Starting phenix.real_space_refine on Sat Dec 16 07:18:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7d_33661/12_2023/7y7d_33661_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7d_33661/12_2023/7y7d_33661.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7d_33661/12_2023/7y7d_33661_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7d_33661/12_2023/7y7d_33661_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7d_33661/12_2023/7y7d_33661_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7d_33661/12_2023/7y7d_33661.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7d_33661/12_2023/7y7d_33661.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7d_33661/12_2023/7y7d_33661_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7d_33661/12_2023/7y7d_33661_updated.pdb" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4556 5.49 5 Mg 258 5.21 5 S 150 5.16 5 C 71103 2.51 5 N 26433 2.21 5 O 39417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 82": "OD1" <-> "OD2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ASP 165": "OD1" <-> "OD2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "C PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C ASP 34": "OD1" <-> "OD2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C ASP 181": "OD1" <-> "OD2" Residue "C ASP 183": "OD1" <-> "OD2" Residue "C TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "E GLU 13": "OE1" <-> "OE2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 41": "OD1" <-> "OD2" Residue "E PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 33": "OE1" <-> "OE2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F ASP 82": "OD1" <-> "OD2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "G GLU 74": "OE1" <-> "OE2" Residue "G TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G ASP 126": "OD1" <-> "OD2" Residue "G PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 5": "OD1" <-> "OD2" Residue "H ASP 9": "OD1" <-> "OD2" Residue "H PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 52": "OE1" <-> "OE2" Residue "H GLU 124": "OE1" <-> "OE2" Residue "I TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 59": "OE1" <-> "OE2" Residue "I ARG 95": "NH1" <-> "NH2" Residue "I ASP 107": "OD1" <-> "OD2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "I ARG 124": "NH1" <-> "NH2" Residue "I PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 47": "OE1" <-> "OE2" Residue "J ASP 60": "OD1" <-> "OD2" Residue "J ASP 63": "OD1" <-> "OD2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J ASP 97": "OD1" <-> "OD2" Residue "K ASP 112": "OD1" <-> "OD2" Residue "L ARG 14": "NH1" <-> "NH2" Residue "L ARG 56": "NH1" <-> "NH2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "M ASP 42": "OD1" <-> "OD2" Residue "M ASP 58": "OD1" <-> "OD2" Residue "M GLU 59": "OE1" <-> "OE2" Residue "M GLU 72": "OE1" <-> "OE2" Residue "M ASP 82": "OD1" <-> "OD2" Residue "M TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 26": "OE1" <-> "OE2" Residue "N ASP 54": "OD1" <-> "OD2" Residue "N ARG 65": "NH1" <-> "NH2" Residue "N GLU 92": "OE1" <-> "OE2" Residue "O GLU 14": "OE1" <-> "OE2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "P GLU 77": "OE1" <-> "OE2" Residue "R PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 22": "OD1" <-> "OD2" Residue "R TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 3": "NH1" <-> "NH2" Residue "S ARG 32": "NH1" <-> "NH2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "S GLU 73": "OE1" <-> "OE2" Residue "S ARG 81": "NH1" <-> "NH2" Residue "T GLU 53": "OE1" <-> "OE2" Residue "U ARG 66": "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 GLU 82": "OE1" <-> "OE2" Residue "c ASP 114": "OD1" <-> "OD2" Residue "c ARG 133": "NH1" <-> "NH2" Residue "c GLU 145": "OE1" <-> "OE2" Residue "c ARG 167": "NH1" <-> "NH2" Residue "c ARG 177": "NH1" <-> "NH2" Residue "c ARG 182": "NH1" <-> "NH2" Residue "c ASP 187": "OD1" <-> "OD2" Residue "c ARG 189": "NH1" <-> "NH2" Residue "c GLU 199": "OE1" <-> "OE2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c ARG 212": "NH1" <-> "NH2" Residue "c GLU 236": "OE1" <-> "OE2" Residue "c PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d GLU 17": "OE1" <-> "OE2" Residue "d GLU 30": "OE1" <-> "OE2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ASP 39": "OD1" <-> "OD2" Residue "d ARG 59": "NH1" <-> "NH2" Residue "d ARG 83": "NH1" <-> "NH2" Residue "d GLU 86": "OE1" <-> "OE2" Residue "d ASP 108": "OD1" <-> "OD2" Residue "d GLU 168": "OE1" <-> "OE2" Residue "d ARG 169": "NH1" <-> "NH2" Residue "d ASP 176": "OD1" <-> "OD2" Residue "d GLU 183": "OE1" <-> "OE2" Residue "d ASP 200": "OD1" <-> "OD2" Residue "e GLU 25": "OE1" <-> "OE2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e GLU 51": "OE1" <-> "OE2" Residue "e ARG 61": "NH1" <-> "NH2" Residue "e ARG 88": "NH1" <-> "NH2" Residue "e TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 102": "NH1" <-> "NH2" Residue "e GLU 111": "OE1" <-> "OE2" Residue "e PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 162": "NH1" <-> "NH2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "e ASP 176": "OD1" <-> "OD2" Residue "e GLU 197": "OE1" <-> "OE2" Residue "f TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 32": "OE1" <-> "OE2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 92": "NH1" <-> "NH2" 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 PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 133": "NH1" <-> "NH2" Residue "f GLU 134": "OE1" <-> "OE2" Residue "f GLU 140": "OE1" <-> "OE2" Residue "f PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 3": "NH1" <-> "NH2" Residue "g ASP 39": "OD1" <-> "OD2" Residue "g GLU 42": "OE1" <-> "OE2" Residue "g PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 114": "OD1" <-> "OD2" Residue "g ASP 147": "OD1" <-> "OD2" Residue "g ARG 153": "NH1" <-> "NH2" Residue "g TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 163": "NH1" <-> "NH2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "h ARG 27": "NH1" <-> "NH2" Residue "i ARG 13": "NH1" <-> "NH2" Residue "i TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 31": "OE1" <-> "OE2" Residue "i ARG 37": "NH1" <-> "NH2" Residue "i ASP 52": "OD1" <-> "OD2" Residue "i GLU 91": "OE1" <-> "OE2" Residue "i ARG 96": "NH1" <-> "NH2" Residue "i ARG 120": "NH1" <-> "NH2" Residue "j GLU 4": "OE1" <-> "OE2" Residue "j ASP 12": "OD1" <-> "OD2" Residue "j ASP 37": "OD1" <-> "OD2" Residue "j GLU 106": "OE1" <-> "OE2" Residue "k GLU 10": "OE1" <-> "OE2" Residue "k ARG 21": "NH1" <-> "NH2" Residue "k ARG 33": "NH1" <-> "NH2" Residue "k ARG 41": "NH1" <-> "NH2" Residue "k ARG 47": "NH1" <-> "NH2" Residue "k TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 60": "NH1" <-> "NH2" Residue "k PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 78": "NH1" <-> "NH2" Residue "k GLU 106": "OE1" <-> "OE2" Residue "k ARG 123": "NH1" <-> "NH2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "l ARG 10": "NH1" <-> "NH2" Residue "l ARG 18": "NH1" <-> "NH2" Residue "l ASP 25": "OD1" <-> "OD2" Residue "l ARG 40": "NH1" <-> "NH2" Residue "l ARG 44": "NH1" <-> "NH2" Residue "l GLU 47": "OE1" <-> "OE2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "l PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 90": "OE1" <-> "OE2" Residue "l GLU 104": "OE1" <-> "OE2" Residue "l ASP 106": "OD1" <-> "OD2" Residue "l ARG 114": "NH1" <-> "NH2" Residue "m ARG 12": "NH1" <-> "NH2" Residue "m ARG 17": "NH1" <-> "NH2" Residue "m ARG 22": "NH1" <-> "NH2" Residue "m GLU 32": "OE1" <-> "OE2" Residue "m ARG 46": "NH1" <-> "NH2" Residue "m ASP 58": "OD1" <-> "OD2" Residue "m ARG 63": "NH1" <-> "NH2" Residue "m ARG 64": "NH1" <-> "NH2" Residue "m ARG 69": "NH1" <-> "NH2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "m ARG 96": "NH1" <-> "NH2" Residue "m GLU 114": "OE1" <-> "OE2" Residue "m ASP 117": "OD1" <-> "OD2" Residue "m ARG 118": "NH1" <-> "NH2" Residue "n ARG 10": "NH1" <-> "NH2" Residue "n ARG 16": "NH1" <-> "NH2" Residue "n ARG 25": "NH1" <-> "NH2" Residue "n TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 81": "NH1" <-> "NH2" Residue "n ARG 94": "NH1" <-> "NH2" Residue "n ARG 102": "NH1" <-> "NH2" Residue "n ASP 108": "OD1" <-> "OD2" Residue "n ARG 111": "NH1" <-> "NH2" Residue "o ARG 21": "NH1" <-> "NH2" Residue "o GLU 27": "OE1" <-> "OE2" Residue "o ARG 39": "NH1" <-> "NH2" Residue "o GLU 68": "OE1" <-> "OE2" Residue "o ASP 82": "OD1" <-> "OD2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "o TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 101": "NH1" <-> "NH2" Residue "o GLU 102": "OE1" <-> "OE2" Residue "o ARG 