Starting phenix.real_space_refine (version: dev) on Sun Apr 10 22:19:26 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbv_6486/04_2022/3jbv_6486_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbv_6486/04_2022/3jbv_6486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbv_6486/04_2022/3jbv_6486.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbv_6486/04_2022/3jbv_6486.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbv_6486/04_2022/3jbv_6486_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbv_6486/04_2022/3jbv_6486_neut_updated.pdb" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "P GLU 45": "OE1" <-> "OE2" Residue "P GLU 48": "OE1" <-> "OE2" Residue "P ASP 55": "OD1" <-> "OD2" Residue "U GLU 30": "OE1" <-> "OE2" Residue "0 ARG 3": "NH1" <-> "NH2" Residue "0 ARG 11": "NH1" <-> "NH2" Residue "0 ARG 18": "NH1" <-> "NH2" Residue "0 ARG 37": "NH1" <-> "NH2" Residue "0 GLU 43": "OE1" <-> "OE2" Residue "0 ARG 50": "NH1" <-> "NH2" Residue "0 ARG 57": "NH1" <-> "NH2" Residue "0 ARG 74": "NH1" <-> "NH2" Residue "1 GLU 12": "OE1" <-> "OE2" Residue "1 ARG 29": "NH1" <-> "NH2" Residue "1 ARG 47": "NH1" <-> "NH2" Residue "1 ARG 52": "NH1" <-> "NH2" Residue "1 GLU 59": "OE1" <-> "OE2" Residue "2 ARG 11": "NH1" <-> "NH2" Residue "2 ARG 30": "NH1" <-> "NH2" Residue "2 GLU 37": "OE1" <-> "OE2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "2 GLU 59": "OE1" <-> "OE2" Residue "3 ARG 10": "NH1" <-> "NH2" Residue "3 ARG 16": "NH1" <-> "NH2" Residue "3 ARG 52": "NH1" <-> "NH2" Residue "4 GLU 32": "OE1" <-> "OE2" Residue "4 GLU 35": "OE1" <-> "OE2" Residue "4 ARG 44": "NH1" <-> "NH2" Residue "6 ARG 3": "NH1" <-> "NH2" Residue "6 ARG 12": "NH1" <-> "NH2" Residue "6 ARG 14": "NH1" <-> "NH2" Residue "6 ARG 19": "NH1" <-> "NH2" Residue "6 ARG 21": "NH1" <-> "NH2" Residue "6 ARG 33": "NH1" <-> "NH2" Residue "6 ARG 41": "NH1" <-> "NH2" Residue "7 ARG 13": "NH1" <-> "NH2" Residue "7 ARG 30": "NH1" <-> "NH2" Residue "7 ARG 40": "NH1" <-> "NH2" Residue "7 ARG 42": "NH1" <-> "NH2" Residue "8 ARG 24": "NH1" <-> "NH2" Residue "c GLU 35": "OE1" <-> "OE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ARG 63": "NH1" <-> "NH2" Residue "c ARG 80": "NH1" <-> "NH2" Residue "c TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 133": "NH1" <-> "NH2" Residue "c GLU 145": "OE1" <-> "OE2" Residue "c ARG 167": "NH1" <-> "NH2" Residue "c ARG 177": "NH1" <-> "NH2" Residue "c ARG 182": "NH1" <-> "NH2" Residue "c ARG 189": "NH1" <-> "NH2" Residue "c GLU 194": "OE1" <-> "OE2" Residue "c GLU 199": "OE1" <-> "OE2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c ARG 212": "NH1" <-> "NH2" Residue "i ASP 46": "OD1" <-> "OD2" Residue "i TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 141": "OD1" <-> "OD2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d GLU 17": "OE1" <-> "OE2" Residue "d GLU 28": "OE1" <-> "OE2" Residue "d GLU 30": "OE1" <-> "OE2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 59": "NH1" <-> "NH2" Residue "d GLU 64": "OE1" <-> "OE2" Residue "d GLU 74": "OE1" <-> "OE2" Residue "d ARG 77": "NH1" <-> "NH2" Residue "d GLU 81": "OE1" <-> "OE2" Residue "d ARG 83": "NH1" <-> "NH2" Residue "d GLU 88": "OE1" <-> "OE2" Residue "d PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 168": "OE1" <-> "OE2" Residue "d ARG 169": "NH1" <-> "NH2" Residue "d GLU 183": "OE1" <-> "OE2" Residue "d ARG 184": "NH1" <-> "NH2" Residue "e ARG 21": "NH1" <-> "NH2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e ARG 61": "NH1" <-> "NH2" Residue "e ARG 88": "NH1" <-> "NH2" Residue "e ARG 102": "NH1" <-> "NH2" Residue "e GLU 152": "OE1" <-> "OE2" Residue "e ARG 162": "NH1" <-> "NH2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "e ASP 191": "OD1" <-> "OD2" Residue "f GLU 32": "OE1" <-> "OE2" Residue "f GLU 42": "OE1" <-> "OE2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f GLU 94": "OE1" <-> "OE2" Residue "f GLU 98": "OE1" <-> "OE2" Residue "f ARG 102": "NH1" <-> "NH2" Residue "f ARG 110": "NH1" <-> "NH2" Residue "f ARG 112": "NH1" <-> "NH2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f ASP 123": "OD1" <-> "OD2" Residue "f ARG 133": "NH1" <-> "NH2" Residue "f GLU 134": "OE1" <-> "OE2" Residue "f GLU 140": "OE1" <-> "OE2" Residue "f ASP 142": "OD1" <-> "OD2" Residue "f GLU 164": "OE1" <-> "OE2" Residue "g ARG 3": "NH1" <-> "NH2" Residue "g ASP 16": "OD1" <-> "OD2" Residue "g GLU 32": "OE1" <-> "OE2" Residue "g PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 81": "OE1" <-> "OE2" Residue "g ASP 114": "OD1" <-> "OD2" Residue "g GLU 130": "OE1" <-> "OE2" Residue "g ARG 153": "NH1" <-> "NH2" Residue "g ARG 163": "NH1" <-> "NH2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "g GLU 173": "OE1" <-> "OE2" Residue "h ARG 27": "NH1" <-> "NH2" Residue "h PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ASP 14": "OD1" <-> "OD2" Residue "j GLU 31": "OE1" <-> "OE2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j GLU 91": "OE1" <-> "OE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "k GLU 92": "OE1" <-> "OE2" Residue "k GLU 121": "OE1" <-> "OE2" Residue "l ARG 21": "NH1" <-> "NH2" Residue "l ARG 33": "NH1" <-> "NH2" Residue "l ARG 41": "NH1" <-> "NH2" Residue "l ARG 47": "NH1" <-> "NH2" Residue "l GLU 51": "OE1" <-> "OE2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 76": "OE1" <-> "OE2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m GLU 47": "OE1" <-> "OE2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m GLU 75": "OE1" <-> "OE2" Residue "m GLU 90": "OE1" <-> "OE2" Residue "m TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 104": "OE1" <-> "OE2" Residue "m ASP 106": "OD1" <-> "OD2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n GLU 82": "OE1" <-> "OE2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 114": "OE1" <-> "OE2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "n GLU 120": "OE1" <-> "OE2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o GLU 46": "OE1" <-> "OE2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "p GLU 11": "OE1" <-> "OE2" Residue "p ARG 21": "NH1" <-> "NH2" Residue "p ARG 39": "NH1" <-> "NH2" Residue "p GLU 44": "OE1" <-> "OE2" Residue "p ARG 62": "NH1" <-> "NH2" Residue "p GLU 68": "OE1" <-> "OE2" Residue "p GLU 71": "OE1" <-> "OE2" Residue "p ARG 89": "NH1" <-> "NH2" Residue "p TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 101": "NH1" <-> "NH2" Residue "p ARG 109": "NH1" <-> "NH2" Residue "q ARG 3": "NH1" <-> "NH2" Residue "q ARG 6": "NH1" <-> "NH2" Residue "q ARG 13": "NH1" <-> "NH2" Residue "q TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 33": "NH1" <-> "NH2" Residue "q ARG 48": "NH1" <-> "NH2" Residue "q ARG 70": "NH1" <-> "NH2" Residue "q GLU 111": "OE1" <-> "OE2" Residue "r GLU 16": "OE1" <-> "OE2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 23": "OE1" <-> "OE2" Residue "r GLU 31": "OE1" <-> "OE2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r GLU 70": "OE1" <-> "OE2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r ARG 79": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "r PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 2": "OE1" <-> "OE2" Residue "s GLU 59": "OE1" <-> "OE2" Residue "s GLU 78": "OE1" <-> "OE2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "t GLU 4": "OE1" <-> "OE2" Residue "t GLU 52": "OE1" <-> "OE2" Residue "t GLU 54": "OE1" <-> "OE2" Residue "t GLU 56": "OE1" <-> "OE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ARG 7": "NH1" <-> "NH2" Residue "u GLU 10": "OE1" <-> "OE2" Residue "u ARG 82": "NH1" <-> "NH2" Residue "u PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 86": "NH1" <-> "NH2" Residue "u GLU 88": "OE1" <-> "OE2" Residue "u ARG 94": "NH1" <-> "NH2" Residue "u PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 101": "OE1" <-> "OE2" Residue "w ASP 45": "OD1" <-> "OD2" Residue "w GLU 55": "OE1" <-> "OE2" Residue "w TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 69": "OE1" <-> "OE2" Residue "w TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 17": "OE1" <-> "OE2" Residue "y PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 83": "OE1" <-> "OE2" Residue "z GLU 10": "OE1" <-> "OE2" Residue "z PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 145911 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 32831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1530, 32831 Classifications: {'RNA': 1530} Modifications used: {'rna3p_pyr': 569, 'rna2p_pur': 121, 'rna3p_pur': 751, 'rna2p_pyr': 89} Link IDs: {'rna3p': 1319, 'rna2p': 210} Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1105 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "G" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1174 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "M" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 876 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "N" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "O" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 716 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "S" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "T" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "U" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "V" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1620 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna3p_pur': 33, 'rna2p_pyr': 7, 'rna3p_pyr': 30} Link IDs: {'rna3p': 62, 'rna2p': 13} Chain: "W" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1599 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna3p_pur': 27, 'rna2p_pyr': 6, 'rna3p_pyr': 31} Link IDs: {'rna3p': 58, 'rna2p': 16} Chain: "X" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 231 Classifications: {'RNA': 11} Modifications used: {'rna3p_pyr': 5, 'p5*END': 1, 'rna3p_pur': 4, 'rna2p_pyr': 2} Link IDs: {'rna3p': 8, 'rna2p': 2} Chain: "0" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "1" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "2" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "3" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "4" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "6" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "7" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "8" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "a" Number of atoms: 2506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2506 Classifications: {'RNA': 117} Modifications used: {'rna3p_pyr': 50, 'rna2p_pur': 10, 'rna3p_pur': 53, 'rna2p_pyr': 4} Link IDs: {'rna3p': 102, 'rna2p': 14} Chain: "b" Number of atoms: 62321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62321 Classifications: {'RNA': 2903} Modifications used: {'rna2p_pyr': 144, 'rna3p_pyr': 1085, 'p5*END': 1, 'rna3p_pur': 1425, 'rna2p_pur': 249} Link IDs: {'rna3p': 2509, 'rna2p': 393} Chain: "c" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "i" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 976 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "d" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "e" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "f" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "g" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "h" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 145, 'PCIS': 1} Chain: "j" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "k" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "l" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "m" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1063 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain breaks: 1 Chain: "n" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "o" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "p" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "r" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "s" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "t" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "u" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "w" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "y" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 569 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "z" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 211 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 2, 'CIS': 4, 'TRANS': 20} Chain: "b" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'CLM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 60.00, per 1000 atoms: 0.41 Number of scatterers: 145911 At special positions: 0 Unit cell: (265.32, 287.76, 224.