Starting phenix.real_space_refine (version: dev) on Sat Apr 9 22:32:06 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbu_6483/04_2022/3jbu_6483_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbu_6483/04_2022/3jbu_6483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbu_6483/04_2022/3jbu_6483.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbu_6483/04_2022/3jbu_6483.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbu_6483/04_2022/3jbu_6483_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbu_6483/04_2022/3jbu_6483_neut.pdb" } resolution = 3.64 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 "I ASP 106": "OD1" <-> "OD2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "P GLU 45": "OE1" <-> "OE2" Residue "P GLU 48": "OE1" <-> "OE2" Residue "P ASP 55": "OD1" <-> "OD2" Residue "0 ARG 3": "NH1" <-> "NH2" Residue "0 ARG 11": "NH1" <-> "NH2" Residue "0 ARG 18": "NH1" <-> "NH2" Residue "0 ARG 37": "NH1" <-> "NH2" Residue "0 GLU 43": "OE1" <-> "OE2" Residue "0 ARG 50": "NH1" <-> "NH2" Residue "0 ARG 57": "NH1" <-> "NH2" Residue "0 ARG 74": "NH1" <-> "NH2" Residue "1 GLU 12": "OE1" <-> "OE2" Residue "1 ARG 29": "NH1" <-> "NH2" Residue "1 ARG 47": "NH1" <-> "NH2" Residue "1 ARG 52": "NH1" <-> "NH2" Residue "1 GLU 59": "OE1" <-> "OE2" Residue "2 ARG 11": "NH1" <-> "NH2" Residue "2 ARG 30": "NH1" <-> "NH2" Residue "2 GLU 37": "OE1" <-> "OE2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "2 GLU 59": "OE1" <-> "OE2" Residue "3 ARG 10": "NH1" <-> "NH2" Residue "3 ARG 16": "NH1" <-> "NH2" Residue "3 ARG 52": "NH1" <-> "NH2" Residue "4 GLU 32": "OE1" <-> "OE2" Residue "4 GLU 35": "OE1" <-> "OE2" Residue "4 ARG 44": "NH1" <-> "NH2" Residue "6 ARG 3": "NH1" <-> "NH2" Residue "6 ARG 12": "NH1" <-> "NH2" Residue "6 ARG 14": "NH1" <-> "NH2" Residue "6 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 19": "NH1" <-> "NH2" Residue "6 ARG 21": "NH1" <-> "NH2" Residue "6 ARG 33": "NH1" <-> "NH2" Residue "6 ARG 41": "NH1" <-> "NH2" Residue "7 ARG 13": "NH1" <-> "NH2" Residue "7 ARG 30": "NH1" <-> "NH2" Residue "7 ARG 40": "NH1" <-> "NH2" Residue "7 ARG 42": "NH1" <-> "NH2" Residue "8 ARG 24": "NH1" <-> "NH2" Residue "c GLU 35": "OE1" <-> "OE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ARG 63": "NH1" <-> "NH2" Residue "c ARG 80": "NH1" <-> "NH2" Residue "c TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 133": "NH1" <-> "NH2" Residue "c GLU 145": "OE1" <-> "OE2" Residue "c TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 167": "NH1" <-> "NH2" Residue "c ARG 177": "NH1" <-> "NH2" Residue "c ARG 182": "NH1" <-> "NH2" Residue "c ARG 189": "NH1" <-> "NH2" Residue "c GLU 194": "OE1" <-> "OE2" Residue "c GLU 199": "OE1" <-> "OE2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c ARG 212": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d GLU 17": "OE1" <-> "OE2" Residue "d GLU 28": "OE1" <-> "OE2" Residue "d GLU 30": "OE1" <-> "OE2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 59": "NH1" <-> "NH2" Residue "d GLU 64": "OE1" <-> "OE2" Residue "d GLU 74": "OE1" <-> "OE2" Residue "d ARG 77": "NH1" <-> "NH2" Residue "d GLU 81": "OE1" <-> "OE2" Residue "d ARG 83": "NH1" <-> "NH2" Residue "d GLU 88": "OE1" <-> "OE2" Residue "d GLU 168": "OE1" <-> "OE2" Residue "d ARG 169": "NH1" <-> "NH2" Residue "d GLU 183": "OE1" <-> "OE2" Residue "d ARG 184": "NH1" <-> "NH2" Residue "e ARG 21": "NH1" <-> "NH2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e ARG 61": "NH1" <-> "NH2" Residue "e ARG 88": "NH1" <-> "NH2" Residue "e ARG 102": "NH1" <-> "NH2" Residue "e GLU 152": "OE1" <-> "OE2" Residue "e ARG 162": "NH1" <-> "NH2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "e ASP 191": "OD1" <-> "OD2" Residue "f GLU 32": "OE1" <-> "OE2" Residue "f GLU 42": "OE1" <-> "OE2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f GLU 94": "OE1" <-> "OE2" Residue "f GLU 98": "OE1" <-> "OE2" Residue "f ARG 102": "NH1" <-> "NH2" Residue "f ARG 110": "NH1" <-> "NH2" Residue "f ARG 112": "NH1" <-> "NH2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f ASP 123": "OD1" <-> "OD2" Residue "f ARG 133": "NH1" <-> "NH2" Residue "f GLU 134": "OE1" <-> "OE2" Residue "f GLU 140": "OE1" <-> "OE2" Residue "f ASP 142": "OD1" <-> "OD2" Residue "f TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 164": "OE1" <-> "OE2" Residue "g ARG 3": "NH1" <-> "NH2" Residue "g ASP 16": "OD1" <-> "OD2" Residue "g GLU 32": "OE1" <-> "OE2" Residue "g PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 81": "OE1" <-> "OE2" Residue "g ASP 114": "OD1" <-> "OD2" Residue "g GLU 130": "OE1" <-> "OE2" Residue "g ARG 153": "NH1" <-> "NH2" Residue "g ARG 163": "NH1" <-> "NH2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "g GLU 173": "OE1" <-> "OE2" Residue "h ARG 27": "NH1" <-> "NH2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j GLU 31": "OE1" <-> "OE2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j GLU 91": "OE1" <-> "OE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "k GLU 92": "OE1" <-> "OE2" Residue "k GLU 110": "OE1" <-> "OE2" Residue "k GLU 121": "OE1" <-> "OE2" Residue "l GLU 10": "OE1" <-> "OE2" Residue "l ARG 21": "NH1" <-> "NH2" Residue "l ARG 33": "NH1" <-> "NH2" Residue "l ARG 41": "NH1" <-> "NH2" Residue "l ARG 47": "NH1" <-> "NH2" Residue "l GLU 51": "OE1" <-> "OE2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 76": "OE1" <-> "OE2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m GLU 47": "OE1" <-> "OE2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m GLU 75": "OE1" <-> "OE2" Residue "m GLU 90": "OE1" <-> "OE2" Residue "m TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 104": "OE1" <-> "OE2" Residue "m ASP 106": "OD1" <-> "OD2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n GLU 82": "OE1" <-> "OE2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 114": "OE1" <-> "OE2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "n GLU 120": "OE1" <-> "OE2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o GLU 46": "OE1" <-> "OE2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "p GLU 11": "OE1" <-> "OE2" Residue "p ARG 21": "NH1" <-> "NH2" Residue "p ARG 39": "NH1" <-> "NH2" Residue "p GLU 44": "OE1" <-> "OE2" Residue "p ARG 62": "NH1" <-> "NH2" Residue "p GLU 68": "OE1" <-> "OE2" Residue "p GLU 71": "OE1" <-> "OE2" Residue "p ARG 89": "NH1" <-> "NH2" Residue "p ARG 101": "NH1" <-> "NH2" Residue "p ARG 109": "NH1" <-> "NH2" Residue "q ARG 3": "NH1" <-> "NH2" Residue "q ARG 6": "NH1" <-> "NH2" Residue "q ARG 13": "NH1" <-> "NH2" Residue "q ARG 33": "NH1" <-> "NH2" Residue "q PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 48": "NH1" <-> "NH2" Residue "q ARG 70": "NH1" <-> "NH2" Residue "q GLU 111": "OE1" <-> "OE2" Residue "r GLU 16": "OE1" <-> "OE2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 23": "OE1" <-> "OE2" Residue "r GLU 31": "OE1" <-> "OE2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r GLU 70": "OE1" <-> "OE2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r ARG 79": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "r PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 2": "OE1" <-> "OE2" Residue "s GLU 59": "OE1" <-> "OE2" Residue "s PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 78": "OE1" <-> "OE2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "t GLU 4": "OE1" <-> "OE2" Residue "t GLU 52": "OE1" <-> "OE2" Residue "t GLU 54": "OE1" <-> "OE2" Residue "t GLU 56": "OE1" <-> "OE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ARG 7": "NH1" <-> "NH2" Residue "u GLU 10": "OE1" <-> "OE2" Residue "u ARG 82": "NH1" <-> "NH2" Residue "u PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 86": "NH1" <-> "NH2" Residue "u GLU 88": "OE1" <-> "OE2" Residue "u ARG 94": "NH1" <-> "NH2" Residue "u PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 101": "OE1" <-> "OE2" Residue "w ASP 45": "OD1" <-> "OD2" Residue "w GLU 55": "OE1" <-> "OE2" Residue "w TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 69": "OE1" <-> "OE2" Residue "w ASP 76": "OD1" <-> "OD2" Residue "y GLU 17": "OE1" <-> "OE2" Residue "y PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 83": "OE1" <-> "OE2" Residue "z GLU 3": "OE1" <-> "OE2" Residue "z PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 143334 Number of models: 1 Model: "" Number of chains: 54 Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1105 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "G" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1174 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "M" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 876 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "N" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "O" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 716 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "S" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "T" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "U" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "0" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "1" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "2" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "3" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "4" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "6" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "7" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "8" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "c" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "d" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "e" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "f" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "g" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "h" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'CIS': 