Starting phenix.real_space_refine on Sat Dec 16 06:49:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pva_17959/12_2023/8pva_17959_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pva_17959/12_2023/8pva_17959.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pva_17959/12_2023/8pva_17959_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pva_17959/12_2023/8pva_17959_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pva_17959/12_2023/8pva_17959_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pva_17959/12_2023/8pva_17959.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pva_17959/12_2023/8pva_17959.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pva_17959/12_2023/8pva_17959_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pva_17959/12_2023/8pva_17959_updated.pdb" } resolution = 4.5 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= 0.003 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 Zn 2 6.06 5 P 4554 5.49 5 S 149 5.16 5 C 71046 2.51 5 N 26426 2.21 5 O 39388 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 123": "OD1" <-> "OD2" Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 127": "OD1" <-> "OD2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ASP 188": "OD1" <-> "OD2" Residue "B ASP 197": "OD1" <-> "OD2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "C ASP 34": "OD1" <-> "OD2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C ASP 118": "OD1" <-> "OD2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C ASP 181": "OD1" <-> "OD2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D ASP 174": "OD1" <-> "OD2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "E GLU 10": "OE1" <-> "OE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "F GLU 16": "OE1" <-> "OE2" Residue "F GLU 33": "OE1" <-> "OE2" Residue "F GLU 73": "OE1" <-> "OE2" Residue "F ASP 82": "OD1" <-> "OD2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "G ASP 126": "OD1" <-> "OD2" Residue "H GLU 43": "OE1" <-> "OE2" Residue "H GLU 47": "OE1" <-> "OE2" Residue "H GLU 58": "OE1" <-> "OE2" Residue "I PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 36": "OE1" <-> "OE2" Residue "I TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 42": "OE1" <-> "OE2" Residue "I GLU 53": "OE1" <-> "OE2" Residue "I ASP 62": "OD1" <-> "OD2" Residue "I GLU 89": "OE1" <-> "OE2" Residue "I GLU 92": "OE1" <-> "OE2" Residue "I ARG 95": "NH1" <-> "NH2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "I ARG 124": "NH1" <-> "NH2" Residue "J GLU 27": "OE1" <-> "OE2" Residue "J PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 75": "OD1" <-> "OD2" Residue "J GLU 78": "OE1" <-> "OE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "K ASP 18": "OD1" <-> "OD2" Residue "K PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 72": "OD1" <-> "OD2" Residue "K GLU 76": "OE1" <-> "OE2" Residue "L ARG 14": "NH1" <-> "NH2" Residue "L GLU 25": "OE1" <-> "OE2" Residue "L ARG 56": "NH1" <-> "NH2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L ASP 109": "OD1" <-> "OD2" Residue "M ASP 11": "OD1" <-> "OD2" Residue "M GLU 50": "OE1" <-> "OE2" Residue "M ASP 58": "OD1" <-> "OD2" Residue "N ASP 18": "OD1" <-> "OD2" Residue "N ASP 33": "OD1" <-> "OD2" Residue "N ASP 38": "OD1" <-> "OD2" Residue "N ASP 40": "OD1" <-> "OD2" Residue "N ARG 65": "NH1" <-> "NH2" Residue "O GLU 14": "OE1" <-> "OE2" Residue "O PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 83": "OE1" <-> "OE2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "P GLU 45": "OE1" <-> "OE2" Residue "P GLU 47": "OE1" <-> "OE2" Residue "P GLU 48": "OE1" <-> "OE2" Residue "Q ASP 15": "OD1" <-> "OD2" Residue "Q GLU 49": "OE1" <-> "OE2" Residue "Q GLU 52": "OE1" <-> "OE2" Residue "Q GLU 60": "OE1" <-> "OE2" Residue "Q GLU 63": "OE1" <-> "OE2" Residue "Q GLU 80": "OE1" <-> "OE2" Residue "R GLU 20": "OE1" <-> "OE2" Residue "R ASP 22": "OD1" <-> "OD2" Residue "R GLU 35": "OE1" <-> "OE2" Residue "S ARG 3": "NH1" <-> "NH2" Residue "S ARG 32": "NH1" <-> "NH2" Residue "S PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 64": "OD1" <-> "OD2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "S ARG 81": "NH1" <-> "NH2" Residue "T TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 53": "OE1" <-> "OE2" Residue "T ASP 59": "OD1" <-> "OD2" Residue "U GLU 10": "OE1" <-> "OE2" Residue "U GLU 39": "OE1" <-> "OE2" Residue "U ARG 66": "NH1" <-> "NH2" Residue "c GLU 23": "OE1" <-> "OE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ARG 63": "NH1" <-> "NH2" Residue "c ARG 80": "NH1" <-> "NH2" Residue "c ASP 114": "OD1" <-> "OD2" Residue "c ARG 133": "NH1" <-> "NH2" Residue "c ARG 167": "NH1" <-> "NH2" Residue "c ASP 168": "OD1" <-> "OD2" Residue "c TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 177": "NH1" <-> "NH2" Residue "c ARG 182": "NH1" <-> "NH2" Residue "c ARG 189": "NH1" <-> "NH2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c ARG 212": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ASP 39": "OD1" <-> "OD2" Residue "d ASP 43": "OD1" <-> "OD2" Residue "d ARG 59": "NH1" <-> "NH2" Residue "d GLU 74": "OE1" <-> "OE2" Residue "d GLU 81": "OE1" <-> "OE2" Residue "d ARG 83": "NH1" <-> "NH2" Residue "d PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 99": "OE1" <-> "OE2" Residue "d ASP 103": "OD1" <-> "OD2" Residue "d ARG 169": "NH1" <-> "NH2" Residue "d GLU 183": "OE1" <-> "OE2" Residue "e TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e ARG 61": "NH1" <-> "NH2" Residue "e ARG 88": "NH1" <-> "NH2" Residue "e ASP 91": "OD1" <-> "OD2" Residue "e ARG 102": "NH1" <-> "NH2" Residue "e ASP 116": "OD1" <-> "OD2" Residue "e GLU 122": "OE1" <-> "OE2" Residue "e PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 155": "OE1" <-> "OE2" Residue "e ARG 162": "NH1" <-> "NH2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "e PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 184": "OD1" <-> "OD2" Residue "f ASP 6": "OD1" <-> "OD2" Residue "f ASP 10": "OD1" <-> "OD2" Residue "f GLU 32": "OE1" <-> "OE2" Residue "f GLU 42": "OE1" <-> "OE2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f GLU 94": "OE1" <-> "OE2" Residue "f ARG 102": "NH1" <-> "NH2" Residue "f ARG 110": "NH1" <-> "NH2" Residue "f ARG 112": "NH1" <-> "NH2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 133": "NH1" <-> "NH2" Residue "f ASP 144": "OD1" <-> "OD2" Residue "f ASP 147": "OD1" <-> "OD2" Residue "f GLU 164": "OE1" <-> "OE2" Residue "f GLU 165": "OE1" <-> "OE2" Residue "f ASP 174": "OD1" <-> "OD2" Residue "g ARG 3": "NH1" <-> "NH2" Residue "g GLU 32": "OE1" <-> "OE2" Residue "g ASP 39": "OD1" <-> "OD2" Residue "g GLU 42": "OE1" <-> "OE2" Residue "g ASP 47": "OD1" <-> "OD2" Residue "g ASP 56": "OD1" <-> "OD2" Residue "g TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 81": "OE1" <-> "OE2" Residue "g GLU 124": "OE1" <-> "OE2" Residue "g GLU 130": "OE1" <-> "OE2" Residue "g ASP 137": "OD1" <-> "OD2" Residue "g ASP 147": "OD1" <-> "OD2" Residue "g ARG 153": "NH1" <-> "NH2" Residue "g GLU 155": "OE1" <-> "OE2" Residue "g ARG 163": "NH1" <-> "NH2" Residue "g GLU 167": "OE1" <-> "OE2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "h ASP 7": "OD1" <-> "OD2" Residue "h ASP 17": "OD1" <-> "OD2" Residue "h ARG 27": "NH1" <-> "NH2" Residue "i PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 13": "NH1" <-> "NH2" Residue "i ASP 14": "OD1" <-> "OD2" Residue "i TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 37": "NH1" <-> "NH2" Residue "i GLU 43": "OE1" <-> "OE2" Residue "i TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 60": "OD1" <-> "OD2" Residue "i ASP 71": "OD1" <-> "OD2" Residue "i PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 96": "NH1" <-> "NH2" Residue "i ARG 120": "NH1" <-> "NH2" Residue "j ASP 56": "OD1" <-> "OD2" Residue "j GLU 110": "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 ARG 60": "NH1" <-> "NH2" Residue "k PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 78": "NH1" <-> "NH2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "k GLU 143": "OE1" <-> "OE2" 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 ARG 50": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "l GLU 90": "OE1" <-> "OE2" 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 ARG 46": "NH1" <-> "NH2" 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 