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 144 16.00 P 4710 15.00 O 40726 8.00 N 27167 7.00 C 73162 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 83655 O4' U b1058 .*. O " rejected from bonding due to valence issues. Atom "ATOM 84080 O5' U b1078 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83698 O4' U b1060 .*. O " rejected from bonding due to valence issues. Atom "ATOM 84021 O4' C b1075 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83735 O5' G b1062 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83695 O5' U b1060 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83715 O5' U b1061 .*. O " rejected from bonding due to valence issues. Atom "ATOM 84080 O5' U b1078 .*. O " rejected from bonding due to valence issues. Atom "ATOM 84021 O4' C b1075 .*. O " rejected from bonding due to valence issues. Atom "ATOM 84061 O4' A b1077 .*. O " rejected from bonding due to valence issues. Atom "ATOM 84165 O4' U b1082 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83715 O5' U b1061 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83698 O4' U b1060 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83698 O4' U b1060 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83761 O4' G b1063 .*. O " rejected from bonding due to valence issues. Atom "ATOM 84021 O4' C b1075 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83761 O4' G b1063 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83784 O4' C b1064 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83655 O4' U b1058 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83695 O5' U b1060 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83761 O4' G b1063 .*. O " rejected from bonding due to valence issues. Atom "ATOM 84080 O5' U b1078 .*. O " rejected from bonding due to valence issues. Atom "ATOM 84145 O4' U b1081 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83738 O4' G b1062 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83695 O5' U b1060 .*. O " rejected from bonding due to valence issues. Atom "ATOM 7958 O5' U A 375 .*. O " rejected from bonding due to valence issues. Atom "ATOM 28832 O5' U A1348 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83781 O5' C b1064 .*. O " rejected from bonding due to valence issues. Atom "ATOM 84061 O4' A b1077 .*. O " rejected from bonding due to valence issues. Atom "ATOM 83863 O5' G b1068 .*. O " rejected from bonding due to valence issues. Atom "ATOM 84165 O4' U b1082 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 58.61 Conformation dependent library (CDL) restraints added in 5.9 seconds 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10528 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 171 helices and 64 sheets defined 37.6% alpha, 18.2% beta 1129 base pairs and 1774 stacking pairs defined. Time for finding SS restraints: 58.12 Creating SS restraints... Processing helix chain 'B' and resid 23 through 28 removed outlier: 4.372A pdb=" N LYS B 27 " --> pdb=" O ASN B 23 " (cutoff:3.500A) Proline residue: B 28 - end of helix No H-bonds generated for 'chain 'B' and resid 23 through 28' Processing helix chain 'B' and resid 42 through 63 removed outlier: 3.746A pdb=" N VAL B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Proline residue: B 47 - end of helix removed outlier: 3.583A pdb=" N ARG B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 63 " --> pdb=" O ILE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 83 removed outlier: 3.500A pdb=" N VAL B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 127 removed outlier: 4.678A pdb=" N GLN B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLN B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N THR B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N PHE B 125 " --> pdb=" O GLN B 121 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASP B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS B 127 " --> pdb=" O GLY B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 146 removed outlier: 4.195A pdb=" N ALA B 133 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASN B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 154 removed outlier: 4.847A pdb=" N MET B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLY B 154 " --> pdb=" O ILE B 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 149 through 154' Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.887A pdb=" N GLU B 168 " --> pdb=" O ASP B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 179 removed outlier: 3.861A pdb=" N ASN B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 224 removed outlier: 4.010A pdb=" N VAL B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N THR B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N GLY B 223 " --> pdb=" O THR B 219 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG B 224 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 11 removed outlier: 6.379A pdb=" N ARG C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU C 11 " --> pdb=" O ASN C 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 6 through 11' Processing helix chain 'C' and resid 27 through 47 removed outlier: 3.665A pdb=" N ASN C 31 " --> pdb=" O GLU C 27 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 removed outlier: 4.040A pdb=" N VAL C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 94 removed outlier: 3.743A pdb=" N ARG C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL C 89 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.569A pdb=" N VAL C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 144 removed outlier: 3.708A pdb=" N MET C 133 " --> pdb=" O PHE C 129 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY C 144 " --> pdb=" O ALA C 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 15 removed outlier: 4.878A pdb=" N LEU D 10 " --> pdb=" O PRO D 6 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 65 removed outlier: 3.647A pdb=" N VAL D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.710A pdb=" N ARG D 80 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LYS D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 96 removed outlier: 4.021A pdb=" N LEU D 89 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU D 90 " --> pdb=" O GLY D 86 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 109 through 120 removed outlier: 4.005A pdb=" N HIS D 119 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 164 removed outlier: 4.348A pdb=" N LYS D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLN D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ARG D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 191 removed outlier: 3.845A pdb=" N LEU D 190 " --> pdb=" O GLU D 186 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N SER D 191 " --> pdb=" O ARG D 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 186 through 191' Processing helix chain 'D' and resid 196 through 205 removed outlier: 3.751A pdb=" N VAL D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 43 removed outlier: 4.321A pdb=" N ALA D 42 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG D 43 " --> pdb=" O HIS D 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 70 removed outlier: 3.588A pdb=" N ASN E 69 " --> pdb=" O LYS E 65 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N MET E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 removed outlier: 4.685A pdb=" N ALA E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 146 removed outlier: 3.901A pdb=" N ARG E 137 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA E 138 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N THR E 139 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ILE E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLU E 144 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ASN E 145 " --> pdb=" O ASP E 141 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET E 146 " --> pdb=" O GLY E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 158 removed outlier: 3.805A pdb=" N LYS E 155 " --> pdb=" O MET E 151 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG E 156 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 33 removed outlier: 4.429A pdb=" N VAL F 18 " --> pdb=" O GLN F 14 " (cutoff:3.500A) Proline residue: F 19 - end of helix removed outlier: 3.661A pdb=" N ILE F 22 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU F 23 " --> pdb=" O PRO F 19 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG F 24 " --> pdb=" O GLY F 20 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ALA F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 removed outlier: 3.811A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP F 72 " --> pdb=" O GLN F 68 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 30 Processing helix chain 'G' and resid 34 through 53 removed outlier: 5.550A pdb=" N ALA G 38 " --> pdb=" O LYS G 34 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR G 43 " --> pdb=" O GLU G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 69 removed outlier: 4.126A pdb=" N GLU G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN G 67 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 110 removed outlier: 3.856A pdb=" N ARG G 95 " --> pdb=" O ARG G 91 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN G 96 " --> pdb=" O PRO G 92 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 129 removed outlier: 3.738A pdb=" N GLU G 128 " --> pdb=" O SER G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 148 removed outlier: 3.627A pdb=" N ASP G 139 " --> pdb=" O LYS G 135 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL G 140 " --> pdb=" O LYS G 136 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA G 144 " --> pdb=" O VAL G 140 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU G 145 " --> pdb=" O HIS G 141 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASN G 147 " --> pdb=" O MET G 143 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 20 removed outlier: 3.806A pdb=" N ASN H 20 " --> pdb=" O GLY H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 43 Processing helix chain 'H' and resid 111 through 119 removed outlier: 3.675A pdb=" N GLN H 117 " --> pdb=" O ARG H 113 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA H 118 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 38 Processing helix chain 'I' and resid 41 through 55 removed outlier: 3.945A pdb=" N MET I 45 " --> pdb=" O GLU I 41 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG I 48 " --> pdb=" O ARG I 44 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN I 49 " --> pdb=" O MET I 45 " (cutoff:3.500A) Proline residue: I 50 - end of helix removed outlier: 3.730A pdb=" N LEU I 53 " --> pdb=" O GLN I 49 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL I 54 " --> pdb=" O PRO I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 90 removed outlier: 4.027A pdb=" N ALA I 85 " --> pdb=" O GLY I 81 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET I 87 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU I 88 " --> pdb=" O ARG I 84 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR I 89 " --> pdb=" O ALA I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 101 removed outlier: 3.871A pdb=" N GLU I 96 " --> pdb=" O SER I 92 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS I 99 " --> pdb=" O SER I 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 30 removed outlier: 3.950A pdb=" N ILE J 18 " --> pdb=" O ASP J 14 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR J 28 " --> pdb=" O GLU J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 89 removed outlier: 4.982A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N MET J 88 " --> pdb=" O VAL J 84 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG J 89 " --> pdb=" O ASP J 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 50 removed outlier: 3.773A pdb=" N GLY K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 59 removed outlier: 4.113A pdb=" N SER K 57 " --> pdb=" O GLY K 53 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 59 - end of helix No H-bonds generated for 'chain 'K' and resid 53 through 59' Processing