1, 'TRANS': 144, '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: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 203 Classifications: {'peptide': 26} Link IDs: {'CIS': 4, 'PTRANS': 1, 'TRANS': 20} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 32831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1530, 32831 Classifications: {'RNA': 1530} Modifications used: {'rna3p_pyr': 569, 'rna2p_pur': 120, 'rna3p_pur': 752, 'rna2p_pyr': 89} Link IDs: {'rna3p': 1320, 'rna2p': 209} Chain: "X" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 232 Classifications: {'RNA': 11} Modifications used: {'rna3p_pyr': 6, 'rna2p_pur': 1, 'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 3} Link IDs: {'rna3p': 8, 'rna2p': 2} Chain: "a" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2528 Classifications: {'RNA': 118} Modifications used: {'rna3p_pyr': 49, 'rna2p_pur': 8, 'rna3p_pur': 56, 'rna2p_pyr': 5} Link IDs: {'rna3p': 104, 'rna2p': 13} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 62321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62321 Classifications: {'RNA': 2903} Modifications used: {'rna2p_pyr': 139, 'rna3p_pyr': 1090, 'p5*END': 1, 'rna3p_pur': 1428, 'rna2p_pur': 246} Link IDs: {'rna3p': 2517, 'rna2p': 385} Chain: "v" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Classifications: {'RNA': 76} Modifications used: {'rna3p_pyr': 33, 'p5*END': 1, 'rna2p_pur': 7, 'rna3p_pur': 31, 'rna2p_pyr': 5} Link IDs: {'rna3p': 64, 'rna2p': 11} Time building chain proxies: 56.95, per 1000 atoms: 0.40 Number of scatterers: 143334 At special positions: 0 Unit cell: (271.92, 291.72, 228.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 138 16.00 P 4637 15.00 O 40018 8.00 N 26713 7.00 C 71828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 51757 O5' U A 375 .*. O " rejected from bonding due to valence issues. Atom "ATOM 51780 O4' G A 376 .*. O " rejected from bonding due to valence issues. Atom "ATOM 51757 O5' U A 375 .*. O " rejected from bonding due to valence issues. Atom "ATOM 72631 O5' U A1348 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 56.38 Conformation dependent library (CDL) restraints added in 5.4 seconds 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10280 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 69 sheets defined 34.1% alpha, 15.8% beta 1001 base pairs and 1615 stacking pairs defined. Time for finding SS restraints: 40.79 Creating SS restraints... Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 32 through 36 removed outlier: 3.975A pdb=" N ASN B 35 " --> pdb=" O GLY B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.566A pdb=" N MET B 48 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA B 54 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE B 59 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 removed outlier: 4.112A pdb=" N ASP B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 121 removed outlier: 3.598A pdb=" N VAL B 106 " --> pdb=" O ASN B 102 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLN B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 145 removed outlier: 4.142A pdb=" N ALA B 133 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASN B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 4.230A pdb=" N ASP B 152 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 177 removed outlier: 3.741A pdb=" N ILE B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.943A pdb=" N TYR B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 224 removed outlier: 4.412A pdb=" N VAL B 220 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ARG B 221 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG B 224 " --> pdb=" O ARG B 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 45 removed outlier: 3.916A pdb=" N ASN C 31 " --> pdb=" O GLU C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 removed outlier: 3.884A pdb=" N VAL C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 Processing helix chain 'C' and resid 83 through 94 removed outlier: 3.910A pdb=" N LYS C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL C 89 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.873A pdb=" N ILE C 119 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN C 122 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 143 removed outlier: 4.265A pdb=" N MET C 133 " --> pdb=" O PHE C 129 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN C 139 " --> pdb=" O ARG C 135 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'D' and resid 7 through 15 removed outlier: 3.973A pdb=" N SER D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 43 removed outlier: 3.719A pdb=" N ALA D 42 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG D 43 " --> pdb=" O HIS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 62 removed outlier: 3.810A pdb=" N VAL D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 79 Processing helix chain 'D' and resid 84 through 96 removed outlier: 3.627A pdb=" N ASN D 88 " --> pdb=" O ASN D 84 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU D 89 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU D 90 " --> pdb=" O GLY D 86 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 103 Processing helix chain 'D' and resid 109 through 119 removed outlier: 3.516A pdb=" N ALA D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 149 Processing helix chain 'D' and resid 151 through 160 removed outlier: 3.578A pdb=" N LYS D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU D 159 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU D 160 " --> pdb=" O ALA D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 190 Processing helix chain 'D' and resid 196 through 204 removed outlier: 4.064A pdb=" N VAL D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 69 removed outlier: 4.006A pdb=" N ALA E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 114 removed outlier: 3.934A pdb=" N VAL E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 136 Processing helix chain 'E' and resid 137 through 142 removed outlier: 3.823A pdb=" N GLY E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 157 Processing helix chain 'F' and resid 14 through 16 No H-bonds generated for 'chain 'F' and resid 14 through 16' Processing helix chain 'F' and resid 17 through 31 removed outlier: 3.633A pdb=" N MET F 21 " --> pdb=" O GLN F 17 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE F 29 " --> pdb=" O TYR F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 removed outlier: 3.834A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP F 72 " --> pdb=" O GLN F 68 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE F 80 " --> pdb=" O THR F 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 30 removed outlier: 3.666A pdb=" N LYS G 24 " --> pdb=" O GLU G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 53 removed outlier: 3.726A pdb=" N TYR G 43 " --> pdb=" O GLU G 39 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR G 48 " --> pdb=" O SER G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 66 Processing helix chain 'G' and resid 67 through 69 No H-bonds generated for 'chain 'G' and resid 67 through 69' Processing helix chain 'G' and resid 91 through 108 removed outlier: 3.831A pdb=" N ARG G 95 " --> pdb=" O ARG G 91 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASN G 96 " --> pdb=" O PRO G 92 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA G 99 " --> pdb=" O ARG G 95 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG G 108 " --> pdb=" O VAL G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 125 removed outlier: 4.126A pdb=" N LEU G 117 " --> pdb=" O LYS G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 140 removed outlier: 3.987A pdb=" N LYS G 136 " --> pdb=" O THR G 132 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG G 137 " --> pdb=" O ALA G 133 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP G 139 " --> pdb=" O LYS G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 147 Processing helix chain 'H' and resid 4 through 19 Processing helix chain 'H' and resid 29 through 42 removed outlier: 3.512A pdb=" N GLU H 42 " --> pdb=" O VAL H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 118 removed outlier: 4.574A pdb=" N GLN H 117 " --> pdb=" O ARG H 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 38 Processing helix chain 'I' and resid 43 through 48 removed outlier: 3.905A pdb=" N ARG I 48 " --> pdb=" O ARG I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 54 removed outlier: 3.950A pdb=" N VAL I 54 " --> pdb=" O PRO I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 87 removed outlier: 3.815A pdb=" N THR I 83 " --> pdb=" O ARG I 79 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG I 84 " --> pdb=" O HIS I 80 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA I 85 " --> pdb=" O GLY I 81 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET I 87 " --> pdb=" O THR I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 101 removed outlier: 3.772A pdb=" N ARG I 94 " --> pdb=" O ASP I 90 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU I 96 " --> pdb=" O SER I 92 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYS I 99 " --> pdb=" O SER I 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 32 removed outlier: 5.948A pdb=" N GLN J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR J 28 " --> pdb=" O GLU J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 87 removed outlier: 4.264A pdb=" N ASP J 85 " --> pdb=" O LYS J 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 57 removed outlier: 3.527A pdb=" N SER K 57 " --> pdb=" O SER K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 