109": "NH1" <-> "NH2" Residue "p ARG 3": "NH1" <-> "NH2" Residue "p ARG 6": "NH1" <-> "NH2" Residue "p ARG 13": "NH1" <-> "NH2" Residue "p ARG 33": "NH1" <-> "NH2" Residue "p ARG 48": "NH1" <-> "NH2" Residue "p TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 91": "OD1" <-> "OD2" Residue "p ASP 97": "OD1" <-> "OD2" Residue "p GLU 111": "OE1" <-> "OE2" Residue "q TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q GLU 23": "OE1" <-> "OE2" Residue "q GLU 31": "OE1" <-> "OE2" Residue "q ARG 68": "NH1" <-> "NH2" Residue "q GLU 70": "OE1" <-> "OE2" Residue "q ARG 79": "NH1" <-> "NH2" Residue "q ARG 84": "NH1" <-> "NH2" Residue "q ASP 95": "OD1" <-> "OD2" Residue "r GLU 2": "OE1" <-> "OE2" Residue "r ASP 22": "OD1" <-> "OD2" Residue "r GLU 52": "OE1" <-> "OE2" Residue "r ASP 62": "OD1" <-> "OD2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "r ARG 88": "NH1" <-> "NH2" Residue "r ARG 95": "NH1" <-> "NH2" Residue "r ARG 110": "NH1" <-> "NH2" Residue "s PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 54": "OE1" <-> "OE2" Residue "s ARG 73": "NH1" <-> "NH2" Residue "s ASP 79": "OD1" <-> "OD2" Residue "t ARG 6": "NH1" <-> "NH2" Residue "t ARG 7": "NH1" <-> "NH2" Residue "t GLU 10": "OE1" <-> "OE2" Residue "t ASP 18": "OD1" <-> "OD2" Residue "t GLU 37": "OE1" <-> "OE2" Residue "t ASP 81": "OD1" <-> "OD2" Residue "t ARG 82": "NH1" <-> "NH2" Residue "t ARG 86": "NH1" <-> "NH2" Residue "t PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 94": "NH1" <-> "NH2" Residue "u GLU 41": "OE1" <-> "OE2" Residue "u TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 59": "OE1" <-> "OE2" Residue "u GLU 69": "OE1" <-> "OE2" Residue "u ASP 90": "OD1" <-> "OD2" Residue "v ASP 15": "OD1" <-> "OD2" Residue "v PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 70": "OE1" <-> "OE2" Residue "w ARG 3": "NH1" <-> "NH2" Residue "w ARG 11": "NH1" <-> "NH2" Residue "w ARG 37": "NH1" <-> "NH2" Residue "w GLU 43": "OE1" <-> "OE2" Residue "w PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 50": "NH1" <-> "NH2" Residue "w ARG 57": "NH1" <-> "NH2" Residue "w ASP 60": "OD1" <-> "OD2" Residue "w ARG 74": "NH1" <-> "NH2" Residue "w GLU 76": "OE1" <-> "OE2" Residue "x ARG 29": "NH1" <-> "NH2" Residue "x ARG 47": "NH1" <-> "NH2" Residue "x ARG 52": "NH1" <-> "NH2" Residue "y ARG 11": "NH1" <-> "NH2" Residue "y ARG 30": "NH1" <-> "NH2" Residue "y ARG 45": "NH1" <-> "NH2" Residue "y PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 16": "NH1" <-> "NH2" Residue "z GLU 36": "OE1" <-> "OE2" Residue "z ARG 52": "NH1" <-> "NH2" Residue "0 GLU 7": "OE1" <-> "OE2" Residue "0 GLU 35": "OE1" <-> "OE2" Residue "0 ASP 40": "OD1" <-> "OD2" Residue "0 ARG 44": "NH1" <-> "NH2" Residue "0 GLU 51": "OE1" <-> "OE2" Residue "1 ARG 3": "NH1" <-> "NH2" Residue "1 ARG 12": "NH1" <-> "NH2" Residue "1 ARG 14": "NH1" <-> "NH2" Residue "1 ARG 21": "NH1" <-> "NH2" Residue "1 ARG 33": "NH1" <-> "NH2" Residue "1 ARG 41": "NH1" <-> "NH2" Residue "2 ARG 13": "NH1" <-> "NH2" Residue "2 ARG 30": "NH1" <-> "NH2" Residue "2 ARG 40": "NH1" <-> "NH2" Residue "3 ARG 24": "NH1" <-> "NH2" Residue "4 TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 141917 Number of models: 1 Model: "" Number of chains: 63 Chain: "A" Number of atoms: 32634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1520, 32634 Classifications: {'RNA': 1520} Modifications used: {'rna2p': 1, 'rna2p_pur': 122, 'rna2p_pyr': 82, 'rna3p': 10, 'rna3p_pur': 741, 'rna3p_pyr': 564} Link IDs: {'rna2p': 205, 'rna3p': 1314} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} 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: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 839 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "G" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1203 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} 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: {'PCIS': 1, 'PTRANS': 4, '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 breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'IAS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "Q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 641 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "S" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 668 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "a" Number of atoms: 59130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2753, 59130 Classifications: {'RNA': 2753} Modifications used: {'rna2p': 7, 'rna2p_pur': 267, 'rna2p_pyr': 140, 'rna3p': 17, 'rna3p_pur': 1318, 'rna3p_pyr': 1004} Link IDs: {'rna2p': 413, 'rna3p': 2339} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Chain: "b" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} 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: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 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: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 303 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "i" 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: "j" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "k" 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: "l" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Unusual residues: {'MS6': 1} Classifications: {'peptide': 135, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126, None: 2} Not linked: pdbres="4D4 l 81 " pdbres="MS6 l 82 " Not linked: pdbres="MS6 l 82 " pdbres="GLY l 83 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "n" 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: "o" 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: "p" 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: "q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "r" 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: "s" 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: "t" 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: "u" 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: "v" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 628 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} 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: "w" 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: "x" 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: "y" 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: "z" 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: "0" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1" 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: "2" 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: "3" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "4" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 480 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain breaks: 1 Chain: "X" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 279 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 10} Chain: "Z" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1645 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 5, 'rna2p_pyr': 3, 'rna3p': 4, 'rna3p_pur': 34, 'rna3p_pyr': 30} Link IDs: {'rna2p': 8, 'rna3p': 68} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 Chain: "V" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1612 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p': 3, 'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p': 8, 'rna3p_pur': 31, 'rna3p_pyr': 27} Link IDs: {'rna2p': 9, 'rna3p': 65} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Unusual residues: {' MG': 58} Classifications: {'undetermined': 58} Link IDs: {None: 57} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 191 Unusual residues: {' MG': 191} Classifications: {'undetermined': 191} Link IDs: {None: 190} Chain: "b" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 53.78, per 1000 atoms: 0.38 Number of scatterers: 141917 At special positions: 0 Unit cell: (251.035, 236.122, 246.893, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 150 16.00 P 4556 15.00 Mg 258 11.99 O 39417 8.00 N 26433 7.00 C 71103 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 60.00 Conformation dependent library (CDL) restraints added in 7.7 seconds 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10272 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 169 helices and 65 sheets defined 38.7% alpha, 18.4% beta 1592 base pairs and 2418 stacking pairs defined. Time for finding SS restraints: 72.83 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 removed outlier: 3.579A pdb=" N MET B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 64 Proline residue: B 48 - end of helix removed outlier: 3.559A pdb=" N LYS