GLU 82": "OE1" <-> "OE2" Residue "m ARG 96": "NH1" <-> "NH2" 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 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 46": "OE1" <-> "OE2" Residue "n GLU 60": "OE1" <-> "OE2" Residue "n GLU 80": "OE1" <-> "OE2" Residue "n ARG 81": "NH1" <-> "NH2" Residue "n ASP 89": "OD1" <-> "OD2" Residue "n ARG 94": "NH1" <-> "NH2" Residue "n ARG 102": "NH1" <-> "NH2" Residue "n ARG 111": "NH1" <-> "NH2" Residue "n PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 21": "NH1" <-> "NH2" Residue "o ARG 39": "NH1" <-> "NH2" Residue "o PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "o ARG 101": "NH1" <-> "NH2" 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 TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 48": "NH1" <-> "NH2" Residue "p TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 97": "OD1" <-> "OD2" Residue "p PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 111": "OE1" <-> "OE2" Residue "q GLU 16": "OE1" <-> "OE2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q ASP 26": "OD1" <-> "OD2" Residue "q GLU 34": "OE1" <-> "OE2" Residue "q GLU 45": "OE1" <-> "OE2" Residue "q ARG 68": "NH1" <-> "NH2" Residue "q ARG 79": "NH1" <-> "NH2" Residue "q ARG 84": "NH1" <-> "NH2" Residue "r ASP 34": "OD1" <-> "OD2" Residue "r GLU 59": "OE1" <-> "OE2" Residue "r ASP 62": "OD1" <-> "OD2" Residue "r ASP 65": "OD1" <-> "OD2" Residue "r PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 52": "OE1" <-> "OE2" Residue "s ARG 73": "NH1" <-> "NH2" Residue "t ARG 6": "NH1" <-> "NH2" Residue "t ARG 7": "NH1" <-> "NH2" Residue "t ASP 9": "OD1" <-> "OD2" Residue "t ARG 82": "NH1" <-> "NH2" Residue "t ARG 86": "NH1" <-> "NH2" Residue "t ASP 89": "OD1" <-> "OD2" Residue "t ARG 94": "NH1" <-> "NH2" Residue "t PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 11": "OE1" <-> "OE2" Residue "u GLU 41": "OE1" <-> "OE2" Residue "u ASP 43": "OD1" <-> "OD2" Residue "u PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 59": "OE1" <-> "OE2" Residue "u GLU 69": "OE1" <-> "OE2" Residue "v PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 70": "OE1" <-> "OE2" Residue "v GLU 83": "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 ARG 50": "NH1" <-> "NH2" Residue "w ARG 57": "NH1" <-> "NH2" Residue "w ASP 65": "OD1" <-> "OD2" Residue "w ARG 74": "NH1" <-> "NH2" Residue "x GLU 8": "OE1" <-> "OE2" Residue "x GLU 17": "OE1" <-> "OE2" Residue "x ARG 29": "NH1" <-> "NH2" Residue "x ARG 47": "NH1" <-> "NH2" Residue "x ASP 49": "OD1" <-> "OD2" Residue "x ARG 52": "NH1" <-> "NH2" Residue "x GLU 59": "OE1" <-> "OE2" Residue "y ARG 11": "NH1" <-> "NH2" Residue "y ARG 30": "NH1" <-> "NH2" Residue "y GLU 37": "OE1" <-> "OE2" Residue "y ARG 45": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 16": "NH1" <-> "NH2" Residue "z ASP 31": "OD1" <-> "OD2" Residue "z GLU 36": "OE1" <-> "OE2" Residue "z ASP 46": "OD1" <-> "OD2" Residue "z ARG 52": "NH1" <-> "NH2" Residue "0 GLU 7": "OE1" <-> "OE2" Residue "0 TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 44": "NH1" <-> "NH2" 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 PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 30": "NH1" <-> "NH2" Residue "2 ARG 40": "NH1" <-> "NH2" Residue "3 ARG 24": "NH1" <-> "NH2" Residue "4 GLU 11": "OE1" <-> "OE2" Residue "4 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 141565 Number of models: 1 Model: "" Number of chains: 58 Chain: "A" Number of atoms: 32612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32612 Classifications: {'RNA': 1519} Modifications used: {'rna2p': 1, 'rna2p_pur': 120, 'rna2p_pyr': 81, 'rna3p': 10, 'rna3p_pur': 742, 'rna3p_pyr': 565} Link IDs: {'rna2p': 202, 'rna3p': 1316} 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': 138, 'rna3p': 16, 'rna3p_pur': 1318, 'rna3p_pyr': 1006} Link IDs: {'rna2p': 411, 'rna3p': 2341} Chain breaks: 3 Unresolved chain link angles: 1 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: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 586 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} 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: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 260 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 9} Chain: "Y" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1579 Classifications: {'RNA': 74} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 3, 'rna3p_pur': 32, 'rna3p_pyr': 32} Link IDs: {'rna2p': 10, 'rna3p': 63} Chain breaks: 1 Chain: "Z" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 33} Link IDs: {'rna2p': 9, 'rna3p': 66} Chain: "5" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Classifications: {'RNA': 2} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1} Link IDs: {'rna2p': 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0STU SG CYS 3 11 49.375 107.114 143.705 1.00120.94 S ATOM A0SUJ SG CYS 3 14 50.809 107.952 139.899 1.00117.70 S ATOM A0SXE SG CYS 3 27 48.938 110.392 142.393 1.00119.98 S ATOM A0T3H SG CYS 4 16 120.585 23.537 163.017 1.00169.13 S ATOM A0T3T SG CYS 4 18 118.012 20.582 164.062 1.00171.05 S ATOM A0T7R SG CYS 4 37 117.253 23.013 161.322 1.00168.60 S ATOM A0T8C SG CYS 4 40 117.384 24.271 164.845 1.00169.82 S Time building chain proxies: 53.89, per 1000 atoms: 0.38 Number of scatterers: 141565 At special positions: 0 Unit cell: (218.572, 244.347, 271.153, 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) Zn 2 29.99 S 149 16.00 P 4554 15.00 O 39388 8.00 N 26426 7.00 C 71046 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: 58.80 Conformation dependent library (CDL) restraints added in 6.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" ND1 HIS 3 33 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 40 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 37 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 16 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 18 " Number of angles added : 9 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10262 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: 173 helices and 73 sheets defined 39.2% alpha, 19.9% beta 1570 base pairs and 2394 stacking pairs defined. Time for finding SS restraints: 73.51 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.693A pdb=" N ILE B 31 " --> pdb=" O MET B 27 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N PHE B 32 " --> pdb=" O LYS B 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 27 through 32' Processing helix chain 'B' and resid 42 through 64 Proline residue: B 48 - end of helix removed outlier: 3.801A pdb=" N ARG B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 88 removed outlier: 4.080A pdb=" N CYS B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 124 removed outlier: 4.802A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 130 removed outlier: 4.446A pdb=" N LEU B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N THR B 130 " --> pdb=" O PHE B 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 125 through 130' Processing helix chain 'B' and resid 131 through 148 removed outlier: 3.799A pdb=" N LEU B 135 " --> pdb=" O LYS B 131 " (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: 3.697A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 48 Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 81 through 96 removed outlier: 3.737A pdb=" N GLU C 85 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 113 removed outlier: 3.867A pdb=" N ASP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 5.645A 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 Processing helix chain 'C' and resid 129 through 145 Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.521A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.857A 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: 5.223A pdb=" N LYS D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.629A 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 removed outlier: 3.526A pdb=" N LYS D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 151 removed outlier: 4.402A pdb=" N LYS D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 166 removed outlier: 3.589A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 removed outlier: 4.235A pdb=" N LEU D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 6.176A 