73 removed outlier: 3.794A pdb=" N ASP K 71 " --> pdb=" O GLU K 67 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL K 73 " --> pdb=" O CYS K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 77 Processing helix chain 'K' and resid 91 through 102 removed outlier: 4.301A pdb=" N ILE K 96 " --> pdb=" O ARG K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 7 removed outlier: 3.783A pdb=" N VAL L 7 " --> pdb=" O VAL L 3 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 18 Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 43 through 47 removed outlier: 3.650A pdb=" N LEU M 47 " --> pdb=" O ILE M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 61 Processing helix chain 'M' and resid 64 through 81 removed outlier: 4.074A pdb=" N LEU M 68 " --> pdb=" O VAL M 64 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER M 75 " --> pdb=" O GLU M 71 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE M 76 " --> pdb=" O ILE M 72 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS M 77 " --> pdb=" O SER M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 91 Processing helix chain 'N' and resid 2 through 19 removed outlier: 3.827A pdb=" N LYS N 6 " --> pdb=" O LYS N 2 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP N 17 " --> pdb=" O VAL N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 27 Processing helix chain 'N' and resid 41 through 43 No H-bonds generated for 'chain 'N' and resid 41 through 43' Processing helix chain 'N' and resid 44 through 49 Processing helix chain 'N' and resid 73 through 77 Processing helix chain 'N' and resid 81 through 88 removed outlier: 3.679A pdb=" N GLU N 85 " --> pdb=" O ILE N 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 13 Processing helix chain 'O' and resid 23 through 42 removed outlier: 3.632A pdb=" N GLN O 27 " --> pdb=" O SER O 23 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL O 28 " --> pdb=" O THR O 24 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA O 29 " --> pdb=" O GLU O 25 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS O 37 " --> pdb=" O ALA O 33 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN O 39 " --> pdb=" O ILE O 35 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLY O 40 " --> pdb=" O ASN O 36 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N HIS O 41 " --> pdb=" O HIS O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 73 removed outlier: 3.723A pdb=" N GLY O 54 " --> pdb=" O HIS O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 85 removed outlier: 4.093A pdb=" N LEU O 80 " --> pdb=" O ARG O 76 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE O 81 " --> pdb=" O TYR O 77 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG O 83 " --> pdb=" O ARG O 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 61 Processing helix chain 'P' and resid 70 through 76 removed outlier: 4.023A pdb=" N LEU P 74 " --> pdb=" O ARG P 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 30 Processing helix chain 'R' and resid 40 through 45 removed outlier: 3.527A pdb=" N THR R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 62 Processing helix chain 'S' and resid 11 through 19 removed outlier: 3.690A pdb=" N LYS S 17 " --> pdb=" O HIS S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 44 removed outlier: 3.866A pdb=" N MET S 43 " --> pdb=" O PHE S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 66 removed outlier: 3.594A pdb=" N VAL S 66 " --> pdb=" O ASP S 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 73 Processing helix chain 'T' and resid 6 through 39 removed outlier: 3.572A pdb=" N ILE T 11 " --> pdb=" O LYS T 7 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU T 14 " --> pdb=" O ALA T 10 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N HIS T 19 " --> pdb=" O LYS T 15 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER T 22 " --> pdb=" O LYS T 18 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET T 27 " --> pdb=" O ARG T 23 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS T 32 " --> pdb=" O ARG T 28 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS T 33 " --> pdb=" O THR T 29 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL T 34 " --> pdb=" O PHE T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 61 Proline residue: T 55 - end of helix Processing helix chain 'T' and resid 66 through 84 removed outlier: 4.474A pdb=" N LYS T 70 " --> pdb=" O ILE T 66 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA T 71 " --> pdb=" O HIS T 67 " (cutoff:3.500A) Processing helix chain 'U' and resid 15 through 22 removed outlier: 3.713A pdb=" N SER U 21 " --> pdb=" O PHE U 18 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS U 22 " --> pdb=" O LYS U 19 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 53 removed outlier: 4.334A pdb=" N LYS U 48 " --> pdb=" O ARG U 44 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA U 49 " --> pdb=" O LYS U 45 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL U 52 " --> pdb=" O LYS U 48 " (cutoff:3.500A) Processing helix chain '0' and resid 41 through 44 Processing helix chain '0' and resid 53 through 63 Processing helix chain '0' and resid 63 through 74 Processing helix chain '1' and resid 3 through 8 removed outlier: 3.834A pdb=" N ARG 1 7 " --> pdb=" O ALA 1 3 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU 1 8 " --> pdb=" O LYS 1 4 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 3 through 8' Processing helix chain '1' and resid 10 through 34 Processing helix chain '1' and resid 39 through 42 Processing helix chain '1' and resid 43 through 61 removed outlier: 4.094A pdb=" N ARG 1 47 " --> pdb=" O LEU 1 43 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG 1 48 " --> pdb=" O LYS 1 44 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ASP 1 49 " --> pdb=" O GLN 1 45 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU 1 59 " --> pdb=" O THR 1 55 " (cutoff:3.500A) Processing helix chain '2' and resid 17 through 28 Processing helix chain '2' and resid 41 through 51 removed outlier: 3.517A pdb=" N MET 2 47 " --> pdb=" O ALA 2 43 " (cutoff:3.500A) Processing helix chain '3' and resid 9 through 17 Processing helix chain '3' and resid 18 through 20 No H-bonds generated for 'chain '3' and resid 18 through 20' Processing helix chain '6' and resid 8 through 17 Processing helix chain '6' and resid 17 through 23 Processing helix chain '6' and resid 24 through 38 Processing helix chain '7' and resid 37 through 43 Processing helix chain '7' and resid 51 through 53 No H-bonds generated for 'chain '7' and resid 51 through 53' Processing helix chain '7' and resid 54 through 62 Processing helix chain '8' and resid 30 through 33 Processing helix chain 'c' and resid 30 through 32 No H-bonds generated for 'chain 'c' and resid 30 through 32' Processing helix chain 'c' and resid 133 through 135 No H-bonds generated for 'chain 'c' and resid 133 through 135' Processing helix chain 'c' and resid 197 through 203 removed outlier: 3.559A pdb=" N MET c 201 " --> pdb=" O ALA c 198 " (cutoff:3.500A) Processing helix chain 'c' and resid 207 through 213 removed outlier: 3.970A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 225 Processing helix chain 'c' and resid 263 through 265 No H-bonds generated for 'chain 'c' and resid 263 through 265' Processing helix chain 'd' and resid 39 through 44 Processing helix chain 'd' and resid 56 through 60 Processing helix chain 'd' and resid 61 through 72 removed outlier: 3.756A pdb=" N ALA d 71 " --> pdb=" O HIS d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 102 Processing helix chain 'd' and resid 120 through 126 Processing helix chain 'd' and resid 182 through 184 No H-bonds generated for 'chain 'd' and resid 182 through 184' Processing helix chain 'e' and resid 15 through 20 Processing helix chain 'e' and resid 24 through 38 Processing helix chain 'e' and resid 97 through 115 Processing helix chain 'e' and resid 130 through 141 Processing helix chain 'e' and resid 154 through 161 Processing helix chain 'e' and resid 173 through 175 No H-bonds generated for 'chain 'e' and resid 173 through 175' Processing helix chain 'e' and resid 176 through 183 removed outlier: 3.684A pdb=" N LEU e 180 " --> pdb=" O ASP e 176 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE e 181 " --> pdb=" O PRO e 177 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE e 183 " --> pdb=" O SER e 179 " (cutoff:3.500A) Processing helix chain 'e' and resid 190 through 201 Processing helix chain 'f' and resid 3 through 20 removed outlier: 4.099A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR f 18 " --> pdb=" O LYS f 14 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU f 19 " --> pdb=" O LYS f 15 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE f 20 " --> pdb=" O LEU f 16 " (cutoff:3.500A) Processing helix chain 'f' and resid 24 through 28 Processing helix chain 'f' and resid 41 through 46 removed outlier: 4.237A pdb=" N ILE f 44 " --> pdb=" O GLY f 41 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP f 46 " --> pdb=" O ALA f 43 " (cutoff:3.500A) Processing helix chain 'f' and resid 47 through 61 removed outlier: 3.888A pdb=" N ASP f 51 " --> pdb=" O LYS f 47 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 106 removed outlier: 3.512A pdb=" N ILE f 106 " --> pdb=" O ARG f 102 " (cutoff:3.500A) Processing helix chain 'f' and resid 107 through 111 Processing helix chain 'f' and resid 134 through 138 removed outlier: 3.540A pdb=" N ILE f 137 " --> pdb=" O GLU f 134 " (cutoff:3.500A) Processing helix chain 'f' and resid 162 through 172 Processing helix chain 'g' and resid 3 through 7 Processing helix chain 'g' and resid 61 through 79 removed