B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 88 removed outlier: 4.090A pdb=" N VAL B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N CYS B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 124 removed outlier: 3.537A pdb=" N GLY B 124 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 148 removed outlier: 6.415A pdb=" N ALA B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 171 through 180 Processing helix chain 'B' and resid 206 through 227 Processing helix chain 'C' and resid 6 through 12 removed outlier: 4.033A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 48 removed outlier: 3.808A pdb=" N ASN C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.590A pdb=" N VAL C 76 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY C 78 " --> pdb=" O GLY C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 96 Processing helix chain 'C' and resid 108 through 113 removed outlier: 4.619A pdb=" N ASP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 108 through 113' Processing helix chain 'C' and resid 114 through 127 removed outlier: 3.521A pdb=" N ARG C 127 " --> pdb=" O GLN C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 145 Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.658A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.521A pdb=" N LYS D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 68 through 83 removed outlier: 5.184A pdb=" N LYS D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.654A pdb=" N GLY D 96 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 106 Processing helix chain 'D' and resid 110 through 121 Processing helix chain 'D' and resid 146 through 151 removed outlier: 4.504A pdb=" N LYS D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 166 removed outlier: 3.531A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 removed outlier: 3.650A pdb=" N LEU D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N SER D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 187 through 192' Processing helix chain 'D' and resid 196 through 206 removed outlier: 3.818A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 3.911A pdb=" N MET E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 119 Processing helix chain 'E' and resid 132 through 147 Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 160 through 165 removed outlier: 3.567A pdb=" N ILE E 164 " --> pdb=" O SER E 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 16 removed outlier: 3.840A pdb=" N SER F 15 " --> pdb=" O HIS F 11 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLU F 16 " --> pdb=" O PRO F 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 11 through 16' Processing helix chain 'F' and resid 17 through 33 removed outlier: 3.620A pdb=" N GLU F 33 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 removed outlier: 3.524A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 31 removed outlier: 3.742A pdb=" N ALA G 24 " --> pdb=" O SER G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 55 removed outlier: 3.558A pdb=" N ALA G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 70 removed outlier: 4.203A pdb=" N ALA G 61 " --> pdb=" O SER G 57 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 112 removed outlier: 3.522A pdb=" N LYS G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG G 111 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLY G 112 " --> pdb=" O ALA G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 130 removed outlier: 3.560A pdb=" N GLU G 129 " --> pdb=" O SER G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 149 removed outlier: 3.536A pdb=" N LYS G 136 " --> pdb=" O GLY G 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 21 Processing helix chain 'H' and resid 30 through 44 Processing helix chain 'H' and resid 112 through 120 Processing helix chain 'I' and resid 34 through 40 removed outlier: 4.628A pdb=" N GLY I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 56 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 71 through 92 removed outlier: 3.695A pdb=" N GLU I 92 " --> pdb=" O MET I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 102 Processing helix chain 'J' and resid 14 through 33 removed outlier: 3.571A pdb=" N ILE J 18 " --> pdb=" O ASP J 14 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 91 removed outlier: 3.565A pdb=" N LEU J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ASP J 91 " --> pdb=" O LEU J 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 51 removed outlier: 4.385A pdb=" N GLY K 51 " --> pdb=" O ALA K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 59 removed outlier: 3.928A pdb=" N SER K 58 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR K 59 " --> pdb=" O SER K 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 54 through 59' Processing helix chain 'K' and resid 60 through 75 Processing helix chain 'K' and resid 92 through 104 removed outlier: 4.892A pdb=" N THR K 96 " --> pdb=" O GLY K 92 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY K 104 " --> pdb=" O LEU K 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 11 Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 113 through 118 removed outlier: 3.705A pdb=" N TYR L 117 " --> pdb=" O ALA L 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 22 removed outlier: 3.904A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE M 22 " --> pdb=" O ALA M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 64 removed outlier: 4.545A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N PHE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N VAL M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 removed outlier: 3.627A pdb=" N GLY M 84 " --> pdb=" O LEU M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 21 removed outlier: 3.528A pdb=" N LYS N 7 " --> pdb=" O LYS N 3 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE N 21 " --> pdb=" O ALA N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 33 Processing helix chain 'N' and resid 37 through 51 removed outlier: 3.506A pdb=" N ARG N 41 " --> pdb=" O SER N 37 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU N 51 " --> pdb=" O LYS N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 91 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 43 removed outlier: 4.396A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.924A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 85 Processing helix chain 'P' and resid 53 through 64 Processing helix chain 'P' and resid 68 through 80 removed outlier: 3.813A pdb=" N LYS P 80 " --> pdb=" O LYS P 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 17 removed outlier: 3.634A pdb=" N ALA R 15 " --> pdb=" O CYS R 11 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU R 16 " --> pdb=" O ARG R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 34 removed outlier: 4.357A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N THR R 34 " --> pdb=" O LYS R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 removed outlier: 3.542A pdb=" N THR R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 66 Processing helix chain 'S' and resid 12 through 26 Processing helix chain 'S' and resid 70 through 76 removed outlier: 4.820A pdb=" N PHE S 74 " --> pdb=" O LYS S 70 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA S 75 " --> pdb=" O LEU S 71 " (cutoff:3.500A) Proline residue: S 76 - end of helix No H-bonds generated for 'chain 'S' and resid 70 through 76' Processing helix chain 'T' and resid 4 through 41 Processing helix chain 'T' and resid 44 through 65 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 87 Processing helix chain 'U' and resid 11 through 27 Processing helix chain 'U' and resid 28 through 36 Processing helix chain 'U' and resid 40 through 69 removed outlier: 5.130A pdb=" N ARG U 69 " --> pdb=" O ALA U 65 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 15 removed outlier: 5.104A pdb=" N HIS c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 35 removed outlier: 4.184A pdb=" N LEU c 34 " --> pdb=" O PHE c 30 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N GLU c 35 " --> pdb=" O ALA c 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 30 through 35' Processing helix chain 'c' and resid 131 through 136 removed outlier: 3.790A pdb=" N ILE c 135 " --> pdb=" O PRO c 131 " (cutoff:3.500A) Proline residue: c 136 - end of helix No H-bonds generated for 'chain 'c' and resid 131 through 136' Processing helix chain 'c' and resid 207 through 215 removed outlier: 3.710A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG c 214 " --> pdb=" O ALA c 210 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY c 215 " --> pdb=" O ALA c 211 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 226 removed outlier: 4.055A pdb=" N MET c 225 " --> pdb=" O ARG c 221 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASN c 226 " --> pdb=" O GLY c 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 221 through 226' Processing helix chain 'c' and resid 260 through 268 removed outlier: 3.573A pdb=" N ASP c 264 " --> pdb=" O ASN c 260 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LYS c 265 " --> pdb=" O LYS c 261 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE c 266 " --> pdb=" O ARG c 262 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE c 267 " --> pdb=" O THR c 263 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N VAL c 268 " --> pdb=" O ASP c 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 260 through 268' Processing helix chain 'c' and resid 197 through 202 removed outlier: 4.278A pdb=" N MET c 201 " --> pdb=" O ALA c 198 " (cutoff:3.500A) Processing helix chain 'd' and resid 56 through 61 removed outlier: 5.722A pdb=" N THR d 61 " --> pdb=" O ALA d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 72 Processing helix chain 'd' and resid 98 through 103 removed outlier: 3.934A pdb=" N ALA d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASP d 103 " --> pdb=" O GLU d 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 98 through 103' Processing helix chain 'd' and resid 120 through 125 Processing helix chain 'd' and resid 39 through 44 Processing helix chain 'e' and resid 15 through 20 Processing helix chain 'e' and resid 24 through 40 removed outlier: 3.519A pdb=" N ALA e 39 " --> pdb=" O TYR e 35 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG e 40 " --> pdb=" O ALA e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 97 through 116 Processing helix chain 'e' and resid 130 through 142 Processing helix chain 'e' and resid 154 through 163 removed outlier: 3.624A pdb=" N ARG e 162 " --> pdb=" O PHE e 158 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN e 163 " --> pdb=" O LEU e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 184 removed outlier: 5.922A pdb=" N ASP e 184 " --> pdb=" O LEU e 180 " (cutoff:3.500A) Processing helix chain 'e' and resid 189 through 201 Processing helix chain 'f' and resid 2 through 21 removed outlier: 5.661A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 46 through 62 removed outlier: 4.322A pdb=" N LEU f 50 " --> pdb=" O ASP f 46 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 111 removed outlier: 5.837A pdb=" N VAL f 108 " --> pdb=" O ILE f 104 " (cutoff:3.500A) Proline residue: f 109 - end of helix Processing helix chain 'f' and resid 162 through 174 Processing helix chain 'f' and resid 40 through 45 removed outlier: 3.620A pdb=" N ALA f 43 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE f 44 " --> pdb=" O GLY f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 134 through 139 removed outlier: 3.969A pdb=" N ILE f 137 " --> pdb=" O GLU f 134 " (cutoff:3.500A) Proline residue: f 139 - end of helix Processing helix chain 'g' and resid 2 through 8 removed outlier: 3.634A pdb=" N ALA g 7 " --> pdb=" O ARG g 3 " (cutoff:3.500A) Proline residue: g 8 - end of helix Processing helix chain 'g' and resid 60 through 81 removed outlier: 5.537A pdb=" N GLN g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 153 removed outlier: 4.267A pdb=" N ARG g 152 " --> pdb=" O LEU g 148 " (cutoff:3.500A) Processing helix chain 'h' and resid 22 through 28 Processing helix chain 'h' and resid 29 through 34 removed outlier: 3.667A pdb=" N GLN h 33 " --> pdb=" O PHE h 29 " (cutoff:3.500A) Processing helix chain 'i' and resid 24 through 38 removed outlier: 3.875A pdb=" N GLU i 31 " --> pdb=" O ARG i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 88 through 96 Processing helix chain 'i' and resid 97 through 110 removed outlier: 4.435A pdb=" N ILE i 101 " --> pdb=" O PRO i 97 " (cutoff:3.500A) Proline residue: i 110 - end of helix Processing helix chain 'i' and resid 112 through 122 removed outlier: 4.040A pdb=" N LYS i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU i 122 " --> pdb=" O MET i 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 119 Processing helix chain 'k' and resid 37 through 42 removed outlier: 3.589A pdb=" N ARG k 41 " --> pdb=" O GLY k 37 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N SER k 42 " --> pdb=" O GLN k 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 37 through 42' Processing helix chain 'k' and resid 56 through 62 removed outlier: 3.682A pdb=" N LEU k 61 " --> pdb=" O LEU k 57 " (cutoff:3.500A) Proline residue: k 62 - end of helix Processing helix chain 'k' and resid 68 through 75 removed outlier: 4.265A pdb=" N ALA k 72 " --> pdb=" O SER k 68 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE k 73 " --> pdb=" O ARG k 69 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR k 74 " --> pdb=" O LYS k 70 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ALA k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 68 through 75' Processing helix chain 'k' and resid 78 through 85 removed outlier: 4.084A pdb=" N LEU k 82 " --> pdb=" O ARG k 78 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA k 83 " --> pdb=" O LEU k 79 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LYS k 84 " --> pdb=" O SER k 80 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL k 85 " --> pdb=" O ASP k 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 78 through 85' Processing helix chain 'k' and resid 91 through 99 Processing helix chain 'k' and resid 128 through 139 Processing helix chain 'l' and resid 42 through 58 Processing helix chain 'l' and resid 109 through 125 removed outlier: 3.996A pdb=" N LYS l 123 " --> pdb=" O LEU l 119 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU l 124 " --> pdb=" O ALA l 120 " (cutoff:3.500A) Proline residue: l 125 - end of helix Processing helix chain 'm' and resid 13 through 32 Processing helix chain 'm' and resid 38 through 57 removed outlier: 4.225A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL m 47 " --> pdb=" O GLU m 43 " (cutoff:3.500A) Proline residue: m 50 - end of helix removed outlier: 4.527A pdb=" N THR m 57 " --> pdb=" O THR m 53 " (cutoff:3.500A) Processing helix chain 'm' and resid 59 through 71 removed outlier: 4.582A pdb=" N THR m 70 " --> pdb=" O ALA m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 72 through 88 removed outlier: 3.528A pdb=" N VAL m 76 " --> pdb=" O ASP m 72 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLY m 84 " --> pdb=" O PHE m 80 " (cutoff:3.500A) Proline residue: m 85 - end of helix Processing helix chain 'n' and resid 2 through 22 removed outlier: 4.487A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 63 removed outlier: 5.180A pdb=" N GLN n 61 " --> pdb=" O ALA n 57 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU n 62 " --> pdb=" O ILE n 58 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N LYS n 63 " --> pdb=" O ALA n 59 " (cutoff:3.500A) Processing helix chain 'n' and resid 67 through 86 Processing helix chain 'n' and resid 101 through 114 Processing helix chain 'o' and resid 2 through 13 removed outlier: 3.604A pdb=" N GLU o 11 " --> pdb=" O GLN o 7 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN o 12 " --> pdb=" O LEU o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 104 removed outlier: 4.635A pdb=" N ARG o 101 " --> pdb=" O LEU o 97 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU o 102 " --> pdb=" O TYR o 98 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG o 103 " --> pdb=" O TYR o 99 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N THR o 104 " --> pdb=" O LEU o 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 97 through 104' Processing helix chain 'p' and resid 6 through 22 removed outlier: 3.855A pdb=" N LYS p 22 " --> pdb=" O LEU p 18 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 31 removed outlier: 3.886A pdb=" N ARG p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) Processing helix chain 'p' and resid 32 through 37 removed outlier: 4.198A pdb=" N GLN p 37 " --> pdb=" O ARG p 33 " (cutoff:3.500A) Processing helix chain 'p' and resid 39 through 73 removed outlier: 4.117A pdb=" N ARG p 51 " --> pdb=" O TYR p 47 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN p 72 " --> pdb=" O ALA p 68 " (cutoff:3.500A) Processing helix chain 'p' and resid 75 through 87 Processing helix chain 'p' and resid 91 through 102 Processing helix chain 'p' and resid 103 through 118 Processing helix chain 'r' and resid 13 through 25 removed outlier: 3.742A