helix chain 'K' and resid 60 through 75 removed outlier: 3.512A pdb=" N VAL K 73 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLU K 75 " --> pdb=" O ASP K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 103 removed outlier: 4.726A pdb=" N ILE K 96 " --> pdb=" O ARG K 92 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY K 103 " --> pdb=" O LEU K 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 10 Proline residue: L 10 - end of helix Processing helix chain 'L' and resid 112 through 117 removed outlier: 4.788A pdb=" N TYR L 116 " --> pdb=" O ALA L 112 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLY L 117 " --> pdb=" O ARG L 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 112 through 117' Processing helix chain 'M' and resid 13 through 21 removed outlier: 4.095A pdb=" N THR M 19 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER M 20 " --> pdb=" O ILE M 16 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 37 removed outlier: 3.519A pdb=" N ALA M 36 " --> pdb=" O ILE M 32 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY M 37 " --> pdb=" O LEU M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 63 removed outlier: 4.644A pdb=" N ASP M 53 " --> pdb=" O GLU M 49 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS M 61 " --> pdb=" O ASP M 57 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N VAL M 63 " --> pdb=" O VAL M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 82 Processing helix chain 'M' and resid 84 through 93 Processing helix chain 'M' and resid 105 through 110 removed outlier: 3.580A pdb=" N LYS M 109 " --> pdb=" O ALA M 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 21 removed outlier: 3.940A pdb=" N LYS N 6 " --> pdb=" O LYS N 2 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR N 19 " --> pdb=" O LEU N 15 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA N 21 " --> pdb=" O ASP N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 28 removed outlier: 4.661A pdb=" N LYS N 27 " --> pdb=" O ARG N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 49 removed outlier: 4.149A pdb=" N LEU N 45 " --> pdb=" O TRP N 41 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU N 47 " --> pdb=" O ALA N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 90 removed outlier: 3.771A pdb=" N ARG N 84 " --> pdb=" O ARG N 80 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU N 85 " --> pdb=" O ILE N 81 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG N 89 " --> pdb=" O GLU N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 15 removed outlier: 5.095A pdb=" N GLY O 15 " --> pdb=" O VAL O 11 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 46 removed outlier: 3.671A pdb=" N VAL O 28 " --> pdb=" O THR O 24 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA O 29 " --> pdb=" O GLU O 25 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N HIS O 37 " --> pdb=" O ALA O 33 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN O 39 " --> pdb=" O ILE O 35 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLY O 40 " --> pdb=" O ASN O 36 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA O 43 " --> pdb=" O GLN O 39 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLU O 44 " --> pdb=" O GLY O 40 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS O 45 " --> pdb=" O HIS O 41 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LYS O 46 " --> pdb=" O PHE O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 73 removed outlier: 4.783A pdb=" N ARG O 52 " --> pdb=" O ASP O 48 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG O 53 " --> pdb=" O HIS O 49 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLY O 54 " --> pdb=" O HIS O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 85 removed outlier: 3.500A pdb=" N LEU O 80 " --> pdb=" O ARG O 76 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 64 Processing helix chain 'P' and resid 68 through 79 removed outlier: 3.826A pdb=" N ALA P 73 " --> pdb=" O ASP P 69 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU P 74 " --> pdb=" O ARG P 70 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN P 79 " --> pdb=" O ILE P 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 32 removed outlier: 4.300A pdb=" N ASN R 30 " --> pdb=" O ALA R 26 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TYR R 31 " --> pdb=" O THR R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 removed outlier: 3.695A pdb=" N THR R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 65 removed outlier: 4.226A pdb=" N TYR R 63 " --> pdb=" O LYS R 59 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU R 64 " --> pdb=" O ARG R 60 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 24 removed outlier: 3.942A pdb=" N LYS S 16 " --> pdb=" O LEU S 12 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LYS S 17 " --> pdb=" O HIS S 13 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU S 19 " --> pdb=" O LEU S 15 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LYS S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ALA S 21 " --> pdb=" O LYS S 17 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL S 22 " --> pdb=" O VAL S 18 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU S 23 " --> pdb=" O GLU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 75 removed outlier: 4.061A pdb=" N PHE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA S 74 " --> pdb=" O LEU S 70 " (cutoff:3.500A) Proline residue: S 75 - end of helix No H-bonds generated for 'chain 'S' and resid 69 through 75' Processing helix chain 'T' and resid 7 through 41 removed outlier: 3.701A pdb=" N ILE T 11 " --> pdb=" O LYS T 7 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU T 14 " --> pdb=" O ALA T 10 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER T 22 " --> pdb=" O LYS T 18 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG T 23 " --> pdb=" O HIS T 19 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET T 27 " --> pdb=" O ARG T 23 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS T 32 " --> pdb=" O ARG T 28 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 64 removed outlier: 4.179A pdb=" N ALA T 46 " --> pdb=" O ASP T 42 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLN T 47 " --> pdb=" O LYS T 43 " (cutoff:3.500A) Proline residue: T 55 - end of helix removed outlier: 4.250A pdb=" N ALA T 61 " --> pdb=" O VAL T 57 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA T 62 " --> pdb=" O ASP T 58 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS T 63 " --> pdb=" O ARG T 59 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY T 64 " --> pdb=" O GLN T 60 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 86 removed outlier: 3.711A pdb=" N ALA T 71 " --> pdb=" O HIS T 67 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS T 84 " --> pdb=" O ALA T 80 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA T 86 " --> pdb=" O ILE T 82 " (cutoff:3.500A) Processing helix chain 'U' and resid 15 through 23 removed outlier: 3.710A pdb=" N LYS U 19 " --> pdb=" O LEU U 15 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG U 20 " --> pdb=" O ARG U 16 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER U 21 " --> pdb=" O ARG U 17 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N CYS U 22 " --> pdb=" O PHE U 18 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU U 23 " --> pdb=" O LYS U 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 15 through 23' Processing helix chain 'U' and resid 26 through 31 removed outlier: 7.291A pdb=" N GLU U 30 " --> pdb=" O GLY U 26 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL U 31 " --> pdb=" O VAL U 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 26 through 31' Processing helix chain 'U' and resid 36 through 44 Proline residue: U 40 - end of helix removed outlier: 3.952A pdb=" N GLU U 43 " --> pdb=" O LYS U 39 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ARG U 44 " --> pdb=" O PRO U 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 36 through 44' Processing helix chain 'U' and resid 46 through 53 removed outlier: 3.970A pdb=" N VAL U 52 " --> pdb=" O LYS U 48 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS U 53 " --> pdb=" O ALA U 49 " (cutoff:3.500A) Processing helix chain '0' and resid 52 through 63 Processing helix chain '0' and resid 64 through 75 Processing helix chain '1' and resid 2 through 9 removed outlier: 6.070A pdb=" N LEU 1 6 " --> pdb=" O LYS 1 2 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG 1 7 " --> pdb=" O ALA 1 3 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU 1 8 " --> pdb=" O LYS 1 4 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LYS 1 9 " --> pdb=" O GLU 1 5 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 2 through 9' Processing helix chain '1' and resid 10 through 35 removed outlier: 3.601A pdb=" N GLY 1 35 " --> pdb=" O GLN 1 31 " (cutoff:3.500A) Processing helix chain '1' and resid 39 through 61 removed outlier: 4.733A pdb=" N LEU 1 43 " --> pdb=" O GLN 1 39 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LYS 1 44 " --> pdb=" O SER 1 40 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN 1 45 " --> pdb=" O HIS 1 41 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL 1 46 " --> pdb=" O LEU 1 42 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG 1 47 " --> pdb=" O LEU 1 43 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG 1 48 " --> pdb=" O LYS 1 44 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ASP 1 49 " --> pdb=" O GLN 1 45 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU 1 59 " --> pdb=" O THR 1 55 " (cutoff:3.500A) Processing helix chain '2' and resid 17 through 28 Processing helix chain '2' and resid 41 through 52 Processing helix chain '3' and resid 9 through 19 removed outlier: 4.871A pdb=" N HIS 3 19 " --> pdb=" O MET 3 15 " (cutoff:3.500A) Processing helix chain '6' and resid 8 through 16 Processing helix chain '6' and resid 17 through 25 removed outlier: 4.222A pdb=" N THR 6 24 " --> pdb=" O ALA 6 20 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LYS 6 25 " --> pdb=" O ARG 6 21 " (cutoff:3.500A) Processing helix chain '6' and resid 26 through 38 Processing helix chain '7' and resid 7 through 14 removed outlier: 3.545A pdb=" N LYS 7 12 " --> pdb=" O ARG 7 8 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG 7 13 " --> pdb=" O GLY 7 9 " (cutoff:3.500A) Processing helix chain '7' and resid 32 through 37 removed outlier: 4.390A pdb=" N LYS 7 36 " --> pdb=" O ILE 7 32 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ALA 7 37 " --> pdb=" O LEU 7 33 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 32 through 37' Processing helix chain '7' and resid 38 through 46 Proline residue: 7 46 - end of helix Processing helix chain '7' and resid 51 through 63 removed outlier: 4.883A pdb=" N GLY 7 56 " --> pdb=" O LYS 7 52 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU 7 57 " --> pdb=" O GLY 7 53 " (cutoff:3.500A) Proline residue: 7 63 - end of helix Processing helix chain 'c' and resid 10 through 16 removed outlier: 7.432A pdb=" N HIS c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL c 16 " --> pdb=" O GLY c 12 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 35 removed outlier: 4.004A pdb=" N LEU c 34 " --> pdb=" O PHE c 30 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLU c 35 " --> pdb=" O ALA c 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 30 through 35' Processing helix chain 'c' and resid 131 through 136 removed outlier: 3.718A pdb=" N ILE c 135 " --> pdb=" O PRO c 131 " (cutoff:3.500A) Proline residue: c 136 - end of helix No H-bonds generated for 'chain 'c' and resid 131 through 136' Processing helix chain 'c' and resid 207 through 215 removed outlier: 3.924A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG c 214 " --> pdb=" O ALA c 210 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 226 removed outlier: 3.736A pdb=" N MET c 225 " --> pdb=" O ARG c 221 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ASN c 226 " --> pdb=" O GLY c 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 221 through 226' Processing helix chain 'c' and resid 260 through 268 removed outlier: 5.907A pdb=" N ASP c 264 " --> pdb=" O ASN c 260 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LYS c 265 " --> pdb=" O LYS c 261 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N PHE c 266 " --> pdb=" O ARG c 262 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE c 267 " --> pdb=" O THR c 263 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL c 268 " --> pdb=" O ASP c 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 260 through 268' Processing helix chain 'c' and resid 197 through 202 removed outlier: 3.621A pdb=" N MET c 201 " --> pdb=" O ALA c 198 " (cutoff:3.500A) Processing helix chain 'i' and resid 24 through 29 removed outlier: 4.212A pdb=" N GLY i 28 " --> pdb=" O GLY i 24 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN i 29 " --> pdb=" O PRO i 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 24 through 29' Processing helix chain 'i' and resid 33 through 46 removed outlier: 5.564A pdb=" N CYS i 38 " --> pdb=" O ILE i 34 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LYS i 39 " --> pdb=" O MET i 35 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA i 40 " --> pdb=" O GLU i 36 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N PHE i 41 " --> pdb=" O PHE i 37 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASN i 42 " --> pdb=" O CYS i 38 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS i 44 " --> pdb=" O ALA i 40 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP i 46 " --> pdb=" O ASN i 42 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 82 removed outlier: 4.132A pdb=" N LEU i 78 " --> pdb=" O PRO i 74 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU i 79 " --> pdb=" O ALA i 75 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LYS i 80 " --> pdb=" O ALA i 76 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS i 81 " --> pdb=" O VAL i 77 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA i 82 " --> pdb=" O LEU i 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 74 through 82' Processing helix chain 'i' and resid 101 through 113 removed outlier: 4.808A pdb=" N LEU i 105 " --> pdb=" O SER i 101 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLN i 106 " --> pdb=" O ARG i 102 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLU i 107 " --> pdb=" O ALA i 103 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE i 108 " --> pdb=" O GLN i 104 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS i 112 " --> pdb=" O ILE i 108 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ALA i 113 " --> pdb=" O ALA i 109 " (cutoff:3.500A) Processing helix chain 'i' and resid 120 through 134 removed outlier: 3.573A pdb=" N MET i 124 " --> pdb=" O ASP i 120 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N THR i 125 " --> pdb=" O ILE i 121 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ARG i 126 " --> pdb=" O GLU i 122 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER i 127 " --> pdb=" O ALA i 123 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE i 128 " --> pdb=" O MET i 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 56 through 61 removed outlier: 5.448A pdb=" N THR d 61 " --> pdb=" O ALA d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 72 removed outlier: 3.735A pdb=" N ALA d 71 " --> pdb=" O HIS d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 103 removed outlier: 4.482A pdb=" N ALA d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASP d 103 " --> pdb=" O GLU d 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 98 through 103' Processing helix chain 'd' and resid 120 through 125 Processing helix chain 'e' and resid 15 through 20 Processing helix chain 'e' and resid 24 through 40 removed outlier: 3.924A pdb=" N ARG e 40 " --> pdb=" O ALA e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 97 through 116 Processing helix chain 'e' and resid 130 through 142 Processing helix chain 'e' and resid 154 through 163 removed outlier: 3.711A pdb=" N ARG e 162 " --> pdb=" O PHE e 158 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ASN e 163 " --> pdb=" O LEU e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 183 removed outlier: 3.671A pdb=" N LEU e 180 " --> pdb=" O ASP e 176 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE e 181 " --> pdb=" O PRO e 177 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE e 183 " --> pdb=" O SER e 179 " (cutoff:3.500A) Processing helix chain 'e' and resid 189 through 201 Processing helix chain 'f' and resid 2 through 21 removed outlier: 3.537A pdb=" N ASP f 6 " --> pdb=" O ALA f 2 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS f 9 " --> pdb=" O HIS f 5 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR f 18 " --> pdb=" O LYS f 14 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE f 20 " --> pdb=" O LEU f 16 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 47 removed outlier: 3.625A pdb=" N ASP f 46 " --> pdb=" O GLU f 42 " (cutoff:3.500A) Processing helix chain 'f' and resid 48 through 62 Processing helix chain 'f' and resid 93 through 111 removed outlier: 3.519A pdb=" N ILE f 106 " --> pdb=" O ARG f 102 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL f 108 " --> pdb=" O ILE f 104 " (cutoff:3.500A) Proline residue: f 109 - end of helix Processing helix chain 'f' and resid 162 through 174 removed outlier: 3.712A pdb=" N PHE f 173 " --> pdb=" O LEU f 169 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP f 174 " --> pdb=" O LEU f 170 " (cutoff:3.500A) Processing helix chain 'f' and resid 134 through 139 removed outlier: 3.550A pdb=" N ILE f 137 " --> pdb=" O GLU f 134 " (cutoff:3.500A) Proline residue: f 139 - end of helix Processing helix chain 'g' and resid 2 through 8 Proline residue: g 8 - end of helix Processing helix chain 'g' and resid 60 through 81 removed outlier: 5.056A pdb=" N GLN g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER g 74 " --> pdb=" O ALA g 70 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR g 80 " --> pdb=" O VAL g 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 153 removed outlier: 4.446A pdb=" N ARG g 152 " --> pdb=" O LEU g 148 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG g 153 " --> pdb=" O ARG g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 22 through 34 removed outlier: 3.755A pdb=" N ALA h 26 " --> pdb=" O LYS h 22 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ARG h 27 " --> pdb=" O ALA h 23 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN h 28 " --> pdb=" O GLY h 24 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE h 29 " --> pdb=" O TYR h 25 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LEU h 30 " --> pdb=" O ALA h 26 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL h 31 " --> pdb=" O ARG h 27 " (cutoff:3.500A) Proline residue: h 32 - end of helix No H-bonds generated for 'chain 'h' and resid 22 through 34' Processing helix chain 'h' and resid 43 through 54 removed outlier: 3.585A pdb=" N ALA h 49 " --> pdb=" O GLU h 45 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA h 52 " --> pdb=" O GLU h 48 " (cutoff:3.500A) Processing helix chain 'h' and resid 55 through 66 removed outlier: 6.396A pdb=" N ALA h 59 " --> pdb=" O GLU h 55 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU h 60 " --> pdb=" O ALA h 56 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL h 61 " --> pdb=" O LYS h 57 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU h 62 " --> pdb=" O LEU h 58 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA h 63 " --> pdb=" O ALA h 59 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA h 64 " --> pdb=" O GLU h 60 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ALA h 65 " --> pdb=" O VAL h 61 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN h 66 " --> pdb=" O LEU h 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 55 through 66' Processing helix chain 'h' and resid 67 through 75 removed outlier: 4.076A pdb=" N LYS h 71 " --> pdb=" O ALA h 67 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ALA h 74 " --> pdb=" O GLU h 70 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU h 75 " --> pdb=" O LYS h 71 " (cutoff:3.500A) Processing helix chain 'h' and resid 95 through 100 removed outlier: 4.377A pdb=" N ILE h 99 " --> pdb=" O GLY h 95 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 removed outlier: 4.969A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 88 through 96 Processing helix chain 'j' and resid 97 through 110 removed outlier: 4.175A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET j 108 " --> pdb=" O ALA j 104 " (cutoff:3.500A) Proline residue: j 110 - end of helix Processing helix chain 'j' and resid 112 through 123 removed outlier: 3.769A pdb=" N ARG j 120 " --> pdb=" O ARG j 116 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS j 121 " --> pdb=" O ALA j 117 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU j 122 " --> pdb=" O MET j 118 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LYS j 123 " --> pdb=" O PHE j 119 " (cutoff:3.500A) Processing helix chain 'k' and resid 109 through 119 removed outlier: 5.707A pdb=" N MET k 113 " --> pdb=" O SER k 109 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LYS k 114 " --> pdb=" O GLU k 110 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE k 115 " --> pdb=" O LYS k 111 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 62 Proline residue: l 62 - end of helix Processing helix chain 'l' and resid 68 through 75 removed outlier: 7.261A pdb=" N ALA l 72 " --> pdb=" O SER l 68 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE l 73 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ALA l 75 " --> pdb=" O ALA l 71 " (cutoff:3.500A) Processing helix chain 'l' and resid 78 through 83 removed outlier: 3.643A pdb=" N LEU l 82 " --> pdb=" O ARG l 78 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA l 83 " --> pdb=" O LEU l 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 78 through 83' Processing helix chain 'l' and resid 91 through 99 removed outlier: 3.707A pdb=" N LEU l 95 " --> pdb=" O ASP l 91 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS l 96 " --> pdb=" O LEU l 92 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 139 removed outlier: 3.776A pdb=" N GLY l 139 " --> pdb=" O ILE l 135 " (cutoff:3.500A) Processing helix chain 'm' and resid 42 through 58 Processing helix chain 'm' and resid 109 through 125 removed outlier: 3.544A pdb=" N ALA m 122 " --> pdb=" O LYS m 118 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS m 123 " --> pdb=" O LEU m 119 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU m 124 " --> pdb=" O ALA m 120 " (cutoff:3.500A) Proline residue: m 125 - end of helix Processing helix chain 'n' and resid 13 through 32 Processing helix chain 'n' and resid 38 through 57 removed outlier: 3.604A pdb=" N ARG n 45 " --> pdb=" O ALA n 41 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) Proline residue: n 50 - end of helix removed outlier: 4.392A pdb=" N THR n 57 " --> pdb=" O THR n 53 " (cutoff:3.500A) Processing helix chain 'n' and resid 59 through 71 removed outlier: 4.017A pdb=" N THR n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 88 removed outlier: 5.103A pdb=" N GLY n 84 " --> pdb=" O PHE n 80 " (cutoff:3.500A) Proline residue: n 85 - end of helix Processing helix chain 'o' and resid 2 through 22 removed outlier: 3.668A pdb=" N ARG o 7 " --> pdb=" O LYS o 3 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG o 9 " --> pdb=" O SER o 5 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG o 15 " --> pdb=" O ALA o 11 " (cutoff:3.500A) Processing helix chain 'o' and resid 56 through 63 removed outlier: 4.581A pdb=" N GLN o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU o 62 " --> pdb=" O ILE o 58 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LYS o 63 " --> pdb=" O ALA o 59 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 86 Processing helix chain 'o' and resid 101 through 114 removed outlier: 3.842A pdb=" N GLY o 114 " --> pdb=" O ALA o 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 14 removed outlier: 3.733A pdb=" N GLU p 11 " --> pdb=" O GLN p 7 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN p 12 " --> pdb=" O LEU p 8 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LYS p 14 " --> pdb=" O GLN p 10 " (cutoff:3.500A) Processing helix chain 'p' and resid 97 through 104 removed outlier: 4.611A pdb=" N ARG p 101 " --> pdb=" O LEU p 97 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU p 102 " --> pdb=" O TYR p 98 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG p 103 " --> pdb=" O TYR p 99 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N THR p 104 " --> pdb=" O LEU p 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 97 through 104' Processing helix chain 'q' and resid 7 through 22 removed outlier: 3.547A pdb=" N ARG q 11 " --> pdb=" O GLY q 7 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE q 17 " --> pdb=" O ARG q 13 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS q 22 " --> pdb=" O LEU q 18 " (cutoff:3.500A) Processing helix chain 'q' and resid 26 through 31 removed outlier: 3.885A pdb=" N ARG q 30 " --> pdb=" O GLY q 26 " (cutoff:3.500A) Processing helix chain 'q' and resid 32 through 37 removed outlier: 3.910A pdb=" N GLN q 37 " --> pdb=" O ARG q 33 " (cutoff:3.500A) Processing helix chain 'q' and resid 39 through 73 removed outlier: 3.825A pdb=" N ARG q 51 " --> pdb=" O TYR q 47 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS q 54 " --> pdb=" O ARG q 50 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG q 55 " --> pdb=" O ARG q 51 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG q 58 " --> pdb=" O LYS q 54 " (cutoff:3.500A) Processing helix chain 'q' and resid 75 through 87 Processing helix chain 'q' and resid 91 through 102 Processing helix chain 'q' and resid 103 through 118 removed outlier: 3.568A pdb=" N ALA q 116 " --> pdb=" O LYS q 112 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 25 removed outlier: 3.667A pdb=" N LEU s 19 " --> pdb=" O GLN s 15 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 39 removed outlier: 3.702A pdb=" N ASP s 34 " --> pdb=" O SER s 30 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 removed outlier: 3.604A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS s 49 " --> pdb=" O VAL s 45 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) Processing helix chain 't' and resid 3 through 11 removed outlier: 3.508A pdb=" N LEU t 7 " --> pdb=" O ARG t 3 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU t 11 " --> pdb=" O LEU t 7 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 27 removed outlier: 5.559A pdb=" N SER t 21 " --> pdb=" O SER t 17 " (cutoff:3.500A) Processing helix chain 't' and resid 39 through 51 Processing helix chain 'u' and resid 66 through 71 removed outlier: 4.032A pdb=" N VAL u 70 " --> pdb=" O GLN u 66 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ALA u 71 " --> pdb=" O VAL u 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 66 through 71' Processing helix chain 'w' and resid 13 through 24 Processing helix chain 'w' and resid 43 through 53 removed outlier: 3.535A pdb=" N VAL w 47 " --> pdb=" O ASP w 43 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET w 50 " --> pdb=" O LYS w 46 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA w 52 " --> pdb=" O MET w 48 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS w 53 " --> pdb=" O ASN w 49 " (cutoff:3.500A) Processing helix chain 'w' and resid 54 through 59 removed outlier: 3.790A pdb=" N SER w 58 " --> pdb=" O ALA w 54 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 29 through 32 removed outlier: 7.049A pdb=" N PHE B 29 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASN B 41 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 88 through 91 removed outlier: 4.484A pdb=" N GLY B 70 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 161 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 69 " --> pdb=" O PHE B 161 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL B 162 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA B 184 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE B 199 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL B 186 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 53 through 58 removed outlier: 4.339A pdb=" N VAL C 55 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C 66 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 63 " --> pdb=" O PRO C 97 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN C 99 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 67 " --> pdb=" O ASN C 101 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 163 through 168 removed outlier: 5.896A pdb=" N ARG C 163 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLY C 154 " --> pdb=" O ARG C 163 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY C 147 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY C 196 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS C 203 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ASP C 180 " --> pdb=" O LYS C 203 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 139 through 143 removed outlier: 4.704A pdb=" N ASP D 140 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE D 181 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU D 178 " --> pdb=" O ASP D 173 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 11 through 15 removed outlier: 4.449A pdb=" N GLN E 11 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU E 35 " --> pdb=" O ILE E 15 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 83 through 87 removed outlier: 3.872A pdb=" N GLN E 96 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN E 121 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 32 through 39 removed outlier: 4.130A pdb=" N ALA E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY E 50 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR E 36 " --> pdb=" O GLY E 48 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY E 48 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY E 46 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F' and resid 38 through 43 removed outlier: 4.272A pdb=" N ARG F 38 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN F 63 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU F 40 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TRP F 42 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE F 8 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE F 6 " --> pdb=" O MET F 62 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET F 90 " --> pdb=" O GLU F 5 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'G' and resid 72 through 77 removed outlier: 4.146A pdb=" N ARG G 77 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR G 84 " --> pdb=" O ARG G 77 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'H' and resid 22 through 28 removed outlier: 5.702A pdb=" N ALA H 22 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER H 28 " --> pdb=" O PRO H 56 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU H 51 " --> pdb=" O GLU H 57 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASP H 47 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'H' and resid 102 through 105 removed outlier: 7.007A pdb=" N VAL H 102 " --> pdb=" O ILE H 125 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'I' and resid 4 through 10 removed outlier: 4.013A pdb=" N LYS I 67 " --> pdb=" O ALA I 15 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR I 63 " --> pdb=" O PHE I 19 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS I 26 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL I 28 " --> pdb=" O LEU I 62 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE I 64 " --> pdb=" O VAL I 28 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'J' and resid 45 through 52 removed outlier: 3.893A pdb=" N ARG J 45 " --> pdb=" O THR J 69 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR J 69 " --> pdb=" O ARG J 45 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU J 47 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N HIS J 70 " --> pdb=" O ALA J 12 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA J 12 " --> pdb=" O HIS J 70 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL J 74 " --> pdb=" O ILE J 8 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE J 8 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE J 76 " --> pdb=" O ILE J 6 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE J 6 " --> pdb=" O ILE J 76 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG J 7 " --> pdb=" O SER J 101 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN J 99 " --> pdb=" O ARG J 9 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS J 11 " --> pdb=" O ASP J 97 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP J 97 " --> pdb=" O LYS J 11 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'K' and resid 29 through 35 removed outlier: 3.849A pdb=" N ILE K 30 " --> pdb=" O HIS K 23 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU K 82 " --> pdb=" O GLY K 18 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL K 83 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'K' and resid 82 through 87 removed outlier: 5.098A pdb=" N GLY K 87 " --> pdb=" O VAL K 112 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'L' and resid 28 through 32 removed outlier: 4.831A pdb=" N LEU L 80 " --> pdb=" O VAL L 97 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG L 82 " --> pdb=" O HIS L 95 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'L' and resid 35 through 40 removed outlier: 3.778A pdb=" N ARG L 35 " --> pdb=" O ARG L 53 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL L 51 " --> pdb=" O TYR L 37 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LYS L 50 " --> pdb=" O ILE L 66 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU L 56 " --> pdb=" O PHE L 60 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N PHE L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'P' and resid 4 through 9 removed outlier: 5.336A pdb=" N PHE P 16 " --> pdb=" O HIS P 9 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY P 49 " --> pdb=" O ASN P 40 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'Q' and resid 6 through 10 Processing sheet with id= 21, first strand: chain 'Q' and resid 18 through 30 No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 'S' and resid 47 through 51 Processing sheet with id= 23, first strand: chain '0' and resid 12 through 19 removed outlier: 4.724A pdb=" N ASN 0 23 " --> pdb=" O SER 0 19 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain '0' and resid 34 through 41 removed outlier: 6.689A pdb=" N SER 0 35 " --> pdb=" O ARG 0 50 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ARG 0 50 " --> pdb=" O SER 0 35 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG 0 37 " --> pdb=" O THR 0 48 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR 0 48 " --> pdb=" O ARG 0 37 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TRP 0 39 " --> pdb=" O PHE 0 46 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N PHE 0 46 " --> pdb=" O TRP 0 39 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLU 0 41 " --> pdb=" O LYS 0 44 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain '2' and resid 34 through 39 removed outlier: 4.497A pdb=" N HIS 2 34 " --> pdb=" O GLN 2 9 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N MET 2 54 " --> pdb=" O THR 2 10 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain '4' and resid 19 through 26 removed outlier: 6.090A pdb=" N HIS 4 19 " --> pdb=" O SER 4 13 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS 4 10 " --> pdb=" O ALA 4 52 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA 4 52 " --> pdb=" O LYS 4 10 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE 4 48 " --> pdb=" O SER 4 14 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU 4 51 " --> pdb=" O LEU 4 34 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU 4 34 " --> pdb=" O GLU 4 51 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain '7' and resid 22 through 25 No H-bonds generated for sheet with id= 27 Processing sheet with id= 28, first strand: chain '8' and resid 1 through 5 removed outlier: 5.485A pdb=" N ILE 8 23 " --> pdb=" O GLN 8 37 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'c' and resid 2 through 5 removed outlier: 3.626A pdb=" N VAL c 20 " --> pdb=" O ALA c 2 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'c' and resid 80 through 83 removed outlier: 3.580A pdb=" N ARG c 80 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU c 93 " --> pdb=" O GLU c 79 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ILE c 74 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N SER c 118 " --> pdb=" O ILE c 74 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASP c 114 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLY c 127 " --> pdb=" O GLN c 115 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN c 117 " --> pdb=" O GLY c 127 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'c' and resid 138 through 142 removed outlier: 4.386A pdb=" N SER c 139 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR c 173 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU c 180 " --> pdb=" O LEU c 176 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'i' and resid 56 through 60 removed outlier: 4.369A pdb=" N VAL i 57 " --> pdb=" O VAL i 69 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL i 69 " --> pdb=" O VAL i 57 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR i 67 " --> pdb=" O THR i 59 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'd' and resid 3 through 9 removed outlier: 4.166A pdb=" N SER d 199 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 13.565A pdb=" N GLY d 198 " --> pdb=" O LYS d 114 " (cutoff:3.500A) removed outlier: 12.262A pdb=" N LYS d 114 " --> pdb=" O GLY d 198 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU d 168 " --> pdb=" O SER d 113 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'd' and resid 11 through 16 removed outlier: 4.310A pdb=" N VAL d 20 " --> pdb=" O THR d 16 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'd' and resid 36 through 40 removed outlier: 3.562A pdb=" N GLN d 36 " --> pdb=" O GLN d 49 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU d 40 " --> pdb=" O TYR d 45 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR d 45 " --> pdb=" O LEU d 40 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN d 94 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'd' and resid 46 through 51 removed outlier: 5.598A pdb=" N ARG d 46 " --> pdb=" O LEU d 84 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'd' and resid 105 through 108 removed outlier: 6.066A pdb=" N LYS d 105 " --> pdb=" O VAL d 177 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'e' and resid 2 through 5 removed outlier: 4.343A pdb=" N LEU e 5 " --> pdb=" O SER e 10 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER e 10 " --> pdb=" O LEU e 5 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'e' and resid 117 through 120 removed outlier: 5.568A pdb=" N ARG e 117 " --> pdb=" O ASP e 184 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'f' and resid 65 through 69 removed outlier: 8.050A pdb=" N ILE f 85 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL f 40 " --> pdb=" O ILE f 85 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLY f 39 " --> pdb=" O GLY f 151 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLY f 151 " --> pdb=" O GLY f 39 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'g' and resid 16 through 19 removed outlier: 3.534A pdb=" N LYS g 27 " --> pdb=" O ASP g 16 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU g 33 " --> pdb=" O ILE g 26 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'g' and resid 41 through 45 removed outlier: 3.736A pdb=" N THR g 51 " --> pdb=" O LYS g 44 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'g' and resid 82 through 89 removed outlier: 3.759A pdb=" N LYS g 85 " --> pdb=" O LEU g 133 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU g 133 " --> pdb=" O LYS g 85 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR g 129 " --> pdb=" O LEU g 89 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU g 130 " --> pdb=" O PRO g 126 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'g' and resid 94 through 98 removed outlier: 3.691A pdb=" N SER g 106 " --> pdb=" O ARG g 95 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'h' and resid 16 through 20 removed outlier: 4.575A pdb=" N ASP h 17 " --> pdb=" O LEU h 5 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLN h 2 " --> pdb=" O ALA h 39 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LYS h 35 " --> pdb=" O LEU h 6 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'j' and resid 52 through 56 Processing sheet with id= 47, first strand: chain 'k' and resid 17 through 21 removed outlier: 6.755A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL k 10 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR k 6 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASN k 82 " --> pdb=" O MET k 7 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'm' and resid 37 through 40 No H-bonds generated for sheet with id= 48 Processing sheet with id= 49, first strand: chain 'm' and resid 62 through 65 removed outlier: 7.489A pdb=" N SER m 30 " --> pdb=" O LYS m 133 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS m 127 " --> pdb=" O VAL m 36 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'n' and resid 33 through 37 removed outlier: 6.228A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N TYR n 94 " --> pdb=" O VAL n 116 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'o' and resid 49 through 52 Processing sheet with id= 52, first strand: chain 'p' and resid 38 through 45 removed outlier: 6.684A pdb=" N THR p 25 " --> pdb=" O LYS p 87 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER p 83 " --> pdb=" O LYS p 29 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'p' and resid 49 through 52 removed outlier: 3.618A pdb=" N ALA p 49 " --> pdb=" O THR p 60 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N SER p 57 " --> pdb=" O THR p 76 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'r' and resid 11 through 15 removed outlier: 3.581A pdb=" N MET r 40 " --> pdb=" O VAL r 4 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'r' and resid 18 through 23 removed outlier: 4.263A pdb=" N GLN r 18 " --> pdb=" O ILE r 98 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'r' and resid 57 through 60 Processing sheet with id= 57, first strand: chain 'r' and resid 71 through 78 removed outlier: 3.962A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 's' and resid 2 through 8 Processing sheet with id= 59, first strand: chain 't' and resid 28 through 33 removed outlier: 6.487A pdb=" N ASN t 28 " --> pdb=" O LEU t 87 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG t 73 " --> pdb=" O HIS t 70 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LYS t 66 " --> pdb=" O ARG t 77 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ASP t 79 " --> pdb=" O LYS t 64 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LYS t 64 " --> pdb=" O ASP t 79 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS t 81 " --> pdb=" O VAL t 62 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL t 62 " --> pdb=" O LYS t 81 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA t 83 " --> pdb=" O THR t 60 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR t 60 " --> pdb=" O ALA t 83 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL t 85 " --> pdb=" O VAL t 58 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL t 58 " --> pdb=" O VAL t 85 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'u' and resid 40 through 45 No H-bonds generated for sheet with id= 60 Processing sheet with id= 61, first strand: chain 'u' and resid 82 through 87 removed outlier: 4.969A pdb=" N ARG u 82 " --> pdb=" O LYS u 97 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG u 86 " --> pdb=" O VAL u 93 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'w' and resid 69 through 72 removed outlier: 6.657A pdb=" N ALA w 39 " --> pdb=" O ARG w 9 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE w 89 " --> pdb=" O PRO w 27 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'y' and resid 27 through 31 removed outlier: 7.341A pdb=" N GLY y 27 " --> pdb=" O PHE y 69 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE y 69 " --> pdb=" O GLY y 27 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU y 29 " --> pdb=" O VAL y 67 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'y' and resid 51 through 54 removed outlier: 4.176A pdb=" N THR y 58 " --> pdb=" O GLY y 54 " (cutoff:3.500A) 1532 hydrogen bonds defined for protein. 4533 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2840 hydrogen bonds 4662 hydrogen bond angles 0 basepair planarities 1129 basepair parallelities 1774 stacking parallelities Total time for adding SS restraints: 216.13 Time building geometry restraints manager: 64.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 11778 1.28 - 1.42: 62746 1.42 - 1.56: 74338 1.56 - 1.69: 9504 1.69 - 1.83: 271 Bond restraints: 158637 Sorted by residual: bond pdb=" O3' C b2610 " pdb=" P C b2611 " ideal model delta sigma weight residual 1.607 1.826 -0.219 1.50e-02 4.44e+03 2.14e+02 bond pdb=" O3' U b2504 " pdb=" P G b2505 " ideal model delta sigma weight residual 1.607 1.810 -0.203 1.50e-02 4.44e+03 1.84e+02 bond pdb=" O3' C b2248 " pdb=" P U b2249 " ideal model delta sigma weight residual 1.607 1.779 -0.172 1.50e-02 4.44e+03 1.31e+02 bond pdb=" C5' U b 399 " pdb=" C4' U b 399 " ideal model delta sigma weight residual 1.508 1.672 -0.164 1.50e-02 4.44e+03 1.20e+02 bond pdb=" O3' C b1323 " pdb=" P G b1324 " ideal model delta sigma weight residual 1.607 1.766 -0.159 1.50e-02 4.44e+03 1.12e+02 ... (remaining 158632 not shown) Histogram of bond angle deviations from ideal: 83.82 - 96.34: 17 96.34 - 108.87: 56895 108.87 - 121.39: 138213 121.39 - 133.91: 42386 133.91 - 146.43: 26 Bond angle restraints: 237537 Sorted by residual: angle pdb=" O3' C W 36 " pdb=" P G W 37 " pdb=" O5' G W 37 " ideal model delta sigma weight residual 104.00 146.43 -42.43 1.50e+00 4.44e-01 8.00e+02 angle pdb=" C2' G b 400 " pdb=" C1' G b 400 " pdb=" N9 G b 400 " ideal model delta sigma weight residual 112.00 132.89 -20.89 1.50e+00 4.44e-01 1.94e+02 angle pdb=" C2' G b2123 " pdb=" C1' G b2123 " pdb=" N9 G b2123 " ideal model delta sigma weight residual 112.00 131.78 -19.78 1.50e+00 4.44e-01 1.74e+02 angle pdb=" C2' A b1275 " pdb=" C1' A b1275 " pdb=" N9 A b1275 " ideal model delta sigma weight residual 114.00 133.61 -19.61 1.50e+00 4.44e-01 1.71e+02 angle pdb=" O3' G b1930 " pdb=" C3' G b1930 " pdb=" C2' G b1930 " ideal model delta sigma weight residual 109.50 128.57 -19.07 1.50e+00 4.44e-01 1.62e+02 ... (remaining 237532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 79032 35.98 - 71.96: 5064 71.96 - 107.93: 446 107.93 - 143.91: 72 143.91 - 179.89: 64 Dihedral angle restraints: 84678 sinusoidal: 68359 harmonic: 16319 Sorted by residual: dihedral pdb=" CA THR d 151 " pdb=" C THR d 151 " pdb=" N PRO d 152 " pdb=" CA PRO d 152 " ideal model delta harmonic sigma weight residual 180.00 -98.45 -81.55 0 5.00e+00 4.00e-02 2.66e+02 dihedral pdb=" C4' C b1079 " pdb=" C3' C b1079 " pdb=" C2' C b1079 " pdb=" C1' C b1079 " ideal model delta sinusoidal sigma weight residual 36.00 -49.81 85.81 1 8.00e+00 1.56e-02 1.39e+02 dihedral pdb=" C5' C b1079 " pdb=" C4' C b1079 " pdb=" C3' C b1079 " pdb=" O3' C b1079 " ideal model delta sinusoidal sigma weight residual 82.00 166.46 -84.46 1 8.00e+00 1.56e-02 1.36e+02 ... (remaining 84675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.293: 29976 0.293 - 0.586: 388 0.586 - 0.879: 23 0.879 - 1.172: 6 1.172 - 1.465: 3 Chirality restraints: 30396 Sorted by residual: chirality pdb=" C4' U b1657 " pdb=" C5' U b1657 " pdb=" O4' U b1657 " pdb=" C3' U b1657 " both_signs ideal model delta sigma weight residual False -2.50 -1.03 -1.47 2.00e-01 2.50e+01 5.37e+01 chirality pdb=" C1' A b1275 " pdb=" O4' A b1275 " pdb=" C2' A b1275 " pdb=" N9 A b1275 " both_signs ideal model delta sigma weight residual False 2.44 1.09 1.35 2.00e-01 2.50e+01 4.54e+01 chirality pdb=" C3' C b2161 " pdb=" C4' C b2161 " pdb=" O3' C b2161 " pdb=" C2' C b2161 " both_signs ideal model delta sigma weight residual False -2.48 -1.14 -1.34 2.00e-01 2.50e+01 4.47e+01 ... (remaining 30393 not shown) Planarity restraints: 12579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G b1059 " 0.058 2.00e-02 2.50e+03 1.62e-01 7.83e+02 pdb=" N9 G b1059 " 0.030 2.00e-02 2.50e+03 pdb=" C8 G b1059 " -0.021 2.00e-02 2.50e+03 pdb=" N7 G b1059 " -0.030 2.00e-02 2.50e+03 pdb=" C5 G b1059 " -0.041 2.00e-02 2.50e+03 pdb=" C6 G b1059 " -0.124 2.00e-02 2.50e+03 pdb=" O6 G b1059 " 0.341 2.00e-02 2.50e+03 pdb=" N1 G b1059 " -0.361 2.00e-02 2.50e+03 pdb=" C2 G b1059 " -0.080 2.00e-02 2.50e+03 pdb=" N2 G b1059 " 0.186 2.00e-02 2.50e+03 pdb=" N3 G b1059 " 0.050 2.00e-02 2.50e+03 pdb=" C4 G b1059 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 CLM b9000 " -0.180 2.00e-02 2.50e+03 2.22e-01 6.18e+02 pdb=" C2 CLM b9000 " 0.071 2.00e-02 2.50e+03 pdb=" C3 CLM b9000 " -0.267 2.00e-02 2.50e+03 pdb=" N2 CLM b9000 " 0.372 2.00e-02 2.50e+03 pdb=" O2 CLM b9000 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G b1382 " -0.019 2.00e-02 2.50e+03 1.41e-01 5.95e+02 pdb=" N9 G b1382 " 0.022 2.00e-02 2.50e+03 pdb=" C8 G b1382 " 0.007 2.00e-02 2.50e+03 pdb=" N7 G b1382 " 0.023 2.00e-02 2.50e+03 pdb=" C5 G b1382 " -0.064 2.00e-02 2.50e+03 pdb=" C6 G b1382 " 0.109 2.00e-02 2.50e+03 pdb=" O6 G b1382 " -0.233 2.00e-02 2.50e+03 pdb=" N1 G b1382 " 0.358 2.00e-02 2.50e+03 pdb=" C2 G b1382 " 0.052 2.00e-02 2.50e+03 pdb=" N2 G b1382 " -0.178 2.00e-02 2.50e+03 pdb=" N3 G b1382 " -0.029 2.00e-02 2.50e+03 pdb=" C4 G b1382 " -0.049 2.00e-02 2.50e+03 ... (remaining 12576 not shown) Histogram of nonbonded interaction distances: 0.39 - 1.29: 125 1.29 - 2.19: 794 2.19 - 3.10: 108094 3.10 - 4.00: 452560 4.00 - 4.90: 746746 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1308319 Sorted by model distance: nonbonded pdb=" N3 G b1062 " pdb=" CD2 LEU i 79 " model vdw 0.389 3.540 nonbonded pdb=" N3 C b1076 " pdb=" CG MET i 135 " model vdw 0.395 3.520 nonbonded pdb=" C4' G b1062 " pdb=" CB LEU i 78 " model vdw 0.434 3.870 nonbonded pdb=" C3' G b1062 " pdb=" CA LEU i 78 " model vdw 0.445 3.900 nonbonded pdb=" C2 A b1077 " pdb=" C ARG i 133 " model vdw 0.479 3.570 ... (remaining 1308314 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4710 5.49 5 S 144 5.16 5 Cl 2 4.86 5 C 73162 2.51 5 N 27167 2.21 5 O 40726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 17.110 Check model and map are aligned: 1.600 Convert atoms to be neutral: 0.930 Process input model: 497.810 Find NCS groups from input model: 3.470 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.040 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 527.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.219 158637 Z= 0.442 Angle : 1.324 42.429 237537 Z= 0.889 Chirality : 0.099 1.465 30396 Planarity : 0.012 0.222 12579 Dihedral : 19.577 179.891 74150 Min Nonbonded Distance : 0.389 Molprobity Statistics. All-atom Clashscore : 31.38 Ramachandran Plot: Outliers : 3.00 % Allowed : 8.13 % Favored : 88.86 % Rotamer Outliers : 3.04 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.07 % Twisted Proline : 0.52 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.10), residues: 5630 helix: -2.65 (0.09), residues: 1647 sheet: -2.12 (0.15), residues: 941 loop : -1.07 (0.11), residues: 3042 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2068 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1926 time to evaluate : 6.048 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 outliers start: 142 outliers final: 26 residues processed: 2019 average time/residue: 1.4212 time to fit residues: 4817.6994 Evaluate side-chains 1306 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1280 time to evaluate : 5.778 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 2 residues processed: 26 average time/residue: 1.0661 time to fit residues: 59.0687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 861 optimal weight: 20.0000 chunk 773 optimal weight: 9.9990 chunk 428 optimal weight: 6.9990 chunk 264 optimal weight: 3.9990 chunk 521 optimal weight: 10.0000 chunk 413 optimal weight: 0.9980 chunk 799 optimal weight: 3.9990 chunk 309 optimal weight: 10.0000 chunk 486 optimal weight: 3.9990 chunk 595 optimal weight: 10.0000 chunk 926 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN B 176 ASN ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN D 119 HIS ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN D 135 GLN D 139 ASN ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN E 77 ASN E 82 HIS E 88 HIS E 147 ASN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN I 80 HIS K 23 HIS K 39 ASN K 80 ASN L 19 ASN L 58 ASN ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 HIS ** O 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 HIS O 50 HIS ** P 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN P 59 HIS Q 30 HIS Q 50 ASN S 51 HIS S 56 HIS T 12 GLN T 74 HIS 1 25 GLN 1 58 ASN 7 28 ASN 8 13 ASN ** c 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 260 ASN ** i 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 110 GLN ** d 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 30 ASN g 38 ASN g 45 HIS g 115 HIS h 28 ASN ** h 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 128 HIS k 3 GLN n 18 GLN ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 100 HIS q 44 GLN q 52 GLN s 7 HIS s 61 ASN t 59 ASN t 91 GLN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 78 GLN z 21 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.194 158637 Z= 0.285 Angle : 0.889 28.439 237537 Z= 0.453 Chirality : 0.048 1.585 30396 Planarity : 0.007 0.143 12579 Dihedral : 18.043 179.652 62889 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 1.17 % Allowed : 6.80 % Favored : 92.02 % Rotamer Outliers : 5.19 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.07 % Twisted Proline : 2.08 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.11), residues: 5630 helix: -0.72 (0.12), residues: 1688 sheet: -1.59 (0.15), residues: 1004 loop : -1.24 (0.11), residues: 2938 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1616 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 1373 time to evaluate : 6.006 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 outliers start: 243 outliers final: 137 residues processed: 1507 average time/residue: 1.3666 time to fit residues: 3577.5412 Evaluate side-chains 1330 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1193 time to evaluate : 6.074 Switching outliers to nearest non-outliers outliers start: 137 outliers final: 0 residues processed: 137 average time/residue: 1.0947 time to fit residues: 293.4752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 514 optimal weight: 10.0000 chunk 287 optimal weight: 6.9990 chunk 770 optimal weight: 7.9990 chunk 630 optimal weight: 10.0000 chunk 255 optimal weight: 0.9990 chunk 927 optimal weight: 2.9990 chunk 1002 optimal weight: 8.9990 chunk 826 optimal weight: 0.2980 chunk 920 optimal weight: 5.9990 chunk 316 optimal weight: 8.9990 chunk 744 optimal weight: 5.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS E 121 ASN ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 GLN O 41 HIS P 18 GLN P 63 GLN T 69 ASN 0 6 GLN 8 35 GLN c 153 GLN c 226 ASN d 150 GLN ** f 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 22 GLN ** h 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 54 GLN ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 82 HIS s 31 GLN s 61 ASN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 74 ASN ** w 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.248 158637 Z= 0.227 Angle : 0.709 19.565 237537 Z= 0.368 Chirality : 0.041 0.627 30396 Planarity : 0.006 0.115 12579 Dihedral : 17.361 179.721 62889 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.82 % Favored : 91.33 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.07 % Twisted Proline : 2.08 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.11), residues: 5630 helix: -0.14 (0.12), residues: 1683 sheet: -1.56 (0.15), residues: 1073 loop : -1.28 (0.11), residues: 2874 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1462 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1306 time to evaluate : 6.140 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 outliers start: 156 outliers final: 69 residues processed: 1394 average time/residue: 1.3611 time to fit residues: 3311.5880 Evaluate side-chains 1208 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1139 time to evaluate : 6.129 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 0 residues processed: 69 average time/residue: 1.1071 time to fit residues: 152.0611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 916 optimal weight: 9.9990 chunk 697 optimal weight: 10.0000 chunk 481 optimal weight: 30.0000 chunk 102 optimal weight: 50.0000 chunk 442 optimal weight: 10.0000 chunk 623 optimal weight: 10.0000 chunk 931 optimal weight: 30.0000 chunk 985 optimal weight: 10.0000 chunk 486 optimal weight: 10.0000 chunk 882 optimal weight: 6.9990 chunk 265 optimal weight: 20.0000 overall best weight: 9.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN F 68 GLN G 129 ASN ** G 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 HIS ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 48 GLN ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 46 HIS T 12 GLN 1 58 ASN ** 8 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 53 HIS c 134 ASN c 153 GLN ** c 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 49 GLN d 150 GLN e 115 GLN f 27 GLN f 52 ASN g 30 ASN ** h 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 119 ASN h 135 HIS j 131 ASN l 99 ASN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 37 GLN r 6 GLN s 9 HIS t 48 GLN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 4 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.258 158637 Z= 0.455 Angle : 0.913 14.831 237537 Z= 0.457 Chirality : 0.050 0.508 30396 Planarity : 0.007 0.149 12579 Dihedral : 17.729 179.975 62889 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.83 % Allowed : 8.90 % Favored : 90.27 % Rotamer Outliers : 5.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.07 % Twisted Proline : 1.56 % 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: -2.02 (0.11), residues: 5630 helix: -0.47 (0.12), residues: 1683 sheet: -1.61 (0.15), residues: 1089 loop : -1.73 (0.11), residues: 2858 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1497 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1252 time to evaluate : 6.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 245 outliers final: 148 residues processed: 1390 average time/residue: 1.3380 time to fit residues: 3249.6540 Evaluate side-chains 1300 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1152 time to evaluate : 6.092 Switching outliers to nearest non-outliers outliers start: 148 outliers final: 0 residues processed: 148 average time/residue: 1.0904 time to fit residues: 315.8598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 821 optimal weight: 5.9990 chunk 559 optimal weight: 8.9990 chunk 14 optimal weight: 40.0000 chunk 734 optimal weight: 10.0000 chunk 406 optimal weight: 0.0030 chunk 841 optimal weight: 20.0000 chunk 681 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 503 optimal weight: 4.9990 chunk 884 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 overall best weight: 4.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 ASN ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 HIS T 19 HIS T 69 ASN 1 39 GLN 1 58 ASN ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 93 ASN ** d 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN ** g 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 73 ASN l 54 GLN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 16 HIS n 62 ASN ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 37 GLN q 44 GLN q 52 GLN r 6 GLN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 74 ASN ** w 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.127 158637 Z= 0.249 Angle : 0.713 19.917 237537 Z= 0.367 Chirality : 0.041 0.467 30396 Planarity : 0.006 0.159 12579 Dihedral : 17.344 179.442 62889 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.19 % Favored : 91.05 % Rotamer Outliers : 2.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.07 % Twisted Proline : 1.04 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.11), residues: 5630 helix: -0.22 (0.12), residues: 1692 sheet: -1.58 (0.15), residues: 1070 loop : -1.71 (0.11), residues: 2868 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1332 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1199 time to evaluate : 6.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 133 outliers final: 71 residues processed: 1263 average time/residue: 1.3072 time to fit residues: 2884.3465 Evaluate side-chains 1188 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1117 time to evaluate : 6.076 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 1.0696 time to fit residues: 151.6782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 331 optimal weight: 9.9990 chunk 887 optimal weight: 0.0030 chunk 194 optimal weight: 10.0000 chunk 578 optimal weight: 10.0000 chunk 243 optimal weight: 20.0000 chunk 986 optimal weight: 10.0000 chunk 819 optimal weight: 5.9990 chunk 456 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 326 optimal weight: 9.9990 chunk 518 optimal weight: 9.9990 overall best weight: 7.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN B 102 ASN C 184 ASN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN F 63 ASN ** G 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 HIS P 63 GLN 1 58 ASN ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 29 GLN ** 8 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 153 GLN ** c 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 49 GLN e 115 GLN g 30 ASN g 128 GLN h 133 GLN l 4 ASN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 18 GLN n 107 ASN o 38 GLN p 3 ASN p 56 HIS ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 74 ASN w 49 ASN ** w 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.089 158637 Z= 0.339 Angle : 0.789 15.252 237537 Z= 0.399 Chirality : 0.044 0.476 30396 Planarity : 0.006 0.158 12579 Dihedral : 17.459 177.873 62889 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.54 % Favored : 89.73 % Rotamer Outliers : 4.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.07 % Twisted Proline : 1.04 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.11), residues: 5630 helix: -0.28 (0.12), residues: 1689 sheet: -1.66 (0.15), residues: 1065 loop : -1.93 (0.11), residues: 2876 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1363 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1176 time to evaluate : 6.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 187 outliers final: 116 residues processed: 1272 average time/residue: 1.3118 time to fit residues: 2921.5337 Evaluate side-chains 1238 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1122 time to evaluate : 6.116 Switching outliers to nearest non-outliers outliers start: 116 outliers final: 0 residues processed: 116 average time/residue: 1.0811 time to fit residues: 246.1647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 951 optimal weight: 6.9990 chunk 111 optimal weight: 30.0000 chunk 562 optimal weight: 10.0000 chunk 720 optimal weight: 10.0000 chunk 558 optimal weight: 10.0000 chunk 830 optimal weight: 8.9990 chunk 551 optimal weight: 30.0000 chunk 983 optimal weight: 6.9990 chunk 615 optimal weight: 10.0000 chunk 599 optimal weight: 30.0000 chunk 453 optimal weight: 10.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 GLN T 12 GLN 1 36 GLN 1 58 ASN ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 29 GLN ** 8 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN g 128 GLN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 88 ASN p 77 HIS q 37 GLN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.428 158637 Z= 0.404 Angle : 0.838 27.369 237537 Z= 0.424 Chirality : 0.046 0.471 30396 Planarity : 0.007 0.149 12579 Dihedral : 17.629 178.493 62889 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.71 % Allowed : 9.80 % Favored : 89.48 % Rotamer Outliers : 3.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.07 % Twisted Proline : 1.04 % 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: -2.31 (0.10), residues: 5630 helix: -0.55 (0.12), residues: 1697 sheet: -1.68 (0.15), residues: 1046 loop : -2.09 (0.11), residues: 2887 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1328 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1173 time to evaluate : 6.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 155 outliers final: 83 residues processed: 1241 average time/residue: 1.3125 time to fit residues: 2837.4386 Evaluate side-chains 1203 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1120 time to evaluate : 6.210 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 0 residues processed: 83 average time/residue: 1.0501 time to fit residues: 173.8251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 608 optimal weight: 10.0000 chunk 392 optimal weight: 20.0000 chunk 587 optimal weight: 30.0000 chunk 296 optimal weight: 5.9990 chunk 193 optimal weight: 7.9990 chunk 190 optimal weight: 7.9990 chunk 625 optimal weight: 8.9990 chunk 669 optimal weight: 10.0000 chunk 486 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 772 optimal weight: 6.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 HIS ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 ASN O 27 GLN ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 59 HIS P 63 GLN 1 36 GLN 1 58 ASN ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 29 GLN ** 8 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN g 30 ASN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 88 ASN n 107 ASN q 44 GLN q 52 GLN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 49 ASN ** w 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.419 158637 Z= 0.355 Angle : 0.797 22.254 237537 Z= 0.405 Chirality : 0.044 0.442 30396 Planarity : 0.007 0.144 12579 Dihedral : 17.557 179.269 62889 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.71 % Allowed : 9.96 % Favored : 89.33 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.07 % Twisted Proline : 1.04 % 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: -2.33 (0.10), residues: 5630 helix: -0.51 (0.12), residues: 1705 sheet: -1.68 (0.15), residues: 1010 loop : -2.15 (0.11), residues: 2915 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1289 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1186 time to evaluate : 6.166 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 outliers start: 103 outliers final: 60 residues processed: 1222 average time/residue: 1.3396 time to fit residues: 2855.8148 Evaluate side-chains 1203 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1143 time to evaluate : 6.186 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 1.1326 time to fit residues: 134.5398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 894 optimal weight: 8.9990 chunk 941 optimal weight: 9.9990 chunk 859 optimal weight: 10.0000 chunk 916 optimal weight: 9.9990 chunk 551 optimal weight: 20.0000 chunk 399 optimal weight: 0.9990 chunk 719 optimal weight: 10.0000 chunk 281 optimal weight: 5.9990 chunk 827 optimal weight: 20.0000 chunk 866 optimal weight: 6.9990 chunk 912 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 ASN L 111 GLN O 27 GLN ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 58 ASN ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 29 GLN ** 8 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 49 GLN ** e 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN h 135 HIS ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 88 ASN n 107 ASN q 44 GLN q 52 GLN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.5849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 1.131 158637 Z= 0.369 Angle : 0.758 88.632 237537 Z= 0.381 Chirality : 0.041 0.391 30396 Planarity : 0.006 0.145 12579 Dihedral : 17.380 179.509 62889 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.60 % Allowed : 9.13 % Favored : 90.27 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.07 % Twisted Proline : 1.04 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.11), residues: 5630 helix: -0.36 (0.12), residues: 1693 sheet: -1.61 (0.15), residues: 1017 loop : -2.08 (0.11), residues: 2920 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1218 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1157 time to evaluate : 6.107 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 outliers start: 61 outliers final: 40 residues processed: 1175 average time/residue: 1.3375 time to fit residues: 2747.4018 Evaluate side-chains 1155 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1115 time to evaluate : 5.800 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 1.1160 time to fit residues: 90.5932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 601 optimal weight: 10.0000 chunk 968 optimal weight: 20.0000 chunk 591 optimal weight: 10.0000 chunk 459 optimal weight: 20.0000 chunk 673 optimal weight: 10.0000 chunk 1016 optimal weight: 3.9990 chunk 935 optimal weight: 20.0000 chunk 809 optimal weight: 6.9990 chunk 84 optimal weight: 30.0000 chunk 625 optimal weight: 10.0000 chunk 496 optimal weight: 10.0000 overall best weight: 8.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 HIS O 27 GLN ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 12 GLN ** T 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 29 GLN ** 8 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN f 21 ASN g 30 ASN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 88 ASN ** q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 44 GLN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 49 ASN ** w 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.146 158637 Z= 0.526 Angle : 0.836 106.099 237537 Z= 0.408 Chirality : 0.043 0.612 30396 Planarity : 0.006 0.167 12579 Dihedral : 17.380 179.604 62889 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.60 % Allowed : 9.40 % Favored : 90.00 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.07 % Twisted Proline : 1.04 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.11), residues: 5630 helix: -0.37 (0.12), residues: 1691 sheet: -1.61 (0.15), residues: 1017 loop : -2.09 (0.11), residues: 2922 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11260 Ramachandran restraints generated. 5630 Oldfield, 0 Emsley, 5630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1124 time to evaluate : 6.324 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 outliers start: 39 outliers final: 31 residues processed: 1133 average time/residue: 1.3199 time to fit residues: 2619.1745 Evaluate side-chains 1135 residues out of total 4679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1104 time to evaluate : 6.105 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 1.1184 time to fit residues: 71.8028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 642 optimal weight: 10.0000 chunk 861 optimal weight: 20.0000 chunk 247 optimal weight: 3.9990 chunk 746 optimal weight: 4.9990 chunk 119 optimal weight: 20.0000 chunk 224 optimal weight: 0.5980 chunk 810 optimal weight: 0.0570 chunk 339 optimal weight: 50.0000 chunk 832 optimal weight: 0.3980 chunk 102 optimal weight: 50.0000 chunk 149 optimal weight: 10.0000 overall best weight: 2.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 27 GLN ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 88 ASN ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 44 GLN q 52 GLN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.155550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.124375 restraints weight = 286241.694| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.18 r_work: 0.3639 rms_B_bonded: 1.12 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 1.22 restraints_weight: 0.2500 r_work: 0.3612 rms_B_bonded: 1.40 restraints_weight: 0.1250 r_work: 0.3596 rms_B_bonded: 1.66 restraints_weight: 0.0625 r_work: 0.3577 rms_B_bonded: 2.02 restraints_weight: 0.0312 r_work: 0.3553 rms_B_bonded: 2.51 restraints_weight: 0.0156 r_work: 0.3522 rms_B_bonded: 3.18 restraints_weight: 0.0078 r_work: 0.3480 rms_B_bonded: 4.15 restraints_weight: 0.0039 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.146 158637 Z= 0.531 Angle : 0.838 106.099 237537 Z= 0.409 Chirality : 0.043 0.612 30396 Planarity : 0.006 0.213 12579 Dihedral : 17.380 179.604 62889 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.60 % Allowed : 9.40 % Favored : 90.00 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.07 % Twisted Proline : 1.04 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.11), residues: 5630 helix: -0.37 (0.12), residues: 1691 sheet: -1.61 (0.15), residues: 1017 loop : -2.09 (0.11), residues: 2922 =============================================================================== Job complete usr+sys time: 42132.60 seconds wall clock time: 724 minutes 22.68 seconds (43462.68 seconds total)