outlier: 3.664A pdb=" N SER g 74 " --> pdb=" O ALA g 70 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 152 removed outlier: 4.472A pdb=" N ARG g 152 " --> pdb=" O LEU g 148 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 34 removed outlier: 3.903A pdb=" N GLN h 33 " --> pdb=" O PHE h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 43 through 49 removed outlier: 4.354A pdb=" N ALA h 49 " --> pdb=" O GLU h 45 " (cutoff:3.500A) Processing helix chain 'h' and resid 49 through 58 removed outlier: 3.736A pdb=" N GLU h 53 " --> pdb=" O ALA h 49 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA h 56 " --> pdb=" O ALA h 52 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS h 57 " --> pdb=" O GLU h 53 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 67 Processing helix chain 'h' and resid 68 through 73 Processing helix chain 'j' and resid 24 through 37 removed outlier: 4.595A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 58 through 62 removed outlier: 3.606A pdb=" N VAL j 62 " --> pdb=" O ALA j 59 " (cutoff:3.500A) Processing helix chain 'j' and resid 67 through 72 Processing helix chain 'j' and resid 89 through 96 Processing helix chain 'j' and resid 97 through 109 removed outlier: 4.248A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 120 removed outlier: 3.559A pdb=" N PHE j 119 " --> pdb=" O GLY j 115 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG j 120 " --> pdb=" O ARG j 116 " (cutoff:3.500A) Processing helix chain 'j' and resid 131 through 136 removed outlier: 4.585A pdb=" N ALA j 134 " --> pdb=" O ASN j 131 " (cutoff:3.500A) Processing helix chain 'k' and resid 104 through 108 Processing helix chain 'k' and resid 112 through 119 Processing helix chain 'l' and resid 37 through 41 Processing helix chain 'l' and resid 56 through 61 Processing helix chain 'l' and resid 70 through 72 No H-bonds generated for 'chain 'l' and resid 70 through 72' Processing helix chain 'l' and resid 81 through 86 removed outlier: 3.963A pdb=" N VAL l 85 " --> pdb=" O LEU l 82 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU l 86 " --> pdb=" O ALA l 83 " (cutoff:3.500A) Processing helix chain 'l' and resid 91 through 98 removed outlier: 3.667A pdb=" N LEU l 95 " --> pdb=" O ASP l 91 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS l 96 " --> pdb=" O LEU l 92 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 138 removed outlier: 3.550A pdb=" N ALA l 133 " --> pdb=" O LYS l 129 " (cutoff:3.500A) Processing helix chain 'm' and resid 43 through 57 removed outlier: 3.507A pdb=" N MET m 53 " --> pdb=" O ALA m 49 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 122 Processing helix chain 'n' and resid 13 through 32 Processing helix chain 'n' and resid 38 through 55 removed outlier: 3.581A pdb=" N ARG n 45 " --> pdb=" O ALA n 41 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) Proline residue: n 50 - end of helix Processing helix chain 'n' and resid 59 through 69 Processing helix chain 'n' and resid 72 through 82 Processing helix chain 'n' and resid 82 through 87 Processing helix chain 'o' and resid 3 through 22 removed outlier: 3.687A pdb=" N ARG o 7 " --> pdb=" O LYS o 3 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG o 9 " --> pdb=" O SER o 5 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG o 15 " --> pdb=" O ALA o 11 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 85 Processing helix chain 'o' and resid 101 through 113 Processing helix chain 'p' and resid 3 through 11 removed outlier: 3.714A pdb=" N GLU p 11 " --> pdb=" O GLN p 7 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 56 Processing helix chain 'p' and resid 97 through 103 Processing helix chain 'p' and resid 104 through 109 removed outlier: 4.000A pdb=" N ARG p 109 " --> pdb=" O LYS p 106 " (cutoff:3.500A) Processing helix chain 'q' and resid 6 through 21 removed outlier: 3.512A pdb=" N ALA q 12 " --> pdb=" O VAL q 8 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE q 17 " --> pdb=" O ARG q 13 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 30 Processing helix chain 'q' and resid 31 through 72 removed outlier: 3.868A pdb=" N GLN q 37 " --> pdb=" O ARG q 33 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG q 51 " --> pdb=" O TYR q 47 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS q 54 " --> pdb=" O ARG q 50 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG q 55 " --> pdb=" O ARG q 51 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG q 58 " --> pdb=" O LYS q 54 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA q 67 " --> pdb=" O ALA q 63 " (cutoff:3.500A) Processing helix chain 'q' and resid 75 through 86 Processing helix chain 'q' and resid 91 through 102 Processing helix chain 'q' and resid 102 through 118 removed outlier: 3.594A pdb=" N ALA q 116 " --> pdb=" O LYS q 112 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 25 removed outlier: 3.641A pdb=" N LEU s 19 " --> pdb=" O GLN s 15 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 38 removed outlier: 3.697A pdb=" N ASP s 34 " --> pdb=" O SER s 30 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 62 removed outlier: 3.697A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL s 47 " --> pdb=" O ALA s 43 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS s 49 " --> pdb=" O VAL s 45 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP s 62 " --> pdb=" O ALA s 58 " (cutoff:3.500A) Processing helix chain 's' and resid 65 through 69 removed outlier: 3.710A pdb=" N LEU s 69 " --> pdb=" O ILE s 66 " (cutoff:3.500A) Processing helix chain 's' and resid 89 through 91 No H-bonds generated for 'chain 's' and resid 89 through 91' Processing helix chain 't' and resid 3 through 10 Processing helix chain 't' and resid 18 through 28 removed outlier: 3.540A pdb=" N GLU t 25 " --> pdb=" O SER t 21 " (cutoff:3.500A) Processing helix chain 't' and resid 39 through 51 Processing helix chain 'w' and resid 13 through 23 Processing helix chain 'w' and resid 44 through 51 Processing helix chain 'w' and resid 52 through 58 removed outlier: 7.036A pdb=" N GLU w 55 " --> pdb=" O ALA w 52 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 160 through 162 removed outlier: 7.880A pdb=" N LEU B 160 " --> pdb=" O PHE B 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 165 through 170 removed outlier: 4.333A pdb=" N GLY C 147 " --> pdb=" O PHE C 202 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 127 through 128 Processing sheet with id= D, first strand: chain 'E' and resid 12 through 13 removed outlier: 3.761A pdb=" N VAL E 37 " --> pdb=" O LYS E 13 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 17 through 24 removed outlier: 3.580A pdb=" N VAL E 24 " --> pdb=" O GLY E 27 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 85 through 88 removed outlier: 3.743A pdb=" N GLN E 96 " --> pdb=" O LEU E 123 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 41 through 46 removed outlier: 5.482A pdb=" N ASP F 41 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU F 61 " --> pdb=" O ASP F 41 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL F 60 " --> pdb=" O PHE F 8 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE F 8 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N MET F 90 " --> pdb=" O GLU F 5 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 72 through 75 Processing sheet with id= I, first strand: chain 'H' and resid 23 through 26 Processing sheet with id= J, first strand: chain 'H' and resid 110 through 111 removed outlier: 6.497A pdb=" N VAL H 102 " --> pdb=" O ILE H 125 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'I' and resid 28 through 29 Processing sheet with id= L, first strand: chain 'J' and resid 10 through 11 Processing sheet with id= M, first strand: chain 'J' and resid 48 through 52 Processing sheet with id= N, first strand: chain 'K' and resid 20 through 22 Processing sheet with id= O, first strand: chain 'K' and resid 83 through 85 Processing sheet with id= P, first strand: chain 'L' and resid 59 through 65 removed outlier: 4.915A pdb=" N PHE L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU L 56 " --> pdb=" O PHE L 60 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL L 51 " --> pdb=" O VAL L 36 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL L 36 " --> pdb=" O VAL L 51 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ARG L 53 " --> pdb=" O THR L 34 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR L 34 " --> pdb=" O ARG L 53 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL L 32 " --> pdb=" O ARG L 55 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'P' and resid 34 through 35 removed outlier: 7.192A pdb=" N VAL P 2 " --> pdb=" O THR P 66 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'P' and resid 37 through 39 Processing sheet with id= S, first strand: chain 'Q' and resid 11 through 13 removed outlier: 7.157A pdb=" N VAL Q 21 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'Q' and resid 58 through 62 removed outlier: 7.298A pdb=" N GLU Q 59 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'S' and resid 50 through 51 Processing sheet with id= V, first strand: chain '0' and resid 13 through 18 Processing sheet with id= W, first strand: chain '0' and resid 33 through 40 removed outlier: 3.569A pdb=" N ARG 0 45 " --> pdb=" O VAL 0 40 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '2' and resid 35 through 38 Processing sheet with id= Y, first strand: chain '3' and resid 28 through 30 Processing sheet with id= Z, first strand: chain '3' and resid 48 through 49 Processing sheet with id= AA, first strand: chain '4' and resid 20 through 25 removed outlier: 3.547A pdb=" N GLN 4 45 " --> pdb=" O ASP 4 40 