pdb=" N VAL r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG r 25 " --> pdb=" O ALA r 21 " (cutoff:3.500A) Processing helix chain 'r' and resid 28 through 39 Processing helix chain 'r' and resid 41 through 61 removed outlier: 3.508A pdb=" N VAL r 45 " --> pdb=" O LYS r 41 " (cutoff:3.500A) Processing helix chain 's' and resid 3 through 11 removed outlier: 4.276A pdb=" N LEU s 11 " --> pdb=" O LEU s 7 " (cutoff:3.500A) Processing helix chain 's' and resid 17 through 27 Processing helix chain 's' and resid 39 through 51 Processing helix chain 't' and resid 66 through 71 removed outlier: 3.806A pdb=" N VAL t 70 " --> pdb=" O GLN t 66 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ALA t 71 " --> pdb=" O VAL t 67 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 66 through 71' Processing helix chain 'u' and resid 13 through 24 removed outlier: 3.560A pdb=" N ALA u 23 " --> pdb=" O ARG u 19 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN u 24 " --> pdb=" O LEU u 20 " (cutoff:3.500A) Processing helix chain 'u' and resid 43 through 53 removed outlier: 3.564A pdb=" N VAL u 47 " --> pdb=" O ASP u 43 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS u 53 " --> pdb=" O ASN u 49 " (cutoff:3.500A) Processing helix chain 'u' and resid 54 through 59 removed outlier: 4.316A pdb=" N SER u 58 " --> pdb=" O ALA u 54 " (cutoff:3.500A) Processing helix chain 'w' and resid 52 through 63 Processing helix chain 'w' and resid 64 through 75 Processing helix chain 'x' and resid 2 through 10 removed outlier: 4.625A pdb=" N LYS x 9 " --> pdb=" O GLU x 5 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N SER x 10 " --> pdb=" O LEU x 6 " (cutoff:3.500A) Processing helix chain 'x' and resid 11 through 35 Processing helix chain 'x' and resid 39 through 62 removed outlier: 4.672A pdb=" N LEU x 43 " --> pdb=" O GLN x 39 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS x 44 " --> pdb=" O SER x 40 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY x 62 " --> pdb=" O ASN x 58 " (cutoff:3.500A) Processing helix chain 'y' and resid 17 through 28 Processing helix chain 'y' and resid 41 through 52 Processing helix chain 'z' and resid 9 through 19 removed outlier: 4.717A pdb=" N HIS z 19 " --> pdb=" O MET z 15 " (cutoff:3.500A) Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 24 removed outlier: 4.503A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) Processing helix chain '1' and resid 25 through 38 Processing helix chain '2' and resid 7 through 14 removed outlier: 4.221A pdb=" N ARG 2 13 " --> pdb=" O GLY 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 37 through 46 Proline residue: 2 46 - end of helix Processing helix chain '2' and resid 51 through 63 removed outlier: 4.633A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LEU 2 57 " --> pdb=" O GLY 2 53 " (cutoff:3.500A) Proline residue: 2 63 - end of helix Processing helix chain '4' and resid 41 through 46 Processing helix chain '4' and resid 55 through 65 removed outlier: 3.844A pdb=" N ARG 4 59 " --> pdb=" O GLY 4 55 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 90 through 93 Processing sheet with id= 2, first strand: chain 'C' and resid 53 through 59 removed outlier: 3.504A pdb=" N ARG C 54 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.736A pdb=" N GLY C 148 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'D' and resid 141 through 144 removed outlier: 3.606A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU D 172 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'E' and resid 12 through 16 removed outlier: 6.839A pdb=" N LEU E 36 " --> pdb=" O ILE E 16 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 84 through 88 removed outlier: 3.624A pdb=" N ALA E 99 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ASN E 122 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 33 through 40 removed outlier: 3.651A pdb=" N GLY E 49 " --> pdb=" O THR E 37 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'F' and resid 38 through 42 removed outlier: 5.479A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F' and resid 43 through 47 removed outlier: 3.999A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N HIS F 55 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'G' and resid 72 through 79 removed outlier: 6.041A pdb=" N THR G 72 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'H' and resid 23 through 29 removed outlier: 6.347A pdb=" N ALA H 23 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.688A pdb=" N SER H 74 " --> pdb=" O ALA H 130 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS H 127 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'I' and resid 5 through 11 Processing sheet with id= 14, first strand: chain 'I' and resid 26 through 30 Processing sheet with id= 15, first strand: chain 'J' and resid 36 through 40 Processing sheet with id= 16, first strand: chain 'J' and resid 44 through 52 Processing sheet with id= 17, first strand: chain 'K' and resid 42 through 45 removed outlier: 3.794A pdb=" N ASN K 29 " --> pdb=" O SER K 26 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG K 106 " --> pdb=" O LYS K 80 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL K 84 " --> pdb=" O THR K 108 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'L' and resid 29 through 33 removed outlier: 5.236A pdb=" N LEU L 81 " --> pdb=" O VAL L 98 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'L' and resid 36 through 41 removed outlier: 5.334A pdb=" N LYS L 51 " --> pdb=" O ILE L 67 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'P' and resid 4 through 10 removed outlier: 3.747A pdb=" N PHE P 16 " --> pdb=" O HIS P 9 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N GLY P 49 " --> pdb=" O ASN P 40 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'Q' and resid 7 through 11 removed outlier: 6.674A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'Q' and resid 19 through 30 No H-bonds generated for sheet with id= 22 Processing sheet with id= 23, first strand: chain 'S' and resid 30 through 34 removed outlier: 4.655A pdb=" N LEU S 47 " --> pdb=" O VAL S 62 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'c' and resid 2 through 6 removed outlier: 5.917A pdb=" N VAL c 16 " --> pdb=" O CYS c 6 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'c' and resid 80 through 83 removed outlier: 3.509A pdb=" N ARG c 80 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU c 93 " --> pdb=" O GLU c 79 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ILE c 74 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N SER c 118 " --> pdb=" O ILE c 74 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP c 114 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLY c 127 " --> pdb=" O GLN c 115 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLN c 117 " --> pdb=" O GLY c 127 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'c' and resid 138 through 142 removed outlier: 4.174A pdb=" N SER c 139 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR c 173 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU c 180 " --> pdb=" O LEU c 176 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'c' and resid 90 through 96 removed outlier: 5.224A pdb=" N ASN c 90 " --> pdb=" O ALA c 106 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU c 100 " --> pdb=" O TYR c 96 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'd' and resid 3 through 8 removed outlier: 4.253A pdb=" N SER d 199 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LYS d 105 " --> pdb=" O VAL d 177 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'd' and resid 11 through 16 removed outlier: 3.638A pdb=" N VAL d 20 " --> pdb=" O THR d 16 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'd' and resid 79 through 84 removed outlier: 5.840A pdb=" N ARG d 46 " --> pdb=" O LEU d 84 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLN d 94 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'e' and resid 1 through 6 removed outlier: 3.761A pdb=" N SER e 10 " --> pdb=" O LEU e 5 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'e' and resid 117 through 120 Processing sheet with id= 33, first strand: chain 'f' and resid 65 through 69 removed outlier: 5.332A pdb=" N GLY f 39 " --> pdb=" O GLY f 151 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N GLY f 151 " --> pdb=" O GLY f 39 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU f 152 " --> pdb=" O VAL f 132 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'g' and resid 16 through 19 Processing sheet with id= 35, first strand: chain 'g' and resid 82 through 89 removed outlier: 5.836A pdb=" N THR g 129 " --> pdb=" O LEU g 89 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'g' and resid 94 through 98 Processing sheet with id= 37, first strand: chain 'h' and resid 1 through 4 No H-bonds generated for sheet with id= 37 Processing sheet with id= 38, first strand: chain 'i' and resid 52 through 57 removed outlier: 5.017A pdb=" N ASP i 19 " --> pdb=" O LEU i 140 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'i' and resid 74 through 78 removed outlier: 7.608A pdb=" N GLY i 83 " --> pdb=" O THR i 78 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'j' and resid 18 through 21 removed outlier: 4.147A pdb=" N THR j 6 " --> pdb=" O CYS j 21 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ASN j 82 " --> pdb=" O MET j 7 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'l' and resid 62 through 65 removed outlier: 6.541A pdb=" N LEU l 33 " --> pdb=" O LEU l 102 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS l 100 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'l' and resid 30 through 36 removed outlier: 7.789A pdb=" N SER l 30 " --> pdb=" O LYS l 133 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LYS l 127 " --> pdb=" O VAL l 36 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'm' and resid 33 through 37 removed outlier: 6.236A pdb=" N MET m 110 " --> pdb=" O CYS m 100 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N TYR m 94 " --> pdb=" O VAL m 116 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'n' and resid 49 through 52 removed outlier: 3.561A pdb=" N VAL n 49 " --> pdb=" O VAL n 39 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'o' and resid 38 through 45 removed outlier: 6.551A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER o 83 " --> pdb=" O LYS o 29 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'o' and resid 49 through 53 removed outlier: 3.612A pdb=" N ALA o 49 " --> pdb=" O THR o 60 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ARG o 53 " --> pdb=" O HIS o 56 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N SER o 57 " --> pdb=" O THR o 76 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'q' and resid 11 through 15 removed outlier: 3.529A pdb=" N MET q 40 " --> pdb=" O VAL q 4 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN q 43 " --> pdb=" O GLU q 46 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU q 46 " --> pdb=" O ASN q 43 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'q' and resid 18 through 23 removed outlier: 4.264A pdb=" N GLN q 18 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP q 95 " --> pdb=" O VAL q 64 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS q 60 " --> pdb=" O THR q 99 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL q 33 " --> pdb=" O ALA q 61 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'q' and resid 57 through 60 removed outlier: 3.581A pdb=" N GLY q 100 " --> pdb=" O LYS q 60 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'q' and resid 65 through 68 Processing sheet with id= 51, first strand: chain 'q' and resid 71 through 78 removed outlier: 4.141A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'r' and resid 2 through 8 Processing sheet with id= 53, first strand: chain 's' and resid 28 through 33 removed outlier: 6.212A pdb=" N ASN s 28 " --> pdb=" O LEU s 87 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS s 66 " --> pdb=" O ARG s 77 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASP s 79 " --> pdb=" O LYS s 64 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LYS s 64 " --> pdb=" O ASP s 79 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS s 81 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL s 62 " --> pdb=" O LYS s 81 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA s 83 " --> pdb=" O THR s 60 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR s 60 " --> pdb=" O ALA s 83 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL s 85 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL s 58 " --> pdb=" O VAL s 85 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 't' and resid 82 through 87 removed outlier: 5.463A pdb=" N ARG t 82 " --> pdb=" O LYS t 97 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'u' and resid 69 through 72 removed outlier: 6.674A pdb=" N ALA u 39 " --> pdb=" O ARG u 9 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE u 89 " --> pdb=" O PRO u 27 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'v' and resid 51 through 54 removed outlier: 4.255A pdb=" N THR v 58 " --> pdb=" O GLY v 54 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'v' and resid 65 through 71 Processing sheet with id= 58, first strand: chain 'w' and resid 12 through 19 removed outlier: 4.562A pdb=" N ASN w 23 " --> pdb=" O SER w 19 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'w' and resid 34 through 41 Processing sheet with id= 60, first strand: chain 'y' and resid 34 through 39 removed outlier: 4.405A pdb=" N HIS y 34 " --> pdb=" O GLN y 9 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE y 7 " --> pdb=" O VAL y 36 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS y 6 " --> pdb=" O GLU y 58 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU y 58 " --> pdb=" O LYS y 6 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N MET y 54 " --> pdb=" O THR y 10 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'z' and resid 29 through 32 removed outlier: 4.649A pdb=" N GLU z 36 " --> pdb=" O ASP z 31 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain '0' and resid 20 through 25 removed outlier: 6.769A pdb=" N ILE 0 48 " --> pdb=" O SER 0 14 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU 0 51 " --> pdb=" O LEU 0 34 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU 0 34 " --> pdb=" O GLU 0 51 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain '2' and resid 22 through 25 removed outlier: 5.724A pdb=" N PHE 2 22 " --> pdb=" O VAL 2 50 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain '3' and resid 14 through 19 Processing sheet with id= 65, first strand: chain '4' and resid 20 through 25 removed outlier: 4.408A pdb=" N ASN 4 20 " --> pdb=" O CYS 4 16 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS 4 16 " --> pdb=" O ASN 4 20 " (cutoff:3.500A) 1855 hydrogen bonds defined for protein. 5472 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4002 hydrogen bonds 6244 hydrogen bond angles 0 basepair planarities 1592 basepair parallelities 2418 stacking parallelities Total time for adding SS restraints: 249.59 Time building geometry restraints manager: 64.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 12644 1.30 - 1.43: 69190 1.43 - 1.57: 62778 1.57 - 1.70: 9110 1.70 - 1.84: 264 Bond restraints: 153986 Sorted by residual: bond pdb=" C5 5MU Z 55 " pdb=" C6 5MU Z 55 " ideal model delta sigma weight residual 1.155 1.443 -0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C5 5MU V 53 " pdb=" C6 5MU V 53 " ideal model delta sigma weight residual 1.155 1.439 -0.284 2.00e-02 2.50e+03 2.01e+02 bond pdb=" C5 5MU a1939 " pdb=" C6 5MU a1939 " ideal model delta sigma weight residual 1.155 1.436 -0.281 2.00e-02 2.50e+03 1.98e+02 bond pdb=" C5 5MU a 747 " pdb=" C6 5MU a 747 " ideal model delta sigma weight residual 1.155 1.435 -0.280 2.00e-02 2.50e+03 1.96e+02 bond pdb=" C MS6 l 82 " pdb=" S MS6 l 82 " ideal model delta sigma weight residual 1.816 1.565 0.251 2.00e-02 2.50e+03 1.57e+02 ... (remaining 153981 not shown) Histogram of bond angle deviations from ideal: 96.22 - 105.29: 21996 105.29 - 114.37: 103907 114.37 - 123.45: 82137 123.45 - 132.53: 22195 132.53 - 141.61: 212 Bond angle restraints: 230447 Sorted by residual: angle pdb=" C1' 2MA a2503 " pdb=" N9 2MA a2503 " pdb=" C8 2MA a2503 " ideal model delta sigma weight residual 106.32 141.61 -35.29 3.00e+00 1.11e-01 1.38e+02 angle pdb=" C1' G7M a2069 " pdb=" N9 G7M a2069 " pdb=" C8 G7M a2069 " ideal model delta sigma weight residual 94.96 126.23 -31.27 3.00e+00 1.11e-01 1.09e+02 angle pdb=" C1' G7M A 527 " pdb=" N9 G7M A 527 " pdb=" C8 G7M A 527 " ideal model delta sigma weight residual 94.96 124.68 -29.72 3.00e+00 1.11e-01 9.82e+01 angle pdb=" C1' 2MA a2503 " pdb=" N9 2MA a2503 " pdb=" C4 2MA a2503 " ideal model delta sigma weight residual 138.88 111.13 27.75 3.00e+00 1.11e-01 8.56e+01 angle pdb=" C1' 1MA V 9 " pdb=" N9 1MA V 9 " pdb=" C8 1MA V 9 " ideal model delta sigma weight residual 100.68 128.22 -27.54 3.00e+00 1.11e-01 8.43e+01 ... (remaining 230442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 85327 35.84 - 71.68: 8482 71.68 - 107.53: 1166 107.53 - 143.37: 14 143.37 - 