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: 4.032A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 3.678A pdb=" N MET E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 132 through 147 removed outlier: 3.574A pdb=" N ASN E 146 " --> pdb=" O ASP E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'F' and resid 15 through 33 Proline residue: F 19 - end of helix removed outlier: 3.513A pdb=" N ALA F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU F 33 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 82 removed outlier: 5.350A pdb=" N ASP F 82 " --> pdb=" O PHE F 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 35 through 55 Processing helix chain 'G' and resid 57 through 70 removed outlier: 4.422A pdb=" N GLU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 112 removed outlier: 3.542A pdb=" N ARG G 111 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLY G 112 " --> pdb=" O ALA G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 130 removed outlier: 3.715A pdb=" N GLU G 129 " --> pdb=" O SER G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 149 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: 4.538A 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 91 Processing helix chain 'I' and resid 94 through 102 Processing helix chain 'J' and resid 14 through 33 removed outlier: 3.675A pdb=" N GLY J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 91 removed outlier: 4.413A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASP J 91 " --> pdb=" O LEU J 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 51 removed outlier: 4.031A pdb=" N GLY K 51 " --> pdb=" O ALA K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 59 removed outlier: 3.632A pdb=" N SER K 58 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 4.943A 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 76 removed outlier: 3.547A pdb=" N LYS K 75 " --> pdb=" O ALA K 71 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLU K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 104 removed outlier: 3.897A pdb=" N THR K 96 " --> pdb=" O GLY K 92 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA K 102 " --> pdb=" O ARG K 98 " (cutoff:3.500A) removed outlier: 3.736A 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: 3.645A pdb=" N TYR L 117 " --> pdb=" O ALA L 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 22 removed outlier: 3.562A pdb=" N THR M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) removed outlier: 4.608A 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: 3.938A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N PHE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 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 Processing helix chain 'N' and resid 22 through 33 Processing helix chain 'N' and resid 37 through 51 removed outlier: 3.633A pdb=" N THR N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 61 removed outlier: 4.298A pdb=" N GLN N 60 " --> pdb=" O SER N 56 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ARG N 61 " --> pdb=" O PRO N 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 56 through 61' 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 44 removed outlier: 4.133A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.793A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 86 removed outlier: 3.641A pdb=" N GLY O 86 " --> pdb=" O ILE O 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 64 Processing helix chain 'P' and resid 68 through 80 removed outlier: 3.834A pdb=" N LYS P 80 " --> pdb=" O LYS P 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 17 removed outlier: 3.872A pdb=" N ALA R 15 " --> pdb=" O CYS R 11 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU R 16 " --> pdb=" O ARG R 12 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY R 17 " --> pdb=" O PHE R 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 11 through 17' Processing helix chain 'R' and resid 25 through 34 removed outlier: 4.066A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N THR R 34 " --> pdb=" O LYS R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 Processing helix chain 'R' and resid 48 through 66 Processing helix chain 'S' and resid 12 through 26 removed outlier: 3.540A pdb=" N SER S 25 " --> pdb=" O LYS S 21 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY S 26 " --> pdb=" O ALA S 22 " (cutoff:3.500A) Processing helix chain 'S' and resid 70 through 76 removed outlier: 4.494A pdb=" N PHE S 74 " --> pdb=" O LYS S 70 " (cutoff:3.500A) removed outlier: 4.115A 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 removed outlier: 3.678A pdb=" N LYS T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 87 removed outlier: 3.773A pdb=" N THR T 80 " --> pdb=" O LYS T 76 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN T 82 " --> pdb=" O ASN T 78 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA T 87 " --> pdb=" O ILE T 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 27 removed outlier: 3.524A pdb=" N ALA U 15 " --> pdb=" O PRO U 11 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 37 removed outlier: 4.879A pdb=" N PHE U 37 " --> pdb=" O ARG U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 68 removed outlier: 4.597A pdb=" N ARG U 67 " --> pdb=" O GLU U 63 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR U 68 " --> pdb=" O ASN U 64 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 15 removed outlier: 4.738A pdb=" N HIS c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 35 removed outlier: 3.987A pdb=" N LEU c 34 " --> pdb=" O PHE c 30 " (cutoff:3.500A) removed outlier: 5.863A 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: 3.571A 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: 3.790A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG c 214 " --> pdb=" O ALA c 210 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY c 215 " --> pdb=" O ALA c 211 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 226 removed outlier: 3.805A pdb=" N MET c 225 " --> pdb=" O ARG c 221 " (cutoff:3.500A) removed outlier: 5.192A 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: 4.714A pdb=" N LYS c 265 " --> pdb=" O LYS c 261 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N PHE c 266 " --> pdb=" O ARG c 262 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE c 267 " --> pdb=" O THR c 263 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL c 268 " --> pdb=" O ASP c 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 56 through 61 removed outlier: 5.575A pdb=" N THR d 61 " --> pdb=" O ALA d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 72 removed outlier: 3.674A pdb=" N ALA d 71 " --> pdb=" O HIS d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 103 removed outlier: 4.151A pdb=" N ALA d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) removed outlier: 5.191A 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: 3.784A pdb=" N ARG e 40 " --> pdb=" O ALA e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 53 removed outlier: 6.437A pdb=" N THR e 53 " --> pdb=" O ARG e 49 " (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: 3.541A pdb=" N PHE e 158 " --> pdb=" O ASP e 154 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASN e 163 " --> pdb=" O LEU e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 183 removed outlier: 3.676A pdb=" N PHE e 183 " --> pdb=" O SER e 179 " (cutoff:3.500A) Processing helix chain 'e' and resid 189 through 201 Processing helix chain 'f' and resid 2 through 21 removed outlier: 5.102A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 24 through 29 removed outlier: 4.017A pdb=" N VAL f 28 " --> pdb=" O SER f 24 " (cutoff:3.500A) Proline residue: f 29 - end of helix No H-bonds generated for 'chain 'f' and resid 24 through 29' Processing helix chain 'f' and resid 42 through 47 removed outlier: 4.073A pdb=" N ASP f 46 " --> pdb=" O GLU f 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS f 47 " --> pdb=" O ALA f 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 42 through 47' Processing helix chain 'f' and resid 48 through 62 Processing helix chain 'f' and resid 93 through 111 removed outlier: 3.564A pdb=" N ALA f 107 " --> pdb=" O LEU f 103 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL f 108 " --> pdb=" O ILE f 104 " (cutoff:3.500A) Proline residue: f 109 - end of helix Processing helix chain 'f' and resid 162 through 174 removed outlier: 3.670A pdb=" N PHE f 173 " --> pdb=" O LEU f 169 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP f 174 " --> pdb=" O LEU f 170 " (cutoff:3.500A) Processing helix chain 'f' and resid 134 through 139 removed outlier: 3.671A 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 7 removed outlier: 3.711A pdb=" N LYS g 6 " --> pdb=" O SER g 2 " (cutoff:3.500A) Processing helix chain 'g' and resid 60 through 81 removed outlier: 6.153A pdb=" N GLN g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR g 80 " --> pdb=" O VAL g 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 153 removed outlier: 4.035A 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 Processing helix chain 'i' and resid 24 through 38 removed outlier: 3.946A 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: 4.174A pdb=" N ILE i 101 " --> pdb=" O PRO i 97 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET i 108 " --> pdb=" O ALA i 104 " (cutoff:3.500A) Proline residue: i 110 - end of helix Processing helix chain 'i' and resid 112 through 122 removed outlier: 3.802A pdb=" N LYS i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) removed outlier: 4.176A 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: 3.816A pdb=" N ARG k 41 " --> pdb=" O GLY k 37 " (cutoff:3.500A) removed outlier: 5.689A 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 Proline residue: k 62 - end of helix Processing helix chain 'k' and resid 68 through 75 removed outlier: 4.028A pdb=" N ALA k 72 " --> pdb=" O SER k 68 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE k 73 " --> pdb=" O ARG k 69 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ALA k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 78 through 85 removed outlier: 3.912A pdb=" N LEU k 82 " --> pdb=" O ARG k 78 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA k 83 " --> pdb=" O LEU k 79 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LYS k 84 " --> pdb=" O SER k 80 " (cutoff:3.500A) removed outlier: 3.929A 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: 4.125A pdb=" N LYS l 123 " --> pdb=" O LEU l 119 " (cutoff:3.500A) removed outlier: 3.892A 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: 4.356A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL m 47 " --> pdb=" O GLU m 43 " (cutoff:3.500A) Proline residue: m 50 - end of helix removed outlier: 4.300A pdb=" N THR m 57 " --> pdb=" O THR m 53 " (cutoff:3.500A) Processing helix chain 'm' and resid 59 through 71 removed outlier: 4.032A pdb=" N THR m 70 " --> pdb=" O ALA m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 72 through 88 removed outlier: 4.990A 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: 3.531A pdb=" N ALA n 6 " --> pdb=" O ASP n 2 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 63 removed outlier: 4.781A pdb=" N GLN n 61 " --> pdb=" O ALA n 57 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU n 62 " --> pdb=" O ILE n 58 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LYS n 63 " --> pdb=" O ALA n 59 " (cutoff:3.500A) Processing helix chain 'n' and resid 67 through 86 removed outlier: 3.509A pdb=" N LYS n 85 " --> pdb=" O ARG n 81 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 114 Processing helix chain 'o' and resid 2 through 13 removed outlier: 3.895A pdb=" N GLN o 12 " --> pdb=" O LEU o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 104 removed outlier: 4.649A pdb=" N ARG o 101 " --> pdb=" O LEU o 97 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLU o 102 " --> pdb=" O TYR o 98 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG o 103 " --> pdb=" O TYR o 99 " (cutoff:3.500A) removed outlier: 5.261A 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 Processing helix chain 'p' and resid 26 through 31 removed outlier: 3.665A pdb=" N ARG p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) Processing helix chain 'p' and resid 32 through 37 removed outlier: 3.775A pdb=" N GLN p 37 " --> pdb=" O ARG p 33 " (cutoff:3.500A) Processing helix chain 'p' and resid 39 through 73 removed outlier: 3.821A pdb=" N ARG p 51 " --> pdb=" O TYR p 47 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG p 55 " --> pdb=" O ARG p 51 " (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: 3.555A pdb=" N LEU r 19 " --> pdb=" O GLN r 15 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) Processing helix chain 'r' and resid 28 through 39 Processing helix chain 'r' and resid 41 through 61 removed outlier: 3.575A pdb=" N VAL r 45 " --> pdb=" O LYS r 41 " (cutoff:3.500A) Processing helix chain 's' and resid 3 through 11 removed outlier: 4.229A 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: 3.996A pdb=" N VAL t 70 " --> pdb=" O GLN t 66 " (cutoff:3.500A) removed outlier: 5.239A 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 Processing helix chain 'u' and resid 43 through 53 removed outlier: 3.792A pdb=" N ALA u 52 " --> pdb=" O MET u 48 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LYS u 53 " --> pdb=" O ASN u 49 " (cutoff:3.500A) Processing helix chain 'u' and resid 54 through 59 removed outlier: 4.181A 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 9 removed outlier: 3.789A pdb=" N LEU x 6 " --> pdb=" O LYS x 2 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU x 8 " --> pdb=" O LYS x 4 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS x 9 " --> pdb=" O GLU x 5 " (cutoff:3.500A) Processing helix chain 'x' and resid 10 through 35 removed outlier: 4.589A pdb=" N GLY x 35 " --> pdb=" O GLN x 31 " (cutoff:3.500A) Processing helix chain 'x' and resid 39 through 62 removed outlier: 4.737A pdb=" N LEU x 43 " --> pdb=" O GLN x 39 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS x 44 " --> pdb=" O SER x 40 " (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: 4.876A 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: 4.263A 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: 3.664A pdb=" N ARG 2 13 " --> pdb=" O GLY 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 32 through 37 removed outlier: 4.507A pdb=" N LYS 2 36 " --> pdb=" O ILE 2 32 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ALA 2 37 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 32 through 37' Processing helix chain '2' and resid 38 through 46 Proline residue: 2 46 - end of helix Processing helix chain '2' and resid 51 through 63 removed outlier: 4.538A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 5.285A 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: 3.665A pdb=" N ARG 4 59 " --> pdb=" O GLY 4 55 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN 4 65 " --> pdb=" O ASN 4 61 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 15 through 18 removed outlier: 4.908A pdb=" N HIS B 15 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N HIS B 39 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 67 through 71 Processing sheet with id= 3, first strand: chain 'C' and resid 53 through 59 removed outlier: 3.540A pdb=" N ARG C 54 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 164 through 170 removed outlier: 6.089A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 141 through 145 removed outlier: 4.028A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE D 145 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N MET D 178 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 12 through 16 removed outlier: 6.659A pdb=" N LEU E 36 " --> pdb=" O ILE E 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 84 through 88 removed outlier: 3.661A pdb=" N ALA E 99 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ASN E 122 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 33 through 40 Processing sheet with id= 9, first strand: chain 'F' and resid 38 through 43 removed outlier: 5.804A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'G' and resid 72 through 79 removed outlier: 6.398A 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: 5.923A pdb=" N ALA H 23 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 3.795A 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: 3.829A pdb=" N SER H 74 " --> pdb=" O ALA H 130 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS H 127 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.639A 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 removed outlier: 3.543A pdb=" N GLY I 24 " --> pdb=" O LYS I 60 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS I 60 " --> pdb=" O GLY I 24 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS I 27 " --> pdb=" O LEU I 61 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'J' and resid 39 through 42 removed outlier: 4.658A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'J' and resid 44 through 52 Processing sheet with id= 16, first strand: chain 'K' and resid 29 through 36 removed outlier: 3.828A pdb=" N ASN K 29 " --> pdb=" O SER K 26 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLY K 19 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL K 84 " --> pdb=" O GLY K 19 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA K 21 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL K 86 " --> pdb=" O ALA K 21 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE K 23 " --> pdb=" O VAL K 86 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N GLY K 88 " --> pdb=" O ILE K 23 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ALA K 25 " --> pdb=" O GLY K 88 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL K 84 " --> pdb=" O THR K 108 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'L' and resid 29 through 32 removed outlier: 5.207A pdb=" N LEU L 81 " --> pdb=" O VAL L 98 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'L' and resid 36 through 41 removed outlier: 3.735A pdb=" N ARG L 36 " --> pdb=" O ARG L 54 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LYS L 51 " --> pdb=" O ILE L 67 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'P' and resid 4 through 10 removed outlier: 3.535A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLY P 49 " --> pdb=" O ASN P 40 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'Q' and resid 7 through 12 removed outlier: 4.843A pdb=" N ASP Q 57 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'Q' and resid 19 through 30 No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 'Q' and resid 56 through 59 removed outlier: 7.112A pdb=" N GLY Q 56 " --> pdb=" O ALA Q 82 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA Q 82 " --> pdb=" O GLY Q 56 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'S' and resid 30 through 34 removed outlier: 4.549A 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: 5.752A pdb=" N VAL c 16 " --> pdb=" O CYS c 6 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'c' and resid 73 through 78 removed outlier: 4.976A pdb=" N ILE c 74 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N SER c 118 " --> pdb=" O ILE c 74 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP c 114 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLY c 127 " --> pdb=" O GLN c 115 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLN c 117 " --> pdb=" O GLY c 127 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'c' and resid 80 through 83 removed outlier: 5.345A pdb=" N ASN c 90 " --> pdb=" O ALA c 106 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'c' and resid 138 through 141 removed outlier: 4.086A pdb=" N SER c 139 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR c 173 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU c 180 " --> pdb=" O LEU c 176 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'd' and resid 3 through 6 removed outlier: 4.046A pdb=" N GLU d 168 " --> pdb=" O SER d 113 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'd' and resid 10 through 16 removed outlier: 3.676A pdb=" N GLY d 10 " --> pdb=" O VAL d 26 " (cutoff:3.500A) removed outlier: 4.013A 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: 6.072A pdb=" N ARG d 46 " --> pdb=" O LEU d 84 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN d 94 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'd' and resid 105 through 108 removed outlier: 6.383A pdb=" N LYS d 105 " --> pdb=" O VAL d 177 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'e' and resid 1 through 5 removed outlier: 4.204A pdb=" N MET e 1 " --> pdb=" O VAL e 14 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL e 14 " --> pdb=" O MET e 1 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU e 5 " --> pdb=" O SER e 10 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N SER e 10 " --> pdb=" O LEU e 5 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'e' and resid 44 through 47 removed outlier: 6.748A pdb=" N ARG e 44 " --> pdb=" O PRO e 89 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ALA e 87 " --> pdb=" O GLN e 46 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'e' and resid 117 through 120 removed outlier: 5.749A pdb=" N ARG e 117 " --> pdb=" O ASP e 184 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'f' and resid 65 through 69 removed outlier: 5.592A pdb=" N ILE f 85 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLY f 39 " --> pdb=" O GLY f 151 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLY f 151 " --> pdb=" O GLY f 39 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'f' and resid 72 through 75 removed outlier: 6.870A pdb=" N LYS f 72 " --> pdb=" O GLN f 81 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLN f 81 " --> pdb=" O LYS f 72 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'g' and resid 15 through 20 removed outlier: 6.464A pdb=" N GLN g 22 " --> pdb=" O LEU g 37 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE g 26 " --> pdb=" O LEU g 33 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU g 33 " --> pdb=" O ILE g 26 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'g' and resid 41 through 44 No H-bonds generated for sheet with id= 38 Processing sheet with id= 39, first strand: chain 'g' and resid 94 through 99 removed outlier: 6.880A pdb=" N ASN g 101 " --> pdb=" O LEU g 117 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'g' and resid 121 through 125 removed outlier: 6.240A pdb=" N THR g 129 " --> pdb=" O LEU g 89 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY g 135 " --> pdb=" O PHE g 83 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE g 83 " --> pdb=" O GLY g 135 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'h' and resid 1 through 5 removed outlier: 3.599A pdb=" N VAL h 3 " --> pdb=" O VAL h 19 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASP h 17 " --> pdb=" O LEU h 5 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'i' and resid 52 through 57 removed outlier: 4.857A pdb=" N ASP i 19 " --> pdb=" O LEU i 140 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'i' and resid 74 through 78 removed outlier: 7.475A pdb=" N GLY i 83 " --> pdb=" O THR i 78 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'j' and resid 6 through 9 removed outlier: 4.182A pdb=" N THR j 6 " --> pdb=" O CYS j 21 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'j' and resid 38 through 42 Processing sheet with id= 46, first strand: chain 'j' and resid 63 through 66 removed outlier: 3.926A pdb=" N LYS j 66 " --> pdb=" O GLY j 81 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLY j 81 " --> pdb=" O LYS j 66 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'j' and resid 68 through 71 removed outlier: 4.172A pdb=" N SER j 75 " --> pdb=" O ARG j 71 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'l' and resid 37 through 40 No H-bonds generated for sheet with id= 48 Processing sheet with id= 49, first strand: chain 'l' and resid 62 through 65 removed outlier: 6.568A pdb=" N LEU l 33 " --> pdb=" O LEU l 102 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS l 100 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'l' and resid 30 through 36 removed outlier: 7.972A pdb=" N SER l 30 " --> pdb=" O LYS l 133 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LYS l 127 " --> pdb=" O VAL l 36 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'm' and resid 33 through 37 removed outlier: 4.919A pdb=" N ARG m 103 " --> pdb=" O ASN m 107 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY m 101 " --> pdb=" O PRO m 109 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ALA m 111 " --> pdb=" O LYS m 99 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS m 99 " --> pdb=" O ALA m 111 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE m 113 " --> pdb=" O ILE m 97 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE m 97 " --> pdb=" O ILE m 113 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU m 115 " --> pdb=" O THR m 95 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR m 95 " --> pdb=" O LEU m 115 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'n' and resid 49 through 53 removed outlier: 6.454A pdb=" N ILE n 35 " --> pdb=" O THR n 53 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'o' and resid 38 through 45 removed outlier: 6.500A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'o' and resid 49 through 52 removed outlier: 3.682A pdb=" N ALA o 49 " --> pdb=" O THR o 60 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N SER o 57 " --> pdb=" O THR o 76 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'q' and resid 11 through 15 removed outlier: 6.927A pdb=" N LEU q 39 " --> pdb=" O GLY q 50 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLU q 46 " --> pdb=" O ASN q 43 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'q' and resid 18 through 23 removed outlier: 4.235A pdb=" N GLN q 18 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASP q 95 " --> pdb=" O VAL q 64 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS q 60 " --> pdb=" O THR q 99 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU q 31 " --> pdb=" O VAL q 63 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'q' and resid 57 through 60 Processing sheet with id= 58, first strand: chain 'q' and resid 65 through 68 Processing sheet with id= 59, first strand: chain 'q' and resid 71 through 78 removed outlier: 4.012A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'r' and resid 2 through 8 Processing sheet with id= 61, first strand: chain 's' and resid 28 through 33 removed outlier: 5.732A pdb=" N ASN s 28 " --> pdb=" O LEU s 87 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS s 66 " --> pdb=" O ARG s 77 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASP s 79 " --> pdb=" O LYS s 64 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS s 64 " --> pdb=" O ASP s 79 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LYS s 81 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL s 62 " --> pdb=" O LYS s 81 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA s 83 " --> pdb=" O THR s 60 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR s 60 " --> pdb=" O ALA s 83 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL s 85 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL s 58 " --> pdb=" O VAL s 85 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 't' and resid 40 through 45 No H-bonds generated for sheet with id= 62 Processing sheet with id= 63, first strand: chain 'u' and resid 69 through 72 removed outlier: 6.558A pdb=" N ALA u 39 " --> pdb=" O ARG u 9 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE u 89 " --> pdb=" O PRO u 27 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'v' and resid 51 through 54 removed outlier: 4.126A pdb=" N THR v 58 " --> pdb=" O GLY v 54 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'v' and resid 65 through 71 Processing sheet with id= 66, first strand: chain 'w' and resid 12 through 19 removed outlier: 4.397A pdb=" N ASN w 23 " --> pdb=" O SER w 19 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'w' and resid 35 through 41 Processing sheet with id= 68, first strand: chain 'y' and resid 33 through 39 removed outlier: 4.358A pdb=" N HIS y 34 " --> pdb=" O GLN y 9 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N MET y 54 " --> pdb=" O THR y 10 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'z' and resid 29 through 32 removed outlier: 4.343A pdb=" N GLU z 36 " --> pdb=" O ASP z 31 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain '0' and resid 19 through 25 removed outlier: 6.328A pdb=" N HIS 0 19 " --> pdb=" O SER 0 13 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE 0 48 " --> pdb=" O SER 0 14 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU 0 34 " --> pdb=" O GLU 0 51 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain '2' and resid 22 through 25 No H-bonds generated for sheet with id= 71 Processing sheet with id= 72, first strand: chain '3' and resid 1 through 5 removed outlier: 6.826A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain '4' and resid 20 through 25 removed outlier: 4.181A pdb=" N ASN 4 20 " --> pdb=" O CYS 4 16 " (cutoff:3.500A) 1878 hydrogen bonds defined for protein. 5553 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3949 hydrogen bonds 6186 hydrogen bond angles 0 basepair planarities 1570 basepair parallelities 2394 stacking parallelities Total time for adding SS restraints: 231.25 Time building geometry restraints manager: 63.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 23309 1.34 - 1.47: 71298 1.47 - 1.59: 49958 1.59 - 1.72: 9056 1.72 - 1.85: 264 Bond restraints: 153885 Sorted by residual: bond pdb=" C4 5MU a 747 " pdb=" C5 5MU a 747 " ideal model delta sigma weight residual 1.802 1.445 0.357 2.00e-02 2.50e+03 3.18e+02 bond pdb=" C4 5MU a1939 " pdb=" C5 5MU a1939 " ideal model delta sigma weight residual 1.802 1.451 0.351 2.00e-02 2.50e+03 3.07e+02 bond pdb=" N1 5MU a1939 " pdb=" C6 5MU a1939 " ideal model delta sigma weight residual 1.635 1.393 0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" N1 5MU a 747 " pdb=" C6 5MU a 747 " ideal model delta sigma weight residual 1.635 1.394 0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" O4' 3TD a1915 " pdb=" C1' 3TD a1915 " ideal model delta sigma weight residual 1.652 1.440 0.212 2.00e-02 2.50e+03 1.12e+02 ... (remaining 153880 not shown) Histogram of bond angle deviations from ideal: 92.97 - 101.37: 5726 101.37 - 109.78: 48780 109.78 - 118.18: 96051 118.18 - 126.59: 66139 126.59 - 135.00: 13600 Bond angle restraints: 230296 Sorted by residual: angle pdb=" C1' G7M a2069 " pdb=" N9 G7M a2069 " pdb=" C8 G7M a2069 " ideal model delta sigma weight residual 94.96 125.82 -30.86 3.00e+00 1.11e-01 1.06e+02 angle pdb=" C1' G7M A 527 " pdb=" N9 G7M A 527 " pdb=" C8 G7M A 527 " ideal model delta sigma weight residual 94.96 125.77 -30.81 3.00e+00 1.11e-01 1.05e+02 angle pdb=" O3' U A 561 " pdb=" P U A 562 " pdb=" O5' U A 562 " ideal model delta sigma weight residual 104.00 92.97 11.03 1.50e+00 4.44e-01 5.41e+01 angle pdb=" O3' U a2519 " pdb=" P C a2520 " pdb=" O5' C a2520 " ideal model delta sigma weight residual 104.00 93.10 10.90 1.50e+00 4.44e-01 5.28e+01 angle pdb=" C1' 2MA a2503 " pdb=" N9 2MA a2503 " pdb=" C8 2MA a2503 " ideal model delta sigma weight residual 106.32 126.61 -20.29 3.00e+00 1.11e-01 4.57e+01 ... (remaining 230291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 84727 35.95 - 71.91: 9071 71.91 - 107.86: 1108 107.86 - 143.82: 18 143.82 - 179.77: 9 Dihedral angle restraints: 94933 sinusoidal: 79026 harmonic: 15907 Sorted by residual: dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 51.97 148.03 1 1.50e+01 4.44e-03 7.89e+01 dihedral pdb=" O4' U a1779 " pdb=" C1' U a1779 " pdb=" N1 U a1779 " pdb=" C2 U a1779 " ideal model delta sinusoidal sigma weight residual 200.00 58.99 141.01 1 1.50e+01 4.44e-03 7.58e+01 dihedral pdb=" O4' C A1158 " pdb=" C1' C A1158 " pdb=" N1 C A1158 " pdb=" C2 C A1158 " ideal model delta sinusoidal sigma weight residual 200.00 62.08 137.92 1 1.50e+01 4.44e-03 7.43e+01 ... (remaining 94930 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 19939 0.115 - 0.230: 9082 0.230 - 0.345: 302 0.345 - 0.460: 8 0.460 - 0.575: 10 Chirality restraints: 29341 Sorted by residual: chirality pdb=" P A A 2 " pdb=" OP1 A A 2 " pdb=" OP2 A A 2 " pdb=" O5' A A 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.26e+00 chirality pdb=" P G Y 18 " pdb=" OP1 G Y 18 " pdb=" OP2 G Y 18 " pdb=" O5' G Y 18 " both_signs ideal model delta sigma weight residual True 2.41 2.98 -0.57 2.00e-01 2.50e+01 8.03e+00 chirality pdb=" P G A 846 " pdb=" OP1 G A 846 " pdb=" OP2 G A 846 " pdb=" O5' G A 846 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.74e+00 ... (remaining 29338 not shown) Planarity restraints: 12246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a2445 " 0.081 2.00e-02 2.50e+03 6.08e-01 8.32e+03 pdb=" C4' 2MG a2445 " 0.440 2.00e-02 2.50e+03 pdb=" O4' 2MG a2445 " 0.747 2.00e-02 2.50e+03 pdb=" C3' 2MG a2445 " -0.638 2.00e-02 2.50e+03 pdb=" O3' 2MG a2445 " -0.617 2.00e-02 2.50e+03 pdb=" C2' 2MG a2445 " -0.182 2.00e-02 2.50e+03 pdb=" O2' 2MG a2445 " 0.910 2.00e-02 2.50e+03 pdb=" C1' 2MG a2445 " 0.198 2.00e-02 2.50e+03 pdb=" N9 2MG a2445 " -0.939 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " -0.079 2.00e-02 2.50e+03 6.02e-01 8.16e+03 pdb=" C4' 2MG A1516 " -0.442 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " -0.638 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " 0.611 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " 0.666 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " 0.130 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " -0.958 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " -0.215 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " 0.926 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC a2498 " -0.054 2.00e-02 2.50e+03 5.99e-01 8.07e+03 pdb=" C4' OMC a2498 " -0.431 2.00e-02 2.50e+03 pdb=" O4' OMC a2498 " -0.651 2.00e-02 2.50e+03 pdb=" C3' OMC a2498 " 0.614 2.00e-02 2.50e+03 pdb=" O3' OMC a2498 " 0.648 2.00e-02 2.50e+03 pdb=" C2' OMC a2498 " 0.149 2.00e-02 2.50e+03 pdb=" O2' OMC a2498 " -0.961 2.00e-02 2.50e+03 pdb=" C1' OMC a2498 " -0.221 2.00e-02 2.50e+03 pdb=" N1 OMC a2498 " 0.907 2.00e-02 2.50e+03 ... (remaining 12243 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 347 2.53 - 3.12: 91713 3.12 - 3.71: 284096 3.71 - 4.31: 406339 4.31 - 4.90: 536235 Nonbonded interactions: 1318730 Sorted by model distance: nonbonded pdb=" NH2 ARG M 71 " pdb=" OD1 ASP f 113 " model vdw 1.936 2.520 nonbonded pdb=" NH2 ARG M 71 " pdb=" OD2 ASP f 113 " model vdw 2.039 2.520 nonbonded pdb=" O2' A Y 58 " pdb=" OP2 C Y 60 " model vdw 2.058 2.440 nonbonded pdb=" O2 U a2554 " pdb=" N4 C Y 74 " model vdw 2.168 2.520 nonbonded pdb=" N1 G Z 18 " pdb=" O2 U Z 55 " model vdw 2.183 2.520 ... (remaining 1318725 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.560 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: 0.090 Extract box with map and model: 17.570 Check model and map are aligned: 1.560 Set scattering table: 0.930 Process input model: 540.930 Find NCS groups from input model: 2.930 Set up NCS constraints: 0.330 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: 0.020 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 570.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 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 : 0.011 0.357 153885 Z= 0.644 Angle : 1.591 30.862 230296 Z= 0.952 Chirality : 0.105 0.575 29341 Planarity : 0.020 0.608 12246 Dihedral : 22.179 179.769 84671 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.60 % Favored : 96.22 % Rotamer: Outliers : 3.61 % Allowed : 11.40 % Favored : 85.00 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.10), residues: 5474 helix: -0.94 (0.10), residues: 1826 sheet: -0.60 (0.15), residues: 993 loop : -1.12 (0.11), residues: 2655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.005 TRP o 31 HIS 0.017 0.003 HIS F 58 PHE 0.034 0.005 PHE 4 43 TYR 0.042 0.006 TYR p 32 ARG 0.040 0.004 ARG e 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2646 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 2481 time to evaluate : 6.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 165 outliers final: 19 residues processed: 2567 average time/residue: 1.4014 time to fit residues: 5971.6700 Evaluate side-chains 1463 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1444 time to evaluate : 5.967 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 1.4203 time to fit residues: 52.5881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 834 optimal weight: 5.9990 chunk 748 optimal weight: 2.9990 chunk 415 optimal weight: 10.0000 chunk 255 optimal weight: 1.9990 chunk 505 optimal weight: 10.0000 chunk 400 optimal weight: 10.0000 chunk 774 optimal weight: 7.9990 chunk 299 optimal weight: 3.9990 chunk 470 optimal weight: 20.0000 chunk 576 optimal weight: 10.0000 chunk 897 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 HIS B 39 HIS ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN B 109 GLN C 41 GLN C 123 GLN C 140 ASN C 190 HIS ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 GLN D 100 ASN D 152 GLN ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS L 6 GLN L 46 ASN L 77 HIS L 112 GLN N 35 ASN N 66 GLN S 14 HIS S 69 HIS ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN T 68 HIS T 84 ASN ** c 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 70 ASN ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 260 ASN d 32 ASN d 49 GLN d 67 HIS ** e 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 5 HIS g 20 ASN ** g 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 128 GLN h 20 ASN h 33 GLN ** i 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 135 GLN j 29 HIS ** k 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 17 ASN m 3 HIS n 100 HIS o 56 HIS p 44 GLN p 71 GLN r 60 HIS s 48 GLN t 40 ASN t 66 GLN u 5 ASN w 6 GLN x 25 GLN x 31 GLN ** 0 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 28 ASN 3 13 ASN 4 20 ASN 4 30 HIS 4 41 HIS Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 153885 Z= 0.220 Angle : 0.731 15.963 230296 Z= 0.388 Chirality : 0.039 0.407 29341 Planarity : 0.007 0.120 12246 Dihedral : 22.391 179.869 73643 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.67 % Favored : 97.28 % Rotamer: Outliers : 0.42 % Allowed : 5.53 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.11), residues: 5474 helix: 0.51 (0.11), residues: 1875 sheet: 0.02 (0.15), residues: 1016 loop : -0.50 (0.12), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP P 60 HIS 0.015 0.002 HIS B 15 PHE 0.024 0.003 PHE I 39 TYR 0.038 0.002 TYR f 7 ARG 0.012 0.001 ARG I 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1833 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1814 time to evaluate : 6.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 1823 average time/residue: 1.3031 time to fit residues: 4084.5221 Evaluate side-chains 1292 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1285 time to evaluate : 5.336 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.9013 time to fit residues: 17.8197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 498 optimal weight: 10.0000 chunk 278 optimal weight: 6.9990 chunk 746 optimal weight: 0.7980 chunk 610 optimal weight: 10.0000 chunk 247 optimal weight: 6.9990 chunk 898 optimal weight: 20.0000 chunk 970 optimal weight: 5.9990 chunk 800 optimal weight: 20.0000 chunk 891 optimal weight: 0.5980 chunk 306 optimal weight: 20.0000 chunk 721 optimal weight: 0.0030 overall best weight: 2.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 ASN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN D 71 GLN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 HIS E 146 ASN G 142 HIS G 153 HIS ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN K 15 GLN ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS ** K 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 ASN ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 69 HIS S 83 HIS ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 29 HIS e 46 GLN e 156 ASN ** f 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 20 ASN g 115 HIS g 139 GLN h 33 GLN i 58 ASN i 128 ASN ** k 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 23 ASN n 29 HIS ** o 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 45 GLN ** 0 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 13 ASN 1 16 HIS 1 26 ASN 3 13 ASN 4 30 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 153885 Z= 0.189 Angle : 0.626 14.322 230296 Z= 0.341 Chirality : 0.035 0.403 29341 Planarity : 0.007 0.134 12246 Dihedral : 22.306 179.238 73643 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.38 % Favored : 96.58 % Rotamer: Outliers : 0.22 % Allowed : 4.46 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.11), residues: 5474 helix: 0.61 (0.12), residues: 1883 sheet: 0.02 (0.15), residues: 1022 loop : -0.42 (0.12), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP Q 73 HIS 0.015 0.002 HIS F 11 PHE 0.039 0.003 PHE k 107 TYR 0.031 0.002 TYR D 76 ARG 0.021 0.001 ARG D 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1729 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1719 time to evaluate : 6.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 1720 average time/residue: 1.2900 time to fit residues: 3836.5425 Evaluate side-chains 1273 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1271 time to evaluate : 5.969 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.9884 time to fit residues: 10.1813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 888 optimal weight: 0.0670 chunk 675 optimal weight: 3.9990 chunk 466 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 428 optimal weight: 10.0000 chunk 603 optimal weight: 10.0000 chunk 902 optimal weight: 6.9990 chunk 955 optimal weight: 9.9990 chunk 471 optimal weight: 30.0000 chunk 854 optimal weight: 6.9990 chunk 257 optimal weight: 6.9990 overall best weight: 5.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 GLN D 89 ASN E 82 GLN E 83 HIS E 132 ASN F 3 HIS ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 GLN G 68 ASN ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 HIS N 66 GLN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 45 HIS R 31 ASN R 52 GLN ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 69 HIS T 13 GLN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 134 ASN d 32 ASN ** e 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 156 ASN ** e 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 63 GLN g 30 ASN ** g 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 29 HIS o 41 GLN o 56 HIS p 72 ASN r 31 GLN r 40 ASN s 28 ASN ** t 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 46 HIS 1 13 ASN ** 1 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 13 ASN ** 3 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 30 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.6234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.153 153885 Z= 0.261 Angle : 0.678 13.986 230296 Z= 0.364 Chirality : 0.036 0.390 29341 Planarity : 0.007 0.126 12246 Dihedral : 22.418 179.285 73643 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.62 % Favored : 96.33 % Rotamer: Outliers : 0.07 % Allowed : 3.96 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.11), residues: 5474 helix: 0.45 (0.12), residues: 1877 sheet: -0.12 (0.15), residues: 1001 loop : -0.51 (0.12), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP Q 73 HIS 0.014 0.002 HIS f 5 PHE 0.036 0.003 PHE B 184 TYR 0.027 0.002 TYR D 76 ARG 0.025 0.001 ARG x 7 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1616 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1613 time to evaluate : 6.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 1616 average time/residue: 1.2993 time to fit residues: 3674.1200 Evaluate side-chains 1238 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1237 time to evaluate : 5.968 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.0143 time to fit residues: 8.2980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 795 optimal weight: 9.9990 chunk 542 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 711 optimal weight: 8.9990 chunk 394 optimal weight: 10.0000 chunk 814 optimal weight: 5.9990 chunk 660 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 487 optimal weight: 20.0000 chunk 857 optimal weight: 9.9990 chunk 240 optimal weight: 5.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 GLN E 70 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 GLN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 HIS ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN R 74 HIS S 83 HIS ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 134 ASN d 140 HIS ** e 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 156 ASN e 165 HIS ** f 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 33 GLN i 128 ASN ** k 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 54 GLN ** l 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 62 ASN n 29 HIS n 38 GLN o 15 GLN o 41 GLN o 56 HIS ** p 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 81 ASN s 28 ASN ** t 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 36 HIS ** x 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 34 HIS ** z 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 13 ASN ** 1 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 31 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.8300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 153885 Z= 0.380 Angle : 0.839 13.826 230296 Z= 0.441 Chirality : 0.043 0.452 29341 Planarity : 0.008 0.133 12246 Dihedral : 22.845 179.266 73643 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 23.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.12 % Favored : 94.81 % Rotamer: Outliers : 0.11 % Allowed : 5.34 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.10), residues: 5474 helix: -0.49 (0.11), residues: 1885 sheet: -0.28 (0.16), residues: 967 loop : -1.11 (0.11), residues: 2622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP P 60 HIS 0.013 0.003 HIS 4 30 PHE 0.039 0.003 PHE i 119 TYR 0.047 0.003 TYR D 76 ARG 0.017 0.001 ARG y 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1569 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1564 time to evaluate : 6.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 1567 average time/residue: 1.2763 time to fit residues: 3501.5280 Evaluate side-chains 1195 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1193 time to evaluate : 5.940 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.9878 time to fit residues: 10.0549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 321 optimal weight: 6.9990 chunk 860 optimal weight: 0.7980 chunk 188 optimal weight: 5.9990 chunk 560 optimal weight: 10.0000 chunk 235 optimal weight: 5.9990 chunk 955 optimal weight: 0.4980 chunk 793 optimal weight: 6.9990 chunk 442 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 316 optimal weight: 7.9990 chunk 501 optimal weight: 10.0000 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 54 GLN D 71 GLN E 70 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 HIS G 148 ASN ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 GLN N 66 GLN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 134 ASN c 163 GLN ** c 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 49 GLN ** e 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN e 156 ASN f 5 HIS ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 132 HIS ** k 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 54 GLN ** l 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 23 ASN m 62 ASN n 29 HIS o 56 HIS ** p 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 72 ASN ** t 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 69 ASN ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 13 ASN ** 1 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.8481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 153885 Z= 0.215 Angle : 0.655 17.971 230296 Z= 0.354 Chirality : 0.036 0.414 29341 Planarity : 0.006 0.124 12246 Dihedral : 22.621 178.988 73643 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.95 % Favored : 96.00 % Rotamer: Outliers : 0.02 % Allowed : 2.58 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.11), residues: 5474 helix: 0.01 (0.11), residues: 1882 sheet: -0.31 (0.16), residues: 973 loop : -0.87 (0.12), residues: 2619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 23 HIS 0.013 0.001 HIS B 15 PHE 0.036 0.002 PHE f 20 TYR 0.052 0.002 TYR D 76 ARG 0.013 0.001 ARG J 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1596 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1595 time to evaluate : 6.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 1595 average time/residue: 1.2743 time to fit residues: 3563.7646 Evaluate side-chains 1241 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1241 time to evaluate : 5.903 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.3401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 921 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 544 optimal weight: 10.0000 chunk 698 optimal weight: 20.0000 chunk 540 optimal weight: 10.0000 chunk 804 optimal weight: 0.0980 chunk 533 optimal weight: 10.0000 chunk 952 optimal weight: 8.9990 chunk 595 optimal weight: 10.0000 chunk 580 optimal weight: 10.0000 chunk 439 optimal weight: 10.0000 overall best weight: 7.8194 ------------------------------------------------------------------------------- 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: