarity : 0.006 0.114 12326 Dihedral : 24.509 179.752 78630 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.81 % Favored : 89.67 % Rotamer: Outliers : 6.82 % Allowed : 25.98 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.09 % Twisted Proline : 0.55 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.11), residues: 5497 helix: -0.36 (0.13), residues: 1596 sheet: -1.78 (0.16), residues: 964 loop : -1.96 (0.11), residues: 2937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 103 HIS 0.011 0.002 HIS Q 30 PHE 0.024 0.002 PHE N 76 TYR 0.026 0.002 TYR R 50 ARG 0.009 0.001 ARG q 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1241 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 929 time to evaluate : 6.243 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: B 10 LYS cc_start: 0.5134 (tmtt) cc_final: 0.4734 (mttt) REVERT: B 15 PHE cc_start: 0.5451 (m-80) cc_final: 0.5100 (m-80) REVERT: B 203 ASP cc_start: 0.4506 (p0) cc_final: 0.2931 (t0) REVERT: B 211 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6892 (mt) REVERT: C 17 TRP cc_start: 0.7325 (m-90) cc_final: 0.6507 (m-10) REVERT: C 27 GLU cc_start: 0.7792 (tp30) cc_final: 0.6796 (mp0) REVERT: C 71 ARG cc_start: 0.5615 (mtm-85) cc_final: 0.5315 (mmp80) REVERT: C 203 LYS cc_start: 0.6348 (pttt) cc_final: 0.5084 (tptt) REVERT: D 25 ARG cc_start: 0.3171 (ptp90) cc_final: 0.2060 (mtm180) REVERT: F 9 MET cc_start: 0.7176 (mtp) cc_final: 0.6724 (mtt) REVERT: F 41 ASP cc_start: 0.6933 (t70) cc_final: 0.6123 (m-30) REVERT: F 45 ARG cc_start: 0.6473 (tpp80) cc_final: 0.5954 (tpp80) REVERT: F 49 TYR cc_start: 0.8338 (p90) cc_final: 0.7778 (p90) REVERT: F 56 LYS cc_start: 0.6145 (pttm) cc_final: 0.5454 (ptmt) REVERT: G 30 MET cc_start: 0.6629 (ttp) cc_final: 0.5041 (mpp) REVERT: G 51 GLN cc_start: 0.6427 (tp40) cc_final: 0.5818 (mt0) REVERT: H 26 MET cc_start: 0.3915 (ptp) cc_final: 0.3665 (ptp) REVERT: H 30 LYS cc_start: 0.8469 (tttt) cc_final: 0.7691 (pttp) REVERT: I 12 LYS cc_start: 0.6057 (ptpt) cc_final: 0.5689 (ptmm) REVERT: I 38 PHE cc_start: 0.6180 (OUTLIER) cc_final: 0.5579 (t80) REVERT: I 45 MET cc_start: 0.6770 (mtt) cc_final: 0.6407 (mmt) REVERT: I 79 ARG cc_start: 0.7324 (ttp-170) cc_final: 0.6407 (mmm-85) REVERT: J 60 ASP cc_start: 0.7717 (m-30) cc_final: 0.7385 (t0) REVERT: J 64 GLN cc_start: 0.7993 (pm20) cc_final: 0.7776 (pm20) REVERT: L 8 ARG cc_start: 0.6475 (OUTLIER) cc_final: 0.5691 (mmt90) REVERT: L 95 HIS cc_start: 0.6699 (m90) cc_final: 0.6066 (m90) REVERT: M 26 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7454 (mptt) REVERT: M 103 THR cc_start: 0.7916 (m) cc_final: 0.7530 (t) REVERT: O 16 ARG cc_start: 0.5528 (mtt180) cc_final: 0.5225 (ptt-90) REVERT: Q 47 ASP cc_start: 0.6804 (t0) cc_final: 0.6358 (t0) REVERT: Q 67 SER cc_start: 0.6183 (m) cc_final: 0.5689 (t) REVERT: U 4 LYS cc_start: 0.6007 (tttt) cc_final: 0.5784 (tttp) REVERT: U 38 GLU cc_start: 0.7523 (tt0) cc_final: 0.7125 (pt0) REVERT: 0 44 LYS cc_start: 0.8875 (tptt) cc_final: 0.8384 (mptt) REVERT: 0 54 LYS cc_start: 0.8682 (tppt) cc_final: 0.8396 (tmtt) REVERT: 1 4 LYS cc_start: 0.7866 (tttp) cc_final: 0.7268 (mptt) REVERT: 1 25 GLN cc_start: 0.8250 (tt0) cc_final: 0.7486 (tp40) REVERT: 3 37 LYS cc_start: 0.8600 (mtmt) cc_final: 0.7861 (tptt) REVERT: 4 33 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.7042 (mmtp) REVERT: 6 41 ARG cc_start: 0.8315 (mtt90) cc_final: 0.7705 (ptm160) REVERT: 7 15 LYS cc_start: 0.7156 (tttt) cc_final: 0.6718 (mmtt) REVERT: 8 1 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7556 (ptm) REVERT: c 35 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8104 (tp30) REVERT: c 117 GLN cc_start: 0.8237 (tt0) cc_final: 0.7888 (tp40) REVERT: c 167 ARG cc_start: 0.8175 (ttm170) cc_final: 0.7923 (ttm170) REVERT: c 181 MET cc_start: 0.6813 (mtp) cc_final: 0.6292 (mmt) REVERT: c 261 LYS cc_start: 0.6954 (mttt) cc_final: 0.6515 (mtpp) REVERT: d 28 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8004 (tm-30) REVERT: d 46 ARG cc_start: 0.6137 (mtp-110) cc_final: 0.4659 (ptp90) REVERT: e 23 PHE cc_start: 0.7286 (OUTLIER) cc_final: 0.6605 (m-80) REVERT: e 111 GLU cc_start: 0.6399 (mm-30) cc_final: 0.5900 (mm-30) REVERT: e 122 GLU cc_start: 0.7782 (tp30) cc_final: 0.7284 (tp30) REVERT: e 148 ILE cc_start: 0.7966 (mm) cc_final: 0.7680 (mt) REVERT: f 83 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.7694 (m-10) REVERT: f 175 PHE cc_start: 0.5246 (OUTLIER) cc_final: 0.4757 (m-80) REVERT: g 77 ILE cc_start: 0.8023 (mm) cc_final: 0.7694 (tp) REVERT: g 81 GLU cc_start: 0.7588 (tt0) cc_final: 0.7241 (tm-30) REVERT: g 88 GLN cc_start: 0.6173 (pt0) cc_final: 0.5774 (mp10) REVERT: g 153 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7900 (mtt90) REVERT: g 155 GLU cc_start: 0.9243 (pt0) cc_final: 0.8636 (pp20) REVERT: g 157 TYR cc_start: 0.7471 (m-80) cc_final: 0.7245 (m-10) REVERT: g 160 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7501 (ttmm) REVERT: h 33 GLN cc_start: 0.7776 (mp10) cc_final: 0.7415 (mt0) REVERT: j 2 LYS cc_start: 0.7898 (mttt) cc_final: 0.7650 (mttm) REVERT: j 41 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.8553 (mtpt) REVERT: j 102 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6969 (mt-10) REVERT: k 7 MET cc_start: 0.8077 (mmm) cc_final: 0.7763 (mmt) REVERT: k 58 LEU cc_start: 0.8665 (pt) cc_final: 0.8111 (mt) REVERT: k 98 ARG cc_start: 0.7822 (ttm110) cc_final: 0.7487 (ttm110) REVERT: m 53 MET cc_start: 0.7872 (mtt) cc_final: 0.7319 (mtp) REVERT: m 59 ARG cc_start: 0.7883 (mtt180) cc_final: 0.6710 (ptp-170) REVERT: m 119 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.7665 (mt) REVERT: n 72 ASP cc_start: 0.8257 (t0) cc_final: 0.8040 (t0) REVERT: o 93 ASP cc_start: 0.7557 (t0) cc_final: 0.7336 (t0) REVERT: p 11 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8570 (tm-30) REVERT: p 12 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.6622 (mp10) REVERT: p 50 ILE cc_start: 0.8791 (mm) cc_final: 0.8468 (mm) REVERT: p 70 VAL cc_start: 0.8585 (t) cc_final: 0.8262 (p) REVERT: p 110 ILE cc_start: 0.8484 (mt) cc_final: 0.8231 (mt) REVERT: p 111 LYS cc_start: 0.5987 (mmtt) cc_final: 0.5016 (ptmt) REVERT: q 84 LYS cc_start: 0.7680 (ttpt) cc_final: 0.7450 (mtmt) REVERT: q 87 SER cc_start: 0.9108 (m) cc_final: 0.8862 (t) REVERT: r 20 VAL cc_start: 0.7562 (OUTLIER) cc_final: 0.7322 (m) REVERT: r 37 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7407 (mm-30) REVERT: r 84 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8311 (ptt-90) REVERT: s 57 ASN cc_start: 0.8172 (m-40) cc_final: 0.7961 (m-40) REVERT: t 8 LEU cc_start: 0.8665 (mt) cc_final: 0.8330 (tp) REVERT: t 79 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7852 (m-30) REVERT: u 101 GLU cc_start: 0.7592 (tp30) cc_final: 0.7072 (mm-30) REVERT: w 11 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6868 (mm-30) REVERT: w 20 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6953 (mt) REVERT: w 51 GLN cc_start: 0.8501 (pp30) cc_final: 0.8049 (pp30) REVERT: y 29 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7633 (mt-10) REVERT: y 68 LYS cc_start: 0.8685 (mmmm) cc_final: 0.7646 (pttt) REVERT: z 10 GLU cc_start: 0.4964 (OUTLIER) cc_final: 0.3564 (mt-10) outliers start: 312 outliers final: 261 residues processed: 1122 average time/residue: 1.2050 time to fit residues: 2372.6939 Evaluate side-chains 1199 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 918 time to evaluate : 8.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 91 ARG Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 5 TYR Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 126 PHE Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 116 TYR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 26 LYS Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 112 ARG Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 44 GLU Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 51 GLN Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain T residue 50 PHE Chi-restraints excluded: chain T residue 67 HIS Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain 0 residue 14 THR Chi-restraints excluded: chain 0 residue 42 SER Chi-restraints excluded: chain 0 residue 52 SER Chi-restraints excluded: chain 0 residue 56 MET Chi-restraints excluded: chain 0 residue 58 VAL Chi-restraints excluded: chain 1 residue 6 LEU Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 2 residue 10 THR Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 2 residue 57 VAL Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 4 residue 5 ILE Chi-restraints excluded: chain 4 residue 33 LYS Chi-restraints excluded: chain 6 residue 30 VAL Chi-restraints excluded: chain 6 residue 44 VAL Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 8 residue 1 MET Chi-restraints excluded: chain 8 residue 2 LYS Chi-restraints excluded: chain 8 residue 20 ASP Chi-restraints excluded: chain 8 residue 22 VAL Chi-restraints excluded: chain 8 residue 28 SER Chi-restraints excluded: chain c residue 6 CYS Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 140 THR Chi-restraints excluded: chain c residue 180 GLU Chi-restraints excluded: chain c residue 228 VAL Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 28 GLU Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 51 THR Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain d residue 168 GLU Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain d residue 171 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain d residue 193 VAL Chi-restraints excluded: chain d residue 200 ASP Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 23 PHE Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 55 SER Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 115 GLN Chi-restraints excluded: chain e residue 159 LEU Chi-restraints excluded: chain e residue 175 ILE Chi-restraints excluded: chain f residue 14 LYS Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 69 LYS Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 127 ASN Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain f residue 175 PHE Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 56 ASP Chi-restraints excluded: chain g residue 107 LEU Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 121 ILE Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain g residue 151 TYR Chi-restraints excluded: chain g residue 153 ARG Chi-restraints excluded: chain g residue 160 LYS Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 11 ASN Chi-restraints excluded: chain h residue 40 THR Chi-restraints excluded: chain h residue 91 PHE Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain h residue 147 VAL Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 25 LEU Chi-restraints excluded: chain j residue 31 GLU Chi-restraints excluded: chain j residue 41 LYS Chi-restraints excluded: chain j residue 44 TYR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 69 ARG Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 117 SER Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 94 THR Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain m residue 13 HIS Chi-restraints excluded: chain m residue 25 ASP 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 m residue 129 THR 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 o residue 4 LYS Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 8 LEU Chi-restraints excluded: chain p residue 12 GLN Chi-restraints excluded: chain p residue 20 PHE Chi-restraints excluded: chain p residue 30 VAL Chi-restraints excluded: chain p residue 48 ILE Chi-restraints excluded: chain p residue 64 ILE Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 112 GLU Chi-restraints excluded: chain p residue 115 ASN Chi-restraints excluded: chain q residue 6 ARG Chi-restraints excluded: chain q residue 40 ILE Chi-restraints excluded: chain q residue 74 ILE Chi-restraints excluded: chain q residue 80 ILE Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 84 ARG Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 24 ILE Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 25 GLU Chi-restraints excluded: chain t residue 70 HIS Chi-restraints excluded: chain t residue 78 SER Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain u residue 12 ILE Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 15 THR Chi-restraints excluded: chain w residue 7 GLU Chi-restraints excluded: chain w residue 17 SER Chi-restraints excluded: chain w residue 20 LEU Chi-restraints excluded: chain w residue 29 ILE Chi-restraints excluded: chain w residue 45 ASP Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 53 LYS Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 64 VAL Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 59 LEU Chi-restraints excluded: chain y residue 71 VAL Chi-restraints excluded: chain y residue 81 SER Chi-restraints excluded: chain z residue 10 GLU Chi-restraints excluded: chain z residue 25 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 589 optimal weight: 20.0000 chunk 949 optimal weight: 10.0000 chunk 579 optimal weight: 40.0000 chunk 450 optimal weight: 6.9990 chunk 660 optimal weight: 20.0000 chunk 996 optimal weight: 20.0000 chunk 916 optimal weight: 50.0000 chunk 793 optimal weight: 20.0000 chunk 82 optimal weight: 8.9990 chunk 612 optimal weight: 20.0000 chunk 486 optimal weight: 9.9990 overall best weight: 11.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 ASN ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 GLN P 79 ASN ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 74 HIS ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 130 GLN ** e 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 41 GLN q 59 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.7326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.144 155858 Z= 0.459 Angle : 0.941 18.602 233415 Z= 0.464 Chirality : 0.048 0.345 29864 Planarity : 0.007 0.116 12326 Dihedral : 24.819 179.248 78630 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.53 % Allowed : 11.12 % Favored : 88.36 % Rotamer: Outliers : 7.06 % Allowed : 25.90 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.09 % Twisted Proline : 0.55 % Twisted General : 0.06 % 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: -2.67 (0.10), residues: 5497 helix: -0.87 (0.12), residues: 1588 sheet: -1.89 (0.16), residues: 935 loop : -2.28 (0.10), residues: 2974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP B 103 HIS 0.010 0.002 HIS D 119 PHE 0.029 0.003 PHE N 76 TYR 0.033 0.003 TYR M 22 ARG 0.030 0.001 ARG R 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1240 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 917 time to evaluate : 6.042 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: B 67 LEU cc_start: 0.4396 (OUTLIER) cc_final: 0.4034 (tt) REVERT: B 203 ASP cc_start: 0.4352 (p0) cc_final: 0.2536 (t70) REVERT: B 204 ASP cc_start: 0.5169 (m-30) cc_final: 0.4743 (m-30) REVERT: B 221 ARG cc_start: 0.3991 (mtt-85) cc_final: 0.3753 (ptp-170) REVERT: C 17 TRP cc_start: 0.7312 (m-90) cc_final: 0.6548 (m-10) REVERT: C 71 ARG cc_start: 0.5678 (mtm-85) cc_final: 0.5387 (mmp80) REVERT: D 3 TYR cc_start: 0.6108 (t80) cc_final: 0.5839 (t80) REVERT: D 25 ARG cc_start: 0.3611 (ptp90) cc_final: 0.2379 (mtm180) REVERT: F 9 MET cc_start: 0.7345 (mtp) cc_final: 0.6820 (mtt) REVERT: F 41 ASP cc_start: 0.6908 (t70) cc_final: 0.6317 (m-30) REVERT: F 49 TYR cc_start: 0.8368 (p90) cc_final: 0.7805 (p90) REVERT: F 56 LYS cc_start: 0.6356 (pttm) cc_final: 0.5675 (ptmt) REVERT: H 30 LYS cc_start: 0.8569 (tttt) cc_final: 0.7806 (pttp) REVERT: H 63 LYS cc_start: 0.6195 (ptmt) cc_final: 0.5678 (ptmt) REVERT: I 12 LYS cc_start: 0.6105 (ptpt) cc_final: 0.5769 (ptmm) REVERT: I 38 PHE cc_start: 0.6065 (OUTLIER) cc_final: 0.5726 (t80) REVERT: I 45 MET cc_start: 0.6860 (mtt) cc_final: 0.6443 (mmt) REVERT: I 79 ARG cc_start: 0.7396 (ttp-170) cc_final: 0.6511 (mmm-85) REVERT: L 8 ARG cc_start: 0.6364 (OUTLIER) cc_final: 0.6010 (mmt90) REVERT: L 95 HIS cc_start: 0.6886 (m90) cc_final: 0.6322 (m90) REVERT: L 115 LYS cc_start: 0.4911 (mttm) cc_final: 0.4551 (pttt) REVERT: M 21 ILE cc_start: 0.6376 (mp) cc_final: 0.5982 (mm) REVERT: M 26 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7503 (mptt) REVERT: M 65 GLU cc_start: 0.7295 (mm-30) cc_final: 0.7047 (mm-30) REVERT: O 16 ARG cc_start: 0.5486 (mtt180) cc_final: 0.5233 (ptt-90) REVERT: Q 47 ASP cc_start: 0.6818 (t0) cc_final: 0.6429 (t0) REVERT: R 51 GLN cc_start: 0.8284 (tp40) cc_final: 0.7942 (tm-30) REVERT: R 56 ARG cc_start: 0.8524 (ttm170) cc_final: 0.8284 (ttm170) REVERT: S 9 PHE cc_start: 0.6761 (t80) cc_final: 0.6362 (t80) REVERT: U 38 GLU cc_start: 0.7480 (tt0) cc_final: 0.7104 (pt0) REVERT: 0 44 LYS cc_start: 0.8900 (tptt) cc_final: 0.8431 (mptt) REVERT: 1 4 LYS cc_start: 0.7953 (tttp) cc_final: 0.7345 (mptt) REVERT: 1 23 ARG cc_start: 0.6828 (ttm170) cc_final: 0.6260 (ttt-90) REVERT: 1 25 GLN cc_start: 0.8361 (tt0) cc_final: 0.7396 (tp40) REVERT: 1 45 GLN cc_start: 0.7666 (mt0) cc_final: 0.7300 (mt0) REVERT: 3 37 LYS cc_start: 0.8608 (mtmt) cc_final: 0.8212 (mtpt) REVERT: 4 33 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6960 (mmtp) REVERT: 6 41 ARG cc_start: 0.8361 (mtt90) cc_final: 0.7804 (ptm160) REVERT: 8 1 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7563 (ptm) REVERT: c 35 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8123 (tp30) REVERT: c 117 GLN cc_start: 0.8289 (tt0) cc_final: 0.8010 (tp-100) REVERT: c 167 ARG cc_start: 0.8228 (ttm170) cc_final: 0.7462 (ttm170) REVERT: c 171 TYR cc_start: 0.8349 (m-10) cc_final: 0.8146 (m-10) REVERT: c 181 MET cc_start: 0.7023 (mtp) cc_final: 0.6528 (mmt) REVERT: c 261 LYS cc_start: 0.7130 (mttt) cc_final: 0.6553 (mtpp) REVERT: d 28 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.7913 (tm-30) REVERT: d 46 ARG cc_start: 0.6185 (mtp-110) cc_final: 0.4671 (ptp90) REVERT: e 23 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.6891 (m-80) REVERT: e 122 GLU cc_start: 0.7944 (tp30) cc_final: 0.7574 (tp30) REVERT: e 148 ILE cc_start: 0.8247 (mm) cc_final: 0.7983 (mt) REVERT: f 83 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.7724 (m-10) REVERT: f 87 CYS cc_start: 0.5865 (p) cc_final: 0.5238 (p) REVERT: f 175 PHE cc_start: 0.5268 (OUTLIER) cc_final: 0.4659 (m-80) REVERT: g 77 ILE cc_start: 0.7962 (mm) cc_final: 0.7619 (tp) REVERT: g 88 GLN cc_start: 0.6084 (pt0) cc_final: 0.5786 (mp10) REVERT: g 155 GLU cc_start: 0.9271 (pt0) cc_final: 0.8653 (pp20) REVERT: g 160 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7495 (ttmm) REVERT: h 33 GLN cc_start: 0.7901 (mp10) cc_final: 0.7539 (mt0) REVERT: j 2 LYS cc_start: 0.7951 (mttt) cc_final: 0.7676 (mttm) REVERT: j 9 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7145 (mp0) REVERT: j 41 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.8591 (mtpt) REVERT: j 102 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6796 (mt-10) REVERT: j 118 MET cc_start: 0.7929 (mmt) cc_final: 0.7705 (mmt) REVERT: k 7 MET cc_start: 0.8305 (mmm) cc_final: 0.7675 (mmt) REVERT: k 58 LEU cc_start: 0.8736 (pt) cc_final: 0.8144 (mt) REVERT: l 7 SER cc_start: 0.8305 (p) cc_final: 0.7958 (t) REVERT: l 21 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8882 (mmp80) REVERT: m 13 HIS cc_start: 0.8778 (OUTLIER) cc_final: 0.8255 (m-70) REVERT: m 59 ARG cc_start: 0.7832 (mtt180) cc_final: 0.6606 (ptp-170) REVERT: m 65 ILE cc_start: 0.9042 (mt) cc_final: 0.8813 (mt) REVERT: o 93 ASP cc_start: 0.8168 (t0) cc_final: 0.7882 (t0) REVERT: p 11 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8635 (tm-30) REVERT: p 12 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7912 (tt0) REVERT: p 50 ILE cc_start: 0.8860 (mm) cc_final: 0.8528 (mm) REVERT: p 70 VAL cc_start: 0.8663 (t) cc_final: 0.8348 (p) REVERT: p 110 ILE cc_start: 0.8545 (mt) cc_final: 0.8310 (mt) REVERT: p 111 LYS cc_start: 0.5802 (mmtt) cc_final: 0.4918 (ptmt) REVERT: q 87 SER cc_start: 0.9148 (m) cc_final: 0.8709 (t) REVERT: r 20 VAL cc_start: 0.7562 (OUTLIER) cc_final: 0.7332 (m) REVERT: r 37 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7407 (mm-30) REVERT: r 40 MET cc_start: 0.7590 (tmm) cc_final: 0.7189 (tmm) REVERT: r 84 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8354 (ptt-90) REVERT: t 8 LEU cc_start: 0.8581 (mt) cc_final: 0.8307 (tp) REVERT: t 69 ARG cc_start: 0.5791 (ttm-80) cc_final: 0.5491 (mtm110) REVERT: t 79 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7888 (m-30) REVERT: t 88 LYS cc_start: 0.6382 (mmtt) cc_final: 0.6051 (tmtt) REVERT: u 101 GLU cc_start: 0.7582 (tp30) cc_final: 0.7024 (mm-30) REVERT: w 11 GLU cc_start: 0.7329 (mm-30) cc_final: 0.6936 (mm-30) REVERT: w 20 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6953 (mt) REVERT: w 41 GLU cc_start: 0.8642 (pt0) cc_final: 0.8418 (pt0) REVERT: w 51 GLN cc_start: 0.8598 (pp30) cc_final: 0.8089 (pp30) REVERT: y 29 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7568 (mt-10) REVERT: y 68 LYS cc_start: 0.8705 (mmmm) cc_final: 0.7692 (pttt) REVERT: z 10 GLU cc_start: 0.4407 (OUTLIER) cc_final: 0.3324 (mt-10) outliers start: 323 outliers final: 265 residues processed: 1119 average time/residue: 1.2371 time to fit residues: 2415.9103 Evaluate side-chains 1180 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 895 time to evaluate : 6.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 91 ARG Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 5 TYR Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 20 GLN Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 116 TYR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 26 LYS Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 112 ARG Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 44 GLU Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain T residue 50 PHE Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain 0 residue 14 THR Chi-restraints excluded: chain 0 residue 42 SER Chi-restraints excluded: chain 0 residue 52 SER Chi-restraints excluded: chain 0 residue 56 MET Chi-restraints excluded: chain 0 residue 58 VAL Chi-restraints excluded: chain 1 residue 6 LEU Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 2 residue 10 THR Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 2 residue 57 VAL Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 4 residue 5 ILE Chi-restraints excluded: chain 4 residue 33 LYS Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 2 LYS Chi-restraints excluded: chain 6 residue 30 VAL Chi-restraints excluded: chain 6 residue 44 VAL Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 8 residue 1 MET Chi-restraints excluded: chain 8 residue 2 LYS Chi-restraints excluded: chain 8 residue 20 ASP Chi-restraints excluded: chain 8 residue 22 VAL Chi-restraints excluded: chain 8 residue 28 SER Chi-restraints excluded: chain c residue 6 CYS Chi-restraints excluded: chain c residue 114 ASP Chi-restraints excluded: chain c residue 140 THR Chi-restraints excluded: chain c residue 180 GLU Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 28 GLU Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 51 THR Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain d residue 168 GLU Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain d residue 171 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain d residue 193 VAL Chi-restraints excluded: chain d residue 200 ASP Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 23 PHE Chi-restraints excluded: chain e residue 33 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 52 VAL Chi-restraints excluded: chain e residue 55 SER Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 105 LEU Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 115 GLN Chi-restraints excluded: chain e residue 159 LEU Chi-restraints excluded: chain e residue 175 ILE Chi-restraints excluded: chain f residue 14 LYS Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 69 LYS Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 127 ASN Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain f residue 175 PHE Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 56 ASP Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain g residue 107 LEU Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 121 ILE Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain g residue 160 LYS Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain h residue 11 ASN Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 40 THR Chi-restraints excluded: chain h residue 91 PHE Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain h residue 147 VAL Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 31 GLU Chi-restraints excluded: chain j residue 41 LYS Chi-restraints excluded: chain j residue 44 TYR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 69 ARG Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 108 MET Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 117 SER Chi-restraints excluded: chain l residue 21 ARG Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain m residue 13 HIS Chi-restraints excluded: chain m residue 25 ASP 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 m residue 129 THR 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 o residue 4 LYS Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain p residue 8 LEU Chi-restraints excluded: chain p residue 12 GLN Chi-restraints excluded: chain p residue 20 PHE Chi-restraints excluded: chain p residue 30 VAL Chi-restraints excluded: chain p residue 48 ILE Chi-restraints excluded: chain p residue 64 ILE Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 112 GLU Chi-restraints excluded: chain p residue 115 ASN Chi-restraints excluded: chain q residue 6 ARG Chi-restraints excluded: chain q residue 40 ILE Chi-restraints excluded: chain q residue 74 ILE Chi-restraints excluded: chain q residue 80 ILE Chi-restraints excluded: chain q residue 117 LEU Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 70 GLU Chi-restraints excluded: chain r residue 84 ARG Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 24 ILE Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 25 GLU Chi-restraints excluded: chain t residue 70 HIS Chi-restraints excluded: chain t residue 78 SER Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain u residue 12 ILE Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 15 THR Chi-restraints excluded: chain w residue 7 GLU Chi-restraints excluded: chain w residue 17 SER Chi-restraints excluded: chain w residue 20 LEU Chi-restraints excluded: chain w residue 29 ILE Chi-restraints excluded: chain w residue 45 ASP Chi-restraints excluded: chain w residue 53 LYS Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 64 VAL Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain y residue 36 ILE Chi-restraints excluded: chain y residue 59 LEU Chi-restraints excluded: chain y residue 71 VAL Chi-restraints excluded: chain y residue 81 SER Chi-restraints excluded: chain z residue 10 GLU Chi-restraints excluded: chain z residue 25 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 630 optimal weight: 20.0000 chunk 845 optimal weight: 10.0000 chunk 243 optimal weight: 6.9990 chunk 731 optimal weight: 30.0000 chunk 117 optimal weight: 4.9990 chunk 220 optimal weight: 5.9990 chunk 794 optimal weight: 10.0000 chunk 332 optimal weight: 2.9990 chunk 815 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN D 40 HIS D 130 ASN D 135 GLN ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 HIS R 51 GLN ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 130 GLN ** e 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 41 GLN w 87 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.128039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.104930 restraints weight = 391716.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.106071 restraints weight = 231973.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.105883 restraints weight = 141157.799| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.7387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 155858 Z= 0.242 Angle : 0.711 14.482 233415 Z= 0.361 Chirality : 0.039 0.370 29864 Planarity : 0.005 0.110 12326 Dihedral : 24.555 179.449 78630 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.08 % Favored : 90.45 % Rotamer: Outliers : 6.21 % Allowed : 27.12 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.09 % Twisted Proline : 0.55 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.11), residues: 5497 helix: -0.46 (0.13), residues: 1597 sheet: -1.77 (0.16), residues: 917 loop : -2.11 (0.11), residues: 2983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 103 HIS 0.010 0.001 HIS T 67 PHE 0.024 0.002 PHE N 76 TYR 0.029 0.002 TYR L 65 ARG 0.015 0.001 ARG I 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36958.87 seconds wall clock time: 645 minutes 34.32 seconds (38734.32 seconds total)