179.21: 11 Dihedral angle restraints: 95000 sinusoidal: 79077 harmonic: 15923 Sorted by residual: dihedral pdb=" CA ASP g 47 " pdb=" C ASP g 47 " pdb=" N ASN g 48 " pdb=" CA ASN g 48 " ideal model delta harmonic sigma weight residual -180.00 -113.78 -66.22 0 5.00e+00 4.00e-02 1.75e+02 dihedral pdb=" CA HIS 2 31 " pdb=" C HIS 2 31 " pdb=" N ILE 2 32 " pdb=" CA ILE 2 32 " ideal model delta harmonic sigma weight residual -180.00 -130.29 -49.71 0 5.00e+00 4.00e-02 9.89e+01 dihedral pdb=" O4' C V 73 " pdb=" C1' C V 73 " pdb=" N1 C V 73 " pdb=" C2 C V 73 " ideal model delta sinusoidal sigma weight residual -160.00 5.76 -165.76 1 1.50e+01 4.44e-03 8.40e+01 ... (remaining 94997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 26991 0.082 - 0.165: 2158 0.165 - 0.247: 140 0.247 - 0.329: 6 0.329 - 0.412: 4 Chirality restraints: 29299 Sorted by residual: chirality pdb=" C1* PSU A 516 " pdb=" O4* PSU A 516 " pdb=" C2* PSU A 516 " pdb=" C5 PSU A 516 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" C1* PSU a2580 " pdb=" O4* PSU a2580 " pdb=" C2* PSU a2580 " pdb=" C5 PSU a2580 " both_signs ideal model delta sigma weight residual False 2.55 2.18 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" C1' A a 983 " pdb=" O4' A a 983 " pdb=" C2' A a 983 " pdb=" N9 A a 983 " both_signs ideal model delta sigma weight residual False 2.46 2.11 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 29296 not shown) Planarity restraints: 12266 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " -0.075 2.00e-02 2.50e+03 6.12e-01 8.42e+03 pdb=" C4' 2MG A1516 " -0.434 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " -0.612 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " 0.602 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " 0.673 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " 0.154 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " -1.018 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " -0.224 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " 0.935 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG a2251 " 0.031 2.00e-02 2.50e+03 5.98e-01 8.04e+03 pdb=" C4' OMG a2251 " 0.443 2.00e-02 2.50e+03 pdb=" O4' OMG a2251 " 0.747 2.00e-02 2.50e+03 pdb=" C3' OMG a2251 " -0.601 2.00e-02 2.50e+03 pdb=" O3' OMG a2251 " -0.573 2.00e-02 2.50e+03 pdb=" C2' OMG a2251 " -0.224 2.00e-02 2.50e+03 pdb=" O2' OMG a2251 " 0.904 2.00e-02 2.50e+03 pdb=" C1' OMG a2251 " 0.204 2.00e-02 2.50e+03 pdb=" N9 OMG a2251 " -0.929 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1207 " -0.068 2.00e-02 2.50e+03 5.98e-01 8.04e+03 pdb=" C4' 2MG A1207 " -0.442 2.00e-02 2.50e+03 pdb=" O4' 2MG A1207 " -0.624 2.00e-02 2.50e+03 pdb=" C3' 2MG A1207 " 0.598 2.00e-02 2.50e+03 pdb=" O3' 2MG A1207 " 0.642 2.00e-02 2.50e+03 pdb=" C2' 2MG A1207 " 0.183 2.00e-02 2.50e+03 pdb=" O2' 2MG A1207 " -0.980 2.00e-02 2.50e+03 pdb=" C1' 2MG A1207 " -0.213 2.00e-02 2.50e+03 pdb=" N9 2MG A1207 " 0.903 2.00e-02 2.50e+03 ... (remaining 12263 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 650 2.42 - 3.04: 80435 3.04 - 3.66: 263093 3.66 - 4.28: 416383 4.28 - 4.90: 560573 Nonbonded interactions: 1321134 Sorted by model distance: nonbonded pdb=" O6 G A1222 " pdb="MG MG A1604 " model vdw 1.795 2.170 nonbonded pdb=" OP1 C a 787 " pdb="MG MG a6124 " model vdw 1.805 2.170 nonbonded pdb=" OP2 A A 964 " pdb="MG MG A1611 " model vdw 1.810 2.170 nonbonded pdb=" OP1 C a2385 " pdb="MG MG a6112 " model vdw 1.830 2.170 nonbonded pdb=" OP2 C A 980 " pdb="MG MG A1604 " model vdw 1.834 2.170 ... (remaining 1321129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 35.370 Check model and map are aligned: 1.540 Set scattering table: 1.020 Process input model: 538.970 Find NCS groups from input model: 3.100 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 600.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 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 : 0.010 0.288 153986 Z= 0.626 Angle : 0.775 35.288 230447 Z= 0.401 Chirality : 0.046 0.412 29299 Planarity : 0.025 0.612 12266 Dihedral : 21.733 179.209 84728 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.00 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.60 (0.11), residues: 5480 helix: 0.70 (0.12), residues: 1835 sheet: -0.86 (0.15), residues: 1110 loop : -0.93 (0.12), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 23 HIS 0.028 0.002 HIS K 118 PHE 0.027 0.002 PHE P 32 TYR 0.020 0.002 TYR F 25 ARG 0.015 0.001 ARG s 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1138 time to evaluate : 6.032 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 1138 average time/residue: 2.3527 time to fit residues: 3731.9358 Evaluate side-chains 826 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 824 time to evaluate : 5.970 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 1.6492 time to fit residues: 11.4855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 835 optimal weight: 0.8980 chunk 750 optimal weight: 8.9990 chunk 416 optimal weight: 10.0000 chunk 256 optimal weight: 8.9990 chunk 506 optimal weight: 8.9990 chunk 400 optimal weight: 10.0000 chunk 775 optimal weight: 7.9990 chunk 300 optimal weight: 7.9990 chunk 471 optimal weight: 30.0000 chunk 577 optimal weight: 3.9990 chunk 899 optimal weight: 10.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 198 HIS E 70 ASN E 77 ASN E 121 HIS ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 HIS N 4 GLN N 49 GLN ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 ASN c 134 ASN ** d 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 20 ASN ** g 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 3 GLN n 29 HIS n 38 GLN o 12 GLN p 37 GLN q 6 GLN ** s 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 75 GLN w 36 HIS x 38 GLN x 45 GLN 1 29 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 153986 Z= 0.322 Angle : 0.820 16.003 230447 Z= 0.433 Chirality : 0.042 0.373 29299 Planarity : 0.008 0.152 12266 Dihedral : 22.368 178.292 73690 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.91 % Favored : 96.04 % Rotamer: Outliers : 3.83 % Allowed : 12.83 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.47 (0.11), residues: 5480 helix: 0.82 (0.12), residues: 1842 sheet: -0.76 (0.15), residues: 1080 loop : -0.88 (0.12), residues: 2558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 248 HIS 0.018 0.002 HIS K 118 PHE 0.025 0.003 PHE p 57 TYR 0.020 0.003 TYR f 83 ARG 0.012 0.001 ARG p 51 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1037 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 862 time to evaluate : 5.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 175 outliers final: 72 residues processed: 944 average time/residue: 2.2498 time to fit residues: 3003.8890 Evaluate side-chains 885 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 813 time to evaluate : 5.566 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 35 residues processed: 37 average time/residue: 1.4432 time to fit residues: 95.4949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 499 optimal weight: 10.0000 chunk 279 optimal weight: 20.0000 chunk 748 optimal weight: 9.9990 chunk 612 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 chunk 900 optimal weight: 4.9990 chunk 972 optimal weight: 5.9990 chunk 802 optimal weight: 0.0970 chunk 893 optimal weight: 6.9990 chunk 307 optimal weight: 9.9990 chunk 722 optimal weight: 6.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN D 198 HIS E 70 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 GLN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN O 37 ASN P 40 ASN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 36 GLN e 24 ASN f 27 GLN ** g 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 86 GLN k 104 GLN ** s 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 75 GLN v 76 ASN x 45 GLN 1 29 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 153986 Z= 0.243 Angle : 0.725 15.029 230447 Z= 0.395 Chirality : 0.039 0.390 29299 Planarity : 0.008 0.141 12266 Dihedral : 22.280 176.790 73690 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.91 % Favored : 96.04 % Rotamer: Outliers : 4.33 % Allowed : 16.20 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.33 (0.11), residues: 5480 helix: 0.95 (0.12), residues: 1847 sheet: -0.66 (0.15), residues: 1076 loop : -0.83 (0.12), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 248 HIS 0.012 0.001 HIS K 118 PHE 0.027 0.002 PHE F 8 TYR 0.019 0.002 TYR f 7 ARG 0.011 0.001 ARG p 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1028 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 830 time to evaluate : 6.