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain '7' and resid 15 through 16 Processing sheet with id= AC, first strand: chain '8' and resid 2 through 4 removed outlier: 6.410A pdb=" N LYS 8 2 " --> pdb=" O ARG 8 36 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ILE 8 23 " --> pdb=" O GLN 8 37 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'c' and resid 4 through 5 Processing sheet with id= AE, first strand: chain 'c' and resid 34 through 35 Processing sheet with id= AF, first strand: chain 'c' and resid 101 through 105 removed outlier: 6.755A pdb=" N ILE c 91 " --> pdb=" O LEU c 81 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU c 81 " --> pdb=" O ILE c 91 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU c 93 " --> pdb=" O GLU c 79 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'c' and resid 129 through 131 removed outlier: 5.892A pdb=" N ILE c 164 " --> pdb=" O ARG c 175 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG c 175 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA c 166 " --> pdb=" O THR c 173 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS c 183 " --> pdb=" O ILE c 267 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE c 267 " --> pdb=" O LYS c 183 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'c' and resid 144 through 145 removed outlier: 6.174A pdb=" N VAL c 144 " --> pdb=" O GLN c 153 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'd' and resid 4 through 15 removed outlier: 5.680A pdb=" N LYS d 8 " --> pdb=" O GLU d 28 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU d 28 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY d 10 " --> pdb=" O VAL d 26 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU d 186 " --> pdb=" O VAL d 180 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL d 180 " --> pdb=" O LEU d 186 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU d 188 " --> pdb=" O VAL d 178 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP d 176 " --> pdb=" O LYS d 190 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL d 107 " --> pdb=" O SER d 174 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'd' and resid 80 through 83 removed outlier: 3.507A pdb=" N GLN d 36 " --> pdb=" O GLN d 49 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR d 51 " --> pdb=" O VAL d 34 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL d 34 " --> pdb=" O THR d 51 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'd' and resid 115 through 119 removed outlier: 6.043A pdb=" N MET d 165 " --> pdb=" O LYS d 116 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE d 118 " --> pdb=" O GLY d 163 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY d 163 " --> pdb=" O PHE d 118 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'e' and resid 2 through 3 Processing sheet with id= AM, first strand: chain 'e' and resid 118 through 121 removed outlier: 6.536A pdb=" N LEU e 147 " --> pdb=" O VAL e 187 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N THR e 189 " --> pdb=" O LEU e 147 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ILE e 149 " --> pdb=" O THR e 189 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'f' and resid 66 through 69 Processing sheet with id= AO, first strand: chain 'g' and resid 9 through 10 removed outlier: 3.741A pdb=" N THR g 51 " --> pdb=" O LYS g 44 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'g' and resid 18 through 20 Processing sheet with id= AQ, first strand: chain 'g' and resid 122 through 124 Processing sheet with id= AR, first strand: chain 'g' and resid 95 through 99 removed outlier: 3.733A pdb=" N SER g 106 " --> pdb=" O ARG g 95 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'h' and resid 18 through 19 removed outlier: 3.604A pdb=" N VAL h 19 " --> pdb=" O VAL h 3 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'h' and resid 131 through 132 Processing sheet with id= AU, first strand: chain 'j' and resid 122 through 124 removed outlier: 6.867A pdb=" N ILE j 54 " --> pdb=" O LYS j 123 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TYR j 16 " --> pdb=" O ILE j 55 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU j 57 " --> pdb=" O TYR j 16 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL j 18 " --> pdb=" O LEU j 57 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP j 15 " --> pdb=" O GLN j 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain 'j' and resid 73 through 76 Processing sheet with id= AW, first strand: chain 'k' and resid 92 through 94 removed outlier: 4.989A pdb=" N GLN k 93 " --> pdb=" O ASN k 88 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA k 83 " --> pdb=" O VAL k 63 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS k 59 " --> pdb=" O LEU k 87 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE k 39 " --> pdb=" O LYS k 23 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS k 23 " --> pdb=" O ILE k 39 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE k 41 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N CYS k 21 " --> pdb=" O ILE k 41 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE k 43 " --> pdb=" O VAL k 19 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL k 19 " --> pdb=" O ILE k 43 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLU k 45 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL k 10 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N CYS k 84 " --> pdb=" O MET k 7 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASN k 9 " --> pdb=" O CYS k 84 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU k 86 " --> pdb=" O ASN k 9 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'k' and resid 69 through 70 removed outlier: 3.657A pdb=" N VAL k 76 " --> pdb=" O VAL p 73 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA p 49 " --> pdb=" O THR p 60 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG p 62 " --> pdb=" O VAL p 47 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VAL p 47 " --> pdb=" O ARG p 62 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N ILE p 64 " --> pdb=" O GLY p 45 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N GLY p 45 " --> pdb=" O ILE p 64 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N THR p 25 " --> pdb=" O VAL p 86 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL p 86 " --> pdb=" O THR p 25 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU p 27 " --> pdb=" O ILE p 84 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE p 84 " --> pdb=" O GLU p 27 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS p 29 " --> pdb=" O ASP p 82 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'l' and resid 74 through 76 removed outlier: 3.614A pdb=" N LYS l 109 " --> pdb=" O ALA l 75 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'l' and resid 89 through 90 removed outlier: 3.583A pdb=" N GLU l 143 " --> pdb=" O VAL l 122 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'm' and resid 62 through 65 removed outlier: 6.716A pdb=" N LEU m 33 " --> pdb=" O LEU m 102 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU m 104 " --> pdb=" O PHE m 31 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N PHE m 31 " --> pdb=" O GLU m 104 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'm' and resid 39 through 42 removed outlier: 5.745A pdb=" N VAL m 89 " --> pdb=" O GLU m 75 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU m 75 " --> pdb=" O VAL m 89 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR m 91 " --> pdb=" O ILE m 73 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'n' and resid 33 through 37 removed outlier: 6.228A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'o' and resid 47 through 52 Processing sheet with id= BE, first strand: chain 'r' and resid 11 through 15 removed outlier: 3.554A pdb=" N MET r 40 " --> pdb=" O VAL r 4 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLN r 6 " --> pdb=" O VAL r 38 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL r 38 " --> pdb=" O GLN r 6 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'r' and resid 19 through 22 removed outlier: 6.994A pdb=" N PHE r 93 " --> pdb=" O HIS r 66 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N HIS r 66 " --> pdb=" O PHE r 93 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE r 101 " --> pdb=" O VAL r 58 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL r 58 " --> pdb=" O ILE r 101 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'r' and resid 72 through 78 removed outlier: 3.882A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 's' and resid 3 through 10 removed outlier: 5.361A pdb=" N SER s 101 " --> pdb=" O HIS s 9 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS s 73 " --> pdb=" O VAL s 106 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N SER s 108 " --> pdb=" O VAL s 71 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL s 71 " --> pdb=" O SER s 108 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 's' and resid 82 through 87 Processing sheet with id= BJ, first strand: chain 't' and resid 11 through 14 removed outlier: 4.422A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL t 57 " --> pdb=" O THR t 86 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 't' and resid 67 through 70 removed outlier: 3.833A pdb=" N ARG t 73 " --> pdb=" O HIS t 70 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'u' and resid 65 through 66 removed outlier: 3.545A pdb=" N LYS u 33 " --> pdb=" O LEU u 29 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLU u 10 " --> pdb=" O PHE u 73 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE u 72 " --> pdb=" O ASP u 81 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'u' and resid 41 through 45 Processing sheet with id= BN, first strand: chain 'u' and resid 83 through 88 removed outlier: 3.644A pdb=" N ARG u 86 " --> pdb=" O VAL u 93 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'w' and resid 3 through 8 removed outlier: 7.975A pdb=" N ASN w 5 " --> pdb=" O ASP w 43 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASP w 43 " --> pdb=" O ASN w 5 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N LYS w 25 " --> pdb=" O GLN w 87 " (cutoff:3.500A) removed outlier: 10.163A pdb=" N ILE w 89 " --> pdb=" O LYS w 25 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N PHE w 91 " --> pdb=" O PRO w 27 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE w 29 " --> pdb=" O PHE w 91 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP w 76 " --> pdb=" O ASP w 90 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N VAL w 92 " --> pdb=" O ALA w 74 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ALA w 74 " --> pdb=" O VAL w 92 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE w 4 " --> pdb=" O VAL w 64 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'y' and resid 22 through 23 removed outlier: 6.716A pdb=" N LEU y 59 " --> pdb=" O ILE y 37 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'y' and resid 30 through 31 1497 hydrogen bonds defined for protein. 4053 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2552 hydrogen bonds 4258 hydrogen bond angles 0 basepair planarities 1001 basepair parallelities 1615 stacking parallelities Total time for adding SS restraints: 197.27 Time building geometry restraints manager: 62.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 14229 1.31 - 1.44: 67731 1.44 - 1.57: 64373 1.57 - 1.70: 9266 1.70 - 1.83: 259 Bond restraints: 155858 Sorted by residual: bond pdb=" C2 G A 230 " pdb=" N3 G A 230 " ideal model delta sigma weight residual 1.323 1.765 -0.442 2.00e-02 2.50e+03 4.87e+02 bond pdb=" N1 G A 230 " pdb=" C2 G A 230 " ideal model delta sigma weight residual 1.373 1.804 -0.431 2.00e-02 2.50e+03 4.64e+02 bond pdb=" C6 G A 230 " pdb=" N1 G A 230 " ideal model delta sigma weight residual 1.391 1.817 -0.426 2.00e-02 2.50e+03 4.53e+02 bond pdb=" N3 G A 230 " pdb=" C4 G A 230 " ideal model delta sigma weight residual 1.350 1.760 -0.410 2.00e-02 2.50e+03 4.20e+02 bond pdb=" C5 G A 230 " pdb=" C6 G A 230 " ideal model delta sigma weight residual 1.419 1.818 -0.399 2.00e-02 2.50e+03 3.97e+02 ... (remaining 155853 not shown) Histogram of bond angle deviations from ideal: 74.20 - 88.45: 1 88.45 - 102.69: 8874 102.69 - 116.94: 131689 116.94 - 131.19: 91527 131.19 - 145.43: 1324 Bond angle restraints: 233415 Sorted by residual: angle pdb=" O3' C v 74 " pdb=" P C v 75 " pdb=" O5' C v 75 " ideal model delta sigma weight residual 104.00 74.20 29.80 1.50e+00 4.44e-01 3.95e+02 angle pdb=" N LEU h 62 " pdb=" CA LEU h 62 " pdb=" C LEU h 62 " ideal model delta sigma weight residual 111.07 131.26 -20.19 1.07e+00 8.73e-01 3.56e+02 angle pdb=" N VAL h 61 " pdb=" CA VAL h 61 " pdb=" C VAL h 61 " ideal model delta sigma weight residual 110.72 129.45 -18.73 1.01e+00 9.80e-01 3.44e+02 angle pdb=" C2' C b1102 " pdb=" C1' C b1102 " pdb=" N1 C b1102 " ideal model delta sigma weight residual 112.00 135.47 -23.47 1.50e+00 4.44e-01 2.45e+02 angle pdb=" C2' A b1509 " pdb=" C1' A b1509 " pdb=" N9 A b1509 " ideal model delta sigma weight residual 114.00 137.32 -23.32 1.50e+00 4.44e-01 2.42e+02 ... (remaining 233410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 77674 35.83 - 71.66: 4942 71.66 - 107.50: 434 107.50 - 143.33: 61 143.33 - 179.16: 49 Dihedral angle restraints: 83160 sinusoidal: 67224 harmonic: 15936 Sorted by residual: dihedral pdb=" CA THR d 151 " pdb=" C THR d 151 " pdb=" N PRO d 152 " pdb=" CA PRO d 152 " ideal model delta harmonic sigma weight residual -180.00 -96.19 -83.81 0 5.00e+00 4.00e-02 2.81e+02 dihedral pdb=" O4' U b2118 " pdb=" C2' U b2118 " pdb=" C1' U b2118 " pdb=" C3' U b2118 " ideal model delta sinusoidal sigma weight residual 25.00 -54.18 79.18 1 8.00e+00 1.56e-02 1.22e+02 dihedral pdb=" O4' G b 801 " pdb=" C4' G b 801 " pdb=" C3' G b 801 " pdb=" C2' G b 801 " ideal model delta sinusoidal sigma weight residual -35.00 43.90 -78.90 1 8.00e+00 1.56e-02 1.21e+02 ... (remaining 83157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.279: 29391 0.279 - 0.558: 435 0.558 - 0.837: 29 0.837 - 1.116: 5 1.116 - 1.395: 4 Chirality restraints: 29864 Sorted by residual: chirality pdb=" CG LEU d 4 " pdb=" CB LEU d 4 " pdb=" CD1 LEU d 4 " pdb=" CD2 LEU d 4 " both_signs ideal model delta sigma weight residual False -2.59 -1.19 -1.40 2.00e-01 2.50e+01 4.87e+01 chirality pdb=" C1' A b1275 " pdb=" O4' A b1275 " pdb=" C2' A b1275 " pdb=" N9 A b1275 " both_signs ideal model delta sigma weight residual False 2.44 1.06 1.38 2.00e-01 2.50e+01 4.76e+01 chirality pdb=" C1' A b1509 " pdb=" O4' A b1509 " pdb=" C2' A b1509 " pdb=" N9 A b1509 " both_signs ideal model delta sigma weight residual False 2.44 1.10 1.34 2.00e-01 2.50e+01 4.48e+01 ... (remaining 29861 not shown) Planarity restraints: 12326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U b1943 " 0.222 2.00e-02 2.50e+03 1.08e-01 2.65e+02 pdb=" N1 U b1943 " -0.212 2.00e-02 2.50e+03 pdb=" C2 U b1943 " -0.032 2.00e-02 2.50e+03 pdb=" O2 U b1943 " -0.031 2.00e-02 2.50e+03 pdb=" N3 U b1943 " 0.033 2.00e-02 2.50e+03 pdb=" C4 U b1943 " 0.024 2.00e-02 2.50e+03 pdb=" O4 U b1943 " 0.057 2.00e-02 2.50e+03 pdb=" C5 U b1943 " 0.006 2.00e-02 2.50e+03 pdb=" C6 U b1943 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A b1088 " -0.232 2.00e-02 2.50e+03 9.50e-02 2.48e+02 pdb=" N9 A b1088 " 0.172 2.00e-02 2.50e+03 pdb=" C8 A b1088 " 0.064 2.00e-02 2.50e+03 pdb=" N7 A b1088 " -0.009 2.00e-02 2.50e+03 pdb=" C5 A b1088 " 0.020 2.00e-02 2.50e+03 pdb=" C6 A b1088 " -0.023 2.00e-02 2.50e+03 pdb=" N6 A b1088 " -0.064 2.00e-02 2.50e+03 pdb=" N1 A b1088 " -0.039 2.00e-02 2.50e+03 pdb=" C2 A b1088 " 0.008 2.00e-02 2.50e+03 pdb=" N3 A b1088 " 0.061 2.00e-02 2.50e+03 pdb=" C4 A b1088 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A b1272 " -0.192 2.00e-02 2.50e+03 8.73e-02 2.10e+02 pdb=" N9 A b1272 " 0.200 2.00e-02 2.50e+03 pdb=" C8 A b1272 " 0.016 2.00e-02 2.50e+03 pdb=" N7 A b1272 " -0.029 2.00e-02 2.50e+03 pdb=" C5 A b1272 " -0.017 2.00e-02 2.50e+03 pdb=" C6 A b1272 " -0.025 2.00e-02 2.50e+03 pdb=" N6 A b1272 " -0.023 2.00e-02 2.50e+03 pdb=" N1 A b1272 " -0.024 2.00e-02 2.50e+03 pdb=" C2 A b1272 " 0.009 2.00e-02 2.50e+03 pdb=" N3 A b1272 " 0.040 2.00e-02 2.50e+03 pdb=" C4 A b1272 " 0.046 2.00e-02 2.50e+03 ... (remaining 12323 not shown) Histogram of nonbonded interaction distances: 0.23 - 1.17: 12 1.17 - 2.10: 233 2.10 - 3.03: 85548 3.03 - 3.97: 438074 3.97 - 4.90: 733349 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1257216 Sorted by model distance: nonbonded pdb=" O ARG P 28 " pdb=" N1 G A 376 " model vdw 0.232 2.520 nonbonded pdb=" O2 C b1349 " pdb=" O6 G b1382 " model vdw 0.610 3.040 nonbonded pdb=" CB ARG P 5 " pdb=" O2' G A 376 " model vdw 0.862 3.440 nonbonded pdb=" NH2 ARG I 108 " pdb=" O6 G A1347 " model vdw 0.871 2.520 nonbonded pdb=" C ARG P 28 " pdb=" N1 G A 376 " model vdw 1.025 3.350 ... (remaining 1257211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4637 5.49 5 S 138 5.16 5 C 71828 2.51 5 N 26713 2.21 5 O 40018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.150 Extract box with map and model: 17.080 Check model and map are aligned: 1.560 Convert atoms to be neutral: 0.930 Process input model: 453.420 Find NCS groups from input model: 2.930 Set up NCS constraints: 0.450 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: 0.020 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 480.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.442 155858 Z= 0.480 Angle : 1.319 29.801 233415 Z= 0.888 Chirality : 0.100 1.395 29864 Planarity : 0.012 0.123 12326 Dihedral : 19.187 179.158 72880 Min Nonbonded Distance : 0.232 Molprobity Statistics. All-atom Clashscore : 33.71 Ramachandran Plot: Outliers : 2.89 % Allowed : 8.00 % Favored : 89.10 % Rotamer Outliers : 2.84 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.09 % Twisted Proline : 0.55 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.10), residues: 5497 helix: -2.58 (0.09), residues: 1550 sheet: -2.26 (0.16), residues: 865 loop : -1.06 (0.11), residues: 3082 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2109 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1979 time to evaluate : 6.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 130 outliers final: 23 residues processed: 2063 average time/residue: 1.5056 time to fit residues: 5257.0030 Evaluate side-chains 1089 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1066 time to evaluate : 6.045 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 1.2369 time to fit residues: 59.3099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 844 optimal weight: 20.0000 chunk 757 optimal weight: 20.0000 chunk 420 optimal weight: 10.0000 chunk 258 optimal weight: 9.9990 chunk 511 optimal weight: 5.9990 chunk 404 optimal weight: 6.9990 chunk 783 optimal weight: 8.9990 chunk 303 optimal weight: 9.9990 chunk 476 optimal weight: 2.9990 chunk 583 optimal weight: 40.0000 chunk 908 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 ASN B 167 HIS ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 HIS ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN G 121 ASN H 3 GLN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN K 39 ASN ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 ASN ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 ASN ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 45 HIS O 50 HIS P 9 HIS P 63 GLN Q 46 HIS Q 49 ASN Q 50 ASN R 51 GLN ** S 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 81 GLN 1 36 GLN ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 26 ASN c 115 GLN c 226 ASN ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 136 GLN f 27 GLN f 37 ASN f 52 ASN g 38 ASN g 88 GLN g 116 GLN h 2 GLN ** h 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 88 ASN ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 104 GLN p 41 GLN p 52 ASN q 37 GLN q 56 GLN r 6 GLN s 7 HIS s 40 ASN s 61 ASN ** t 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 45 HIS ** w 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 78 GLN w 87 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.226 155858 Z= 0.346 Angle : 0.915 18.137 233415 Z= 0.456 Chirality : 0.048 0.635 29864 Planarity : 0.007 0.195 12326 Dihedral : 17.629 179.852 61861 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.39 % Favored : 91.87 % Rotamer Outliers : 5.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.09 % Twisted Proline : 0.55 % Twisted General : 0.04 % 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: -2.08 (0.11), residues: 5497 helix: -1.04 (0.12), residues: 1607 sheet: -1.94 (0.15), residues: 974 loop : -1.30 (0.11), residues: 2916 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1457 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1198 time to evaluate : 6.055 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 outliers start: 259 outliers final: 153 residues processed: 1346 average time/residue: 1.4256 time to fit residues: 3392.2347 Evaluate side-chains 1132 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 979 time to evaluate : 6.036 Switching outliers to nearest non-outliers outliers start: 153 outliers final: 0 residues processed: 153 average time/residue: 1.1806 time to fit residues: 349.9859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 504 optimal weight: 3.9990 chunk 281 optimal weight: 3.9990 chunk 755 optimal weight: 10.0000 chunk 618 optimal weight: 10.0000 chunk 250 optimal weight: 9.9990 chunk 909 optimal weight: 10.0000 chunk 982 optimal weight: 30.0000 chunk 810 optimal weight: 30.0000 chunk 902 optimal weight: 10.0000 chunk 310 optimal weight: 8.9990 chunk 729 optimal weight: 20.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 175 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 151 GLN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN I 80 HIS ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 71 HIS ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 GLN Q 30 HIS R 51 GLN S 13 HIS ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 67 HIS T 77 ASN 0 23 ASN 0 32 ASN 1 25 GLN ** 1 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 29 GLN ** d 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 163 ASN ** h 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 128 ASN ** j 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 35 HIS n 9 GLN o 19 GLN p 52 ASN q 72 ASN r 18 GLN ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 4 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.161 155858 Z= 0.335 Angle : 0.810 19.122 233415 Z= 0.413 Chirality : 0.044 0.336 29864 Planarity : 0.007 0.128 12326 Dihedral : 17.312 179.914 61861 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.08 % Favored : 91.32 % Rotamer Outliers : 4.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.09 % Twisted Proline : 0.55 % Twisted General : 0.04 % 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: -2.08 (0.11), residues: 5497 helix: -0.67 (0.12), residues: 1613 sheet: -1.79 (0.15), residues: 1034 loop : -1.60 (0.11), residues: 2850 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1271 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1067 time to evaluate : 6.159 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: 204 outliers final: 112 residues processed: 1188 average time/residue: 1.2722 time to fit residues: 2650.6521 Evaluate side-chains 1026 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 914 time to evaluate : 5.837 Switching outliers to nearest non-outliers outliers start: 112 outliers final: 0 residues processed: 112 average time/residue: 1.0533 time to fit residues: 229.4035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 898 optimal weight: 10.0000 chunk 683 optimal weight: 20.0000 chunk 472 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 434 optimal weight: 5.9990 chunk 610 optimal weight: 20.0000 chunk 913 optimal weight: 30.0000 chunk 966 optimal weight: 10.0000 chunk 477 optimal weight: 6.9990 chunk 865 optimal weight: 10.0000 chunk 260 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN P 63 GLN R 51 GLN ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 32 ASN 1 25 GLN ** 1 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 58 HIS ** d 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 28 ASN h 33 GLN ** j 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 131 ASN p 52 ASN s 61 ASN t 28 ASN ** t 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 70 HIS t 91 GLN z 4 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.141 155858 Z= 0.267 Angle : 0.722 21.095 233415 Z= 0.369 Chirality : 0.040 0.332 29864 Planarity : 0.006 0.109 12326 Dihedral : 17.066 179.697 61861 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.66 % Favored : 91.78 % Rotamer Outliers : 4.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.09 % Twisted Proline : 0.55 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.11), residues: 5497 helix: -0.37 (0.13), residues: 1628 sheet: -1.67 (0.15), residues: 987 loop : -1.69 (0.11), residues: 2882 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1200 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1015 time to evaluate : 6.050 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: 185 outliers final: 95 residues processed: 1126 average time/residue: 1.2981 time to fit residues: 2583.9761 Evaluate side-chains 998 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 903 time to evaluate : 6.018 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 0 residues processed: 95 average time/residue: 1.1700 time to fit residues: 216.4557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 805 optimal weight: 9.9990 chunk 548 optimal weight: 20.0000 chunk 14 optimal weight: 30.0000 chunk 719 optimal weight: 20.0000 chunk 398 optimal weight: 20.0000 chunk 824 optimal weight: 10.0000 chunk 668 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 493 optimal weight: 10.0000 chunk 867 optimal weight: 10.0000 chunk 243 optimal weight: 0.9990 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 71 HIS ** N 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 ASN ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 54 GLN T 60 GLN 0 32 ASN 1 25 GLN ** 1 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 53 HIS d 32 ASN ** d 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 41 GLN p 52 ASN q 14 HIS q 59 GLN ** t 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 87 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.6268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.130 155858 Z= 0.344 Angle : 0.815 19.205 233415 Z= 0.411 Chirality : 0.044 0.367 29864 Planarity : 0.007 0.113 12326 Dihedral : 17.361 179.798 61861 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.46 % Favored : 89.96 % Rotamer Outliers : 4.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.09 % Twisted Proline : 0.55 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.11), residues: 5497 helix: -0.53 (0.13), residues: 1595 sheet: -1.74 (0.15), residues: 1008 loop : -1.92 (0.11), residues: 2894 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1188 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 975 time to evaluate : 6.040 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 outliers start: 213 outliers final: 119 residues processed: 1101 average time/residue: 1.2939 time to fit residues: 2509.7353 Evaluate side-chains 1008 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 889 time to evaluate : 6.124 Switching outliers to nearest non-outliers outliers start: 119 outliers final: 0 residues processed: 119 average time/residue: 1.0862 time to fit residues: 253.0025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 325 optimal weight: 10.0000 chunk 870 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 567 optimal weight: 20.0000 chunk 238 optimal weight: 10.0000 chunk 967 optimal weight: 10.0000 chunk 803 optimal weight: 10.0000 chunk 447 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 320 optimal weight: 3.9990 chunk 507 optimal weight: 6.9990 overall best weight: 5.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN D 73 ASN D 130 ASN F 3 HIS ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 ASN L 71 HIS ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 GLN ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 32 ASN 1 25 GLN ** 1 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 33 GLN ** j 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 41 GLN t 28 ASN t 59 ASN t 70 HIS w 51 GLN w 87 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.6518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.182 155858 Z= 0.255 Angle : 0.704 14.948 233415 Z= 0.360 Chirality : 0.039 0.290 29864 Planarity : 0.006 0.113 12326 Dihedral : 17.098 179.815 61861 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.95 % Favored : 91.50 % Rotamer Outliers : 2.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.09 % Twisted Proline : 0.55 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.11), residues: 5497 helix: -0.32 (0.13), residues: 1609 sheet: -1.60 (0.16), residues: 950 loop : -1.97 (0.11), residues: 2938 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 964 time to evaluate : 6.069 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: 131 outliers final: 76 residues processed: 1037 average time/residue: 1.3537 time to fit residues: 2481.8395 Evaluate side-chains 964 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 888 time to evaluate : 6.113 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 0 residues processed: 76 average time/residue: 1.1777 time to fit residues: 176.5947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 932 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 551 optimal weight: 30.0000 chunk 706 optimal weight: 10.0000 chunk 547 optimal weight: 40.0000 chunk 814 optimal weight: 20.0000 chunk 540 optimal weight: 30.0000 chunk 963 optimal weight: 10.0000 chunk 603 optimal weight: 30.0000 chunk 587 optimal weight: 40.0000 chunk 444 optimal weight: 3.9990 overall best weight: 8.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 73 ASN D 130 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 GLN ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 25 GLN ** 1 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 49 GLN ** d 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 52 GLN ** w 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 87 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.6589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.591 155858 Z= 0.360 Angle : 0.799 73.900 233415 Z= 0.398 Chirality : 0.042 0.303 29864 Planarity : 0.006 0.122 12326 Dihedral : 17.155 179.809 61861 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.86 % Favored : 90.63 % Rotamer Outliers : 3.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.09 % Twisted Proline : 0.55 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.11), residues: 5497 helix: -0.41 (0.13), residues: 1614 sheet: -1.64 (0.16), residues: 962 loop : -2.07 (0.11), residues: 2921 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1062 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 909 time to evaluate : 8.007 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: 153 outliers final: 100 residues processed: 995 average time/residue: 1.3384 time to fit residues: 2352.2685 Evaluate side-chains 986 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 886 time to evaluate : 6.023 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 0 residues processed: 100 average time/residue: 1.1760 time to fit residues: 228.0144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 596 optimal weight: 30.0000 chunk 384 optimal weight: 4.9990 chunk 575 optimal weight: 30.0000 chunk 290 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 612 optimal weight: 20.0000 chunk 656 optimal weight: 30.0000 chunk 476 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 757 optimal weight: 20.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 73 ASN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN F 3 HIS ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 ASN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 11 HIS ** N 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 7 GLN t 70 HIS ** w 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 87 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.6596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.861 155858 Z= 0.395 Angle : 0.839 106.099 233415 Z= 0.412 Chirality : 0.042 0.568 29864 Planarity : 0.006 0.111 12326 Dihedral : 17.156 179.792 61861 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.82 % Favored : 90.65 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.09 % Twisted Proline : 0.55 % Twisted General : 0.04 % 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: -2.23 (0.11), residues: 5497 helix: -0.41 (0.13), residues: 1613 sheet: -1.63 (0.16), residues: 972 loop : -2.08 (0.11), residues: 2912 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 897 time to evaluate : 8.339 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 outliers start: 49 outliers final: 38 residues processed: 920 average time/residue: 1.3258 time to fit residues: 2153.7825 Evaluate side-chains 915 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 877 time to evaluate : 6.162 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 1.2066 time to fit residues: 90.1304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 876 optimal weight: 20.0000 chunk 923 optimal weight: 20.0000 chunk 842 optimal weight: 10.0000 chunk 898 optimal weight: 10.0000 chunk 540 optimal weight: 20.0000 chunk 391 optimal weight: 9.9990 chunk 705 optimal weight: 10.0000 chunk 275 optimal weight: 7.9990 chunk 811 optimal weight: 30.0000 chunk 849 optimal weight: 20.0000 chunk 895 optimal weight: 10.0000 overall best weight: 9.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 73 ASN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 28 ASN ** w 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 87 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.6603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.946 155858 Z= 0.448 Angle : 0.854 83.710 233415 Z= 0.417 Chirality : 0.043 0.722 29864 Planarity : 0.006 0.133 12326 Dihedral : 17.161 179.825 61861 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.91 % Favored : 90.58 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.09 % Twisted Proline : 0.55 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.11), residues: 5497 helix: -0.44 (0.13), residues: 1613 sheet: -1.66 (0.16), residues: 978 loop : -2.10 (0.11), residues: 2906 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 955 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 896 time to evaluate : 6.001 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 outliers start: 59 outliers final: 46 residues processed: 921 average time/residue: 1.2770 time to fit residues: 2073.5270 Evaluate side-chains 925 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 879 time to evaluate : 6.062 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 1.0972 time to fit residues: 101.6373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 589 optimal weight: 20.0000 chunk 949 optimal weight: 9.9990 chunk 579 optimal weight: 40.0000 chunk 450 optimal weight: 6.9990 chunk 660 optimal weight: 20.0000 chunk 996 optimal weight: 20.0000 chunk 916 optimal weight: 50.0000 chunk 793 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 chunk 612 optimal weight: 30.0000 chunk 486 optimal weight: 6.9990 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 73 ASN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN F 3 HIS ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 11 HIS ** N 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 70 HIS ** w 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 87 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.6607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.021 155858 Z= 0.506 Angle : 0.883 97.826 233415 Z= 0.430 Chirality : 0.043 0.460 29864 Planarity : 0.006 0.132 12326 Dihedral : 17.166 179.820 61861 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.08 % Favored : 90.47 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.09 % Twisted Proline : 0.55 % Twisted General : 0.04 % 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: -2.28 (0.11), residues: 5497 helix: -0.45 (0.13), residues: 1613 sheet: -1.66 (0.16), residues: 978 loop : -2.11 (0.11), residues: 2906 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10994 Ramachandran restraints generated. 5497 Oldfield, 0 Emsley, 5497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 891 time to evaluate : 6.069 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 outliers start: 28 outliers final: 19 residues processed: 901 average time/residue: 1.3050 time to fit residues: 2067.5586 Evaluate side-chains 896 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 877 time to evaluate : 6.108 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 1.1653 time to fit residues: 46.9737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 630 optimal weight: 20.0000 chunk 845 optimal weight: 10.0000 chunk 243 optimal weight: 2.9990 chunk 731 optimal weight: 30.0000 chunk 117 optimal weight: 30.0000 chunk 220 optimal weight: 20.0000 chunk 794 optimal weight: 10.0000 chunk 332 optimal weight: 5.9990 chunk 815 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 146 optimal weight: 0.3980 overall best weight: 4.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 73 ASN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 87 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.127735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.104378 restraints weight = 396456.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.104743 restraints weight = 256490.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.104915 restraints weight = 169895.514| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.6609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.021 155858 Z= 0.507 Angle : 0.884 97.826 233415 Z= 0.431 Chirality : 0.043 0.460 29864 Planarity : 0.006 0.132 12326 Dihedral : 17.166 179.820 61861 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.08 % Favored : 90.47 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.09 % Twisted Proline : 0.55 % Twisted General : 0.04 % 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: -2.28 (0.11), residues: 5497 helix: -0.45 (0.13), residues: 1613 sheet: -1.66 (0.16), residues: 978 loop : -2.11 (0.11), residues: 2906 =============================================================================== Job complete usr+sys time: 37088.15 seconds wall clock time: 639 minutes 34.62 seconds (38374.62 seconds total)