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 198 outliers final: 96 residues processed: 940 average time/residue: 2.2763 time to fit residues: 3034.7907 Evaluate side-chains 899 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 803 time to evaluate : 6.000 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 57 residues processed: 39 average time/residue: 1.3977 time to fit residues: 97.8358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 889 optimal weight: 8.9990 chunk 677 optimal weight: 6.9990 chunk 467 optimal weight: 10.0000 chunk 99 optimal weight: 40.0000 chunk 429 optimal weight: 10.0000 chunk 604 optimal weight: 10.0000 chunk 903 optimal weight: 5.9990 chunk 956 optimal weight: 1.9990 chunk 472 optimal weight: 30.0000 chunk 856 optimal weight: 0.0970 chunk 257 optimal weight: 3.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 198 HIS E 77 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN T 21 ASN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 36 GLN d 42 ASN ** g 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 104 GLN ** s 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 39 GLN x 45 GLN 1 29 GLN 4 48 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 153986 Z= 0.216 Angle : 0.700 14.116 230447 Z= 0.384 Chirality : 0.037 0.390 29299 Planarity : 0.007 0.137 12266 Dihedral : 22.246 175.787 73690 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.98 % Favored : 95.97 % Rotamer: Outliers : 4.90 % Allowed : 17.60 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.20 (0.11), residues: 5480 helix: 1.10 (0.12), residues: 1848 sheet: -0.54 (0.15), residues: 1109 loop : -0.81 (0.12), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 201 HIS 0.010 0.001 HIS D 198 PHE 0.029 0.002 PHE F 8 TYR 0.020 0.002 TYR f 7 ARG 0.011 0.001 ARG i 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 824 time to evaluate : 5.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 224 outliers final: 112 residues processed: 958 average time/residue: 2.2041 time to fit residues: 3017.2430 Evaluate side-chains 896 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 784 time to evaluate : 5.710 Switching outliers to nearest non-outliers outliers start: 112 outliers final: 76 residues processed: 37 average time/residue: 1.2776 time to fit residues: 88.7187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 796 optimal weight: 20.0000 chunk 543 optimal weight: 10.0000 chunk 13 optimal weight: 30.0000 chunk 712 optimal weight: 0.9990 chunk 394 optimal weight: 10.0000 chunk 816 optimal weight: 0.0870 chunk 661 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 488 optimal weight: 30.0000 chunk 858 optimal weight: 8.9990 chunk 241 optimal weight: 1.9990 overall best weight: 4.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 198 HIS E 77 ASN E 121 HIS ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN T 3 ASN T 21 ASN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 36 GLN d 42 ASN e 136 GLN i 131 ASN j 5 GLN k 104 GLN p 72 ASN ** s 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 45 GLN 1 29 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 153986 Z= 0.241 Angle : 0.724 14.505 230447 Z= 0.394 Chirality : 0.039 0.395 29299 Planarity : 0.008 0.141 12266 Dihedral : 22.276 175.737 73690 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.18 % Favored : 95.77 % Rotamer: Outliers : 5.05 % Allowed : 18.47 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.25 (0.11), residues: 5480 helix: 1.04 (0.12), residues: 1853 sheet: -0.58 (0.15), residues: 1096 loop : -0.83 (0.12), residues: 2531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 23 HIS 0.007 0.001 HIS K 118 PHE 0.030 0.002 PHE F 8 TYR 0.021 0.002 TYR f 7 ARG 0.009 0.001 ARG p 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1028 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 797 time to evaluate : 6.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 231 outliers final: 128 residues processed: 939 average time/residue: 2.2620 time to fit residues: 3020.7905 Evaluate side-chains 899 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 771 time to evaluate : 6.023 Switching outliers to nearest non-outliers outliers start: 128 outliers final: 89 residues processed: 39 average time/residue: 1.2501 time to fit residues: 92.0188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 321 optimal weight: 2.9990 chunk 861 optimal weight: 3.9990 chunk 189 optimal weight: 9.9990 chunk 561 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 chunk 957 optimal weight: 7.9990 chunk 795 optimal weight: 4.9990 chunk 443 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 316 optimal weight: 0.0050 chunk 502 optimal weight: 10.0000 overall best weight: 3.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN E 121 HIS G 68 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN T 21 ASN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 36 GLN d 42 ASN k 104 GLN p 20 GLN ** s 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 45 GLN ** 1 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 153986 Z= 0.194 Angle : 0.690 14.029 230447 Z= 0.381 Chirality : 0.037 0.392 29299 Planarity : 0.007 0.138 12266 Dihedral : 22.266 175.580 73690 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.09 % Favored : 95.86 % Rotamer: Outliers : 4.35 % Allowed : 19.54 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.15 (0.11), residues: 5480 helix: 1.15 (0.12), residues: 1846 sheet: -0.52 (0.15), residues: 1090 loop : -0.79 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 201 HIS 0.007 0.001 HIS o 77 PHE 0.033 0.002 PHE F 8 TYR 0.022 0.002 TYR f 7 ARG 0.007 0.001 ARG p 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 790 time to evaluate : 5.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 199 outliers final: 131 residues processed: 918 average time/residue: 2.2252 time to fit residues: 2917.8518 Evaluate side-chains 912 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 781 time to evaluate : 6.071 Switching outliers to nearest non-outliers outliers start: 131 outliers final: 96 residues processed: 35 average time/residue: 1.3310 time to fit residues: 86.3129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 923 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 545 optimal weight: 10.0000 chunk 699 optimal weight: 10.0000 chunk 541 optimal weight: 10.0000 chunk 806 optimal weight: 10.0000 chunk 534 optimal weight: 10.0000 chunk 954 optimal weight: 0.0470 chunk 597 optimal weight: 20.0000 chunk 581 optimal weight: 10.0000 chunk 440 optimal weight: 9.9990 overall best weight: 8.0092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 GLN D 71 GLN D 198 HIS E 77 ASN E 121 HIS H 18 GLN ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 HIS N 49 GLN T 21 ASN c 163 GLN d 36 GLN d 42 ASN e 136 GLN f 127 ASN k 104 GLN p 20 GLN p 37 GLN ** s 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 45 GLN 1 29 GLN 4 20 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 153986 Z= 0.388 Angle : 0.880 17.457 230447 Z= 0.458 Chirality : 0.046 0.404 29299 Planarity : 0.009 0.150 12266 Dihedral : 22.445 177.105 73690 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.96 % Favored : 94.98 % Rotamer: Outliers : 4.83 % Allowed : 19.80 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.63 (0.11), residues: 5480 helix: 0.64 (0.12), residues: 1846 sheet: -0.76 (0.15), residues: 1088 loop : -0.98 (0.12), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP c 248 HIS 0.009 0.002 HIS F 11 PHE 0.033 0.003 PHE F 8 TYR 0.024 0.003 TYR p 32 ARG 0.012 0.001 ARG p 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1029 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 808 time to evaluate : 5.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 221 outliers final: 150 residues processed: 943 average time/residue: 2.2465 time to fit residues: 3018.5285 Evaluate side-chains 937 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 787 time to evaluate : 5.393 Switching outliers to nearest non-outliers outliers start: 150 outliers final: 105 residues processed: 45 average time/residue: 1.1281 time to fit residues: 98.2982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 590 optimal weight: 10.0000 chunk 381 optimal weight: 7.9990 chunk 569 optimal weight: 10.0000 chunk 287 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 chunk 606 optimal weight: 10.0000 chunk 650 optimal weight: 10.0000 chunk 471 optimal weight: 30.0000 chunk 88 optimal weight: 10.0000 chunk 750 optimal weight: 0.9980 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: