Starting phenix.real_space_refine on Mon Apr 15 00:17:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7c_33660/04_2024/7y7c_33660_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7c_33660/04_2024/7y7c_33660.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7c_33660/04_2024/7y7c_33660_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7c_33660/04_2024/7y7c_33660_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7c_33660/04_2024/7y7c_33660_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7c_33660/04_2024/7y7c_33660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7c_33660/04_2024/7y7c_33660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7c_33660/04_2024/7y7c_33660_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7c_33660/04_2024/7y7c_33660_updated.pdb" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4556 5.49 5 Mg 283 5.21 5 S 150 5.16 5 C 71096 2.51 5 N 26433 2.21 5 O 39415 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 123": "OD1" <-> "OD2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 188": "OD1" <-> "OD2" Residue "B PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 204": "OD1" <-> "OD2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 34": "OD1" <-> "OD2" Residue "C PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 29": "OD1" <-> "OD2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 142": "OD1" <-> "OD2" Residue "E GLU 145": "OE1" <-> "OE2" Residue "F TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 33": "OE1" <-> "OE2" Residue "F ASP 41": "OD1" <-> "OD2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 82": "OD1" <-> "OD2" Residue "G PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G ASP 33": "OD1" <-> "OD2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "G GLU 74": "OE1" <-> "OE2" Residue "G GLU 106": "OE1" <-> "OE2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 43": "OE1" <-> "OE2" Residue "H GLU 52": "OE1" <-> "OE2" Residue "H PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 113": "OD1" <-> "OD2" Residue "I GLU 36": "OE1" <-> "OE2" Residue "I TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 95": "NH1" <-> "NH2" Residue "I ASP 107": "OD1" <-> "OD2" Residue "I ARG 124": "NH1" <-> "NH2" Residue "J GLU 66": "OE1" <-> "OE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J ASP 91": "OD1" <-> "OD2" Residue "K ASP 18": "OD1" <-> "OD2" Residue "K PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "K PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 14": "NH1" <-> "NH2" Residue "L GLU 25": "OE1" <-> "OE2" Residue "L ARG 56": "NH1" <-> "NH2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "L TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L ASP 103": "OD1" <-> "OD2" Residue "L TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 11": "OD1" <-> "OD2" Residue "M ASP 42": "OD1" <-> "OD2" Residue "M PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 82": "OD1" <-> "OD2" Residue "N GLU 10": "OE1" <-> "OE2" Residue "N PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 26": "OE1" <-> "OE2" Residue "N ARG 65": "NH1" <-> "NH2" Residue "N GLU 86": "OE1" <-> "OE2" Residue "N GLU 92": "OE1" <-> "OE2" Residue "O PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 21": "OD1" <-> "OD2" Residue "O GLU 45": "OE1" <-> "OE2" Residue "O GLU 83": "OE1" <-> "OE2" Residue "P TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 23": "OD1" <-> "OD2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "P PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 15": "OD1" <-> "OD2" Residue "Q GLU 60": "OE1" <-> "OE2" Residue "Q GLU 63": "OE1" <-> "OE2" Residue "R ASP 22": "OD1" <-> "OD2" Residue "R TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 3": "NH1" <-> "NH2" Residue "S ARG 32": "NH1" <-> "NH2" Residue "S ARG 81": "NH1" <-> "NH2" Residue "T TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 59": "OD1" <-> "OD2" Residue "U PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 66": "NH1" <-> "NH2" Residue "U TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 23": "OE1" <-> "OE2" Residue "c GLU 35": "OE1" <-> "OE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ARG 63": "NH1" <-> "NH2" Residue "c ASP 66": "OD1" <-> "OD2" Residue "c GLU 79": "OE1" <-> "OE2" Residue "c ARG 80": "NH1" <-> "NH2" Residue "c ASP 84": "OD1" <-> "OD2" Residue "c TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 100": "OE1" <-> "OE2" Residue "c TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 114": "OD1" <-> "OD2" Residue "c ARG 133": "NH1" <-> "NH2" Residue "c ARG 167": "NH1" <-> "NH2" Residue "c ARG 177": "NH1" <-> "NH2" Residue "c ARG 182": "NH1" <-> "NH2" Residue "c ARG 189": "NH1" <-> "NH2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c ARG 212": "NH1" <-> "NH2" Residue "c ASP 229": "OD1" <-> "OD2" Residue "c ASP 264": "OD1" <-> "OD2" Residue "c PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ASP 18": "OD1" <-> "OD2" 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 64": "OE1" <-> "OE2" Residue "d PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 83": "NH1" <-> "NH2" Residue "d GLU 86": "OE1" <-> "OE2" Residue "d GLU 89": "OE1" <-> "OE2" Residue "d PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 168": "OE1" <-> "OE2" Residue "d ARG 169": "NH1" <-> "NH2" Residue "d ASP 176": "OD1" <-> "OD2" Residue "e GLU 25": "OE1" <-> "OE2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e ARG 61": "NH1" <-> "NH2" Residue "e ARG 88": "NH1" <-> "NH2" Residue "e ARG 102": "NH1" <-> "NH2" Residue "e GLU 111": "OE1" <-> "OE2" Residue "e PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 127": "OE1" <-> "OE2" Residue "e GLU 155": "OE1" <-> "OE2" Residue "e ARG 162": "NH1" <-> "NH2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "e ASP 176": "OD1" <-> "OD2" Residue "e PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 10": "OD1" <-> "OD2" Residue "f GLU 11": "OE1" <-> "OE2" Residue "f PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 56": "OD1" <-> "OD2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f GLU 94": "OE1" <-> "OE2" Residue "f ARG 102": "NH1" <-> "NH2" Residue "f ARG 110": "NH1" <-> "NH2" Residue "f ARG 112": "NH1" <-> "NH2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 133": "NH1" <-> "NH2" Residue "f GLU 134": "OE1" <-> "OE2" Residue "f ASP 142": "OD1" <-> "OD2" Residue "f GLU 165": "OE1" <-> "OE2" Residue "g ARG 3": "NH1" <-> "NH2" Residue "g GLU 42": "OE1" <-> "OE2" Residue "g PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 153": "NH1" <-> "NH2" Residue "g ARG 163": "NH1" <-> "NH2" Residue "g GLU 167": "OE1" <-> "OE2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "h ARG 27": "NH1" <-> "NH2" Residue "i ARG 13": "NH1" <-> "NH2" Residue "i TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 19": "OD1" <-> "OD2" Residue "i ARG 37": "NH1" <-> "NH2" Residue "i ASP 52": "OD1" <-> "OD2" Residue "i ASP 60": "OD1" <-> "OD2" Residue "i ASP 71": "OD1" <-> "OD2" Residue "i TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 90": "OE1" <-> "OE2" Residue "i ARG 96": "NH1" <-> "NH2" Residue "i GLU 102": "OE1" <-> "OE2" Residue "i ARG 120": "NH1" <-> "NH2" Residue "i TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 56": "OD1" <-> "OD2" Residue "j GLU 92": "OE1" <-> "OE2" Residue "j PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 51": "OE1" <-> "OE2" Residue "k ARG 60": "NH1" <-> "NH2" Residue "k PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 78": "NH1" <-> "NH2" Residue "k ARG 123": "NH1" <-> "NH2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "l ARG 10": "NH1" <-> "NH2" Residue "l ARG 18": "NH1" <-> "NH2" Residue "l ARG 40": "NH1" <-> "NH2" Residue "l ARG 44": "NH1" <-> "NH2" Residue "l GLU 47": "OE1" <-> "OE2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "l TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 104": "OE1" <-> "OE2" Residue "l ASP 106": "OD1" <-> "OD2" Residue "l ARG 114": "NH1" <-> "NH2" Residue "m ARG 12": "NH1" <-> "NH2" Residue "m ARG 17": "NH1" <-> "NH2" Residue "m ARG 22": "NH1" <-> "NH2" Residue "m GLU 43": "OE1" <-> "OE2" 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 ASP 72": "OD1" <-> "OD2" Residue "m GLU 82": "OE1" <-> "OE2" Residue "m ARG 96": "NH1" <-> "NH2" Residue "m ASP 117": "OD1" <-> "OD2" Residue "m ARG 118": "NH1" <-> "NH2" Residue "n ARG 10": "NH1" <-> "NH2" Residue "n ARG 16": "NH1" <-> "NH2" Residue "n ARG 25": "NH1" <-> "NH2" Residue "n TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 55": "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 GLU 9": "OE1" <-> "OE2" Residue "o ARG 21": "NH1" <-> "NH2" Residue "o ASP 24": "OD1" <-> "OD2" Residue "o ARG 39": "NH1" <-> "NH2" Residue "o PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 82": "OD1" <-> "OD2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "o TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 101": "NH1" <-> "NH2" Residue "o ARG 109": "NH1" <-> "NH2" Residue "o GLU 112": "OE1" <-> "OE2" Residue "p ARG 3": "NH1" <-> "NH2" Residue "p ARG 6": "NH1" <-> "NH2" Residue "p ARG 13": "NH1" <-> "NH2" Residue "p ARG 33": "NH1" <-> "NH2" Residue "p ARG 48": "NH1" <-> "NH2" Residue "p GLU 89": "OE1" <-> "OE2" Residue "p ASP 97": "OD1" <-> "OD2" Residue "p ASP 102": "OD1" <-> "OD2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q GLU 34": "OE1" <-> "OE2" Residue "q GLU 46": "OE1" <-> "OE2" Residue "q PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 55": "OD1" <-> "OD2" Residue "q ARG 68": "NH1" <-> "NH2" Residue "q ARG 79": "NH1" <-> "NH2" Residue "q ARG 84": "NH1" <-> "NH2" Residue "r GLU 2": "OE1" <-> "OE2" Residue "r ASP 34": "OD1" <-> "OD2" Residue "r TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 65": "OD1" <-> "OD2" Residue "r PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 78": "OE1" <-> "OE2" 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 25": "OE1" <-> "OE2" Residue "s ASP 37": "OD1" <-> "OD2" Residue "s GLU 56": "OE1" <-> "OE2" Residue "s ARG 73": "NH1" <-> "NH2" Residue "s ASP 79": "OD1" <-> "OD2" Residue "t ARG 6": "NH1" <-> "NH2" Residue "t ARG 7": "NH1" <-> "NH2" Residue "t ASP 9": "OD1" <-> "OD2" Residue "t GLU 10": "OE1" <-> "OE2" Residue "t ASP 18": "OD1" <-> "OD2" Residue "t ARG 82": "NH1" <-> "NH2" Residue "t ARG 86": "NH1" <-> "NH2" Residue "t ARG 94": "NH1" <-> "NH2" Residue "u GLU 11": "OE1" <-> "OE2" Residue "u ASP 45": "OD1" <-> "OD2" Residue "u PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 59": "OE1" <-> "OE2" Residue "u GLU 69": "OE1" <-> "OE2" Residue "u ASP 76": "OD1" <-> "OD2" Residue "v GLU 29": "OE1" <-> "OE2" Residue "v PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 64": "OD1" <-> "OD2" Residue "v PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 3": "NH1" <-> "NH2" Residue "w ARG 11": "NH1" <-> "NH2" Residue "w ARG 37": "NH1" <-> "NH2" Residue "w PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 50": "NH1" <-> "NH2" Residue "w ARG 57": "NH1" <-> "NH2" Residue "w ASP 60": "OD1" <-> "OD2" Residue "w ASP 65": "OD1" <-> "OD2" Residue "w ARG 74": "NH1" <-> "NH2" Residue "x GLU 13": "OE1" <-> "OE2" Residue "x GLU 17": "OE1" <-> "OE2" Residue "x ARG 29": "NH1" <-> "NH2" Residue "x ARG 47": "NH1" <-> "NH2" Residue "x ARG 52": "NH1" <-> "NH2" Residue "y ARG 11": "NH1" <-> "NH2" Residue "y ARG 30": "NH1" <-> "NH2" Residue "y ARG 45": "NH1" <-> "NH2" Residue "y GLU 58": "OE1" <-> "OE2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 16": "NH1" <-> "NH2" Residue "z ARG 52": "NH1" <-> "NH2" Residue "0 PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 44": "NH1" <-> "NH2" Residue "0 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 51": "OE1" <-> "OE2" Residue "1 ARG 3": "NH1" <-> "NH2" Residue "1 ARG 12": "NH1" <-> "NH2" Residue "1 ARG 14": "NH1" <-> "NH2" Residue "1 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 21": "NH1" <-> "NH2" Residue "1 ARG 33": "NH1" <-> "NH2" Residue "1 ARG 41": "NH1" <-> "NH2" Residue "2 ARG 13": "NH1" <-> "NH2" Residue "2 ARG 30": "NH1" <-> "NH2" Residue "2 ARG 40": "NH1" <-> "NH2" Residue "2 ASP 54": "OD1" <-> "OD2" Residue "2 TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 24": "NH1" <-> "NH2" Residue "3 GLU 30": "OE1" <-> "OE2" Residue "4 TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 141933 Number of models: 1 Model: "" Number of chains: 62 Chain: "A" Number of atoms: 32634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1520, 32634 Classifications: {'RNA': 1520} Modifications used: {'rna2p': 1, 'rna2p_pur': 121, 'rna2p_pyr': 82, 'rna3p': 10, 'rna3p_pur': 742, 'rna3p_pyr': 564} Link IDs: {'rna2p': 204, 'rna3p': 1315} 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': 141, 'rna3p': 17, 'rna3p_pur': 1318, 'rna3p_pyr': 1003} Link IDs: {'rna2p': 414, 'rna3p': 2338} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Chain: "b" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Chain: "c" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "d" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "f" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "g" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "h" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 303 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "i" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "j" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "k" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "l" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Unusual residues: {'MS6': 1} Classifications: {'peptide': 135, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126, None: 2} Not linked: pdbres="4D4 l 81 " pdbres="MS6 l 82 " Not linked: pdbres="MS6 l 82 " pdbres="GLY l 83 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "n" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "o" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "p" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "r" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "s" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "t" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "u" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "v" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 628 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "w" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "x" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "y" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "z" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "0" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "2" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "3" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "4" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 480 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain breaks: 1 Chain: "X" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 279 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 10} Chain: "Z" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1645 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 5, 'rna2p_pyr': 3, 'rna3p': 4, 'rna3p_pur': 34, 'rna3p_pyr': 30} Link IDs: {'rna2p': 8, 'rna3p': 68} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 Chain: "V" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1603 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p': 3, 'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p': 7, 'rna3p_pur': 32, 'rna3p_pyr': 27} Link IDs: {'rna2p': 9, 'rna3p': 65} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Unusual residues: {' MG': 73} Classifications: {'undetermined': 73} Link IDs: {None: 72} Chain: "a" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 200 Unusual residues: {' MG': 200} Classifications: {'undetermined': 200} Link IDs: {None: 199} Chain: "b" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 55.35, per 1000 atoms: 0.39 Number of scatterers: 141933 At special positions: 0 Unit cell: (251.035, 238.608, 247.721, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 150 16.00 P 4556 15.00 Mg 283 11.99 O 39415 8.00 N 26433 7.00 C 71096 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: 58.41 Conformation dependent library (CDL) restraints added in 7.7 seconds 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10270 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: 168 helices and 69 sheets defined 38.6% alpha, 18.7% beta 1584 base pairs and 2426 stacking pairs defined. Time for finding SS restraints: 73.24 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 43 through 64 Proline residue: B 48 - end of helix removed outlier: 3.548A pdb=" N LYS B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 88 Processing helix chain 'B' and resid 103 through 124 removed outlier: 4.026A pdb=" N GLY B 124 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 148 removed outlier: 6.428A pdb=" N ALA B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N MET B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 removed outlier: 3.741A pdb=" N GLU B 169 " --> pdb=" O ASP B 165 " (cutoff:3.500A) 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: 3.942A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 48 removed outlier: 4.769A pdb=" N ALA C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASP C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 81 through 96 Processing helix chain 'C' and resid 108 through 113 removed outlier: 4.584A pdb=" N ASP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 5.830A 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: 4.629A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.764A 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: 5.213A pdb=" N LYS D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.809A 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: 3.507A pdb=" N LYS D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 151 removed outlier: 4.842A pdb=" N LYS D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 166 removed outlier: 3.833A pdb=" N ARG D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLU D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 removed outlier: 5.038A pdb=" N SER D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 206 removed outlier: 3.842A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 3.840A 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: 3.531A pdb=" N MET E 147 " --> pdb=" O GLY E 143 " (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: 3.720A pdb=" N GLU F 33 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 35 through 55 removed outlier: 3.521A pdb=" N ALA G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 70 removed outlier: 3.715A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 111 removed outlier: 3.625A pdb=" N LYS G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG G 111 " --> pdb=" O ALA G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 130 removed outlier: 3.914A pdb=" N GLU G 129 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN G 130 " --> pdb=" O ASP G 126 " (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 39 Processing helix chain 'I' and resid 41 through 56 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 71 through 92 Processing helix chain 'I' and resid 93 through 102 removed outlier: 5.210A pdb=" N GLU I 97 " --> pdb=" O SER I 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 33 removed outlier: 3.728A pdb=" N THR J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 90 removed outlier: 3.607A pdb=" N ARG J 89 " --> pdb=" O ASP J 85 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 51 removed outlier: 4.243A pdb=" N GLY K 51 " --> pdb=" O ALA K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 59 removed outlier: 3.883A pdb=" N SER K 58 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 4.511A 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: 4.902A pdb=" N GLU K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 104 removed outlier: 4.504A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 3.941A 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: 3.795A pdb=" N TYR L 117 " --> pdb=" O ALA L 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 22 removed outlier: 3.795A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) removed outlier: 4.536A 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 44 through 49 removed outlier: 3.988A pdb=" N LEU M 48 " --> pdb=" O LYS M 44 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N SER M 49 " --> pdb=" O ILE M 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 44 through 49' Processing helix chain 'M' and resid 50 through 64 removed outlier: 4.801A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N PHE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VAL M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 removed outlier: 3.711A pdb=" N GLY M 84 " --> pdb=" O LEU M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 21 removed outlier: 3.562A pdb=" N LYS N 7 " --> pdb=" O LYS N 3 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE N 21 " --> pdb=" O ALA N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 33 Processing helix chain 'N' and resid 37 through 51 removed outlier: 4.452A pdb=" N ARG N 41 " --> pdb=" O SER N 37 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU N 51 " --> pdb=" O LYS N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 91 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 43 removed outlier: 4.372A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.882A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'P' and resid 53 through 64 Processing helix chain 'P' and resid 68 through 80 removed outlier: 3.556A pdb=" N ASN P 79 " --> pdb=" O ILE P 75 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS P 80 " --> pdb=" O LYS P 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 17 removed outlier: 3.613A pdb=" N ALA R 15 " --> pdb=" O CYS R 11 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU R 16 " --> pdb=" O ARG R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 34 removed outlier: 3.585A pdb=" N LEU R 29 " --> pdb=" O ASP R 25 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N THR R 34 " --> pdb=" O LYS R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 removed outlier: 3.570A pdb=" N THR R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 66 Processing helix chain 'S' and resid 12 through 26 Processing helix chain 'S' and resid 70 through 76 removed outlier: 4.420A pdb=" N PHE S 74 " --> pdb=" O LYS S 70 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA S 75 " --> pdb=" O LEU S 71 " (cutoff:3.500A) Proline residue: S 76 - end of helix No H-bonds generated for 'chain 'S' and resid 70 through 76' Processing helix chain 'T' and resid 4 through 41 Processing helix chain 'T' and resid 44 through 65 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 87 removed outlier: 4.017A pdb=" N ALA T 87 " --> pdb=" O ILE T 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 27 Processing helix chain 'U' and resid 28 through 36 Processing helix chain 'U' and resid 40 through 69 removed outlier: 5.083A pdb=" N ARG U 69 " --> pdb=" O ALA U 65 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 15 removed outlier: 5.102A pdb=" N HIS c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 35 removed outlier: 4.185A pdb=" N LEU c 34 " --> pdb=" O PHE c 30 " (cutoff:3.500A) removed outlier: 5.848A 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: 3.823A 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: 3.752A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG c 214 " --> pdb=" O ALA c 210 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY c 215 " --> pdb=" O ALA c 211 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 226 removed outlier: 4.069A pdb=" N MET c 225 " --> pdb=" O ARG c 221 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASN c 226 " --> pdb=" O GLY c 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 221 through 226' Processing helix chain 'c' and resid 260 through 268 removed outlier: 3.660A pdb=" N ASP c 264 " --> pdb=" O ASN c 260 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LYS c 265 " --> pdb=" O LYS c 261 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHE c 266 " --> pdb=" O ARG c 262 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE c 267 " --> pdb=" O THR c 263 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N VAL c 268 " --> pdb=" O ASP c 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 260 through 268' Processing helix chain 'c' and resid 197 through 202 removed outlier: 4.153A pdb=" N MET c 201 " --> pdb=" O ALA c 198 " (cutoff:3.500A) Processing helix chain 'd' and resid 61 through 72 Processing helix chain 'd' and resid 98 through 103 removed outlier: 4.089A pdb=" N ALA d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) removed outlier: 5.086A 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: 3.995A pdb=" N ARG e 40 " --> pdb=" O ALA e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 97 through 116 Processing helix chain 'e' and resid 130 through 142 Processing helix chain 'e' and resid 154 through 163 removed outlier: 4.724A pdb=" N ASN e 163 " --> pdb=" O LEU e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 183 Processing helix chain 'e' and resid 189 through 201 Processing helix chain 'f' and resid 2 through 21 removed outlier: 5.198A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 24 through 29 removed outlier: 4.149A 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: 3.824A pdb=" N ASP f 46 " --> pdb=" O GLU f 42 " (cutoff:3.500A) removed outlier: 4.032A 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: 4.512A pdb=" N VAL f 108 " --> pdb=" O ILE f 104 " (cutoff:3.500A) Proline residue: f 109 - end of helix Processing helix chain 'f' and resid 162 through 174 Processing helix chain 'f' and resid 134 through 139 removed outlier: 3.752A pdb=" N ILE f 137 " --> pdb=" O GLU f 134 " (cutoff:3.500A) Proline residue: f 139 - end of helix Processing helix chain 'g' and resid 2 through 8 Proline residue: g 8 - end of helix Processing helix chain 'g' and resid 60 through 81 removed outlier: 5.025A pdb=" N GLN g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 153 removed outlier: 4.146A pdb=" N ARG g 152 " --> pdb=" O LEU g 148 " (cutoff:3.500A) Processing helix chain 'h' and resid 22 through 29 Processing helix chain 'i' and resid 24 through 38 removed outlier: 4.100A 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: 4.296A pdb=" N ILE i 101 " --> pdb=" O PRO i 97 " (cutoff:3.500A) removed outlier: 3.582A 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: 4.140A pdb=" N LYS i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) removed outlier: 4.369A 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: 3.699A pdb=" N ARG k 41 " --> pdb=" O GLY k 37 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N SER k 42 " --> pdb=" O GLN k 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 37 through 42' Processing helix chain 'k' and resid 56 through 62 removed outlier: 3.542A pdb=" N LEU k 61 " --> pdb=" O LEU k 57 " (cutoff:3.500A) Proline residue: k 62 - end of helix Processing helix chain 'k' and resid 68 through 75 removed outlier: 3.951A pdb=" N ALA k 72 " --> pdb=" O SER k 68 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE k 73 " --> pdb=" O ARG k 69 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR k 74 " --> pdb=" O LYS k 70 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ALA k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 68 through 75' Processing helix chain 'k' and resid 78 through 85 removed outlier: 3.743A pdb=" N LEU k 82 " --> pdb=" O ARG k 78 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ALA k 83 " --> pdb=" O LEU k 79 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS k 84 " --> pdb=" O SER k 80 " (cutoff:3.500A) removed outlier: 4.594A 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: 4.086A pdb=" N LYS l 123 " --> pdb=" O LEU l 119 " (cutoff:3.500A) removed outlier: 3.841A 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 58 removed outlier: 4.059A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL m 47 " --> pdb=" O GLU m 43 " (cutoff:3.500A) Proline residue: m 50 - end of helix removed outlier: 3.538A pdb=" N LYS m 56 " --> pdb=" O ILE m 52 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR m 57 " --> pdb=" O THR m 53 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ASP m 58 " --> pdb=" O LEU m 54 " (cutoff:3.500A) Processing helix chain 'm' and resid 59 through 71 removed outlier: 3.530A pdb=" N ARG m 69 " --> pdb=" O LEU m 65 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR m 70 " --> pdb=" O ALA m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 72 through 88 removed outlier: 4.873A 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: 3.935A pdb=" N ALA n 6 " --> pdb=" O ASP n 2 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 63 removed outlier: 4.808A pdb=" N GLN n 61 " --> pdb=" O ALA n 57 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU n 62 " --> pdb=" O ILE n 58 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LYS n 63 " --> pdb=" O ALA n 59 " (cutoff:3.500A) Processing helix chain 'n' and resid 67 through 86 Processing helix chain 'n' and resid 101 through 114 removed outlier: 3.620A pdb=" N GLY n 114 " --> pdb=" O ALA n 110 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 14 removed outlier: 3.610A pdb=" N GLU o 11 " --> pdb=" O GLN o 7 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN o 12 " --> pdb=" O LEU o 8 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET o 13 " --> pdb=" O GLU o 9 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LYS o 14 " --> pdb=" O GLN o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 104 removed outlier: 4.609A pdb=" N ARG o 101 " --> pdb=" O LEU o 97 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLU o 102 " --> pdb=" O TYR o 98 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG o 103 " --> pdb=" O TYR o 99 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N THR o 104 " --> pdb=" O LEU o 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 97 through 104' Processing helix chain 'p' and resid 6 through 22 removed outlier: 3.952A pdb=" N LYS p 22 " --> pdb=" O LEU p 18 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 31 removed outlier: 3.832A pdb=" N ARG p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) Processing helix chain 'p' and resid 32 through 37 removed outlier: 3.837A pdb=" N GLN p 37 " --> pdb=" O ARG p 33 " (cutoff:3.500A) Processing helix chain 'p' and resid 39 through 73 removed outlier: 3.848A pdb=" N ARG p 51 " --> pdb=" O TYR p 47 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG p 55 " --> pdb=" O ARG p 51 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN p 72 " --> pdb=" O ALA p 68 " (cutoff:3.500A) Processing helix chain 'p' and resid 75 through 87 Processing helix chain 'p' and resid 91 through 102 Processing helix chain 'p' and resid 103 through 118 Processing helix chain 'r' and resid 13 through 25 removed outlier: 3.830A pdb=" N VAL r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG r 25 " --> pdb=" O ALA r 21 " (cutoff:3.500A) Processing helix chain 'r' and resid 28 through 39 Processing helix chain 'r' and resid 41 through 61 removed outlier: 3.649A pdb=" N VAL r 45 " --> pdb=" O LYS r 41 " (cutoff:3.500A) Processing helix chain 's' and resid 3 through 11 removed outlier: 4.166A 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: 4.003A pdb=" N VAL t 70 " --> pdb=" O GLN t 66 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ALA t 71 " --> pdb=" O VAL t 67 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 66 through 71' Processing helix chain 'u' and resid 13 through 24 removed outlier: 3.704A pdb=" N ASN u 24 " --> pdb=" O LEU u 20 " (cutoff:3.500A) Processing helix chain 'u' and resid 43 through 53 removed outlier: 4.108A pdb=" N LYS u 53 " --> pdb=" O ASN u 49 " (cutoff:3.500A) Processing helix chain 'u' and resid 54 through 59 removed outlier: 4.275A pdb=" N SER u 58 " --> pdb=" O ALA u 54 " (cutoff:3.500A) Processing helix chain 'w' and resid 52 through 63 Processing helix chain 'w' and resid 64 through 75 Processing helix chain 'x' and resid 2 through 10 removed outlier: 3.525A pdb=" N LYS x 9 " --> pdb=" O GLU x 5 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N SER x 10 " --> pdb=" O LEU x 6 " (cutoff:3.500A) Processing helix chain 'x' and resid 11 through 35 removed outlier: 3.836A pdb=" N GLY x 35 " --> pdb=" O GLN x 31 " (cutoff:3.500A) Processing helix chain 'x' and resid 40 through 62 removed outlier: 4.228A pdb=" N LYS x 44 " --> pdb=" O SER x 40 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY x 62 " --> pdb=" O ASN x 58 " (cutoff:3.500A) Processing helix chain 'y' and resid 17 through 28 Processing helix chain 'y' and resid 41 through 52 Processing helix chain 'z' and resid 9 through 19 removed outlier: 4.742A 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: 4.343A 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: 3.853A pdb=" N ARG 2 13 " --> pdb=" O GLY 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 37 through 46 Proline residue: 2 46 - end of helix Processing helix chain '2' and resid 51 through 63 removed outlier: 4.716A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 4.819A 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: 4.630A pdb=" N ARG 4 59 " --> pdb=" O GLY 4 55 " (cutoff:3.500A) removed outlier: 3.784A 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: 5.698A pdb=" N HIS B 15 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N HIS B 39 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 89 through 93 removed outlier: 3.612A pdb=" N LEU B 161 " --> pdb=" O PRO B 182 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 53 through 59 Processing sheet with id= 4, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.516A pdb=" N GLY C 148 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY C 194 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 6.563A 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 144 removed outlier: 4.055A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 11 through 16 removed outlier: 6.715A 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: 3.660A pdb=" N ALA E 99 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ASN E 122 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 32 through 41 removed outlier: 6.320A pdb=" N ARG E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F' and resid 38 through 42 removed outlier: 5.761A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 43 through 47 removed outlier: 3.699A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N HIS F 55 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 72 through 79 removed outlier: 6.472A pdb=" N THR G 72 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'H' and resid 23 through 29 removed outlier: 6.461A pdb=" N ALA H 23 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.551A pdb=" N SER H 74 " --> pdb=" O ALA H 130 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS H 127 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'I' and resid 5 through 11 Processing sheet with id= 15, first strand: chain 'I' and resid 26 through 30 Processing sheet with id= 16, first strand: chain 'J' and resid 42 through 52 removed outlier: 4.987A pdb=" N LEU J 71 " --> pdb=" O PRO J 43 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'K' and resid 30 through 35 removed outlier: 7.370A pdb=" N VAL K 84 " --> pdb=" O THR K 108 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'L' and resid 29 through 32 removed outlier: 5.277A pdb=" N LEU L 81 " --> pdb=" O VAL L 98 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ARG L 94 " --> pdb=" O GLY L 85 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'L' and resid 36 through 41 removed outlier: 5.256A pdb=" N LYS L 51 " --> pdb=" O ILE L 67 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'P' and resid 4 through 10 removed outlier: 3.556A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'Q' and resid 7 through 11 removed outlier: 6.695A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'Q' and resid 19 through 30 No H-bonds generated for sheet with id= 22 Processing sheet with id= 23, first strand: chain 'S' and resid 30 through 33 removed outlier: 4.717A 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: 3.675A pdb=" N ALA c 2 " --> pdb=" O VAL c 20 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL c 16 " --> pdb=" O CYS c 6 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'c' and resid 80 through 83 removed outlier: 3.607A pdb=" N ARG c 80 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU c 93 " --> pdb=" O GLU c 79 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ILE c 74 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N SER c 118 " --> pdb=" O ILE c 74 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASP c 114 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLY c 127 " --> pdb=" O GLN c 115 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLN c 117 " --> pdb=" O GLY c 127 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'c' and resid 138 through 142 removed outlier: 4.228A pdb=" N SER c 139 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR c 173 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU c 180 " --> pdb=" O LEU c 176 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'c' and resid 91 through 96 removed outlier: 3.989A pdb=" N GLU c 100 " --> pdb=" O TYR c 96 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'd' and resid 3 through 6 removed outlier: 6.525A pdb=" N LYS d 105 " --> pdb=" O VAL d 177 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'd' and resid 10 through 16 removed outlier: 3.749A pdb=" N GLY d 10 " --> pdb=" O VAL d 26 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL d 20 " --> pdb=" O THR d 16 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'd' and resid 79 through 84 removed outlier: 5.943A pdb=" N ARG d 46 " --> pdb=" O LEU d 84 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLN d 94 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'e' and resid 1 through 6 removed outlier: 3.660A pdb=" N LEU e 3 " --> pdb=" O LEU e 12 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER e 10 " --> pdb=" O LEU e 5 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'e' and resid 44 through 47 No H-bonds generated for sheet with id= 32 Processing sheet with id= 33, first strand: chain 'e' and resid 117 through 120 removed outlier: 5.725A pdb=" N ARG e 117 " --> pdb=" O ASP e 184 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'f' and resid 65 through 69 removed outlier: 5.240A pdb=" N ILE f 85 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLY f 39 " --> pdb=" O GLY f 151 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLY f 151 " --> pdb=" O GLY f 39 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'g' and resid 22 through 25 removed outlier: 5.758A pdb=" N GLN g 22 " --> pdb=" O LEU g 37 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'g' and resid 40 through 44 removed outlier: 7.532A pdb=" N ALA g 40 " --> pdb=" O ARG g 55 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS g 44 " --> pdb=" O THR g 51 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N THR g 51 " --> pdb=" O LYS g 44 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'g' and resid 94 through 99 removed outlier: 3.738A pdb=" N VAL g 102 " --> pdb=" O LYS g 99 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL g 113 " --> pdb=" O LEU g 105 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'g' and resid 121 through 125 removed outlier: 5.655A pdb=" N THR g 129 " --> pdb=" O LEU g 89 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'h' and resid 2 through 5 removed outlier: 4.611A pdb=" N ASP h 17 " --> pdb=" O LEU h 5 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'i' and resid 52 through 57 removed outlier: 4.966A pdb=" N ASP i 19 " --> pdb=" O LEU i 140 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'i' and resid 74 through 78 removed outlier: 7.580A pdb=" N GLY i 83 " --> pdb=" O THR i 78 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'j' and resid 18 through 21 removed outlier: 4.144A pdb=" N THR j 6 " --> pdb=" O CYS j 21 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ASN j 82 " --> pdb=" O MET j 7 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'l' and resid 37 through 40 No H-bonds generated for sheet with id= 43 Processing sheet with id= 44, first strand: chain 'l' and resid 62 through 65 removed outlier: 3.555A pdb=" N TYR l 103 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU l 33 " --> pdb=" O LEU l 102 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS l 100 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'l' and resid 73 through 76 removed outlier: 6.835A pdb=" N ILE l 73 " --> pdb=" O GLU l 90 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN l 88 " --> pdb=" O GLU l 75 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'l' and resid 30 through 36 removed outlier: 7.887A pdb=" N SER l 30 " --> pdb=" O LYS l 133 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS l 127 " --> pdb=" O VAL l 36 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'm' and resid 33 through 37 removed outlier: 5.476A pdb=" N MET m 110 " --> pdb=" O CYS m 100 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'n' and resid 49 through 53 removed outlier: 3.785A pdb=" N VAL n 49 " --> pdb=" O VAL n 39 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE n 35 " --> pdb=" O THR n 53 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'o' and resid 38 through 45 removed outlier: 6.577A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER o 83 " --> pdb=" O LYS o 29 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'o' and resid 49 through 52 removed outlier: 3.588A pdb=" N ALA o 49 " --> pdb=" O THR o 60 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N SER o 57 " --> pdb=" O THR o 76 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'q' and resid 11 through 15 removed outlier: 3.646A pdb=" N MET q 40 " --> pdb=" O VAL q 4 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU q 39 " --> pdb=" O GLY q 50 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLU q 46 " --> pdb=" O ASN q 43 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'q' and resid 18 through 23 removed outlier: 4.113A pdb=" N GLN q 18 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASP q 95 " --> pdb=" O VAL q 64 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS q 60 " --> pdb=" O THR q 99 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'q' and resid 57 through 60 Processing sheet with id= 54, first strand: chain 'q' and resid 65 through 68 Processing sheet with id= 55, first strand: chain 'q' and resid 71 through 78 removed outlier: 4.224A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'r' and resid 2 through 8 Processing sheet with id= 57, first strand: chain 's' and resid 28 through 33 removed outlier: 6.520A pdb=" N ASN s 28 " --> pdb=" O LEU s 87 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG s 73 " --> pdb=" O HIS s 70 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS s 66 " --> pdb=" O ARG s 77 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASP s 79 " --> pdb=" O LYS s 64 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LYS s 64 " --> pdb=" O ASP s 79 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYS s 81 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL s 62 " --> pdb=" O LYS s 81 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA s 83 " --> pdb=" O THR s 60 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR s 60 " --> pdb=" O ALA s 83 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL s 85 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL s 58 " --> pdb=" O VAL s 85 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 't' and resid 83 through 87 Processing sheet with id= 59, first strand: chain 'u' and resid 69 through 72 removed outlier: 6.707A pdb=" N ALA u 39 " --> pdb=" O ARG u 9 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE u 89 " --> pdb=" O PRO u 27 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'v' and resid 51 through 54 removed outlier: 4.187A pdb=" N THR v 58 " --> pdb=" O GLY v 54 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'v' and resid 66 through 71 Processing sheet with id= 62, first strand: chain 'w' and resid 12 through 19 removed outlier: 4.462A pdb=" N ASN w 23 " --> pdb=" O SER w 19 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'w' and resid 35 through 41 removed outlier: 3.534A pdb=" N ARG w 45 " --> pdb=" O VAL w 40 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'y' and resid 33 through 39 removed outlier: 4.434A pdb=" N HIS y 34 " --> pdb=" O GLN y 9 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N MET y 54 " --> pdb=" O THR y 10 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'z' and resid 29 through 32 removed outlier: 4.460A pdb=" N GLU z 36 " --> pdb=" O ASP z 31 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain '0' and resid 19 through 25 removed outlier: 6.055A pdb=" N HIS 0 19 " --> pdb=" O SER 0 13 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE 0 48 " --> pdb=" O SER 0 14 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU 0 51 " --> pdb=" O LEU 0 34 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU 0 34 " --> pdb=" O GLU 0 51 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain '2' and resid 22 through 25 removed outlier: 5.675A pdb=" N PHE 2 22 " --> pdb=" O VAL 2 50 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '3' and resid 14 through 19 Processing sheet with id= 69, first strand: chain '4' and resid 20 through 25 removed outlier: 4.311A pdb=" N ASN 4 20 " --> pdb=" O CYS 4 16 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU 4 32 " --> pdb=" O THR 4 13 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER 4 15 " --> pdb=" O LEU 4 32 " (cutoff:3.500A) 1867 hydrogen bonds defined for protein. 5532 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3986 hydrogen bonds 6242 hydrogen bond angles 0 basepair planarities 1584 basepair parallelities 2426 stacking parallelities Total time for adding SS restraints: 297.47 Time building geometry restraints manager: 63.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 12368 1.30 - 1.43: 69275 1.43 - 1.56: 62959 1.56 - 1.70: 9110 1.70 - 1.83: 264 Bond restraints: 153976 Sorted by residual: bond pdb=" C5 5MU Z 55 " pdb=" C6 5MU Z 55 " ideal model delta sigma weight residual 1.155 1.442 -0.287 2.00e-02 2.50e+03 2.06e+02 bond pdb=" C5 5MU a 747 " pdb=" C6 5MU a 747 " ideal model delta sigma weight residual 1.155 1.437 -0.282 2.00e-02 2.50e+03 1.99e+02 bond pdb=" C5 5MU V 53 " pdb=" C6 5MU V 53 " ideal model delta sigma weight residual 1.155 1.436 -0.281 2.00e-02 2.50e+03 1.97e+02 bond pdb=" C5 5MU a1939 " pdb=" C6 5MU a1939 " ideal model delta sigma weight residual 1.155 1.434 -0.279 2.00e-02 2.50e+03 1.95e+02 bond pdb=" C MS6 l 82 " pdb=" S MS6 l 82 " ideal model delta sigma weight residual 1.829 1.564 0.265 2.00e-02 2.50e+03 1.75e+02 ... (remaining 153971 not shown) Histogram of bond angle deviations from ideal: 97.44 - 106.29: 26554 106.29 - 115.15: 102724 115.15 - 124.01: 80290 124.01 - 132.86: 20775 132.86 - 141.72: 89 Bond angle restraints: 230432 Sorted by residual: angle pdb=" C1' 2MA a2503 " pdb=" N9 2MA a2503 " pdb=" C8 2MA a2503 " ideal model delta sigma weight residual 106.32 141.72 -35.40 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C1' 2MA a2503 " pdb=" N9 2MA a2503 " pdb=" C4 2MA a2503 " ideal model delta sigma weight residual 138.88 110.84 28.04 3.00e+00 1.11e-01 8.74e+01 angle pdb=" C1' 1MA V 9 " pdb=" N9 1MA V 9 " pdb=" C8 1MA V 9 " ideal model delta sigma weight residual 100.68 128.39 -27.71 3.00e+00 1.11e-01 8.53e+01 angle pdb=" C1' 1MA V 57 " pdb=" N9 1MA V 57 " pdb=" C8 1MA V 57 " ideal model delta sigma weight residual 100.68 127.91 -27.23 3.00e+00 1.11e-01 8.24e+01 angle pdb=" C1' 2MG A1516 " pdb=" N9 2MG A1516 " pdb=" C8 2MG A1516 " ideal model delta sigma weight residual 110.07 130.78 -20.71 3.00e+00 1.11e-01 4.76e+01 ... (remaining 230427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 87447 35.85 - 71.71: 9865 71.71 - 107.56: 1182 107.56 - 143.41: 13 143.41 - 179.27: 14 Dihedral angle restraints: 98521 sinusoidal: 82600 harmonic: 15921 Sorted by residual: dihedral pdb=" CA ASP g 47 " pdb=" C ASP g 47 " pdb=" N ASN g 48 " pdb=" CA ASN g 48 " ideal model delta harmonic sigma weight residual -180.00 -111.49 -68.51 0 5.00e+00 4.00e-02 1.88e+02 dihedral pdb=" C5' C a1730 " pdb=" C4' C a1730 " pdb=" C3' C a1730 " pdb=" O3' C a1730 " ideal model delta sinusoidal sigma weight residual 147.00 78.18 68.82 1 8.00e+00 1.56e-02 9.58e+01 dihedral pdb=" C4' C a1730 " pdb=" C3' C a1730 " pdb=" C2' C a1730 " pdb=" C1' C a1730 " ideal model delta sinusoidal sigma weight residual -35.00 33.20 -68.20 1 8.00e+00 1.56e-02 9.43e+01 ... (remaining 98518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 26966 0.082 - 0.164: 2166 0.164 - 0.246: 153 0.246 - 0.329: 10 0.329 - 0.411: 3 Chirality restraints: 29298 Sorted by residual: chirality pdb=" C3' C a1730 " pdb=" C4' C a1730 " pdb=" O3' C a1730 " pdb=" C2' C a1730 " both_signs ideal model delta sigma weight residual False -2.74 -2.33 -0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" C1* PSU A 516 " pdb=" O4* PSU A 516 " pdb=" C2* PSU A 516 " pdb=" C5 PSU A 516 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" C1* PSU a2580 " pdb=" O4* PSU a2580 " pdb=" C2* PSU a2580 " pdb=" C5 PSU a2580 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 29295 not shown) Planarity restraints: 12266 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " -0.069 2.00e-02 2.50e+03 6.05e-01 8.23e+03 pdb=" C4' 2MG A1516 " -0.435 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " -0.615 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " 0.602 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " 0.655 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " 0.164 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " -1.000 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " -0.224 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " 0.922 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1407 " -0.065 2.00e-02 2.50e+03 6.02e-01 8.15e+03 pdb=" C4' 5MC A1407 " -0.440 2.00e-02 2.50e+03 pdb=" O4' 5MC A1407 " -0.626 2.00e-02 2.50e+03 pdb=" C3' 5MC A1407 " 0.602 2.00e-02 2.50e+03 pdb=" O3' 5MC A1407 " 0.650 2.00e-02 2.50e+03 pdb=" C2' 5MC A1407 " 0.174 2.00e-02 2.50e+03 pdb=" O2' 5MC A1407 " -0.986 2.00e-02 2.50e+03 pdb=" C1' 5MC A1407 " -0.222 2.00e-02 2.50e+03 pdb=" N1 5MC A1407 " 0.912 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1207 " -0.054 2.00e-02 2.50e+03 5.99e-01 8.08e+03 pdb=" C4' 2MG A1207 " -0.445 2.00e-02 2.50e+03 pdb=" O4' 2MG A1207 " -0.661 2.00e-02 2.50e+03 pdb=" C3' 2MG A1207 " 0.597 2.00e-02 2.50e+03 pdb=" O3' 2MG A1207 " 0.627 2.00e-02 2.50e+03 pdb=" C2' 2MG A1207 " 0.192 2.00e-02 2.50e+03 pdb=" O2' 2MG A1207 " -0.962 2.00e-02 2.50e+03 pdb=" C1' 2MG A1207 " -0.210 2.00e-02 2.50e+03 pdb=" N9 2MG A1207 " 0.916 2.00e-02 2.50e+03 ... (remaining 12263 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 720 2.47 - 3.08: 91001 3.08 - 3.69: 265536 3.69 - 4.29: 413522 4.29 - 4.90: 550020 Nonbonded interactions: 1320799 Sorted by model distance: nonbonded pdb=" OP1 C a 948 " pdb="MG MG a6030 " model vdw 1.866 2.170 nonbonded pdb=" OP1 G a1026 " pdb="MG MG a6122 " model vdw 1.877 2.170 nonbonded pdb=" OP2 C a2611 " pdb="MG MG a6062 " model vdw 1.883 2.170 nonbonded pdb=" O6 G A1222 " pdb="MG MG A1604 " model vdw 1.892 2.170 nonbonded pdb=" OP1 A a 751 " pdb="MG MG a6020 " model vdw 1.892 2.170 ... (remaining 1320794 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.560 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: 0.150 Extract box with map and model: 34.740 Check model and map are aligned: 1.510 Set scattering table: 0.960 Process input model: 594.740 Find NCS groups from input model: 3.420 Set up NCS constraints: 0.440 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: 0.040 Load rotamer database and sin/cos tables:14.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 657.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 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 0.287 153976 Z= 0.679 Angle : 0.736 35.399 230432 Z= 0.385 Chirality : 0.047 0.411 29298 Planarity : 0.025 0.605 12266 Dihedral : 22.518 179.268 88251 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.22 % Rotamer: Outliers : 0.09 % Allowed : 0.33 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.11), residues: 5480 helix: 1.05 (0.12), residues: 1826 sheet: -0.20 (0.15), residues: 1091 loop : -0.64 (0.12), residues: 2563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 23 HIS 0.025 0.002 HIS c 53 PHE 0.018 0.002 PHE S 10 TYR 0.026 0.002 TYR 4 9 ARG 0.021 0.001 ARG 3 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1057 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1053 time to evaluate : 5.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 LYS cc_start: 0.1124 (mptt) cc_final: 0.0535 (pptt) REVERT: B 154 MET cc_start: 0.2453 (mtm) cc_final: 0.2233 (mtm) REVERT: C 27 LYS cc_start: 0.5807 (ttpt) cc_final: 0.5343 (tttm) REVERT: C 28 GLU cc_start: 0.5862 (mp0) cc_final: 0.5379 (pm20) REVERT: C 58 GLU cc_start: 0.6160 (tt0) cc_final: 0.5819 (tt0) REVERT: C 65 ARG cc_start: 0.6543 (ttm170) cc_final: 0.5977 (ttm-80) REVERT: C 72 ARG cc_start: 0.6114 (mtp85) cc_final: 0.5625 (mtm180) REVERT: C 87 LEU cc_start: 0.6420 (mt) cc_final: 0.6115 (mt) REVERT: C 88 ARG cc_start: 0.5346 (tmm-80) cc_final: 0.4913 (tmt-80) REVERT: C 100 GLN cc_start: 0.6939 (tt0) cc_final: 0.6618 (tt0) REVERT: C 110 GLU cc_start: 0.6612 (mp0) cc_final: 0.6297 (mp0) REVERT: C 127 ARG cc_start: 0.7126 (mtt90) cc_final: 0.6285 (mtm110) REVERT: C 129 MET cc_start: 0.6159 (mmm) cc_final: 0.5915 (mmm) REVERT: C 144 LEU cc_start: 0.7644 (mm) cc_final: 0.7225 (mm) REVERT: C 161 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6778 (tp30) REVERT: C 183 ASP cc_start: 0.7570 (t0) cc_final: 0.7278 (t0) REVERT: C 185 ASN cc_start: 0.8432 (t0) cc_final: 0.7866 (m-40) REVERT: D 40 GLN cc_start: 0.7117 (pt0) cc_final: 0.6693 (pt0) REVERT: D 73 ARG cc_start: 0.6497 (ttp-170) cc_final: 0.6183 (ttp-110) REVERT: D 88 GLU cc_start: 0.6419 (mt-10) cc_final: 0.5933 (pp20) REVERT: D 105 MET cc_start: 0.6267 (mtm) cc_final: 0.6023 (mtt) REVERT: D 184 ARG cc_start: 0.3841 (ptt90) cc_final: 0.3105 (ppt170) REVERT: D 185 LYS cc_start: 0.5743 (ttmm) cc_final: 0.5417 (mtpt) REVERT: D 205 SER cc_start: 0.6581 (p) cc_final: 0.6205 (m) REVERT: E 11 LEU cc_start: 0.7345 (tp) cc_final: 0.7022 (tt) REVERT: E 23 LYS cc_start: 0.8234 (ptmt) cc_final: 0.7972 (ptmt) REVERT: E 26 LYS cc_start: 0.7607 (ttmt) cc_final: 0.7221 (tttp) REVERT: E 45 ARG cc_start: 0.7196 (mtp85) cc_final: 0.6973 (ttp80) REVERT: E 68 ARG cc_start: 0.7295 (ttm110) cc_final: 0.7034 (ttp-170) REVERT: E 70 ASN cc_start: 0.7005 (m-40) cc_final: 0.6797 (m110) REVERT: E 93 ARG cc_start: 0.7667 (mtm-85) cc_final: 0.7298 (ptp-110) REVERT: F 3 HIS cc_start: 0.7170 (m170) cc_final: 0.6939 (m-70) REVERT: F 8 PHE cc_start: 0.7868 (p90) cc_final: 0.7548 (p90) REVERT: F 9 MET cc_start: 0.7504 (mtm) cc_final: 0.6945 (mtt) REVERT: F 38 ARG cc_start: 0.7667 (ttp-170) cc_final: 0.7318 (ttp-170) REVERT: F 54 LEU cc_start: 0.6676 (mp) cc_final: 0.6430 (mp) REVERT: F 62 MET cc_start: 0.7205 (mtp) cc_final: 0.6258 (mpp) REVERT: F 79 ARG cc_start: 0.6553 (ttm-80) cc_final: 0.6198 (ttp-170) REVERT: F 90 MET cc_start: 0.6133 (mtp) cc_final: 0.5675 (mpp) REVERT: G 76 LYS cc_start: 0.6518 (ptmm) cc_final: 0.6197 (ptpt) REVERT: G 92 ARG cc_start: 0.5855 (mtm110) cc_final: 0.5280 (ptt90) REVERT: G 111 ARG cc_start: 0.5906 (mmt90) cc_final: 0.5427 (mtp-110) REVERT: G 116 MET cc_start: 0.7102 (tpt) cc_final: 0.6896 (tpt) REVERT: G 138 ARG cc_start: 0.6032 (ttp80) cc_final: 0.5649 (ttp80) REVERT: G 139 GLU cc_start: 0.5173 (mt-10) cc_final: 0.4772 (mp0) REVERT: H 38 ASN cc_start: 0.7661 (t0) cc_final: 0.7453 (t0) REVERT: H 39 VAL cc_start: 0.7935 (t) cc_final: 0.7709 (t) REVERT: H 76 GLN cc_start: 0.7502 (tt0) cc_final: 0.7089 (tt0) REVERT: H 88 ARG cc_start: 0.6797 (mtp180) cc_final: 0.6575 (mtp-110) REVERT: H 126 ILE cc_start: 0.7679 (mm) cc_final: 0.7441 (mt) REVERT: I 20 PHE cc_start: 0.7443 (m-80) cc_final: 0.7150 (m-80) REVERT: I 64 TYR cc_start: 0.6964 (t80) cc_final: 0.6675 (t80) REVERT: I 68 LYS cc_start: 0.7580 (mttp) cc_final: 0.7346 (mtpt) REVERT: I 97 GLU cc_start: 0.5237 (pm20) cc_final: 0.4986 (pm20) REVERT: J 9 ARG cc_start: 0.7805 (mtp85) cc_final: 0.7501 (mtp85) REVERT: J 88 MET cc_start: 0.3001 (mmt) cc_final: 0.2746 (mpt) REVERT: K 94 GLU cc_start: 0.5981 (mm-30) cc_final: 0.5726 (mp0) REVERT: M 19 LEU cc_start: 0.7184 (mt) cc_final: 0.6889 (tp) REVERT: M 75 MET cc_start: 0.6196 (mmp) cc_final: 0.5622 (mtp) REVERT: M 93 ARG cc_start: 0.6215 (mmt90) cc_final: 0.5634 (mmt180) REVERT: M 95 LEU cc_start: 0.8199 (mt) cc_final: 0.7742 (mt) REVERT: M 108 THR cc_start: 0.7946 (t) cc_final: 0.7690 (m) REVERT: N 6 MET cc_start: 0.7573 (mmm) cc_final: 0.7236 (mmm) REVERT: N 21 PHE cc_start: 0.6874 (t80) cc_final: 0.6449 (t80) REVERT: N 74 LEU cc_start: 0.7644 (mt) cc_final: 0.7359 (mt) REVERT: N 86 GLU cc_start: 0.6804 (mt-10) cc_final: 0.6269 (tt0) REVERT: O 47 LYS cc_start: 0.7786 (mttp) cc_final: 0.7271 (mtmt) REVERT: O 48 LYS cc_start: 0.7774 (mmtm) cc_final: 0.7358 (mmtt) REVERT: O 62 GLN cc_start: 0.7382 (tt0) cc_final: 0.6947 (tt0) REVERT: O 72 ARG cc_start: 0.6813 (ttp-110) cc_final: 0.6385 (ttm170) REVERT: O 77 ARG cc_start: 0.6751 (mtp85) cc_final: 0.6461 (mtp85) REVERT: O 84 ARG cc_start: 0.6440 (ttm170) cc_final: 0.6209 (mmm-85) REVERT: O 89 ARG cc_start: 0.5458 (ptm-80) cc_final: 0.4996 (ptm160) REVERT: P 34 GLU cc_start: 0.7339 (tt0) cc_final: 0.7015 (tt0) REVERT: P 35 ARG cc_start: 0.7035 (ttp80) cc_final: 0.6798 (ttt90) REVERT: Q 8 LEU cc_start: 0.7518 (tp) cc_final: 0.7117 (tt) REVERT: Q 30 LYS cc_start: 0.8231 (tttt) cc_final: 0.7888 (tttt) REVERT: Q 69 LYS cc_start: 0.7798 (ttmm) cc_final: 0.7357 (tttt) REVERT: R 24 LYS cc_start: 0.6576 (mtmm) cc_final: 0.6121 (mtpt) REVERT: R 32 TYR cc_start: 0.8044 (m-80) cc_final: 0.7804 (m-80) REVERT: R 40 VAL cc_start: 0.7815 (t) cc_final: 0.7455 (p) REVERT: R 51 TYR cc_start: 0.6963 (m-80) cc_final: 0.6096 (m-80) REVERT: R 55 LEU cc_start: 0.7552 (tp) cc_final: 0.7072 (tp) REVERT: R 57 ARG cc_start: 0.7229 (mtm-85) cc_final: 0.6854 (mtp180) REVERT: R 61 ARG cc_start: 0.7355 (mtt90) cc_final: 0.6897 (mtt90) REVERT: S 43 ASN cc_start: 0.6194 (p0) cc_final: 0.5895 (p0) REVERT: S 44 MET cc_start: 0.5905 (mtp) cc_final: 0.5625 (ttm) REVERT: S 51 VAL cc_start: 0.6994 (p) cc_final: 0.6685 (t) REVERT: S 70 LYS cc_start: 0.7606 (mmtt) cc_final: 0.6928 (mmtt) REVERT: S 73 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6725 (mt-10) REVERT: T 16 LYS cc_start: 0.6610 (ttpp) cc_final: 0.6257 (mttp) REVERT: T 18 ARG cc_start: 0.6814 (ttp80) cc_final: 0.6156 (tmm160) REVERT: T 24 ARG cc_start: 0.6706 (mmp80) cc_final: 0.5789 (mtt-85) REVERT: T 27 MET cc_start: 0.6199 (tmm) cc_final: 0.5506 (ttp) REVERT: T 64 LYS cc_start: 0.6029 (mmtt) cc_final: 0.5739 (mptm) REVERT: T 68 HIS cc_start: 0.6858 (t-90) cc_final: 0.6405 (t70) REVERT: U 36 GLU cc_start: 0.6386 (tt0) cc_final: 0.6088 (tt0) REVERT: U 37 PHE cc_start: 0.6734 (m-80) cc_final: 0.6445 (m-80) REVERT: c 5 LYS cc_start: 0.7869 (mtpp) cc_final: 0.7574 (mtpp) REVERT: c 26 LYS cc_start: 0.8359 (mttm) cc_final: 0.7938 (mttt) REVERT: c 28 LYS cc_start: 0.7132 (mmtt) cc_final: 0.6869 (mmtp) REVERT: c 66 ASP cc_start: 0.7962 (t0) cc_final: 0.7755 (t0) REVERT: c 97 LYS cc_start: 0.7240 (ttmm) cc_final: 0.6791 (mttt) REVERT: c 102 ARG cc_start: 0.8077 (ttm170) cc_final: 0.7807 (mtp85) REVERT: c 108 LYS cc_start: 0.8145 (tttt) cc_final: 0.7792 (tttm) REVERT: c 111 LYS cc_start: 0.7157 (pttm) cc_final: 0.6585 (pttm) REVERT: c 132 MET cc_start: 0.8353 (mtm) cc_final: 0.8115 (mtm) REVERT: c 167 ARG cc_start: 0.7167 (ttp-170) cc_final: 0.6906 (ttp-110) REVERT: c 185 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6347 (mp0) REVERT: c 269 ARG cc_start: 0.7279 (ttm-80) cc_final: 0.7063 (ttt180) REVERT: c 270 ARG cc_start: 0.7574 (mmm160) cc_final: 0.7346 (mmm160) REVERT: d 105 LYS cc_start: 0.7758 (mmtp) cc_final: 0.7498 (mttm) REVERT: d 176 ASP cc_start: 0.7707 (m-30) cc_final: 0.7446 (m-30) REVERT: e 4 VAL cc_start: 0.6241 (m) cc_final: 0.6025 (t) REVERT: e 21 ARG cc_start: 0.6209 (ptm-80) cc_final: 0.5926 (ptm-80) REVERT: e 25 GLU cc_start: 0.7512 (tt0) cc_final: 0.7287 (tt0) REVERT: e 140 ASP cc_start: 0.5374 (m-30) cc_final: 0.5127 (m-30) REVERT: e 141 MET cc_start: 0.5900 (mtp) cc_final: 0.5662 (mtp) REVERT: e 166 LYS cc_start: 0.6852 (mtmm) cc_final: 0.6091 (mmmt) REVERT: e 170 ARG cc_start: 0.6702 (mmt90) cc_final: 0.6457 (mtt-85) REVERT: e 184 ASP cc_start: 0.6390 (m-30) cc_final: 0.6126 (t0) REVERT: e 195 GLN cc_start: 0.5894 (mt0) cc_final: 0.5630 (mt0) REVERT: e 197 GLU cc_start: 0.6215 (tt0) cc_final: 0.5917 (pp20) REVERT: f 6 ASP cc_start: 0.5966 (m-30) cc_final: 0.5663 (m-30) REVERT: f 10 ASP cc_start: 0.6150 (m-30) cc_final: 0.5875 (m-30) REVERT: f 46 ASP cc_start: 0.4929 (t0) cc_final: 0.4578 (t0) REVERT: f 47 LYS cc_start: 0.6022 (mmtt) cc_final: 0.5173 (tptp) REVERT: f 50 LEU cc_start: 0.6392 (tp) cc_final: 0.6051 (tm) REVERT: f 51 ASP cc_start: 0.6317 (m-30) cc_final: 0.5710 (m-30) REVERT: f 83 TYR cc_start: 0.5866 (m-80) cc_final: 0.5568 (m-80) REVERT: f 98 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6061 (mt-10) REVERT: f 112 ARG cc_start: 0.5399 (mmm-85) cc_final: 0.5192 (mtt-85) REVERT: f 120 LYS cc_start: 0.6645 (mmmm) cc_final: 0.6412 (mmmt) REVERT: f 129 SER cc_start: 0.7948 (m) cc_final: 0.7552 (m) REVERT: f 133 ARG cc_start: 0.6077 (mtm-85) cc_final: 0.5553 (mtt180) REVERT: f 164 GLU cc_start: 0.6066 (pm20) cc_final: 0.5438 (tp30) REVERT: g 18 LYS cc_start: 0.5703 (ptmm) cc_final: 0.5167 (tptp) REVERT: g 75 MET cc_start: 0.6310 (ttt) cc_final: 0.6041 (tpp) REVERT: g 83 PHE cc_start: 0.6959 (m-80) cc_final: 0.6744 (m-80) REVERT: g 85 LYS cc_start: 0.6421 (mtpp) cc_final: 0.6126 (mtmm) REVERT: g 88 GLN cc_start: 0.6814 (pt0) cc_final: 0.6339 (pt0) REVERT: g 106 SER cc_start: 0.7429 (m) cc_final: 0.6882 (p) REVERT: g 163 ARG cc_start: 0.7881 (ptp-170) cc_final: 0.7589 (ptp90) REVERT: i 1 MET cc_start: 0.5622 (ppp) cc_final: 0.4837 (ptt) REVERT: i 31 GLU cc_start: 0.7372 (tp30) cc_final: 0.7113 (tp30) REVERT: i 49 ASP cc_start: 0.8135 (t0) cc_final: 0.7730 (t0) REVERT: i 52 ASP cc_start: 0.8442 (m-30) cc_final: 0.8130 (m-30) REVERT: i 85 LYS cc_start: 0.8373 (mttm) cc_final: 0.8147 (mtpt) REVERT: i 98 GLU cc_start: 0.7505 (mp0) cc_final: 0.7176 (mp0) REVERT: j 9 ASN cc_start: 0.8346 (m-40) cc_final: 0.7915 (m-40) REVERT: j 17 ARG cc_start: 0.7613 (mmt90) cc_final: 0.7105 (mmt90) REVERT: j 51 LYS cc_start: 0.7476 (mttp) cc_final: 0.6959 (mmtm) REVERT: j 105 ARG cc_start: 0.6519 (ttm-80) cc_final: 0.6280 (ttm-80) REVERT: j 113 MET cc_start: 0.6298 (mmm) cc_final: 0.5874 (mmm) REVERT: j 116 ILE cc_start: 0.7714 (mm) cc_final: 0.7340 (tp) REVERT: k 1 MET cc_start: 0.6713 (ttp) cc_final: 0.6413 (ttp) REVERT: k 7 SER cc_start: 0.8161 (p) cc_final: 0.7947 (p) REVERT: k 14 LYS cc_start: 0.7888 (ttpt) cc_final: 0.7590 (tttp) REVERT: k 69 ARG cc_start: 0.7541 (mtp85) cc_final: 0.7090 (mtp-110) REVERT: k 77 ILE cc_start: 0.8324 (mm) cc_final: 0.8030 (mm) REVERT: k 78 ARG cc_start: 0.7066 (mtp85) cc_final: 0.6593 (mtp85) REVERT: k 104 GLN cc_start: 0.8123 (mm110) cc_final: 0.7482 (mt0) REVERT: k 129 LYS cc_start: 0.6812 (mppt) cc_final: 0.6565 (mtmm) REVERT: l 55 ARG cc_start: 0.7807 (tpt170) cc_final: 0.6460 (ttm110) REVERT: l 63 ILE cc_start: 0.8190 (mm) cc_final: 0.7974 (mt) REVERT: l 127 LYS cc_start: 0.7632 (ttmt) cc_final: 0.7166 (tptm) REVERT: l 133 LYS cc_start: 0.7483 (ptmt) cc_final: 0.6997 (pptt) REVERT: m 27 SER cc_start: 0.8374 (m) cc_final: 0.8025 (t) REVERT: m 110 MET cc_start: 0.8379 (mmm) cc_final: 0.8156 (mmm) REVERT: m 117 ASP cc_start: 0.7529 (p0) cc_final: 0.6917 (p0) REVERT: n 13 ARG cc_start: 0.6898 (ttm-80) cc_final: 0.6181 (ttt180) REVERT: n 16 ARG cc_start: 0.7079 (mmp80) cc_final: 0.6695 (mmp-170) REVERT: n 38 GLN cc_start: 0.7882 (mt0) cc_final: 0.7213 (mt0) REVERT: n 46 GLU cc_start: 0.6584 (pt0) cc_final: 0.6163 (tt0) REVERT: o 5 ILE cc_start: 0.7874 (mm) cc_final: 0.7627 (mp) REVERT: o 27 GLU cc_start: 0.7377 (tt0) cc_final: 0.7147 (tt0) REVERT: o 43 PHE cc_start: 0.8300 (t80) cc_final: 0.7758 (t80) REVERT: o 87 LYS cc_start: 0.7710 (mmtm) cc_final: 0.7380 (mmmt) REVERT: o 111 LYS cc_start: 0.7696 (ttpt) cc_final: 0.7159 (tttp) REVERT: p 59 GLN cc_start: 0.8188 (tt0) cc_final: 0.7925 (tt0) REVERT: p 111 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6687 (mm-30) REVERT: q 1 MET cc_start: 0.6410 (ttt) cc_final: 0.6081 (ttt) REVERT: q 2 TYR cc_start: 0.8301 (p90) cc_final: 0.7939 (p90) REVERT: q 15 SER cc_start: 0.7781 (p) cc_final: 0.7394 (m) REVERT: q 23 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8255 (tp30) REVERT: q 40 MET cc_start: 0.7690 (ptm) cc_final: 0.7037 (ppp) REVERT: r 31 GLN cc_start: 0.7057 (mt0) cc_final: 0.6778 (mt0) REVERT: r 73 LYS cc_start: 0.8393 (ptpp) cc_final: 0.7995 (ptmm) REVERT: r 86 MET cc_start: 0.7738 (ttm) cc_final: 0.7127 (ttp) REVERT: r 92 ARG cc_start: 0.7423 (ttp-170) cc_final: 0.7219 (ttp-170) REVERT: s 50 LEU cc_start: 0.8374 (mt) cc_final: 0.8121 (mt) REVERT: t 41 LEU cc_start: 0.7673 (mt) cc_final: 0.7454 (mt) REVERT: t 62 GLU cc_start: 0.6813 (mp0) cc_final: 0.6473 (mp0) REVERT: u 25 LYS cc_start: 0.7812 (mtpp) cc_final: 0.7491 (mtmp) REVERT: u 34 LYS cc_start: 0.5325 (tppt) cc_final: 0.5062 (tptm) REVERT: u 38 LEU cc_start: 0.7762 (tp) cc_final: 0.7541 (mt) REVERT: u 43 ASP cc_start: 0.7321 (t70) cc_final: 0.7092 (t0) REVERT: u 45 ASP cc_start: 0.6945 (m-30) cc_final: 0.6709 (m-30) REVERT: u 68 LYS cc_start: 0.5375 (ttmm) cc_final: 0.5078 (tppt) REVERT: u 69 GLU cc_start: 0.6740 (pt0) cc_final: 0.6493 (pt0) REVERT: v 3 HIS cc_start: 0.7056 (m170) cc_final: 0.6640 (m-70) REVERT: v 25 ARG cc_start: 0.8004 (mmt90) cc_final: 0.7714 (mmt90) REVERT: v 64 ASP cc_start: 0.7971 (m-30) cc_final: 0.7423 (m-30) REVERT: v 72 LYS cc_start: 0.7717 (ptpp) cc_final: 0.7075 (pttt) REVERT: v 75 LYS cc_start: 0.7554 (mttp) cc_final: 0.7353 (mttt) REVERT: x 27 ASN cc_start: 0.7533 (m-40) cc_final: 0.7076 (m-40) REVERT: x 31 GLN cc_start: 0.6669 (tt0) cc_final: 0.6011 (mt0) REVERT: x 39 GLN cc_start: 0.6963 (mt0) cc_final: 0.6345 (mt0) REVERT: x 44 LYS cc_start: 0.7130 (ttmt) cc_final: 0.6707 (tppt) REVERT: x 45 GLN cc_start: 0.6395 (mt0) cc_final: 0.5860 (mt0) REVERT: x 52 ARG cc_start: 0.7358 (ttm110) cc_final: 0.7013 (ttp-170) REVERT: x 54 LYS cc_start: 0.6685 (mttm) cc_final: 0.6300 (mtpp) REVERT: y 6 LYS cc_start: 0.7288 (mmtp) cc_final: 0.7081 (mmtt) REVERT: y 16 ARG cc_start: 0.7896 (mmt180) cc_final: 0.7477 (mmt180) REVERT: y 56 LYS cc_start: 0.7974 (ttpt) cc_final: 0.7400 (ttmp) REVERT: z 31 ASP cc_start: 0.7689 (t70) cc_final: 0.7372 (t70) REVERT: z 46 ASP cc_start: 0.6923 (m-30) cc_final: 0.6235 (t0) REVERT: 0 33 LYS cc_start: 0.7174 (mmmm) cc_final: 0.6964 (mmtm) REVERT: 0 37 LYS cc_start: 0.7890 (mtpp) cc_final: 0.7642 (mtpp) REVERT: 0 45 GLN cc_start: 0.7639 (mm110) cc_final: 0.7350 (mm110) REVERT: 0 53 LYS cc_start: 0.7040 (mtmm) cc_final: 0.6272 (ptpp) REVERT: 1 41 ARG cc_start: 0.7489 (mtm-85) cc_final: 0.7187 (mpp-170) REVERT: 3 9 LYS cc_start: 0.7833 (mtmm) cc_final: 0.7509 (mtpm) REVERT: 3 15 LYS cc_start: 0.7808 (mttm) cc_final: 0.7564 (mttm) REVERT: 3 17 VAL cc_start: 0.8419 (p) cc_final: 0.8020 (m) outliers start: 4 outliers final: 0 residues processed: 1056 average time/residue: 2.3409 time to fit residues: 3429.3500 Evaluate side-chains 886 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 886 time to evaluate : 5.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 835 optimal weight: 5.9990 chunk 750 optimal weight: 0.0870 chunk 416 optimal weight: 10.0000 chunk 256 optimal weight: 5.9990 chunk 506 optimal weight: 3.9990 chunk 400 optimal weight: 10.0000 chunk 775 optimal weight: 6.9990 chunk 300 optimal weight: 8.9990 chunk 471 optimal weight: 30.0000 chunk 577 optimal weight: 0.9980 chunk 899 optimal weight: 0.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN D 54 GLN D 196 ASN E 19 ASN E 43 ASN E 61 GLN E 78 ASN E 97 GLN E 148 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 HIS H 18 GLN J 64 GLN L 112 GLN N 60 GLN O 40 GLN O 80 GLN ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 251 GLN ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 52 ASN ** g 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 58 ASN l 22 GLN m 18 GLN o 75 GLN p 56 GLN q 6 GLN q 18 GLN s 59 ASN t 66 GLN x 20 ASN x 25 GLN 1 29 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 153976 Z= 0.173 Angle : 0.663 15.365 230432 Z= 0.369 Chirality : 0.035 0.375 29298 Planarity : 0.007 0.133 12266 Dihedral : 23.035 179.800 77213 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.14 % Favored : 96.81 % Rotamer: Outliers : 1.77 % Allowed : 9.01 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.11), residues: 5480 helix: 1.43 (0.12), residues: 1852 sheet: 0.01 (0.16), residues: 1077 loop : -0.50 (0.12), residues: 2551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 201 HIS 0.010 0.001 HIS c 53 PHE 0.021 0.001 PHE d 118 TYR 0.016 0.002 TYR 4 9 ARG 0.008 0.001 ARG 3 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 955 time to evaluate : 5.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 LYS cc_start: 0.1187 (mptt) cc_final: 0.0608 (pptt) REVERT: B 49 MET cc_start: 0.2263 (ptt) cc_final: 0.1608 (mpm) REVERT: C 27 LYS cc_start: 0.5779 (ttpt) cc_final: 0.5313 (tttm) REVERT: C 28 GLU cc_start: 0.5707 (mp0) cc_final: 0.5192 (pm20) REVERT: C 72 ARG cc_start: 0.5826 (mtp85) cc_final: 0.5250 (mtt-85) REVERT: C 88 ARG cc_start: 0.5472 (tmm-80) cc_final: 0.5182 (ttt-90) REVERT: C 100 GLN cc_start: 0.6956 (tt0) cc_final: 0.6752 (tt0) REVERT: C 110 GLU cc_start: 0.6701 (mp0) cc_final: 0.6413 (mp0) REVERT: C 127 ARG cc_start: 0.6703 (mtt90) cc_final: 0.5936 (mtm110) REVERT: C 129 MET cc_start: 0.5792 (mmm) cc_final: 0.5569 (mmm) REVERT: C 134 MET cc_start: 0.7775 (mtp) cc_final: 0.7173 (mtm) REVERT: C 144 LEU cc_start: 0.7311 (mm) cc_final: 0.6736 (mm) REVERT: C 161 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6471 (tp30) REVERT: C 183 ASP cc_start: 0.7513 (t0) cc_final: 0.7084 (t0) REVERT: C 188 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6072 (mm-30) REVERT: D 40 GLN cc_start: 0.7283 (pt0) cc_final: 0.6763 (pt0) REVERT: D 73 ARG cc_start: 0.6517 (ttp-170) cc_final: 0.6222 (ttp-110) REVERT: D 160 GLU cc_start: 0.5355 (mm-30) cc_final: 0.5141 (mp0) REVERT: D 184 ARG cc_start: 0.4251 (ptt90) cc_final: 0.3288 (ppt170) REVERT: D 185 LYS cc_start: 0.5732 (ttmm) cc_final: 0.5367 (mtpt) REVERT: E 23 LYS cc_start: 0.8219 (ptmt) cc_final: 0.7823 (ptmt) REVERT: E 54 ARG cc_start: 0.7461 (tpt-90) cc_final: 0.7093 (mmt90) REVERT: E 68 ARG cc_start: 0.7253 (ttm110) cc_final: 0.7004 (ttp-110) REVERT: E 93 ARG cc_start: 0.7590 (mtm-85) cc_final: 0.7106 (mtt-85) REVERT: E 134 ILE cc_start: 0.7939 (mt) cc_final: 0.7606 (mt) REVERT: F 9 MET cc_start: 0.7628 (mtm) cc_final: 0.7053 (mtt) REVERT: F 37 HIS cc_start: 0.6721 (m-70) cc_final: 0.6122 (m90) REVERT: F 39 LEU cc_start: 0.6860 (tm) cc_final: 0.6641 (tm) REVERT: F 54 LEU cc_start: 0.6800 (mp) cc_final: 0.6583 (mp) REVERT: F 62 MET cc_start: 0.7200 (mtp) cc_final: 0.6423 (mpp) REVERT: F 90 MET cc_start: 0.6036 (mtp) cc_final: 0.5730 (mtp) REVERT: F 102 MET cc_start: 0.5482 (mmm) cc_final: 0.5200 (mmm) REVERT: G 92 ARG cc_start: 0.5710 (mtm110) cc_final: 0.5053 (ptt90) REVERT: G 111 ARG cc_start: 0.5773 (mmt90) cc_final: 0.5410 (mtp-110) REVERT: G 116 MET cc_start: 0.7211 (tpt) cc_final: 0.6957 (tpt) REVERT: G 144 MET cc_start: 0.6497 (ttm) cc_final: 0.6148 (mtp) REVERT: H 76 GLN cc_start: 0.7497 (tt0) cc_final: 0.7074 (tt0) REVERT: H 96 MET cc_start: 0.7303 (ttm) cc_final: 0.6995 (ttm) REVERT: I 20 PHE cc_start: 0.7337 (m-80) cc_final: 0.6901 (m-80) REVERT: I 68 LYS cc_start: 0.7636 (mttp) cc_final: 0.7384 (mtpt) REVERT: I 97 GLU cc_start: 0.5338 (pm20) cc_final: 0.4951 (pm20) REVERT: I 98 LEU cc_start: 0.6855 (mt) cc_final: 0.6595 (mp) REVERT: I 110 GLN cc_start: 0.8059 (mm110) cc_final: 0.7821 (mm-40) REVERT: J 11 LYS cc_start: 0.7581 (mttt) cc_final: 0.7220 (mttp) REVERT: J 48 ARG cc_start: 0.8279 (mpt-90) cc_final: 0.8036 (mpt90) REVERT: J 66 GLU cc_start: 0.7711 (pt0) cc_final: 0.7171 (pp20) REVERT: J 73 LEU cc_start: 0.7517 (tp) cc_final: 0.7163 (tm) REVERT: J 88 MET cc_start: 0.3405 (mmt) cc_final: 0.3155 (mpt) REVERT: M 19 LEU cc_start: 0.7337 (mt) cc_final: 0.7004 (tp) REVERT: M 75 MET cc_start: 0.6174 (mmp) cc_final: 0.5614 (mtp) REVERT: M 93 ARG cc_start: 0.6111 (mmt90) cc_final: 0.5650 (mmt90) REVERT: M 95 LEU cc_start: 0.8013 (mt) cc_final: 0.7778 (mt) REVERT: M 108 THR cc_start: 0.7956 (t) cc_final: 0.7737 (m) REVERT: N 6 MET cc_start: 0.7560 (mmm) cc_final: 0.7186 (mmm) REVERT: N 21 PHE cc_start: 0.7032 (t80) cc_final: 0.6643 (t80) REVERT: N 86 GLU cc_start: 0.6707 (mt-10) cc_final: 0.6094 (tt0) REVERT: N 89 MET cc_start: 0.8185 (mmp) cc_final: 0.7870 (mmp) REVERT: O 26 GLU cc_start: 0.7327 (pm20) cc_final: 0.7002 (mp0) REVERT: O 33 THR cc_start: 0.8050 (m) cc_final: 0.7466 (p) REVERT: O 47 LYS cc_start: 0.7618 (mttp) cc_final: 0.7173 (mtmt) REVERT: O 48 LYS cc_start: 0.7712 (mmtm) cc_final: 0.7230 (mmtt) REVERT: O 62 GLN cc_start: 0.7514 (tt0) cc_final: 0.7087 (tt0) REVERT: O 71 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7398 (ttmm) REVERT: O 72 ARG cc_start: 0.6856 (ttp-110) cc_final: 0.6331 (ttm170) REVERT: O 89 ARG cc_start: 0.5497 (ptm-80) cc_final: 0.5011 (ptm160) REVERT: P 34 GLU cc_start: 0.7368 (tt0) cc_final: 0.7111 (tt0) REVERT: P 35 ARG cc_start: 0.7025 (ttp80) cc_final: 0.6537 (ttt90) REVERT: P 63 GLN cc_start: 0.5839 (tp40) cc_final: 0.4394 (mm110) REVERT: Q 30 LYS cc_start: 0.8238 (tttt) cc_final: 0.7787 (tttt) REVERT: Q 62 ARG cc_start: 0.7032 (ttp80) cc_final: 0.6688 (ttp80) REVERT: R 24 LYS cc_start: 0.6392 (mtmm) cc_final: 0.6136 (mtpt) REVERT: R 51 TYR cc_start: 0.6861 (m-80) cc_final: 0.5955 (m-80) REVERT: R 55 LEU cc_start: 0.7286 (tp) cc_final: 0.6843 (tp) REVERT: R 57 ARG cc_start: 0.7222 (mtm-85) cc_final: 0.6986 (ttm110) REVERT: R 61 ARG cc_start: 0.7149 (mtt90) cc_final: 0.6784 (mtt90) REVERT: S 6 LYS cc_start: 0.6928 (pttt) cc_final: 0.6655 (pttt) REVERT: S 43 ASN cc_start: 0.6131 (p0) cc_final: 0.5862 (p0) REVERT: S 44 MET cc_start: 0.6038 (mtp) cc_final: 0.5599 (ttm) REVERT: S 51 VAL cc_start: 0.6791 (p) cc_final: 0.6475 (t) REVERT: S 73 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6707 (mt-10) REVERT: T 16 LYS cc_start: 0.6631 (ttpp) cc_final: 0.6285 (mttp) REVERT: T 24 ARG cc_start: 0.6672 (mmp80) cc_final: 0.5703 (mtt-85) REVERT: T 27 MET cc_start: 0.6463 (tmm) cc_final: 0.5599 (ttp) REVERT: T 31 PHE cc_start: 0.7109 (m-80) cc_final: 0.6787 (m-80) REVERT: c 5 LYS cc_start: 0.7942 (mtpp) cc_final: 0.7331 (mttm) REVERT: c 26 LYS cc_start: 0.8350 (mttm) cc_final: 0.7914 (mttt) REVERT: c 28 LYS cc_start: 0.7180 (mmtt) cc_final: 0.6950 (mmtp) REVERT: c 66 ASP cc_start: 0.7939 (t0) cc_final: 0.7584 (t0) REVERT: c 97 LYS cc_start: 0.7059 (ttmm) cc_final: 0.6703 (mttt) REVERT: c 111 LYS cc_start: 0.7159 (pttm) cc_final: 0.6599 (pttm) REVERT: c 184 VAL cc_start: 0.8293 (m) cc_final: 0.8043 (p) REVERT: c 185 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6427 (mp0) REVERT: c 194 GLU cc_start: 0.7299 (mt-10) cc_final: 0.7064 (mt-10) REVERT: c 269 ARG cc_start: 0.7302 (ttm-80) cc_final: 0.7019 (ttt90) REVERT: d 105 LYS cc_start: 0.7698 (mmtp) cc_final: 0.7418 (mttm) REVERT: e 5 LEU cc_start: 0.4745 (OUTLIER) cc_final: 0.4525 (mp) REVERT: e 21 ARG cc_start: 0.6344 (ptm-80) cc_final: 0.6070 (ptm-80) REVERT: e 25 GLU cc_start: 0.7376 (tt0) cc_final: 0.7166 (tt0) REVERT: e 111 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7164 (mm-30) REVERT: e 114 ARG cc_start: 0.7033 (mtm-85) cc_final: 0.6630 (mtm-85) REVERT: e 115 GLN cc_start: 0.7069 (mt0) cc_final: 0.6865 (mt0) REVERT: e 141 MET cc_start: 0.5843 (mtp) cc_final: 0.5592 (mtp) REVERT: e 166 LYS cc_start: 0.6636 (mtmm) cc_final: 0.5974 (mmmt) REVERT: e 195 GLN cc_start: 0.5828 (mt0) cc_final: 0.5480 (mt0) REVERT: e 198 GLU cc_start: 0.5716 (OUTLIER) cc_final: 0.5266 (mt-10) REVERT: f 46 ASP cc_start: 0.5151 (t0) cc_final: 0.4908 (t0) REVERT: f 47 LYS cc_start: 0.5954 (mmtt) cc_final: 0.5509 (mtpm) REVERT: f 50 LEU cc_start: 0.6294 (tp) cc_final: 0.6087 (tm) REVERT: f 98 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6035 (mt-10) REVERT: f 112 ARG cc_start: 0.5325 (mmm-85) cc_final: 0.5059 (mtt-85) REVERT: f 120 LYS cc_start: 0.6734 (mmmm) cc_final: 0.6494 (mmmt) REVERT: f 133 ARG cc_start: 0.5876 (mtm-85) cc_final: 0.5595 (mtt180) REVERT: f 164 GLU cc_start: 0.5921 (pm20) cc_final: 0.5556 (pt0) REVERT: g 18 LYS cc_start: 0.5724 (ptmm) cc_final: 0.5236 (tptp) REVERT: g 29 LYS cc_start: 0.4454 (ptpp) cc_final: 0.4202 (ptpt) REVERT: g 88 GLN cc_start: 0.6620 (pt0) cc_final: 0.6071 (pt0) REVERT: g 89 LEU cc_start: 0.7936 (mt) cc_final: 0.7673 (mm) REVERT: g 102 VAL cc_start: 0.6968 (p) cc_final: 0.6751 (t) REVERT: i 49 ASP cc_start: 0.8162 (t0) cc_final: 0.7825 (t0) REVERT: i 95 ARG cc_start: 0.7163 (ttt-90) cc_final: 0.6137 (mtm180) REVERT: i 98 GLU cc_start: 0.7526 (mp0) cc_final: 0.7264 (mp0) REVERT: j 17 ARG cc_start: 0.7639 (mmt90) cc_final: 0.7291 (mmt90) REVERT: j 37 ASP cc_start: 0.8017 (m-30) cc_final: 0.7816 (m-30) REVERT: j 51 LYS cc_start: 0.7489 (mttp) cc_final: 0.6969 (mmtm) REVERT: j 111 LYS cc_start: 0.6432 (ttpt) cc_final: 0.6178 (ttpt) REVERT: j 113 MET cc_start: 0.6262 (mmm) cc_final: 0.6014 (mmm) REVERT: j 116 ILE cc_start: 0.7587 (mm) cc_final: 0.7042 (mt) REVERT: k 78 ARG cc_start: 0.7169 (mtp85) cc_final: 0.6699 (mtp85) REVERT: k 104 GLN cc_start: 0.8110 (mm110) cc_final: 0.7519 (mt0) REVERT: k 106 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7218 (mm-30) REVERT: k 129 LYS cc_start: 0.6939 (mppt) cc_final: 0.6697 (mtmm) REVERT: l 44 ARG cc_start: 0.7732 (mtt-85) cc_final: 0.7407 (mmt-90) REVERT: l 55 ARG cc_start: 0.7573 (tpt170) cc_final: 0.6317 (ttm110) REVERT: l 127 LYS cc_start: 0.7595 (ttmt) cc_final: 0.7141 (tptm) REVERT: l 133 LYS cc_start: 0.7557 (ptmt) cc_final: 0.7137 (pptt) REVERT: m 110 MET cc_start: 0.8305 (mmm) cc_final: 0.8043 (mmm) REVERT: m 117 ASP cc_start: 0.7622 (p0) cc_final: 0.7074 (p0) REVERT: n 13 ARG cc_start: 0.6916 (ttm-80) cc_final: 0.6232 (ttm170) REVERT: n 16 ARG cc_start: 0.7096 (mmp80) cc_final: 0.6297 (mmt90) REVERT: n 46 GLU cc_start: 0.6722 (pt0) cc_final: 0.6204 (tt0) REVERT: n 76 LYS cc_start: 0.6541 (tttt) cc_final: 0.6094 (tmtm) REVERT: o 27 GLU cc_start: 0.7355 (tt0) cc_final: 0.7004 (tt0) REVERT: o 43 PHE cc_start: 0.8240 (t80) cc_final: 0.7653 (t80) REVERT: o 44 GLU cc_start: 0.7344 (tp30) cc_final: 0.6998 (tp30) REVERT: o 111 LYS cc_start: 0.7687 (ttpt) cc_final: 0.7166 (tttp) REVERT: p 59 GLN cc_start: 0.8201 (tt0) cc_final: 0.7953 (tt0) REVERT: p 87 SER cc_start: 0.7440 (p) cc_final: 0.7180 (t) REVERT: p 111 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6581 (mm-30) REVERT: q 15 SER cc_start: 0.7839 (p) cc_final: 0.7452 (m) REVERT: q 22 LEU cc_start: 0.8451 (mt) cc_final: 0.8160 (mp) REVERT: q 40 MET cc_start: 0.7561 (ptm) cc_final: 0.6862 (ppp) REVERT: q 73 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7651 (mttp) REVERT: r 8 ARG cc_start: 0.7958 (mtp-110) cc_final: 0.7728 (mtp-110) REVERT: r 31 GLN cc_start: 0.6908 (mt0) cc_final: 0.6687 (mt0) REVERT: r 73 LYS cc_start: 0.8372 (ptpp) cc_final: 0.7957 (ptmm) REVERT: r 86 MET cc_start: 0.7653 (ttm) cc_final: 0.7062 (ttp) REVERT: r 94 ASP cc_start: 0.8166 (m-30) cc_final: 0.7918 (m-30) REVERT: s 50 LEU cc_start: 0.8403 (mt) cc_final: 0.8150 (mt) REVERT: t 10 GLU cc_start: 0.6846 (tp30) cc_final: 0.6578 (tp30) REVERT: t 62 GLU cc_start: 0.6789 (mp0) cc_final: 0.6490 (mp0) REVERT: u 3 THR cc_start: 0.7331 (m) cc_final: 0.7049 (t) REVERT: u 10 LYS cc_start: 0.6505 (mmmm) cc_final: 0.6118 (mmtm) REVERT: u 25 LYS cc_start: 0.7750 (mtpp) cc_final: 0.7421 (mtmp) REVERT: u 34 LYS cc_start: 0.5498 (tppt) cc_final: 0.5278 (tptm) REVERT: u 38 LEU cc_start: 0.7745 (tp) cc_final: 0.7543 (mt) REVERT: u 45 ASP cc_start: 0.7082 (m-30) cc_final: 0.6781 (m-30) REVERT: u 48 MET cc_start: 0.7417 (tpt) cc_final: 0.6961 (tpt) REVERT: u 68 LYS cc_start: 0.5546 (ttmm) cc_final: 0.5151 (tppt) REVERT: u 69 GLU cc_start: 0.6668 (pt0) cc_final: 0.6466 (pt0) REVERT: v 3 HIS cc_start: 0.6986 (m170) cc_final: 0.6584 (m-70) REVERT: v 25 ARG cc_start: 0.7923 (mmt90) cc_final: 0.7630 (mmt90) REVERT: v 64 ASP cc_start: 0.8044 (m-30) cc_final: 0.7385 (m-30) REVERT: v 72 LYS cc_start: 0.7709 (ptpp) cc_final: 0.7045 (pttt) REVERT: w 11 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.6297 (mtp85) REVERT: x 23 ARG cc_start: 0.7286 (mtm-85) cc_final: 0.6835 (mtt90) REVERT: x 27 ASN cc_start: 0.7585 (m-40) cc_final: 0.7126 (m-40) REVERT: x 31 GLN cc_start: 0.6395 (tt0) cc_final: 0.5996 (mt0) REVERT: x 39 GLN cc_start: 0.6955 (mt0) cc_final: 0.6664 (mt0) REVERT: x 45 GLN cc_start: 0.6409 (mt0) cc_final: 0.5764 (mt0) REVERT: x 46 VAL cc_start: 0.7507 (t) cc_final: 0.7102 (p) REVERT: x 52 ARG cc_start: 0.7278 (ttm110) cc_final: 0.6947 (ttp-110) REVERT: x 54 LYS cc_start: 0.6610 (mttm) cc_final: 0.6312 (mtpp) REVERT: y 56 LYS cc_start: 0.8107 (ttpt) cc_final: 0.7481 (ttmp) REVERT: z 31 ASP cc_start: 0.7954 (t70) cc_final: 0.7494 (t70) REVERT: 0 33 LYS cc_start: 0.7101 (mmmm) cc_final: 0.6845 (mmtm) REVERT: 0 45 GLN cc_start: 0.7546 (mm110) cc_final: 0.7246 (mm110) REVERT: 0 51 GLU cc_start: 0.7407 (tt0) cc_final: 0.7179 (tt0) REVERT: 0 53 LYS cc_start: 0.7013 (mtmm) cc_final: 0.6787 (mtmm) REVERT: 1 1 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7261 (mmm) REVERT: 1 41 ARG cc_start: 0.7569 (mtm-85) cc_final: 0.7257 (mpp-170) REVERT: 2 52 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6754 (tptp) REVERT: 3 9 LYS cc_start: 0.7829 (mtmm) cc_final: 0.7468 (mtpm) REVERT: 3 17 VAL cc_start: 0.8466 (p) cc_final: 0.8157 (m) REVERT: 4 60 PHE cc_start: 0.6337 (t80) cc_final: 0.5923 (t80) outliers start: 81 outliers final: 41 residues processed: 987 average time/residue: 2.3239 time to fit residues: 3206.2484 Evaluate side-chains 929 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 881 time to evaluate : 5.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 97 LYS Chi-restraints excluded: chain O residue 68 ASP Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain O residue 83 GLU Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 144 GLU Chi-restraints excluded: chain e residue 198 GLU Chi-restraints excluded: chain f residue 147 ASP Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain m residue 57 THR Chi-restraints excluded: chain n residue 91 SER Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 48 LYS Chi-restraints excluded: chain q residue 51 VAL Chi-restraints excluded: chain q residue 73 LYS Chi-restraints excluded: chain r residue 22 ASP Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain u residue 64 VAL Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain w residue 11 ARG Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain z residue 30 VAL Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 2 residue 52 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 499 optimal weight: 10.0000 chunk 279 optimal weight: 5.9990 chunk 748 optimal weight: 20.0000 chunk 612 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 900 optimal weight: 9.9990 chunk 972 optimal weight: 20.0000 chunk 802 optimal weight: 5.9990 chunk 893 optimal weight: 10.0000 chunk 307 optimal weight: 7.9990 chunk 722 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN D 36 GLN D 54 GLN D 116 GLN D 198 HIS E 43 ASN E 78 ASN E 97 GLN E 148 ASN F 58 HIS G 142 HIS H 18 GLN H 38 ASN L 112 GLN N 60 GLN O 37 ASN O 80 GLN ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 64 ASN d 32 ASN e 136 GLN g 38 ASN ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 3 GLN m 18 GLN n 38 GLN q 6 GLN q 18 GLN t 46 GLN t 66 GLN x 20 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 153976 Z= 0.369 Angle : 0.831 19.312 230432 Z= 0.440 Chirality : 0.044 0.368 29298 Planarity : 0.008 0.154 12266 Dihedral : 23.197 178.379 77213 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.01 % Favored : 95.88 % Rotamer: Outliers : 3.02 % Allowed : 12.57 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.11), residues: 5480 helix: 0.99 (0.12), residues: 1834 sheet: -0.13 (0.15), residues: 1072 loop : -0.70 (0.12), residues: 2574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP c 248 HIS 0.009 0.002 HIS B 168 PHE 0.028 0.003 PHE S 10 TYR 0.026 0.003 TYR f 83 ARG 0.013 0.001 ARG c 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1018 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 880 time to evaluate : 6.011 Fit side-chains REVERT: B 37 LYS cc_start: 0.0879 (mptt) cc_final: 0.0591 (pptt) REVERT: B 49 MET cc_start: 0.2199 (ptt) cc_final: 0.1624 (mpm) REVERT: B 100 MET cc_start: 0.3456 (mmt) cc_final: 0.3119 (mmm) REVERT: C 27 LYS cc_start: 0.6104 (ttpt) cc_final: 0.5559 (tttm) REVERT: C 28 GLU cc_start: 0.6172 (mp0) cc_final: 0.5375 (pm20) REVERT: C 100 GLN cc_start: 0.6822 (tt0) cc_final: 0.6420 (tt0) REVERT: C 110 GLU cc_start: 0.6664 (mp0) cc_final: 0.6361 (mp0) REVERT: C 127 ARG cc_start: 0.6710 (mtt90) cc_final: 0.5939 (mtm110) REVERT: C 134 MET cc_start: 0.7859 (mtp) cc_final: 0.7349 (mtm) REVERT: C 144 LEU cc_start: 0.7478 (mm) cc_final: 0.6840 (mm) REVERT: C 161 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6540 (tp30) REVERT: C 183 ASP cc_start: 0.7688 (t0) cc_final: 0.7411 (t0) REVERT: D 138 SER cc_start: 0.6896 (OUTLIER) cc_final: 0.6323 (t) REVERT: D 183 LYS cc_start: 0.5659 (mtmm) cc_final: 0.5070 (tmtm) REVERT: D 184 ARG cc_start: 0.4042 (ptt90) cc_final: 0.3294 (ppt170) REVERT: E 23 LYS cc_start: 0.8151 (ptmt) cc_final: 0.7864 (ptmt) REVERT: E 45 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.5879 (ttp80) REVERT: E 93 ARG cc_start: 0.7554 (mtm-85) cc_final: 0.7226 (ptp-110) REVERT: E 146 ASN cc_start: 0.6142 (m-40) cc_final: 0.5635 (p0) REVERT: E 147 MET cc_start: 0.7845 (ttp) cc_final: 0.7487 (ttp) REVERT: F 2 ARG cc_start: 0.7092 (mtt180) cc_final: 0.6848 (mtm-85) REVERT: F 9 MET cc_start: 0.7659 (mtm) cc_final: 0.7018 (mtt) REVERT: F 37 HIS cc_start: 0.6788 (m-70) cc_final: 0.6226 (m170) REVERT: F 54 LEU cc_start: 0.6660 (mp) cc_final: 0.6441 (mp) REVERT: F 62 MET cc_start: 0.7235 (mtp) cc_final: 0.6597 (mpp) REVERT: F 90 MET cc_start: 0.6081 (mtp) cc_final: 0.5770 (mtp) REVERT: F 102 MET cc_start: 0.5396 (mmm) cc_final: 0.5008 (mmm) REVERT: G 40 GLU cc_start: 0.6465 (tt0) cc_final: 0.6261 (tt0) REVERT: G 44 TYR cc_start: 0.7079 (m-10) cc_final: 0.6786 (m-10) REVERT: G 111 ARG cc_start: 0.5505 (mmt90) cc_final: 0.5274 (mtp-110) REVERT: G 144 MET cc_start: 0.6625 (OUTLIER) cc_final: 0.6254 (mtp) REVERT: H 96 MET cc_start: 0.7315 (ttm) cc_final: 0.6936 (ttm) REVERT: I 20 PHE cc_start: 0.7219 (m-80) cc_final: 0.6726 (m-80) REVERT: I 64 TYR cc_start: 0.6854 (t80) cc_final: 0.6458 (t80) REVERT: I 68 LYS cc_start: 0.7736 (mttp) cc_final: 0.7452 (mtpt) REVERT: I 98 LEU cc_start: 0.7024 (mt) cc_final: 0.6774 (mp) REVERT: J 11 LYS cc_start: 0.7707 (mttt) cc_final: 0.7312 (mttp) REVERT: J 73 LEU cc_start: 0.7533 (tp) cc_final: 0.7160 (tm) REVERT: J 88 MET cc_start: 0.3886 (mmt) cc_final: 0.3508 (mpt) REVERT: M 19 LEU cc_start: 0.7372 (mt) cc_final: 0.7130 (mt) REVERT: M 75 MET cc_start: 0.6008 (mmp) cc_final: 0.5549 (mtm) REVERT: M 93 ARG cc_start: 0.6429 (mmt90) cc_final: 0.5676 (mmt180) REVERT: M 95 LEU cc_start: 0.8105 (mt) cc_final: 0.7872 (mt) REVERT: N 6 MET cc_start: 0.7711 (mmm) cc_final: 0.7462 (mmm) REVERT: N 21 PHE cc_start: 0.6861 (t80) cc_final: 0.6558 (t80) REVERT: N 86 GLU cc_start: 0.6707 (mt-10) cc_final: 0.6233 (tt0) REVERT: O 26 GLU cc_start: 0.7289 (pm20) cc_final: 0.7063 (mp0) REVERT: O 47 LYS cc_start: 0.7711 (mttp) cc_final: 0.7273 (mtmt) REVERT: O 48 LYS cc_start: 0.7829 (mmtm) cc_final: 0.7338 (mmtt) REVERT: O 59 MET cc_start: 0.7942 (mtt) cc_final: 0.7710 (mtt) REVERT: O 62 GLN cc_start: 0.7705 (tt0) cc_final: 0.7400 (tt0) REVERT: O 89 ARG cc_start: 0.5643 (ptm-80) cc_final: 0.5180 (ptm160) REVERT: P 35 ARG cc_start: 0.7038 (ttp80) cc_final: 0.6534 (ttt90) REVERT: Q 27 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6885 (ptm-80) REVERT: Q 30 LYS cc_start: 0.8317 (tttt) cc_final: 0.7848 (tttm) REVERT: Q 60 GLU cc_start: 0.7255 (tt0) cc_final: 0.6698 (tt0) REVERT: R 24 LYS cc_start: 0.6464 (mtmm) cc_final: 0.6040 (mtpt) REVERT: R 51 TYR cc_start: 0.6981 (m-80) cc_final: 0.6273 (m-80) REVERT: R 55 LEU cc_start: 0.7310 (tp) cc_final: 0.6976 (tp) REVERT: R 57 ARG cc_start: 0.7281 (mtm-85) cc_final: 0.6975 (mtp180) REVERT: R 61 ARG cc_start: 0.7118 (mtt90) cc_final: 0.6757 (mtt180) REVERT: S 44 MET cc_start: 0.5895 (mtp) cc_final: 0.5371 (ttm) REVERT: S 73 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6623 (mt-10) REVERT: T 16 LYS cc_start: 0.6628 (ttpp) cc_final: 0.6273 (mttp) REVERT: T 24 ARG cc_start: 0.6637 (mmp80) cc_final: 0.5468 (mtt-85) REVERT: U 36 GLU cc_start: 0.6629 (tt0) cc_final: 0.5679 (mt-10) REVERT: c 5 LYS cc_start: 0.8008 (mtpp) cc_final: 0.7373 (mttm) REVERT: c 26 LYS cc_start: 0.8296 (mttm) cc_final: 0.7801 (mttt) REVERT: c 66 ASP cc_start: 0.8014 (t0) cc_final: 0.7769 (OUTLIER) REVERT: c 97 LYS cc_start: 0.7035 (ttmm) cc_final: 0.6686 (mttt) REVERT: c 111 LYS cc_start: 0.7294 (pttm) cc_final: 0.6707 (ptpp) REVERT: c 185 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6386 (tt0) REVERT: c 269 ARG cc_start: 0.7322 (ttm-80) cc_final: 0.6939 (ttt90) REVERT: d 2 ILE cc_start: 0.7157 (pt) cc_final: 0.6858 (pp) REVERT: d 185 ASN cc_start: 0.7781 (m110) cc_final: 0.7243 (m110) REVERT: e 21 ARG cc_start: 0.6104 (ptm-80) cc_final: 0.5793 (ptm-80) REVERT: e 25 GLU cc_start: 0.7312 (tt0) cc_final: 0.7090 (tt0) REVERT: e 111 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7144 (mm-30) REVERT: e 115 GLN cc_start: 0.7092 (mt0) cc_final: 0.6836 (mt0) REVERT: e 136 GLN cc_start: 0.6619 (tp-100) cc_final: 0.5923 (tm-30) REVERT: e 140 ASP cc_start: 0.5045 (m-30) cc_final: 0.4339 (m-30) REVERT: e 166 LYS cc_start: 0.6654 (mtmm) cc_final: 0.6029 (mmmt) REVERT: f 42 GLU cc_start: 0.5981 (pm20) cc_final: 0.5667 (pm20) REVERT: f 47 LYS cc_start: 0.6235 (mmtt) cc_final: 0.5705 (mtpm) REVERT: f 94 GLU cc_start: 0.6400 (tp30) cc_final: 0.6187 (tp30) REVERT: f 98 GLU cc_start: 0.6962 (mt-10) cc_final: 0.6021 (mt-10) REVERT: f 133 ARG cc_start: 0.5822 (mtm-85) cc_final: 0.5596 (mtm180) REVERT: f 164 GLU cc_start: 0.5825 (pm20) cc_final: 0.5479 (pt0) REVERT: g 18 LYS cc_start: 0.5884 (ptmm) cc_final: 0.5677 (tttt) REVERT: g 88 GLN cc_start: 0.6644 (pt0) cc_final: 0.6081 (pt0) REVERT: i 23 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7853 (mttp) REVERT: i 31 GLU cc_start: 0.7048 (tp30) cc_final: 0.6817 (tp30) REVERT: i 49 ASP cc_start: 0.8132 (t0) cc_final: 0.7833 (t0) REVERT: j 4 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7338 (mt-10) REVERT: j 17 ARG cc_start: 0.7636 (mmt90) cc_final: 0.7272 (mmt90) REVERT: j 37 ASP cc_start: 0.8031 (m-30) cc_final: 0.7800 (m-30) REVERT: j 51 LYS cc_start: 0.7432 (mttp) cc_final: 0.7092 (mttm) REVERT: j 111 LYS cc_start: 0.6691 (ttpt) cc_final: 0.6337 (ttpt) REVERT: j 113 MET cc_start: 0.6270 (mmm) cc_final: 0.5953 (mmm) REVERT: k 104 GLN cc_start: 0.8105 (mm110) cc_final: 0.7520 (mt0) REVERT: k 129 LYS cc_start: 0.6855 (mppt) cc_final: 0.6530 (mmpt) REVERT: l 7 THR cc_start: 0.7972 (p) cc_final: 0.7522 (p) REVERT: l 55 ARG cc_start: 0.7661 (tpt170) cc_final: 0.6452 (ttm110) REVERT: l 127 LYS cc_start: 0.7775 (ttmt) cc_final: 0.7256 (tptm) REVERT: m 110 MET cc_start: 0.8310 (mmm) cc_final: 0.8092 (mmm) REVERT: m 114 GLU cc_start: 0.8292 (pt0) cc_final: 0.7998 (pt0) REVERT: m 117 ASP cc_start: 0.7657 (p0) cc_final: 0.7257 (p0) REVERT: n 13 ARG cc_start: 0.6986 (ttm-80) cc_final: 0.6327 (ttm170) REVERT: n 16 ARG cc_start: 0.7252 (mmp80) cc_final: 0.6327 (mmt90) REVERT: n 46 GLU cc_start: 0.6629 (pt0) cc_final: 0.6358 (tt0) REVERT: n 76 LYS cc_start: 0.6567 (tttt) cc_final: 0.6160 (tmtm) REVERT: o 111 LYS cc_start: 0.7724 (ttpt) cc_final: 0.7164 (tttp) REVERT: p 59 GLN cc_start: 0.8329 (tt0) cc_final: 0.8065 (tt0) REVERT: q 22 LEU cc_start: 0.8371 (mt) cc_final: 0.8143 (mp) REVERT: q 40 MET cc_start: 0.7561 (ptm) cc_final: 0.7128 (ppp) REVERT: q 73 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7761 (mttp) REVERT: r 31 GLN cc_start: 0.6890 (mt0) cc_final: 0.6679 (mt0) REVERT: r 73 LYS cc_start: 0.8445 (ptpp) cc_final: 0.7938 (ptmm) REVERT: r 86 MET cc_start: 0.7734 (ttm) cc_final: 0.7132 (ttp) REVERT: t 10 GLU cc_start: 0.6658 (tp30) cc_final: 0.6139 (tp30) REVERT: t 26 LYS cc_start: 0.7078 (tttm) cc_final: 0.6717 (tttm) REVERT: t 47 LYS cc_start: 0.7066 (OUTLIER) cc_final: 0.6542 (mptm) REVERT: u 3 THR cc_start: 0.7257 (m) cc_final: 0.7004 (t) REVERT: u 25 LYS cc_start: 0.7618 (mtpp) cc_final: 0.7346 (mtmp) REVERT: u 34 LYS cc_start: 0.5500 (tppt) cc_final: 0.5291 (tptm) REVERT: u 38 LEU cc_start: 0.7769 (tp) cc_final: 0.7541 (mt) REVERT: u 41 GLU cc_start: 0.6675 (mt-10) cc_final: 0.6379 (mt-10) REVERT: u 45 ASP cc_start: 0.7058 (m-30) cc_final: 0.6773 (m-30) REVERT: u 68 LYS cc_start: 0.5511 (ttmm) cc_final: 0.5063 (tptt) REVERT: u 73 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7247 (tttm) REVERT: v 3 HIS cc_start: 0.7114 (m170) cc_final: 0.6707 (m-70) REVERT: v 25 ARG cc_start: 0.7964 (mmt90) cc_final: 0.7653 (mmt90) REVERT: v 64 ASP cc_start: 0.8000 (m-30) cc_final: 0.7409 (m-30) REVERT: v 72 LYS cc_start: 0.7855 (ptpp) cc_final: 0.7226 (ptmm) REVERT: x 23 ARG cc_start: 0.7227 (mtm-85) cc_final: 0.6808 (mtt90) REVERT: x 27 ASN cc_start: 0.7380 (m-40) cc_final: 0.6965 (m-40) REVERT: x 31 GLN cc_start: 0.6351 (tt0) cc_final: 0.5978 (mt0) REVERT: x 39 GLN cc_start: 0.6910 (mt0) cc_final: 0.6370 (mt0) REVERT: x 45 GLN cc_start: 0.6576 (mt0) cc_final: 0.5871 (mt0) REVERT: y 56 LYS cc_start: 0.8128 (ttpt) cc_final: 0.7456 (ttmp) REVERT: z 31 ASP cc_start: 0.8077 (t70) cc_final: 0.7620 (t70) REVERT: 0 45 GLN cc_start: 0.7666 (mm110) cc_final: 0.7398 (mm110) REVERT: 1 41 ARG cc_start: 0.7499 (mtm-85) cc_final: 0.7216 (mpp-170) REVERT: 2 15 LYS cc_start: 0.8334 (mptt) cc_final: 0.8088 (mptt) REVERT: 3 9 LYS cc_start: 0.7867 (mtmm) cc_final: 0.7550 (mtpp) REVERT: 3 12 ARG cc_start: 0.6570 (mtm110) cc_final: 0.6324 (mtp-110) REVERT: 3 17 VAL cc_start: 0.8358 (p) cc_final: 0.8141 (m) REVERT: 3 18 LYS cc_start: 0.7908 (tttm) cc_final: 0.7584 (tttt) REVERT: 4 22 MET cc_start: 0.6282 (mpp) cc_final: 0.6045 (mpt) REVERT: 4 60 PHE cc_start: 0.6417 (t80) cc_final: 0.6131 (t80) outliers start: 138 outliers final: 70 residues processed: 947 average time/residue: 2.3321 time to fit residues: 3084.8340 Evaluate side-chains 932 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 854 time to evaluate : 5.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 97 LYS Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain O residue 83 GLU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 27 ARG Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 144 GLU Chi-restraints excluded: chain e residue 199 MET Chi-restraints excluded: chain f residue 147 ASP Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 99 LYS Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 14 ASP Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain j residue 4 GLU Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain l residue 24 THR Chi-restraints excluded: chain m residue 36 THR Chi-restraints excluded: chain m residue 57 THR Chi-restraints excluded: chain n residue 91 SER Chi-restraints excluded: chain n residue 103 VAL Chi-restraints excluded: chain p residue 87 SER Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 48 LYS Chi-restraints excluded: chain q residue 73 LYS Chi-restraints excluded: chain r residue 22 ASP Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 35 ILE Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain u residue 64 VAL Chi-restraints excluded: chain u residue 73 LYS Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 30 VAL Chi-restraints excluded: chain 2 residue 59 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 889 optimal weight: 4.9990 chunk 677 optimal weight: 0.8980 chunk 467 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 chunk 429 optimal weight: 8.9990 chunk 604 optimal weight: 10.0000 chunk 903 optimal weight: 5.9990 chunk 956 optimal weight: 4.9990 chunk 472 optimal weight: 30.0000 chunk 856 optimal weight: 0.9980 chunk 257 optimal weight: 3.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN C 140 ASN D 40 GLN D 54 GLN D 71 GLN D 198 HIS E 19 ASN E 43 ASN E 61 GLN E 78 ASN E 97 GLN E 148 ASN G 142 HIS H 18 GLN J 64 GLN L 73 ASN L 112 GLN M 105 ASN N 60 GLN O 37 ASN O 80 GLN ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 45 HIS T 21 ASN g 38 ASN ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 58 ASN m 18 GLN n 38 GLN n 98 GLN ** o 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 6 GLN q 18 GLN t 46 GLN x 20 ASN x 25 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 153976 Z= 0.197 Angle : 0.666 14.792 230432 Z= 0.372 Chirality : 0.036 0.371 29298 Planarity : 0.007 0.136 12266 Dihedral : 23.018 179.718 77213 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.28 % Favored : 96.66 % Rotamer: Outliers : 2.99 % Allowed : 14.69 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.11), residues: 5480 helix: 1.24 (0.12), residues: 1867 sheet: -0.08 (0.15), residues: 1116 loop : -0.59 (0.12), residues: 2497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP c 248 HIS 0.005 0.001 HIS k 35 PHE 0.018 0.002 PHE S 10 TYR 0.018 0.002 TYR p 32 ARG 0.006 0.000 ARG s 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1020 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 883 time to evaluate : 5.930 Fit side-chains REVERT: B 37 LYS cc_start: 0.0968 (mptt) cc_final: 0.0667 (pptt) REVERT: B 49 MET cc_start: 0.2146 (OUTLIER) cc_final: 0.1723 (mpm) REVERT: C 28 GLU cc_start: 0.6185 (mp0) cc_final: 0.5539 (pm20) REVERT: C 100 GLN cc_start: 0.6963 (tt0) cc_final: 0.6517 (tt0) REVERT: C 110 GLU cc_start: 0.6659 (mp0) cc_final: 0.6350 (mp0) REVERT: C 127 ARG cc_start: 0.6580 (mtt90) cc_final: 0.5888 (mtm110) REVERT: C 144 LEU cc_start: 0.7460 (mm) cc_final: 0.6752 (mm) REVERT: C 161 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6356 (tp30) REVERT: C 183 ASP cc_start: 0.7523 (t0) cc_final: 0.7261 (t0) REVERT: D 47 ARG cc_start: 0.4918 (OUTLIER) cc_final: 0.4178 (ptp-170) REVERT: D 73 ARG cc_start: 0.6427 (ttp80) cc_final: 0.6136 (ttp-110) REVERT: D 116 GLN cc_start: 0.6106 (OUTLIER) cc_final: 0.4709 (tp40) REVERT: D 124 MET cc_start: 0.5676 (ttp) cc_final: 0.5382 (ttm) REVERT: D 138 SER cc_start: 0.6868 (OUTLIER) cc_final: 0.6314 (t) REVERT: D 183 LYS cc_start: 0.5579 (mtmm) cc_final: 0.4994 (tmtm) REVERT: D 184 ARG cc_start: 0.3985 (ptt90) cc_final: 0.3096 (ppt170) REVERT: D 200 ILE cc_start: 0.6537 (OUTLIER) cc_final: 0.6308 (mm) REVERT: E 23 LYS cc_start: 0.8144 (ptmt) cc_final: 0.7902 (ptmt) REVERT: E 26 LYS cc_start: 0.7692 (ttmt) cc_final: 0.7241 (tttp) REVERT: E 45 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.5897 (ttp80) REVERT: E 93 ARG cc_start: 0.7501 (mtm-85) cc_final: 0.7057 (mtt180) REVERT: E 146 ASN cc_start: 0.5780 (m-40) cc_final: 0.5428 (p0) REVERT: E 147 MET cc_start: 0.7819 (ttp) cc_final: 0.7404 (ttp) REVERT: F 2 ARG cc_start: 0.7023 (mtt180) cc_final: 0.6792 (mtm-85) REVERT: F 9 MET cc_start: 0.7587 (mtm) cc_final: 0.7016 (mtt) REVERT: F 37 HIS cc_start: 0.6749 (m-70) cc_final: 0.6197 (m170) REVERT: F 62 MET cc_start: 0.7101 (mtp) cc_final: 0.6351 (mpp) REVERT: F 102 MET cc_start: 0.5556 (mmm) cc_final: 0.5194 (mmm) REVERT: G 44 TYR cc_start: 0.7025 (m-10) cc_final: 0.6672 (m-10) REVERT: G 144 MET cc_start: 0.6565 (OUTLIER) cc_final: 0.6243 (mtp) REVERT: H 96 MET cc_start: 0.7299 (ttm) cc_final: 0.6904 (ttm) REVERT: I 20 PHE cc_start: 0.7274 (m-80) cc_final: 0.6768 (m-80) REVERT: I 36 GLU cc_start: 0.6185 (mp0) cc_final: 0.5905 (mp0) REVERT: I 68 LYS cc_start: 0.7769 (mttp) cc_final: 0.7433 (mtpt) REVERT: I 98 LEU cc_start: 0.6909 (mt) cc_final: 0.6624 (mp) REVERT: J 11 LYS cc_start: 0.7721 (mttt) cc_final: 0.7409 (mttp) REVERT: J 73 LEU cc_start: 0.7531 (tp) cc_final: 0.7139 (tm) REVERT: J 88 MET cc_start: 0.3993 (mmt) cc_final: 0.3504 (mpt) REVERT: L 75 GLN cc_start: 0.6922 (pt0) cc_final: 0.6420 (pt0) REVERT: M 19 LEU cc_start: 0.7375 (mt) cc_final: 0.7130 (mt) REVERT: M 31 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7613 (ttmm) REVERT: M 75 MET cc_start: 0.5951 (mmp) cc_final: 0.5500 (mtm) REVERT: M 93 ARG cc_start: 0.6376 (mmt90) cc_final: 0.5612 (mmt180) REVERT: M 95 LEU cc_start: 0.8117 (mt) cc_final: 0.7881 (mt) REVERT: N 6 MET cc_start: 0.7649 (mmm) cc_final: 0.7333 (mmm) REVERT: N 21 PHE cc_start: 0.6820 (t80) cc_final: 0.6524 (t80) REVERT: N 86 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6328 (mt-10) REVERT: O 47 LYS cc_start: 0.7672 (mttp) cc_final: 0.7210 (mtmt) REVERT: O 48 LYS cc_start: 0.7670 (mmtm) cc_final: 0.7295 (mmtt) REVERT: O 62 GLN cc_start: 0.7702 (tt0) cc_final: 0.7426 (tt0) REVERT: O 71 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7374 (ttmm) REVERT: P 35 ARG cc_start: 0.7034 (ttp80) cc_final: 0.6481 (ttt90) REVERT: P 63 GLN cc_start: 0.5704 (tp40) cc_final: 0.4382 (mm110) REVERT: Q 30 LYS cc_start: 0.8209 (tttt) cc_final: 0.7804 (tttm) REVERT: Q 60 GLU cc_start: 0.7147 (tt0) cc_final: 0.6745 (tt0) REVERT: R 24 LYS cc_start: 0.6438 (mtmm) cc_final: 0.6129 (mtpt) REVERT: R 51 TYR cc_start: 0.6923 (m-80) cc_final: 0.6205 (m-80) REVERT: R 55 LEU cc_start: 0.7307 (tp) cc_final: 0.6949 (tp) REVERT: R 57 ARG cc_start: 0.7279 (mtm-85) cc_final: 0.6875 (mtp180) REVERT: R 61 ARG cc_start: 0.7110 (mtt90) cc_final: 0.6174 (mtt-85) REVERT: S 44 MET cc_start: 0.5736 (mtp) cc_final: 0.5438 (ttm) REVERT: S 73 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6691 (mt-10) REVERT: T 16 LYS cc_start: 0.6614 (ttpp) cc_final: 0.6264 (mttp) REVERT: T 24 ARG cc_start: 0.6696 (mmp80) cc_final: 0.5554 (mtt-85) REVERT: U 36 GLU cc_start: 0.6570 (tt0) cc_final: 0.5613 (mt-10) REVERT: c 5 LYS cc_start: 0.7923 (mtpp) cc_final: 0.7327 (mttm) REVERT: c 26 LYS cc_start: 0.8257 (mttm) cc_final: 0.7766 (mttt) REVERT: c 66 ASP cc_start: 0.7993 (t0) cc_final: 0.7738 (t0) REVERT: c 97 LYS cc_start: 0.7005 (ttmm) cc_final: 0.6672 (mttt) REVERT: c 111 LYS cc_start: 0.7302 (pttm) cc_final: 0.6710 (ptpp) REVERT: c 184 VAL cc_start: 0.8407 (m) cc_final: 0.8204 (p) REVERT: c 185 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6411 (tt0) REVERT: c 269 ARG cc_start: 0.7264 (ttm-80) cc_final: 0.6946 (ttt90) REVERT: d 2 ILE cc_start: 0.7129 (pt) cc_final: 0.6856 (pp) REVERT: d 7 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8066 (ptpt) REVERT: d 28 GLU cc_start: 0.7722 (pp20) cc_final: 0.7448 (tm-30) REVERT: e 5 LEU cc_start: 0.4863 (OUTLIER) cc_final: 0.4517 (mp) REVERT: e 21 ARG cc_start: 0.6104 (ptm-80) cc_final: 0.5800 (ptm-80) REVERT: e 25 GLU cc_start: 0.7245 (tt0) cc_final: 0.7011 (tt0) REVERT: e 90 GLN cc_start: 0.8187 (pt0) cc_final: 0.7875 (pt0) REVERT: e 115 GLN cc_start: 0.7039 (mt0) cc_final: 0.6794 (mt0) REVERT: e 136 GLN cc_start: 0.6597 (tp-100) cc_final: 0.6244 (mm-40) REVERT: e 141 MET cc_start: 0.5538 (OUTLIER) cc_final: 0.5298 (OUTLIER) REVERT: e 149 ILE cc_start: 0.7057 (OUTLIER) cc_final: 0.6778 (mt) REVERT: e 166 LYS cc_start: 0.6622 (mtmm) cc_final: 0.5935 (mmmt) REVERT: e 195 GLN cc_start: 0.6117 (mt0) cc_final: 0.5789 (mt0) REVERT: e 198 GLU cc_start: 0.5712 (OUTLIER) cc_final: 0.5317 (mm-30) REVERT: f 11 GLU cc_start: 0.6247 (pm20) cc_final: 0.5787 (mp0) REVERT: f 42 GLU cc_start: 0.5955 (pm20) cc_final: 0.5638 (pm20) REVERT: f 47 LYS cc_start: 0.6259 (mmtt) cc_final: 0.5689 (mtpm) REVERT: f 129 SER cc_start: 0.7904 (m) cc_final: 0.7618 (m) REVERT: f 133 ARG cc_start: 0.5733 (mtm-85) cc_final: 0.5516 (mtm180) REVERT: f 147 ASP cc_start: 0.5837 (OUTLIER) cc_final: 0.5341 (m-30) REVERT: f 164 GLU cc_start: 0.5791 (pm20) cc_final: 0.5442 (pt0) REVERT: g 88 GLN cc_start: 0.6631 (pt0) cc_final: 0.6094 (pt0) REVERT: g 89 LEU cc_start: 0.7791 (mt) cc_final: 0.7492 (mm) REVERT: i 23 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7880 (mttp) REVERT: i 49 ASP cc_start: 0.8119 (t0) cc_final: 0.7800 (t0) REVERT: i 95 ARG cc_start: 0.7109 (ttt-90) cc_final: 0.6134 (mtp-110) REVERT: i 125 TYR cc_start: 0.8093 (m-80) cc_final: 0.7363 (m-80) REVERT: j 4 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7285 (mt-10) REVERT: j 17 ARG cc_start: 0.7615 (mmt90) cc_final: 0.7282 (mmt90) REVERT: j 37 ASP cc_start: 0.8010 (m-30) cc_final: 0.7759 (m-30) REVERT: j 51 LYS cc_start: 0.7406 (mttp) cc_final: 0.7121 (mttm) REVERT: j 111 LYS cc_start: 0.6685 (ttpt) cc_final: 0.6341 (tttt) REVERT: j 113 MET cc_start: 0.6335 (mmm) cc_final: 0.6075 (mmm) REVERT: k 104 GLN cc_start: 0.8072 (mm110) cc_final: 0.7809 (mt0) REVERT: k 129 LYS cc_start: 0.6880 (mppt) cc_final: 0.6550 (mmpt) REVERT: l 55 ARG cc_start: 0.7602 (tpt170) cc_final: 0.6301 (ttm110) REVERT: l 127 LYS cc_start: 0.7734 (ttmt) cc_final: 0.7252 (tptm) REVERT: l 133 LYS cc_start: 0.7673 (ptmt) cc_final: 0.6986 (pptt) REVERT: m 72 ASP cc_start: 0.7383 (p0) cc_final: 0.6610 (p0) REVERT: m 110 MET cc_start: 0.8282 (mmm) cc_final: 0.8062 (mmm) REVERT: m 117 ASP cc_start: 0.7621 (p0) cc_final: 0.7248 (p0) REVERT: n 13 ARG cc_start: 0.6825 (ttm-80) cc_final: 0.6144 (ttm170) REVERT: n 16 ARG cc_start: 0.7159 (mmp80) cc_final: 0.6278 (mmt90) REVERT: n 46 GLU cc_start: 0.6625 (pt0) cc_final: 0.6344 (tt0) REVERT: n 76 LYS cc_start: 0.6462 (tttt) cc_final: 0.6099 (tmtm) REVERT: o 27 GLU cc_start: 0.7315 (tt0) cc_final: 0.7097 (tt0) REVERT: o 111 LYS cc_start: 0.7651 (ttpt) cc_final: 0.7076 (tttm) REVERT: p 59 GLN cc_start: 0.8250 (tt0) cc_final: 0.7990 (tt0) REVERT: q 15 SER cc_start: 0.8201 (p) cc_final: 0.7622 (m) REVERT: q 40 MET cc_start: 0.7470 (ptm) cc_final: 0.7008 (tmm) REVERT: q 48 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7164 (ptmt) REVERT: q 73 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7728 (mttp) REVERT: r 31 GLN cc_start: 0.6806 (mt0) cc_final: 0.6552 (mt0) REVERT: r 73 LYS cc_start: 0.8426 (ptpp) cc_final: 0.7922 (ptmm) REVERT: r 86 MET cc_start: 0.7647 (ttm) cc_final: 0.6990 (ttp) REVERT: r 94 ASP cc_start: 0.8221 (m-30) cc_final: 0.7958 (m-30) REVERT: s 50 LEU cc_start: 0.8190 (mt) cc_final: 0.7777 (mt) REVERT: s 51 PHE cc_start: 0.7847 (m-10) cc_final: 0.7474 (m-10) REVERT: t 10 GLU cc_start: 0.6672 (tp30) cc_final: 0.6155 (tp30) REVERT: t 47 LYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6575 (mptm) REVERT: u 3 THR cc_start: 0.7223 (m) cc_final: 0.6981 (t) REVERT: u 10 LYS cc_start: 0.6973 (mmmt) cc_final: 0.6438 (mmtm) REVERT: u 25 LYS cc_start: 0.7592 (mtpp) cc_final: 0.7318 (mtmp) REVERT: u 34 LYS cc_start: 0.5472 (tppt) cc_final: 0.5152 (tptm) REVERT: u 38 LEU cc_start: 0.7684 (tp) cc_final: 0.7435 (mt) REVERT: u 45 ASP cc_start: 0.7111 (m-30) cc_final: 0.6795 (m-30) REVERT: u 48 MET cc_start: 0.7501 (tpt) cc_final: 0.7185 (tpt) REVERT: u 68 LYS cc_start: 0.5497 (ttmm) cc_final: 0.5045 (tptt) REVERT: u 73 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7274 (tttm) REVERT: v 3 HIS cc_start: 0.7079 (m90) cc_final: 0.6683 (m170) REVERT: v 25 ARG cc_start: 0.7926 (mmt90) cc_final: 0.7616 (mmt90) REVERT: v 64 ASP cc_start: 0.7995 (m-30) cc_final: 0.7446 (m-30) REVERT: v 72 LYS cc_start: 0.7811 (ptpp) cc_final: 0.7219 (ptmm) REVERT: w 11 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.6030 (mtp85) REVERT: x 23 ARG cc_start: 0.7211 (mtm-85) cc_final: 0.6932 (mtt180) REVERT: x 27 ASN cc_start: 0.7390 (m-40) cc_final: 0.6846 (m-40) REVERT: x 31 GLN cc_start: 0.6331 (tt0) cc_final: 0.5934 (mt0) REVERT: x 39 GLN cc_start: 0.6910 (mt0) cc_final: 0.6311 (mt0) REVERT: x 45 GLN cc_start: 0.6582 (mt0) cc_final: 0.5889 (mt0) REVERT: x 46 VAL cc_start: 0.7444 (t) cc_final: 0.7042 (p) REVERT: y 56 LYS cc_start: 0.8109 (ttpt) cc_final: 0.7515 (ttmp) REVERT: z 31 ASP cc_start: 0.8040 (t70) cc_final: 0.7659 (t70) REVERT: 0 45 GLN cc_start: 0.7669 (mm110) cc_final: 0.7400 (mm110) REVERT: 3 9 LYS cc_start: 0.7873 (mtmm) cc_final: 0.7534 (mtpp) REVERT: 3 12 ARG cc_start: 0.6585 (mtm110) cc_final: 0.6350 (mtp-110) REVERT: 3 17 VAL cc_start: 0.8344 (p) cc_final: 0.8100 (m) REVERT: 4 22 MET cc_start: 0.6301 (mpp) cc_final: 0.6053 (mpt) REVERT: 4 60 PHE cc_start: 0.6319 (t80) cc_final: 0.6101 (t80) outliers start: 137 outliers final: 69 residues processed: 954 average time/residue: 2.3017 time to fit residues: 3069.1877 Evaluate side-chains 948 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 858 time to evaluate : 5.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 97 LYS Chi-restraints excluded: chain O residue 68 ASP Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain O residue 83 GLU Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 140 ASP Chi-restraints excluded: chain e residue 141 MET Chi-restraints excluded: chain e residue 149 ILE Chi-restraints excluded: chain e residue 198 GLU Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 147 ASP Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain j residue 4 GLU Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain m residue 36 THR Chi-restraints excluded: chain m residue 57 THR Chi-restraints excluded: chain n residue 91 SER Chi-restraints excluded: chain o residue 115 ASN Chi-restraints excluded: chain p residue 87 SER Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 48 LYS Chi-restraints excluded: chain q residue 73 LYS Chi-restraints excluded: chain r residue 22 ASP Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain s residue 55 VAL Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 64 VAL Chi-restraints excluded: chain u residue 73 LYS Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain w residue 11 ARG Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 5 ILE Chi-restraints excluded: chain z residue 30 VAL Chi-restraints excluded: chain z residue 53 LYS Chi-restraints excluded: chain 2 residue 52 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 796 optimal weight: 10.0000 chunk 543 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 712 optimal weight: 7.9990 chunk 394 optimal weight: 10.0000 chunk 816 optimal weight: 20.0000 chunk 661 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 488 optimal weight: 30.0000 chunk 858 optimal weight: 6.9990 chunk 241 optimal weight: 2.9990 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN C 140 ASN D 40 GLN D 54 GLN D 71 GLN D 198 HIS E 19 ASN E 43 ASN E 78 ASN E 97 GLN G 142 HIS H 18 GLN J 64 GLN K 38 GLN L 112 GLN N 60 GLN O 37 ASN O 80 GLN ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 78 ASN d 36 GLN f 27 GLN ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 11 ASN i 80 HIS m 18 GLN n 38 GLN n 98 GLN ** o 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 6 GLN q 18 GLN t 46 GLN x 20 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 153976 Z= 0.396 Angle : 0.850 19.358 230432 Z= 0.447 Chirality : 0.045 0.383 29298 Planarity : 0.009 0.154 12266 Dihedral : 23.198 176.525 77213 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.20 % Favored : 95.69 % Rotamer: Outliers : 3.76 % Allowed : 15.96 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.11), residues: 5480 helix: 0.77 (0.12), residues: 1851 sheet: -0.14 (0.15), residues: 1102 loop : -0.76 (0.12), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP c 248 HIS 0.008 0.002 HIS k 35 PHE 0.028 0.003 PHE S 10 TYR 0.025 0.003 TYR R 51 ARG 0.012 0.001 ARG c 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 858 time to evaluate : 6.091 Fit side-chains REVERT: B 49 MET cc_start: 0.2154 (OUTLIER) cc_final: 0.1649 (mpm) REVERT: C 100 GLN cc_start: 0.6913 (tt0) cc_final: 0.6503 (tt0) REVERT: C 127 ARG cc_start: 0.6660 (mtt90) cc_final: 0.5879 (mtm110) REVERT: C 134 MET cc_start: 0.7826 (mtp) cc_final: 0.7362 (mtm) REVERT: C 161 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6422 (tp30) REVERT: C 183 ASP cc_start: 0.7664 (t0) cc_final: 0.7370 (t0) REVERT: D 47 ARG cc_start: 0.4928 (OUTLIER) cc_final: 0.4182 (ptp-170) REVERT: D 116 GLN cc_start: 0.6145 (OUTLIER) cc_final: 0.4610 (tp40) REVERT: D 138 SER cc_start: 0.6911 (OUTLIER) cc_final: 0.6344 (t) REVERT: D 183 LYS cc_start: 0.5673 (mtmm) cc_final: 0.5089 (tmtm) REVERT: D 184 ARG cc_start: 0.4115 (ptt90) cc_final: 0.3383 (ppt170) REVERT: D 200 ILE cc_start: 0.6502 (OUTLIER) cc_final: 0.6248 (mm) REVERT: E 23 LYS cc_start: 0.8181 (ptmt) cc_final: 0.7935 (ptmt) REVERT: E 26 LYS cc_start: 0.7696 (ttmt) cc_final: 0.7209 (tttp) REVERT: E 45 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6041 (ttp80) REVERT: E 93 ARG cc_start: 0.7565 (mtm-85) cc_final: 0.7125 (mtt-85) REVERT: E 146 ASN cc_start: 0.5852 (m-40) cc_final: 0.5430 (p0) REVERT: F 2 ARG cc_start: 0.6956 (mtt180) cc_final: 0.6691 (mtm-85) REVERT: F 9 MET cc_start: 0.7616 (mtm) cc_final: 0.6930 (mtt) REVERT: F 37 HIS cc_start: 0.6822 (m-70) cc_final: 0.6305 (m170) REVERT: F 62 MET cc_start: 0.7182 (mtp) cc_final: 0.6584 (mpp) REVERT: G 44 TYR cc_start: 0.6915 (m-10) cc_final: 0.6572 (m-10) REVERT: G 144 MET cc_start: 0.6565 (OUTLIER) cc_final: 0.6229 (mtp) REVERT: H 96 MET cc_start: 0.7290 (ttm) cc_final: 0.6845 (ttm) REVERT: I 20 PHE cc_start: 0.7297 (m-80) cc_final: 0.6865 (m-80) REVERT: I 64 TYR cc_start: 0.6908 (t80) cc_final: 0.6624 (t80) REVERT: I 68 LYS cc_start: 0.7778 (mttp) cc_final: 0.7456 (mtpt) REVERT: I 98 LEU cc_start: 0.7074 (mt) cc_final: 0.6781 (mp) REVERT: J 11 LYS cc_start: 0.7861 (mttt) cc_final: 0.7521 (mttp) REVERT: J 24 GLU cc_start: 0.5292 (OUTLIER) cc_final: 0.4986 (mt-10) REVERT: J 73 LEU cc_start: 0.7551 (tp) cc_final: 0.7179 (tm) REVERT: J 88 MET cc_start: 0.4093 (mmt) cc_final: 0.3510 (mpt) REVERT: L 75 GLN cc_start: 0.6973 (pt0) cc_final: 0.6486 (pt0) REVERT: M 13 LYS cc_start: 0.6518 (mttt) cc_final: 0.5995 (mtmm) REVERT: M 19 LEU cc_start: 0.7464 (mt) cc_final: 0.7243 (mt) REVERT: M 31 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7608 (ttmm) REVERT: M 75 MET cc_start: 0.6028 (mmp) cc_final: 0.5579 (mtm) REVERT: M 81 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.6319 (mtm) REVERT: M 93 ARG cc_start: 0.6509 (mmt90) cc_final: 0.5749 (mmt90) REVERT: M 95 LEU cc_start: 0.8028 (mt) cc_final: 0.7809 (mt) REVERT: N 6 MET cc_start: 0.7761 (mmm) cc_final: 0.7376 (mmm) REVERT: N 19 LYS cc_start: 0.7341 (tttt) cc_final: 0.7098 (tttt) REVERT: N 21 PHE cc_start: 0.6882 (t80) cc_final: 0.6583 (t80) REVERT: N 86 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6400 (mt-10) REVERT: O 47 LYS cc_start: 0.7698 (mttp) cc_final: 0.7259 (mtmt) REVERT: O 48 LYS cc_start: 0.7779 (mmtm) cc_final: 0.7365 (mmtt) REVERT: O 62 GLN cc_start: 0.7810 (tt0) cc_final: 0.7538 (tt0) REVERT: P 35 ARG cc_start: 0.6974 (ttp80) cc_final: 0.6405 (ttt90) REVERT: Q 30 LYS cc_start: 0.8291 (tttt) cc_final: 0.7792 (tttm) REVERT: Q 60 GLU cc_start: 0.7162 (tt0) cc_final: 0.6718 (tt0) REVERT: R 24 LYS cc_start: 0.6461 (mtmm) cc_final: 0.6001 (mtpt) REVERT: R 51 TYR cc_start: 0.7102 (m-80) cc_final: 0.6468 (m-80) REVERT: R 55 LEU cc_start: 0.7334 (tp) cc_final: 0.6989 (tp) REVERT: R 57 ARG cc_start: 0.7298 (mtm-85) cc_final: 0.6958 (mtp180) REVERT: R 61 ARG cc_start: 0.7029 (mtt90) cc_final: 0.6227 (mtt-85) REVERT: S 44 MET cc_start: 0.5840 (mtp) cc_final: 0.5413 (ttm) REVERT: S 73 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6626 (mt-10) REVERT: T 16 LYS cc_start: 0.6627 (ttpp) cc_final: 0.6202 (mtpp) REVERT: T 24 ARG cc_start: 0.6518 (mmp80) cc_final: 0.5548 (mtt-85) REVERT: T 53 GLU cc_start: 0.5903 (OUTLIER) cc_final: 0.5568 (tt0) REVERT: T 80 THR cc_start: 0.6539 (m) cc_final: 0.6134 (t) REVERT: U 36 GLU cc_start: 0.6660 (tt0) cc_final: 0.5734 (mt-10) REVERT: c 5 LYS cc_start: 0.7999 (mtpp) cc_final: 0.7371 (mttm) REVERT: c 26 LYS cc_start: 0.8284 (mttm) cc_final: 0.7786 (mttt) REVERT: c 66 ASP cc_start: 0.8022 (t0) cc_final: 0.7791 (t0) REVERT: c 97 LYS cc_start: 0.6998 (ttmm) cc_final: 0.6653 (mttt) REVERT: c 111 LYS cc_start: 0.7301 (pttm) cc_final: 0.6701 (ptpp) REVERT: c 185 GLU cc_start: 0.6887 (mt-10) cc_final: 0.6306 (tt0) REVERT: c 269 ARG cc_start: 0.7288 (ttm-80) cc_final: 0.6934 (ttt180) REVERT: d 2 ILE cc_start: 0.7132 (pt) cc_final: 0.6858 (pp) REVERT: d 7 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.8064 (ptpt) REVERT: d 28 GLU cc_start: 0.7765 (pp20) cc_final: 0.7553 (tm-30) REVERT: d 185 ASN cc_start: 0.7776 (m110) cc_final: 0.7235 (m-40) REVERT: e 21 ARG cc_start: 0.6239 (ptm-80) cc_final: 0.5977 (ptm-80) REVERT: e 25 GLU cc_start: 0.7311 (tt0) cc_final: 0.7054 (tt0) REVERT: e 127 GLU cc_start: 0.5298 (mt-10) cc_final: 0.5088 (mm-30) REVERT: e 134 LEU cc_start: 0.6319 (tp) cc_final: 0.5982 (tm) REVERT: e 136 GLN cc_start: 0.6729 (tp-100) cc_final: 0.6393 (mm-40) REVERT: e 149 ILE cc_start: 0.7192 (OUTLIER) cc_final: 0.6874 (mt) REVERT: f 11 GLU cc_start: 0.6312 (pm20) cc_final: 0.5874 (mp0) REVERT: f 42 GLU cc_start: 0.5895 (pm20) cc_final: 0.5645 (pm20) REVERT: f 47 LYS cc_start: 0.6238 (mmtt) cc_final: 0.5875 (mtpm) REVERT: f 98 GLU cc_start: 0.6778 (mt-10) cc_final: 0.5971 (mt-10) REVERT: f 129 SER cc_start: 0.7959 (m) cc_final: 0.7647 (m) REVERT: f 133 ARG cc_start: 0.5698 (mtm-85) cc_final: 0.5472 (mtm180) REVERT: f 147 ASP cc_start: 0.6031 (OUTLIER) cc_final: 0.5477 (m-30) REVERT: f 164 GLU cc_start: 0.5849 (pm20) cc_final: 0.5572 (pt0) REVERT: g 139 GLN cc_start: 0.6446 (tm-30) cc_final: 0.5296 (tt0) REVERT: i 23 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7869 (mttp) REVERT: i 49 ASP cc_start: 0.8112 (t0) cc_final: 0.7814 (t0) REVERT: i 125 TYR cc_start: 0.8053 (m-80) cc_final: 0.7344 (m-80) REVERT: j 17 ARG cc_start: 0.7629 (mmt90) cc_final: 0.7275 (mmt90) REVERT: j 37 ASP cc_start: 0.8012 (m-30) cc_final: 0.7741 (m-30) REVERT: j 51 LYS cc_start: 0.7482 (mttp) cc_final: 0.7163 (mttm) REVERT: j 113 MET cc_start: 0.6371 (mmm) cc_final: 0.6086 (mmm) REVERT: k 82 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7481 (mp) REVERT: k 104 GLN cc_start: 0.8072 (mm110) cc_final: 0.7869 (mt0) REVERT: k 129 LYS cc_start: 0.6876 (mppt) cc_final: 0.6553 (mmpt) REVERT: l 7 THR cc_start: 0.7966 (p) cc_final: 0.7553 (p) REVERT: l 55 ARG cc_start: 0.7669 (tpt170) cc_final: 0.6370 (ttm110) REVERT: l 58 LYS cc_start: 0.7582 (mtpp) cc_final: 0.7323 (mtpt) REVERT: l 127 LYS cc_start: 0.7787 (ttmt) cc_final: 0.7273 (tptm) REVERT: m 114 GLU cc_start: 0.8308 (pt0) cc_final: 0.8006 (pt0) REVERT: m 117 ASP cc_start: 0.7629 (p0) cc_final: 0.7219 (p0) REVERT: n 13 ARG cc_start: 0.6977 (ttm-80) cc_final: 0.6382 (ttm170) REVERT: n 16 ARG cc_start: 0.7317 (mmp80) cc_final: 0.6623 (mmp-170) REVERT: n 46 GLU cc_start: 0.6666 (pt0) cc_final: 0.6400 (tm-30) REVERT: n 58 ILE cc_start: 0.6274 (OUTLIER) cc_final: 0.6008 (mm) REVERT: n 76 LYS cc_start: 0.6547 (tttt) cc_final: 0.6157 (tptt) REVERT: o 87 LYS cc_start: 0.7688 (mmmt) cc_final: 0.7383 (mmtt) REVERT: o 111 LYS cc_start: 0.7653 (ttpt) cc_final: 0.7111 (tttp) REVERT: p 59 GLN cc_start: 0.8347 (tt0) cc_final: 0.8087 (tt0) REVERT: q 15 SER cc_start: 0.8406 (p) cc_final: 0.7690 (m) REVERT: q 40 MET cc_start: 0.7432 (ptm) cc_final: 0.7163 (ppp) REVERT: q 48 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7268 (ptmt) REVERT: q 73 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7767 (mttp) REVERT: r 31 GLN cc_start: 0.6896 (mt0) cc_final: 0.6659 (mt0) REVERT: r 86 MET cc_start: 0.7688 (ttm) cc_final: 0.7199 (ttp) REVERT: s 51 PHE cc_start: 0.7801 (m-10) cc_final: 0.7461 (m-10) REVERT: t 10 GLU cc_start: 0.6639 (tp30) cc_final: 0.6061 (tp30) REVERT: t 47 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6625 (mptm) REVERT: u 3 THR cc_start: 0.7284 (m) cc_final: 0.7063 (t) REVERT: u 25 LYS cc_start: 0.7625 (mtpp) cc_final: 0.7324 (mtmp) REVERT: u 34 LYS cc_start: 0.5373 (tppt) cc_final: 0.5128 (tptm) REVERT: u 38 LEU cc_start: 0.7724 (tp) cc_final: 0.7519 (mt) REVERT: u 41 GLU cc_start: 0.6712 (mt-10) cc_final: 0.6444 (mt-10) REVERT: u 45 ASP cc_start: 0.7146 (m-30) cc_final: 0.6864 (m-30) REVERT: u 68 LYS cc_start: 0.5559 (ttmm) cc_final: 0.5051 (tptt) REVERT: u 73 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7252 (tttm) REVERT: v 3 HIS cc_start: 0.7079 (m90) cc_final: 0.6697 (m170) REVERT: v 25 ARG cc_start: 0.7974 (mmt90) cc_final: 0.7656 (mmt90) REVERT: v 64 ASP cc_start: 0.8006 (m-30) cc_final: 0.7431 (m-30) REVERT: v 72 LYS cc_start: 0.7870 (ptpp) cc_final: 0.7088 (pptt) REVERT: w 11 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.6737 (mtp85) REVERT: x 8 GLU cc_start: 0.5530 (mm-30) cc_final: 0.4919 (tp30) REVERT: x 39 GLN cc_start: 0.6920 (mt0) cc_final: 0.6332 (mt0) REVERT: x 45 GLN cc_start: 0.6652 (mt0) cc_final: 0.5861 (mt0) REVERT: y 56 LYS cc_start: 0.8146 (ttpt) cc_final: 0.7498 (ttmp) REVERT: z 31 ASP cc_start: 0.8088 (t70) cc_final: 0.7690 (t70) REVERT: 0 45 GLN cc_start: 0.7670 (mm110) cc_final: 0.7404 (mm110) REVERT: 1 1 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.7103 (mpp) REVERT: 3 9 LYS cc_start: 0.7923 (mtmm) cc_final: 0.7613 (mtpp) REVERT: 3 12 ARG cc_start: 0.6552 (mtm110) cc_final: 0.6340 (mtp-110) REVERT: 3 17 VAL cc_start: 0.8348 (p) cc_final: 0.8131 (m) REVERT: 3 18 LYS cc_start: 0.7954 (tttm) cc_final: 0.7573 (tttt) REVERT: 4 22 MET cc_start: 0.6399 (mpp) cc_final: 0.6123 (mpt) outliers start: 172 outliers final: 106 residues processed: 960 average time/residue: 2.3340 time to fit residues: 3132.4363 Evaluate side-chains 977 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 848 time to evaluate : 5.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain J residue 24 GLU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 97 LYS Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain O residue 83 GLU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 144 GLU Chi-restraints excluded: chain e residue 149 ILE Chi-restraints excluded: chain e residue 170 ARG Chi-restraints excluded: chain e residue 199 MET Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 147 ASP Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 14 ASP Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 24 THR Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 36 THR Chi-restraints excluded: chain m residue 57 THR Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 91 SER Chi-restraints excluded: chain n residue 103 VAL Chi-restraints excluded: chain o residue 115 ASN Chi-restraints excluded: chain p residue 19 LYS Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 48 LYS Chi-restraints excluded: chain q residue 73 LYS Chi-restraints excluded: chain r residue 22 ASP Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain s residue 55 VAL Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain t residue 103 ILE Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 64 VAL Chi-restraints excluded: chain u residue 73 LYS Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain w residue 11 ARG Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 55 VAL Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 30 VAL Chi-restraints excluded: chain z residue 53 LYS Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 2 residue 52 LYS Chi-restraints excluded: chain 2 residue 59 ILE Chi-restraints excluded: chain 3 residue 19 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 321 optimal weight: 6.9990 chunk 861 optimal weight: 0.9980 chunk 189 optimal weight: 20.0000 chunk 561 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 chunk 957 optimal weight: 0.9980 chunk 795 optimal weight: 1.9990 chunk 443 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 316 optimal weight: 10.0000 chunk 502 optimal weight: 7.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN D 40 GLN D 54 GLN D 71 GLN D 198 HIS E 19 ASN E 43 ASN E 78 ASN E 97 GLN G 142 HIS H 18 GLN J 64 GLN L 73 ASN L 112 GLN N 60 GLN O 37 ASN O 80 GLN ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 ASN d 36 GLN f 27 GLN g 38 ASN ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 18 GLN n 38 GLN n 98 GLN ** o 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 6 GLN q 18 GLN t 46 GLN x 20 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 153976 Z= 0.191 Angle : 0.663 14.698 230432 Z= 0.371 Chirality : 0.036 0.380 29298 Planarity : 0.007 0.136 12266 Dihedral : 23.028 179.672 77213 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.23 % Favored : 96.70 % Rotamer: Outliers : 3.37 % Allowed : 17.20 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.11), residues: 5480 helix: 1.19 (0.12), residues: 1860 sheet: -0.04 (0.15), residues: 1098 loop : -0.65 (0.12), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP c 248 HIS 0.005 0.001 HIS E 89 PHE 0.017 0.002 PHE S 10 TYR 0.017 0.002 TYR p 32 ARG 0.007 0.000 ARG s 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 870 time to evaluate : 5.943 Fit side-chains REVERT: B 49 MET cc_start: 0.2058 (OUTLIER) cc_final: 0.1692 (mpm) REVERT: B 100 MET cc_start: 0.3718 (mmt) cc_final: 0.3441 (mmm) REVERT: C 100 GLN cc_start: 0.6936 (tt0) cc_final: 0.6557 (tt0) REVERT: C 127 ARG cc_start: 0.6567 (mtt90) cc_final: 0.5872 (mtm110) REVERT: C 144 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7003 (mm) REVERT: C 161 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6413 (tp30) REVERT: C 183 ASP cc_start: 0.7638 (t0) cc_final: 0.7358 (t0) REVERT: D 47 ARG cc_start: 0.4796 (OUTLIER) cc_final: 0.4107 (ptp-170) REVERT: D 73 ARG cc_start: 0.6455 (ttp80) cc_final: 0.6158 (ttp-110) REVERT: D 78 GLU cc_start: 0.7156 (tp30) cc_final: 0.6656 (tm-30) REVERT: D 116 GLN cc_start: 0.5988 (OUTLIER) cc_final: 0.4581 (tp40) REVERT: D 124 MET cc_start: 0.5662 (ttp) cc_final: 0.5367 (ttp) REVERT: D 138 SER cc_start: 0.6799 (OUTLIER) cc_final: 0.6259 (t) REVERT: D 183 LYS cc_start: 0.5692 (mtmm) cc_final: 0.5085 (tmtm) REVERT: D 184 ARG cc_start: 0.4037 (ptt90) cc_final: 0.3168 (ppt170) REVERT: D 200 ILE cc_start: 0.6539 (OUTLIER) cc_final: 0.6297 (mm) REVERT: E 26 LYS cc_start: 0.7655 (ttmt) cc_final: 0.7252 (tttp) REVERT: E 45 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.5848 (ttp80) REVERT: E 74 VAL cc_start: 0.7680 (t) cc_final: 0.7421 (m) REVERT: E 93 ARG cc_start: 0.7503 (mtm-85) cc_final: 0.7050 (mtt180) REVERT: E 146 ASN cc_start: 0.5715 (m-40) cc_final: 0.5323 (p0) REVERT: E 147 MET cc_start: 0.7761 (ttp) cc_final: 0.7378 (ttp) REVERT: F 2 ARG cc_start: 0.6904 (mtt180) cc_final: 0.6699 (mtm-85) REVERT: F 9 MET cc_start: 0.7591 (mtm) cc_final: 0.7023 (mtt) REVERT: F 37 HIS cc_start: 0.6844 (m-70) cc_final: 0.6528 (m-70) REVERT: F 62 MET cc_start: 0.7122 (mtp) cc_final: 0.6393 (mpp) REVERT: G 11 LYS cc_start: 0.5357 (OUTLIER) cc_final: 0.5102 (mmpt) REVERT: G 21 GLU cc_start: 0.6450 (mt-10) cc_final: 0.6037 (mt-10) REVERT: G 144 MET cc_start: 0.6557 (OUTLIER) cc_final: 0.6240 (mtp) REVERT: H 96 MET cc_start: 0.7238 (ttm) cc_final: 0.6875 (ttm) REVERT: I 20 PHE cc_start: 0.7343 (m-80) cc_final: 0.6934 (m-80) REVERT: I 36 GLU cc_start: 0.6067 (mp0) cc_final: 0.5846 (mp0) REVERT: I 68 LYS cc_start: 0.7786 (mttp) cc_final: 0.7462 (mtpt) REVERT: I 98 LEU cc_start: 0.7031 (mt) cc_final: 0.6711 (mp) REVERT: J 11 LYS cc_start: 0.7842 (mttt) cc_final: 0.7472 (mttp) REVERT: J 73 LEU cc_start: 0.7595 (tp) cc_final: 0.7204 (tm) REVERT: J 88 MET cc_start: 0.4027 (mmt) cc_final: 0.3359 (mpt) REVERT: L 75 GLN cc_start: 0.6907 (pt0) cc_final: 0.6433 (pt0) REVERT: M 19 LEU cc_start: 0.7468 (mt) cc_final: 0.7239 (mt) REVERT: M 31 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7624 (ttmm) REVERT: M 75 MET cc_start: 0.5937 (mmp) cc_final: 0.5498 (mtm) REVERT: M 93 ARG cc_start: 0.6437 (mmt90) cc_final: 0.5796 (mmt90) REVERT: M 95 LEU cc_start: 0.8021 (mt) cc_final: 0.7803 (mt) REVERT: N 6 MET cc_start: 0.7669 (mmm) cc_final: 0.7362 (mmm) REVERT: N 21 PHE cc_start: 0.6792 (t80) cc_final: 0.6469 (t80) REVERT: N 86 GLU cc_start: 0.6751 (mt-10) cc_final: 0.6448 (mt-10) REVERT: O 47 LYS cc_start: 0.7669 (mttp) cc_final: 0.7201 (mtmt) REVERT: O 48 LYS cc_start: 0.7665 (mmtm) cc_final: 0.7275 (mmtt) REVERT: O 62 GLN cc_start: 0.7715 (tt0) cc_final: 0.7461 (tt0) REVERT: P 35 ARG cc_start: 0.6989 (ttp80) cc_final: 0.6382 (ttt90) REVERT: P 63 GLN cc_start: 0.5622 (tp40) cc_final: 0.4257 (mm110) REVERT: Q 30 LYS cc_start: 0.8217 (tttt) cc_final: 0.7804 (tttm) REVERT: Q 60 GLU cc_start: 0.7225 (tt0) cc_final: 0.6744 (tt0) REVERT: R 24 LYS cc_start: 0.6356 (mtmm) cc_final: 0.6117 (mtpt) REVERT: R 48 ARG cc_start: 0.5531 (mmt90) cc_final: 0.4680 (mmp-170) REVERT: R 51 TYR cc_start: 0.6940 (m-80) cc_final: 0.6256 (m-80) REVERT: R 55 LEU cc_start: 0.7352 (tp) cc_final: 0.6900 (tp) REVERT: R 57 ARG cc_start: 0.7298 (mtm-85) cc_final: 0.6901 (mtp180) REVERT: R 61 ARG cc_start: 0.7060 (mtt90) cc_final: 0.6271 (mtt-85) REVERT: S 44 MET cc_start: 0.5758 (mtp) cc_final: 0.5404 (ttm) REVERT: S 73 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6634 (mt-10) REVERT: T 16 LYS cc_start: 0.6581 (ttpp) cc_final: 0.6226 (mttp) REVERT: T 24 ARG cc_start: 0.6589 (mmp80) cc_final: 0.5639 (mtt-85) REVERT: T 53 GLU cc_start: 0.5856 (OUTLIER) cc_final: 0.5531 (tt0) REVERT: U 21 ARG cc_start: 0.5200 (ttt180) cc_final: 0.4608 (mmm160) REVERT: U 36 GLU cc_start: 0.6581 (tt0) cc_final: 0.5618 (mt-10) REVERT: c 5 LYS cc_start: 0.8016 (mtpp) cc_final: 0.7414 (mttm) REVERT: c 20 VAL cc_start: 0.7723 (p) cc_final: 0.7496 (t) REVERT: c 26 LYS cc_start: 0.8210 (mttm) cc_final: 0.7728 (mttt) REVERT: c 66 ASP cc_start: 0.8012 (t0) cc_final: 0.7781 (t0) REVERT: c 97 LYS cc_start: 0.7011 (ttmm) cc_final: 0.6660 (mttt) REVERT: c 111 LYS cc_start: 0.7296 (pttm) cc_final: 0.6701 (ptpp) REVERT: c 167 ARG cc_start: 0.7232 (ttp80) cc_final: 0.6828 (ttp80) REVERT: c 185 GLU cc_start: 0.6920 (mt-10) cc_final: 0.6341 (tt0) REVERT: c 269 ARG cc_start: 0.7296 (ttm-80) cc_final: 0.6907 (ttt180) REVERT: d 1 MET cc_start: 0.4867 (tpt) cc_final: 0.4121 (tpp) REVERT: d 2 ILE cc_start: 0.7100 (pt) cc_final: 0.6870 (pp) REVERT: d 7 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8068 (ptpt) REVERT: d 28 GLU cc_start: 0.7717 (pp20) cc_final: 0.7511 (tm-30) REVERT: d 103 ASP cc_start: 0.6347 (m-30) cc_final: 0.6088 (m-30) REVERT: d 185 ASN cc_start: 0.7681 (m110) cc_final: 0.7129 (m-40) REVERT: e 21 ARG cc_start: 0.6362 (ptm-80) cc_final: 0.6129 (ptm-80) REVERT: e 25 GLU cc_start: 0.7226 (tt0) cc_final: 0.7026 (tt0) REVERT: e 115 GLN cc_start: 0.6995 (mt0) cc_final: 0.6734 (mt0) REVERT: e 136 GLN cc_start: 0.6625 (tp-100) cc_final: 0.6206 (mm-40) REVERT: e 139 LYS cc_start: 0.6741 (tttp) cc_final: 0.6248 (ttpp) REVERT: e 140 ASP cc_start: 0.5675 (m-30) cc_final: 0.5035 (m-30) REVERT: f 11 GLU cc_start: 0.6327 (pm20) cc_final: 0.5886 (mp0) REVERT: f 42 GLU cc_start: 0.5880 (pm20) cc_final: 0.5580 (pm20) REVERT: f 47 LYS cc_start: 0.6349 (mmtt) cc_final: 0.5941 (mtpm) REVERT: f 129 SER cc_start: 0.7898 (m) cc_final: 0.7615 (m) REVERT: f 133 ARG cc_start: 0.5527 (mtm-85) cc_final: 0.5227 (mtt180) REVERT: f 147 ASP cc_start: 0.5894 (OUTLIER) cc_final: 0.5357 (m-30) REVERT: f 164 GLU cc_start: 0.5852 (pm20) cc_final: 0.5629 (pt0) REVERT: g 88 GLN cc_start: 0.6580 (pt0) cc_final: 0.5999 (pt0) REVERT: g 89 LEU cc_start: 0.7753 (mt) cc_final: 0.7424 (mm) REVERT: g 155 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6553 (pp20) REVERT: i 23 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7919 (mttp) REVERT: i 49 ASP cc_start: 0.8118 (t0) cc_final: 0.7805 (t0) REVERT: i 96 ARG cc_start: 0.6616 (mmm-85) cc_final: 0.6282 (mtm180) REVERT: i 125 TYR cc_start: 0.8023 (m-80) cc_final: 0.7331 (m-80) REVERT: j 17 ARG cc_start: 0.7622 (mmt90) cc_final: 0.7283 (mmt90) REVERT: j 37 ASP cc_start: 0.8006 (m-30) cc_final: 0.7737 (m-30) REVERT: j 51 LYS cc_start: 0.7447 (mttp) cc_final: 0.7155 (mttm) REVERT: j 113 MET cc_start: 0.6349 (mmm) cc_final: 0.6088 (mmm) REVERT: k 104 GLN cc_start: 0.8071 (mm110) cc_final: 0.7801 (mt0) REVERT: k 123 ARG cc_start: 0.7101 (ttm170) cc_final: 0.6719 (ttp80) REVERT: k 129 LYS cc_start: 0.6923 (mppt) cc_final: 0.6587 (mmpt) REVERT: l 55 ARG cc_start: 0.7583 (tpt170) cc_final: 0.6282 (ttm110) REVERT: l 127 LYS cc_start: 0.7705 (ttmt) cc_final: 0.7219 (tptm) REVERT: m 72 ASP cc_start: 0.7392 (p0) cc_final: 0.6610 (p0) REVERT: m 82 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7282 (mt-10) REVERT: m 117 ASP cc_start: 0.7555 (p0) cc_final: 0.7194 (p0) REVERT: n 13 ARG cc_start: 0.6865 (ttm-80) cc_final: 0.6239 (ttm170) REVERT: n 16 ARG cc_start: 0.7227 (mmp80) cc_final: 0.6169 (mmt-90) REVERT: n 46 GLU cc_start: 0.6621 (pt0) cc_final: 0.6341 (tm-30) REVERT: n 58 ILE cc_start: 0.6308 (OUTLIER) cc_final: 0.6071 (mm) REVERT: n 76 LYS cc_start: 0.6518 (tttt) cc_final: 0.6069 (tmtm) REVERT: o 27 GLU cc_start: 0.7258 (tt0) cc_final: 0.7006 (tt0) REVERT: o 111 LYS cc_start: 0.7665 (ttpt) cc_final: 0.7086 (tttm) REVERT: p 59 GLN cc_start: 0.8220 (tt0) cc_final: 0.7988 (tt0) REVERT: q 15 SER cc_start: 0.8227 (p) cc_final: 0.7663 (m) REVERT: q 40 MET cc_start: 0.7372 (ptm) cc_final: 0.7052 (tmm) REVERT: q 48 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7143 (ptmt) REVERT: q 60 LYS cc_start: 0.6878 (mmtm) cc_final: 0.6627 (mmtm) REVERT: q 73 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7721 (mttp) REVERT: r 31 GLN cc_start: 0.6877 (mt0) cc_final: 0.6471 (mt0) REVERT: r 33 LEU cc_start: 0.7909 (mt) cc_final: 0.7677 (mt) REVERT: r 86 MET cc_start: 0.7531 (ttm) cc_final: 0.7047 (ttp) REVERT: r 94 ASP cc_start: 0.8167 (m-30) cc_final: 0.7931 (m-30) REVERT: s 30 ILE cc_start: 0.7929 (pt) cc_final: 0.7582 (pp) REVERT: s 51 PHE cc_start: 0.7757 (m-10) cc_final: 0.7474 (m-10) REVERT: t 10 GLU cc_start: 0.6604 (tp30) cc_final: 0.6029 (tp30) REVERT: t 26 LYS cc_start: 0.7015 (tttm) cc_final: 0.6670 (tttm) REVERT: t 47 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6692 (mptm) REVERT: u 3 THR cc_start: 0.7239 (m) cc_final: 0.7003 (t) REVERT: u 25 LYS cc_start: 0.7634 (mtpp) cc_final: 0.7334 (mtmp) REVERT: u 34 LYS cc_start: 0.5413 (tppt) cc_final: 0.5110 (tptm) REVERT: u 38 LEU cc_start: 0.7675 (tp) cc_final: 0.7462 (mt) REVERT: u 41 GLU cc_start: 0.6713 (mt-10) cc_final: 0.6492 (mt-10) REVERT: u 45 ASP cc_start: 0.7093 (m-30) cc_final: 0.6777 (m-30) REVERT: u 48 MET cc_start: 0.7514 (tpt) cc_final: 0.7223 (tpt) REVERT: u 68 LYS cc_start: 0.5610 (ttmm) cc_final: 0.5107 (tptt) REVERT: v 3 HIS cc_start: 0.7071 (m90) cc_final: 0.6690 (m170) REVERT: v 25 ARG cc_start: 0.7928 (mmt90) cc_final: 0.7611 (mmt90) REVERT: v 64 ASP cc_start: 0.7952 (m-30) cc_final: 0.7434 (m-30) REVERT: v 72 LYS cc_start: 0.7763 (ptpp) cc_final: 0.7153 (ptmm) REVERT: w 11 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.6096 (mtp85) REVERT: x 31 GLN cc_start: 0.6358 (OUTLIER) cc_final: 0.5642 (mt0) REVERT: x 39 GLN cc_start: 0.6871 (mt0) cc_final: 0.6282 (mt0) REVERT: x 45 GLN cc_start: 0.6612 (mt0) cc_final: 0.5856 (mt0) REVERT: x 46 VAL cc_start: 0.7425 (t) cc_final: 0.7016 (p) REVERT: y 56 LYS cc_start: 0.8134 (ttpt) cc_final: 0.7523 (ttmp) REVERT: z 31 ASP cc_start: 0.8042 (t70) cc_final: 0.7688 (t70) REVERT: 0 45 GLN cc_start: 0.7655 (mm110) cc_final: 0.7389 (mm110) REVERT: 1 1 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.7105 (mpp) REVERT: 3 9 LYS cc_start: 0.7924 (mtmm) cc_final: 0.7646 (mtpp) REVERT: 3 17 VAL cc_start: 0.8351 (p) cc_final: 0.8127 (m) outliers start: 154 outliers final: 92 residues processed: 960 average time/residue: 2.2826 time to fit residues: 3074.3203 Evaluate side-chains 972 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 858 time to evaluate : 5.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain G residue 11 LYS Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 97 LYS Chi-restraints excluded: chain O residue 72 ARG Chi-restraints excluded: chain O residue 83 GLU Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 199 MET Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 147 ASP Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 14 ASP Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain l residue 24 THR Chi-restraints excluded: chain m residue 36 THR Chi-restraints excluded: chain m residue 57 THR Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 91 SER Chi-restraints excluded: chain n residue 103 VAL Chi-restraints excluded: chain o residue 115 ASN Chi-restraints excluded: chain p residue 87 SER Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 48 LYS Chi-restraints excluded: chain q residue 73 LYS Chi-restraints excluded: chain r residue 22 ASP Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain s residue 55 VAL Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 64 VAL Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain w residue 11 ARG Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain x residue 31 GLN Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain z residue 30 VAL Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 2 residue 52 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 923 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 545 optimal weight: 10.0000 chunk 699 optimal weight: 10.0000 chunk 541 optimal weight: 10.0000 chunk 806 optimal weight: 5.9990 chunk 534 optimal weight: 10.0000 chunk 954 optimal weight: 7.9990 chunk 597 optimal weight: 10.0000 chunk 581 optimal weight: 10.0000 chunk 440 optimal weight: 9.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN D 40 GLN D 54 GLN D 71 GLN D 198 HIS E 19 ASN E 61 GLN E 78 ASN E 97 GLN E 148 ASN G 142 HIS H 18 GLN J 64 GLN L 73 ASN L 112 GLN N 60 GLN O 37 ASN O 80 GLN ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 ASN d 36 GLN f 27 GLN g 38 ASN ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 18 GLN n 38 GLN n 98 GLN q 6 GLN q 18 GLN t 27 ASN t 46 GLN x 20 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 153976 Z= 0.415 Angle : 0.865 19.474 230432 Z= 0.454 Chirality : 0.046 0.388 29298 Planarity : 0.009 0.155 12266 Dihedral : 23.222 176.406 77213 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.36 % Favored : 95.53 % Rotamer: Outliers : 4.02 % Allowed : 17.46 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.11), residues: 5480 helix: 0.74 (0.12), residues: 1839 sheet: -0.13 (0.15), residues: 1081 loop : -0.81 (0.12), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP c 248 HIS 0.009 0.002 HIS k 35 PHE 0.029 0.003 PHE S 10 TYR 0.025 0.003 TYR p 32 ARG 0.014 0.001 ARG s 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 861 time to evaluate : 5.998 Fit side-chains REVERT: B 49 MET cc_start: 0.2234 (OUTLIER) cc_final: 0.1749 (mpm) REVERT: B 100 MET cc_start: 0.3765 (OUTLIER) cc_final: 0.3513 (mmm) REVERT: C 127 ARG cc_start: 0.6693 (mtt90) cc_final: 0.5894 (mtm110) REVERT: C 134 MET cc_start: 0.7815 (mtp) cc_final: 0.7372 (mtm) REVERT: C 161 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6449 (tp30) REVERT: C 183 ASP cc_start: 0.7642 (t0) cc_final: 0.7352 (t0) REVERT: D 47 ARG cc_start: 0.4982 (OUTLIER) cc_final: 0.4202 (ptp-170) REVERT: D 116 GLN cc_start: 0.6125 (OUTLIER) cc_final: 0.4590 (tp40) REVERT: D 138 SER cc_start: 0.6805 (OUTLIER) cc_final: 0.6265 (t) REVERT: D 160 GLU cc_start: 0.5264 (mp0) cc_final: 0.4698 (mt-10) REVERT: D 183 LYS cc_start: 0.5710 (mtmm) cc_final: 0.5057 (tmtm) REVERT: D 184 ARG cc_start: 0.4153 (ptt90) cc_final: 0.3441 (ppt170) REVERT: D 200 ILE cc_start: 0.6515 (OUTLIER) cc_final: 0.6259 (mm) REVERT: E 45 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6073 (ttp80) REVERT: E 74 VAL cc_start: 0.7758 (t) cc_final: 0.7462 (m) REVERT: E 93 ARG cc_start: 0.7549 (mtm-85) cc_final: 0.7132 (mtt-85) REVERT: E 146 ASN cc_start: 0.5797 (m-40) cc_final: 0.5379 (p0) REVERT: F 2 ARG cc_start: 0.6964 (mtt180) cc_final: 0.6692 (mtm-85) REVERT: F 9 MET cc_start: 0.7609 (mtm) cc_final: 0.6968 (mtt) REVERT: F 37 HIS cc_start: 0.6790 (m-70) cc_final: 0.6471 (m-70) REVERT: F 62 MET cc_start: 0.7163 (mtp) cc_final: 0.6545 (mpp) REVERT: G 44 TYR cc_start: 0.6643 (m-10) cc_final: 0.6402 (m-10) REVERT: G 144 MET cc_start: 0.6582 (OUTLIER) cc_final: 0.6257 (mtp) REVERT: H 96 MET cc_start: 0.7319 (ttm) cc_final: 0.6855 (ttm) REVERT: I 20 PHE cc_start: 0.7317 (m-80) cc_final: 0.6984 (m-80) REVERT: I 68 LYS cc_start: 0.7798 (mttp) cc_final: 0.7456 (mtpt) REVERT: I 98 LEU cc_start: 0.7046 (mt) cc_final: 0.6708 (mp) REVERT: J 11 LYS cc_start: 0.7876 (mttt) cc_final: 0.7510 (mttp) REVERT: J 24 GLU cc_start: 0.5247 (OUTLIER) cc_final: 0.4976 (mt-10) REVERT: J 66 GLU cc_start: 0.7736 (pt0) cc_final: 0.7071 (pp20) REVERT: J 73 LEU cc_start: 0.7554 (tp) cc_final: 0.7161 (tm) REVERT: J 88 MET cc_start: 0.3975 (mmt) cc_final: 0.3187 (ptm) REVERT: L 75 GLN cc_start: 0.6934 (pt0) cc_final: 0.6479 (pt0) REVERT: M 13 LYS cc_start: 0.6429 (mttt) cc_final: 0.5958 (mtmm) REVERT: M 19 LEU cc_start: 0.7526 (mt) cc_final: 0.7319 (mt) REVERT: M 31 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7614 (ttmm) REVERT: M 75 MET cc_start: 0.5976 (mmp) cc_final: 0.5538 (mtm) REVERT: M 81 MET cc_start: 0.6636 (OUTLIER) cc_final: 0.6301 (mtm) REVERT: M 93 ARG cc_start: 0.6571 (mmt90) cc_final: 0.5792 (mmt90) REVERT: M 95 LEU cc_start: 0.8032 (mt) cc_final: 0.7812 (mt) REVERT: N 6 MET cc_start: 0.7788 (mmm) cc_final: 0.7479 (mmm) REVERT: N 21 PHE cc_start: 0.6796 (t80) cc_final: 0.6538 (t80) REVERT: N 86 GLU cc_start: 0.6731 (mt-10) cc_final: 0.6399 (mt-10) REVERT: O 47 LYS cc_start: 0.7723 (mttp) cc_final: 0.7271 (mtmt) REVERT: O 48 LYS cc_start: 0.7780 (mmtm) cc_final: 0.7302 (mmtt) REVERT: O 62 GLN cc_start: 0.7832 (tt0) cc_final: 0.7596 (tt0) REVERT: O 71 LYS cc_start: 0.7569 (ttmm) cc_final: 0.7274 (tttm) REVERT: P 35 ARG cc_start: 0.7017 (ttp80) cc_final: 0.6400 (ttt90) REVERT: Q 30 LYS cc_start: 0.8305 (tttt) cc_final: 0.7795 (tttm) REVERT: Q 60 GLU cc_start: 0.7247 (tt0) cc_final: 0.6750 (tt0) REVERT: R 24 LYS cc_start: 0.6512 (mtmm) cc_final: 0.6141 (mtpt) REVERT: R 51 TYR cc_start: 0.7153 (m-80) cc_final: 0.6618 (m-80) REVERT: R 55 LEU cc_start: 0.7359 (tp) cc_final: 0.7044 (tp) REVERT: R 57 ARG cc_start: 0.7338 (mtm-85) cc_final: 0.7020 (mtp180) REVERT: R 61 ARG cc_start: 0.6994 (mtt90) cc_final: 0.6249 (mtt-85) REVERT: S 44 MET cc_start: 0.5816 (mtp) cc_final: 0.5371 (ttm) REVERT: S 73 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6837 (mt-10) REVERT: T 16 LYS cc_start: 0.6546 (ttpp) cc_final: 0.6170 (mttp) REVERT: T 53 GLU cc_start: 0.5929 (OUTLIER) cc_final: 0.5587 (tt0) REVERT: T 80 THR cc_start: 0.6538 (m) cc_final: 0.6115 (t) REVERT: U 36 GLU cc_start: 0.6662 (tt0) cc_final: 0.5738 (mt-10) REVERT: c 5 LYS cc_start: 0.8021 (mtpp) cc_final: 0.7401 (mttm) REVERT: c 26 LYS cc_start: 0.8288 (mttm) cc_final: 0.7794 (mttt) REVERT: c 66 ASP cc_start: 0.8031 (t0) cc_final: 0.7808 (t0) REVERT: c 97 LYS cc_start: 0.7009 (ttmm) cc_final: 0.6624 (mttt) REVERT: c 111 LYS cc_start: 0.7314 (pttm) cc_final: 0.6715 (ptpp) REVERT: c 167 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6229 (tpt-90) REVERT: c 185 GLU cc_start: 0.6790 (mt-10) cc_final: 0.6232 (tt0) REVERT: c 269 ARG cc_start: 0.7307 (ttm-80) cc_final: 0.6951 (ttt90) REVERT: d 1 MET cc_start: 0.4912 (tpt) cc_final: 0.4108 (tpp) REVERT: d 2 ILE cc_start: 0.7108 (pt) cc_final: 0.6874 (pp) REVERT: d 7 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.8059 (ptpt) REVERT: d 28 GLU cc_start: 0.7747 (pp20) cc_final: 0.7508 (tm-30) REVERT: d 103 ASP cc_start: 0.6289 (m-30) cc_final: 0.6087 (m-30) REVERT: d 185 ASN cc_start: 0.7762 (m110) cc_final: 0.7211 (m110) REVERT: e 25 GLU cc_start: 0.7306 (tt0) cc_final: 0.7100 (tt0) REVERT: e 127 GLU cc_start: 0.5653 (mt-10) cc_final: 0.4959 (mm-30) REVERT: e 134 LEU cc_start: 0.6367 (tp) cc_final: 0.6053 (tm) REVERT: e 136 GLN cc_start: 0.6649 (tp-100) cc_final: 0.5954 (mm-40) REVERT: e 139 LYS cc_start: 0.6673 (tttp) cc_final: 0.6196 (ttpm) REVERT: e 140 ASP cc_start: 0.5729 (m-30) cc_final: 0.5093 (m-30) REVERT: e 191 ASP cc_start: 0.5564 (OUTLIER) cc_final: 0.5171 (t70) REVERT: f 42 GLU cc_start: 0.5900 (pm20) cc_final: 0.5671 (pm20) REVERT: f 47 LYS cc_start: 0.6237 (mmtt) cc_final: 0.5995 (mtpm) REVERT: f 112 ARG cc_start: 0.5515 (OUTLIER) cc_final: 0.5215 (mtt-85) REVERT: f 129 SER cc_start: 0.7956 (m) cc_final: 0.7640 (m) REVERT: f 133 ARG cc_start: 0.5616 (mtm-85) cc_final: 0.5409 (mtm180) REVERT: f 147 ASP cc_start: 0.5966 (OUTLIER) cc_final: 0.5435 (m-30) REVERT: f 164 GLU cc_start: 0.5879 (pm20) cc_final: 0.5590 (pt0) REVERT: g 139 GLN cc_start: 0.6427 (tm-30) cc_final: 0.6148 (tm-30) REVERT: i 23 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7853 (mttp) REVERT: i 31 GLU cc_start: 0.7051 (tp30) cc_final: 0.6837 (tp30) REVERT: i 49 ASP cc_start: 0.8112 (t0) cc_final: 0.7816 (t0) REVERT: i 96 ARG cc_start: 0.6714 (mmm-85) cc_final: 0.6363 (mtm180) REVERT: i 125 TYR cc_start: 0.8034 (m-80) cc_final: 0.7378 (m-80) REVERT: j 1 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8310 (ttp) REVERT: j 4 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7343 (mt-10) REVERT: j 17 ARG cc_start: 0.7635 (mmt90) cc_final: 0.7277 (mmt90) REVERT: j 51 LYS cc_start: 0.7469 (mttp) cc_final: 0.7139 (mttm) REVERT: j 113 MET cc_start: 0.6377 (mmm) cc_final: 0.6079 (mmm) REVERT: k 104 GLN cc_start: 0.8061 (mm110) cc_final: 0.7787 (mt0) REVERT: k 106 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7246 (mp0) REVERT: k 123 ARG cc_start: 0.7094 (ttm170) cc_final: 0.6746 (ttp80) REVERT: k 129 LYS cc_start: 0.6854 (mppt) cc_final: 0.6530 (mmpt) REVERT: l 7 THR cc_start: 0.7923 (p) cc_final: 0.7543 (p) REVERT: l 55 ARG cc_start: 0.7692 (tpt170) cc_final: 0.6389 (ttm110) REVERT: l 127 LYS cc_start: 0.7776 (ttmt) cc_final: 0.7323 (tptm) REVERT: m 117 ASP cc_start: 0.7607 (p0) cc_final: 0.7197 (p0) REVERT: n 13 ARG cc_start: 0.6957 (ttm-80) cc_final: 0.6386 (ttm170) REVERT: n 16 ARG cc_start: 0.7288 (mmp80) cc_final: 0.6952 (mmp-170) REVERT: n 46 GLU cc_start: 0.6637 (pt0) cc_final: 0.6390 (tm-30) REVERT: n 58 ILE cc_start: 0.6269 (OUTLIER) cc_final: 0.6007 (mm) REVERT: n 76 LYS cc_start: 0.6536 (tttt) cc_final: 0.6132 (tmtm) REVERT: o 111 LYS cc_start: 0.7647 (ttpt) cc_final: 0.7114 (tttp) REVERT: p 59 GLN cc_start: 0.8302 (tt0) cc_final: 0.8052 (tt0) REVERT: q 15 SER cc_start: 0.8444 (p) cc_final: 0.7721 (m) REVERT: q 40 MET cc_start: 0.7442 (ptm) cc_final: 0.7187 (ppp) REVERT: q 48 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7297 (mttp) REVERT: q 73 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7771 (mttp) REVERT: r 31 GLN cc_start: 0.6953 (mt0) cc_final: 0.6747 (mt0) REVERT: r 86 MET cc_start: 0.7678 (ttm) cc_final: 0.7216 (ttp) REVERT: s 51 PHE cc_start: 0.7683 (m-10) cc_final: 0.7378 (m-10) REVERT: t 10 GLU cc_start: 0.6544 (tp30) cc_final: 0.5965 (tp30) REVERT: t 26 LYS cc_start: 0.7028 (tttm) cc_final: 0.6714 (tttm) REVERT: t 47 LYS cc_start: 0.7073 (OUTLIER) cc_final: 0.6655 (mptm) REVERT: t 77 THR cc_start: 0.5593 (p) cc_final: 0.5310 (t) REVERT: u 3 THR cc_start: 0.7300 (m) cc_final: 0.7092 (t) REVERT: u 25 LYS cc_start: 0.7631 (mtpp) cc_final: 0.7323 (mtmp) REVERT: u 34 LYS cc_start: 0.5394 (tppt) cc_final: 0.5101 (tptm) REVERT: u 41 GLU cc_start: 0.6765 (mt-10) cc_final: 0.6510 (mt-10) REVERT: u 45 ASP cc_start: 0.7147 (m-30) cc_final: 0.6849 (m-30) REVERT: u 68 LYS cc_start: 0.5721 (ttmm) cc_final: 0.5227 (tptt) REVERT: u 73 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7291 (tttm) REVERT: v 3 HIS cc_start: 0.7229 (m90) cc_final: 0.6871 (m170) REVERT: v 25 ARG cc_start: 0.7983 (mmt90) cc_final: 0.7656 (mmt90) REVERT: v 64 ASP cc_start: 0.7983 (m-30) cc_final: 0.7423 (m-30) REVERT: v 72 LYS cc_start: 0.7805 (ptpp) cc_final: 0.7034 (pptt) REVERT: w 11 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.6761 (mtp85) REVERT: x 8 GLU cc_start: 0.5654 (mm-30) cc_final: 0.4954 (tp30) REVERT: x 39 GLN cc_start: 0.6904 (mt0) cc_final: 0.6346 (mt0) REVERT: x 45 GLN cc_start: 0.6673 (mt0) cc_final: 0.5876 (mt0) REVERT: y 56 LYS cc_start: 0.8155 (ttpt) cc_final: 0.7546 (ttmp) REVERT: z 31 ASP cc_start: 0.8091 (t70) cc_final: 0.7675 (t70) REVERT: 0 45 GLN cc_start: 0.7673 (mm110) cc_final: 0.7400 (mm110) REVERT: 1 1 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.7119 (mpp) REVERT: 3 17 VAL cc_start: 0.8368 (p) cc_final: 0.8155 (m) REVERT: 3 24 ARG cc_start: 0.7904 (ptm160) cc_final: 0.7521 (mtt-85) outliers start: 184 outliers final: 122 residues processed: 972 average time/residue: 2.3059 time to fit residues: 3132.8183 Evaluate side-chains 993 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 844 time to evaluate : 5.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain J residue 24 GLU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 97 LYS Chi-restraints excluded: chain O residue 72 ARG Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 83 GLU Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain S residue 3 ARG Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain c residue 167 ARG Chi-restraints excluded: chain c residue 194 GLU Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 144 GLU Chi-restraints excluded: chain e residue 169 VAL Chi-restraints excluded: chain e residue 170 ARG Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain e residue 199 MET Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 112 ARG Chi-restraints excluded: chain f residue 147 ASP Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 14 ASP Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain i residue 131 ASN Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 4 GLU Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain l residue 24 THR Chi-restraints excluded: chain m residue 35 LYS Chi-restraints excluded: chain m residue 36 THR Chi-restraints excluded: chain m residue 57 THR Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 91 SER Chi-restraints excluded: chain n residue 103 VAL Chi-restraints excluded: chain o residue 115 ASN Chi-restraints excluded: chain p residue 87 SER Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 48 LYS Chi-restraints excluded: chain q residue 73 LYS Chi-restraints excluded: chain r residue 22 ASP Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain s residue 55 VAL Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain t residue 103 ILE Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 64 VAL Chi-restraints excluded: chain u residue 73 LYS Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain w residue 11 ARG Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 55 VAL Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 30 VAL Chi-restraints excluded: chain 0 residue 42 VAL Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 52 LYS Chi-restraints excluded: chain 3 residue 19 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 590 optimal weight: 10.0000 chunk 381 optimal weight: 6.9990 chunk 569 optimal weight: 10.0000 chunk 287 optimal weight: 20.0000 chunk 187 optimal weight: 5.9990 chunk 184 optimal weight: 7.9990 chunk 606 optimal weight: 10.0000 chunk 650 optimal weight: 10.0000 chunk 471 optimal weight: 30.0000 chunk 88 optimal weight: 10.0000 chunk 750 optimal weight: 1.9990 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 54 GLN D 71 GLN D 198 HIS E 19 ASN E 43 ASN E 78 ASN E 97 GLN E 148 ASN G 142 HIS H 18 GLN J 64 GLN K 101 ASN L 73 ASN L 112 GLN N 49 GLN N 60 GLN O 37 ASN O 80 GLN ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 ASN ** f 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 27 GLN g 38 ASN ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 18 GLN n 38 GLN n 98 GLN ** o 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 6 GLN q 18 GLN t 46 GLN x 20 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 153976 Z= 0.349 Angle : 0.802 17.691 230432 Z= 0.428 Chirality : 0.043 0.407 29298 Planarity : 0.008 0.150 12266 Dihedral : 23.184 177.212 77213 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.95 % Rotamer: Outliers : 4.00 % Allowed : 18.12 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.11), residues: 5480 helix: 0.74 (0.12), residues: 1847 sheet: -0.14 (0.15), residues: 1087 loop : -0.84 (0.12), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP c 248 HIS 0.009 0.002 HIS k 35 PHE 0.026 0.002 PHE S 10 TYR 0.022 0.002 TYR p 32 ARG 0.012 0.001 ARG s 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 859 time to evaluate : 6.645 Fit side-chains REVERT: B 49 MET cc_start: 0.2124 (OUTLIER) cc_final: 0.1665 (mpm) REVERT: B 100 MET cc_start: 0.3741 (OUTLIER) cc_final: 0.3454 (mmm) REVERT: C 28 GLU cc_start: 0.6371 (OUTLIER) cc_final: 0.6148 (pm20) REVERT: C 127 ARG cc_start: 0.6704 (mtt90) cc_final: 0.5897 (mtm110) REVERT: C 134 MET cc_start: 0.7797 (mtp) cc_final: 0.7359 (mtm) REVERT: C 161 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6402 (tp30) REVERT: C 183 ASP cc_start: 0.7652 (t0) cc_final: 0.7367 (t0) REVERT: D 44 ARG cc_start: 0.5654 (ptm160) cc_final: 0.4390 (ttt90) REVERT: D 47 ARG cc_start: 0.4822 (OUTLIER) cc_final: 0.4157 (ptp-170) REVERT: D 105 MET cc_start: 0.6782 (OUTLIER) cc_final: 0.5929 (mpp) REVERT: D 116 GLN cc_start: 0.6103 (OUTLIER) cc_final: 0.4577 (tp40) REVERT: D 138 SER cc_start: 0.6808 (OUTLIER) cc_final: 0.6269 (t) REVERT: D 160 GLU cc_start: 0.5075 (mp0) cc_final: 0.4502 (mt-10) REVERT: D 183 LYS cc_start: 0.5746 (mtmm) cc_final: 0.5113 (tmtm) REVERT: D 184 ARG cc_start: 0.4131 (ptt90) cc_final: 0.3423 (ppt170) REVERT: D 200 ILE cc_start: 0.6493 (OUTLIER) cc_final: 0.6236 (mm) REVERT: E 26 LYS cc_start: 0.7682 (ttmt) cc_final: 0.7208 (tttp) REVERT: E 45 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6125 (ttp80) REVERT: E 93 ARG cc_start: 0.7560 (mtm-85) cc_final: 0.7133 (mtt-85) REVERT: E 146 ASN cc_start: 0.5726 (m-40) cc_final: 0.5362 (p0) REVERT: E 147 MET cc_start: 0.7781 (ttp) cc_final: 0.7454 (ttp) REVERT: F 2 ARG cc_start: 0.6876 (mtt180) cc_final: 0.6675 (mtm-85) REVERT: F 9 MET cc_start: 0.7608 (mtm) cc_final: 0.6991 (mtt) REVERT: F 37 HIS cc_start: 0.6771 (m-70) cc_final: 0.6497 (m-70) REVERT: F 62 MET cc_start: 0.7187 (mtp) cc_final: 0.6561 (mpp) REVERT: G 11 LYS cc_start: 0.5385 (OUTLIER) cc_final: 0.5140 (mmpt) REVERT: G 144 MET cc_start: 0.6476 (OUTLIER) cc_final: 0.6156 (mtp) REVERT: H 96 MET cc_start: 0.7309 (ttm) cc_final: 0.6887 (ttm) REVERT: I 20 PHE cc_start: 0.7246 (m-80) cc_final: 0.6873 (m-80) REVERT: I 68 LYS cc_start: 0.7804 (mttp) cc_final: 0.7430 (mtpt) REVERT: I 98 LEU cc_start: 0.6932 (mt) cc_final: 0.6643 (mp) REVERT: J 11 LYS cc_start: 0.7877 (mttt) cc_final: 0.7485 (mttp) REVERT: J 66 GLU cc_start: 0.7771 (pt0) cc_final: 0.7113 (pp20) REVERT: J 73 LEU cc_start: 0.7570 (tp) cc_final: 0.7167 (tm) REVERT: J 88 MET cc_start: 0.3997 (mmt) cc_final: 0.3304 (mpt) REVERT: L 75 GLN cc_start: 0.6934 (pt0) cc_final: 0.6470 (pt0) REVERT: M 13 LYS cc_start: 0.6429 (mttt) cc_final: 0.5959 (mtmm) REVERT: M 31 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7633 (ttmm) REVERT: M 75 MET cc_start: 0.5990 (mmp) cc_final: 0.5558 (mtm) REVERT: M 93 ARG cc_start: 0.6529 (mmt90) cc_final: 0.5724 (mmt90) REVERT: M 95 LEU cc_start: 0.8014 (mt) cc_final: 0.7793 (mt) REVERT: N 6 MET cc_start: 0.7753 (mmm) cc_final: 0.7415 (mmm) REVERT: N 21 PHE cc_start: 0.6772 (t80) cc_final: 0.6512 (t80) REVERT: N 86 GLU cc_start: 0.6709 (mt-10) cc_final: 0.6408 (mt-10) REVERT: O 47 LYS cc_start: 0.7713 (mttp) cc_final: 0.7252 (mtmt) REVERT: O 48 LYS cc_start: 0.7750 (mmtm) cc_final: 0.7279 (mmtt) REVERT: O 62 GLN cc_start: 0.7839 (tt0) cc_final: 0.7610 (tt0) REVERT: O 71 LYS cc_start: 0.7600 (ttmm) cc_final: 0.7293 (tttm) REVERT: P 35 ARG cc_start: 0.7003 (ttp80) cc_final: 0.6386 (ttt90) REVERT: Q 30 LYS cc_start: 0.8311 (tttt) cc_final: 0.7789 (tttm) REVERT: Q 60 GLU cc_start: 0.7231 (tt0) cc_final: 0.6764 (tt0) REVERT: R 24 LYS cc_start: 0.6436 (mtmm) cc_final: 0.6112 (mtpt) REVERT: R 51 TYR cc_start: 0.7153 (m-80) cc_final: 0.6675 (m-80) REVERT: R 55 LEU cc_start: 0.7348 (tp) cc_final: 0.7022 (tp) REVERT: R 57 ARG cc_start: 0.7320 (mtm-85) cc_final: 0.7092 (mtp180) REVERT: R 61 ARG cc_start: 0.6998 (mtt90) cc_final: 0.6272 (mtt-85) REVERT: S 44 MET cc_start: 0.5802 (mtp) cc_final: 0.5407 (ttm) REVERT: S 73 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6904 (mt-10) REVERT: T 16 LYS cc_start: 0.6586 (ttpp) cc_final: 0.6147 (mtpp) REVERT: T 53 GLU cc_start: 0.5885 (OUTLIER) cc_final: 0.5483 (tt0) REVERT: T 80 THR cc_start: 0.6529 (m) cc_final: 0.6137 (t) REVERT: U 21 ARG cc_start: 0.5236 (ttt180) cc_final: 0.4636 (mmm160) REVERT: U 36 GLU cc_start: 0.6658 (tt0) cc_final: 0.5733 (mt-10) REVERT: c 5 LYS cc_start: 0.8007 (mtpp) cc_final: 0.7384 (mttm) REVERT: c 26 LYS cc_start: 0.8243 (mttm) cc_final: 0.7748 (mttt) REVERT: c 66 ASP cc_start: 0.8020 (t0) cc_final: 0.7805 (t0) REVERT: c 97 LYS cc_start: 0.7009 (ttmm) cc_final: 0.6461 (ttmt) REVERT: c 102 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7854 (mtp85) REVERT: c 111 LYS cc_start: 0.7278 (pttm) cc_final: 0.6684 (ptpp) REVERT: c 167 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6210 (tpt-90) REVERT: c 185 GLU cc_start: 0.6847 (mt-10) cc_final: 0.6379 (tt0) REVERT: c 269 ARG cc_start: 0.7294 (ttm-80) cc_final: 0.6925 (ttt90) REVERT: d 1 MET cc_start: 0.4841 (tpt) cc_final: 0.4093 (tpp) REVERT: d 7 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8061 (ptpt) REVERT: d 28 GLU cc_start: 0.7737 (pp20) cc_final: 0.7507 (tm-30) REVERT: d 185 ASN cc_start: 0.7788 (m110) cc_final: 0.7252 (m110) REVERT: e 25 GLU cc_start: 0.7287 (tt0) cc_final: 0.7083 (tt0) REVERT: e 134 LEU cc_start: 0.6356 (tp) cc_final: 0.6056 (tm) REVERT: e 136 GLN cc_start: 0.6509 (tp-100) cc_final: 0.5872 (mm-40) REVERT: e 139 LYS cc_start: 0.6664 (tttp) cc_final: 0.6225 (ttpm) REVERT: e 140 ASP cc_start: 0.5391 (m-30) cc_final: 0.4836 (m-30) REVERT: e 191 ASP cc_start: 0.5609 (OUTLIER) cc_final: 0.5241 (t70) REVERT: f 42 GLU cc_start: 0.5834 (pm20) cc_final: 0.5606 (pm20) REVERT: f 47 LYS cc_start: 0.6269 (mmtt) cc_final: 0.6013 (mtpm) REVERT: f 112 ARG cc_start: 0.5542 (OUTLIER) cc_final: 0.5237 (mtt-85) REVERT: f 129 SER cc_start: 0.7937 (m) cc_final: 0.7627 (m) REVERT: f 133 ARG cc_start: 0.5554 (mtm-85) cc_final: 0.5272 (mtm180) REVERT: f 147 ASP cc_start: 0.5922 (OUTLIER) cc_final: 0.5397 (m-30) REVERT: f 164 GLU cc_start: 0.5852 (pm20) cc_final: 0.5556 (pt0) REVERT: g 139 GLN cc_start: 0.6422 (tm-30) cc_final: 0.6131 (tm-30) REVERT: g 155 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6603 (pp20) REVERT: i 23 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7854 (mttp) REVERT: i 31 GLU cc_start: 0.7021 (tp30) cc_final: 0.6804 (tp30) REVERT: i 49 ASP cc_start: 0.8114 (t0) cc_final: 0.7803 (t0) REVERT: i 95 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6800 (mtp-110) REVERT: i 96 ARG cc_start: 0.6652 (mmm-85) cc_final: 0.6363 (ptt-90) REVERT: i 125 TYR cc_start: 0.8034 (m-80) cc_final: 0.7352 (m-80) REVERT: j 1 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8312 (ttp) REVERT: j 17 ARG cc_start: 0.7643 (mmt90) cc_final: 0.7291 (mmt90) REVERT: j 51 LYS cc_start: 0.7505 (mttp) cc_final: 0.7184 (mttm) REVERT: j 113 MET cc_start: 0.6327 (mmm) cc_final: 0.5985 (mmm) REVERT: k 123 ARG cc_start: 0.7104 (ttm170) cc_final: 0.6741 (ttp80) REVERT: k 129 LYS cc_start: 0.6874 (mppt) cc_final: 0.6561 (mmpt) REVERT: l 7 THR cc_start: 0.7937 (p) cc_final: 0.7547 (p) REVERT: l 55 ARG cc_start: 0.7652 (tpt170) cc_final: 0.6337 (ttm110) REVERT: l 127 LYS cc_start: 0.7737 (ttmt) cc_final: 0.7310 (tptm) REVERT: m 117 ASP cc_start: 0.7598 (p0) cc_final: 0.7212 (p0) REVERT: n 13 ARG cc_start: 0.6942 (ttm-80) cc_final: 0.6363 (ttm170) REVERT: n 16 ARG cc_start: 0.7287 (mmp80) cc_final: 0.6959 (mmp-170) REVERT: n 46 GLU cc_start: 0.6610 (pt0) cc_final: 0.6378 (tm-30) REVERT: n 58 ILE cc_start: 0.6257 (OUTLIER) cc_final: 0.6008 (mm) REVERT: n 76 LYS cc_start: 0.6547 (tttt) cc_final: 0.6159 (tptt) REVERT: o 111 LYS cc_start: 0.7644 (ttpt) cc_final: 0.7087 (tttp) REVERT: p 59 GLN cc_start: 0.8289 (tt0) cc_final: 0.8029 (tt0) REVERT: q 15 SER cc_start: 0.8416 (p) cc_final: 0.7751 (m) REVERT: q 48 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.7224 (mttp) REVERT: q 73 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7761 (mttp) REVERT: r 33 LEU cc_start: 0.7964 (mt) cc_final: 0.7755 (mt) REVERT: r 86 MET cc_start: 0.7609 (ttm) cc_final: 0.7172 (ttp) REVERT: s 51 PHE cc_start: 0.7620 (m-10) cc_final: 0.7326 (m-10) REVERT: t 10 GLU cc_start: 0.6566 (tp30) cc_final: 0.5987 (tp30) REVERT: t 47 LYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6654 (mptm) REVERT: u 25 LYS cc_start: 0.7617 (mtpp) cc_final: 0.7305 (mtmp) REVERT: u 34 LYS cc_start: 0.5407 (tppt) cc_final: 0.5203 (tptm) REVERT: u 45 ASP cc_start: 0.7174 (m-30) cc_final: 0.6840 (m-30) REVERT: u 68 LYS cc_start: 0.5662 (ttmm) cc_final: 0.5271 (tptt) REVERT: u 73 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7299 (tttm) REVERT: v 3 HIS cc_start: 0.7226 (m90) cc_final: 0.6867 (m-70) REVERT: v 25 ARG cc_start: 0.7976 (mmt90) cc_final: 0.7655 (mmt90) REVERT: v 64 ASP cc_start: 0.7989 (m-30) cc_final: 0.7454 (m-30) REVERT: v 72 LYS cc_start: 0.7841 (ptpp) cc_final: 0.7072 (pptt) REVERT: w 11 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.6573 (mtp85) REVERT: x 8 GLU cc_start: 0.5591 (mm-30) cc_final: 0.4884 (tp30) REVERT: x 39 GLN cc_start: 0.6895 (mt0) cc_final: 0.6306 (mt0) REVERT: x 45 GLN cc_start: 0.6656 (mt0) cc_final: 0.5855 (mt0) REVERT: y 56 LYS cc_start: 0.8083 (ttpt) cc_final: 0.7479 (ttmp) REVERT: z 31 ASP cc_start: 0.8037 (t70) cc_final: 0.7782 (t70) REVERT: 0 45 GLN cc_start: 0.7669 (mm110) cc_final: 0.7394 (mm110) REVERT: 1 1 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.7118 (mpp) REVERT: 3 17 VAL cc_start: 0.8361 (p) cc_final: 0.8145 (m) outliers start: 183 outliers final: 127 residues processed: 967 average time/residue: 2.2734 time to fit residues: 3072.7009 Evaluate side-chains 1007 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 850 time to evaluate : 5.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain G residue 11 LYS Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 99 ARG Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 97 LYS Chi-restraints excluded: chain O residue 72 ARG Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 83 GLU Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain S residue 3 ARG Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain c residue 102 ARG Chi-restraints excluded: chain c residue 167 ARG Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 144 GLU Chi-restraints excluded: chain e residue 170 ARG Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain e residue 199 MET Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 112 ARG Chi-restraints excluded: chain f residue 147 ASP Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 14 ASP Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain i residue 95 ARG Chi-restraints excluded: chain i residue 131 ASN Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain l residue 24 THR Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 35 LYS Chi-restraints excluded: chain m residue 36 THR Chi-restraints excluded: chain m residue 57 THR Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 91 SER Chi-restraints excluded: chain n residue 103 VAL Chi-restraints excluded: chain o residue 115 ASN Chi-restraints excluded: chain p residue 87 SER Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 48 LYS Chi-restraints excluded: chain q residue 73 LYS Chi-restraints excluded: chain r residue 22 ASP Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain s residue 55 VAL Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain t residue 70 VAL Chi-restraints excluded: chain t residue 103 ILE Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 64 VAL Chi-restraints excluded: chain u residue 73 LYS Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain w residue 11 ARG Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 55 VAL Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 30 VAL Chi-restraints excluded: chain 0 residue 42 VAL Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 52 LYS Chi-restraints excluded: chain 3 residue 19 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 868 optimal weight: 4.9990 chunk 914 optimal weight: 10.0000 chunk 834 optimal weight: 5.9990 chunk 889 optimal weight: 2.9990 chunk 913 optimal weight: 6.9990 chunk 535 optimal weight: 20.0000 chunk 387 optimal weight: 10.0000 chunk 698 optimal weight: 9.9990 chunk 272 optimal weight: 7.9990 chunk 803 optimal weight: 2.9990 chunk 840 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 54 GLN D 71 GLN D 196 ASN D 198 HIS E 19 ASN E 43 ASN E 78 ASN E 97 GLN E 148 ASN G 142 HIS H 18 GLN J 64 GLN L 73 ASN L 112 GLN N 60 GLN O 37 ASN O 80 GLN ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 ASN c 163 GLN d 36 GLN ** f 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 27 GLN g 38 ASN ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 18 GLN ** o 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 6 GLN q 18 GLN t 27 ASN t 46 GLN x 20 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 153976 Z= 0.269 Angle : 0.745 16.671 230432 Z= 0.406 Chirality : 0.040 0.406 29298 Planarity : 0.008 0.146 12266 Dihedral : 23.170 177.224 77213 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.03 % Favored : 95.89 % Rotamer: Outliers : 3.72 % Allowed : 18.75 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.11), residues: 5480 helix: 0.84 (0.12), residues: 1846 sheet: -0.12 (0.15), residues: 1080 loop : -0.81 (0.12), residues: 2554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP c 248 HIS 0.006 0.001 HIS k 35 PHE 0.024 0.002 PHE S 10 TYR 0.020 0.002 TYR R 51 ARG 0.011 0.001 ARG s 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1028 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 858 time to evaluate : 5.993 Fit side-chains REVERT: B 49 MET cc_start: 0.2125 (OUTLIER) cc_final: 0.1665 (mpm) REVERT: B 100 MET cc_start: 0.3711 (OUTLIER) cc_final: 0.3442 (mmm) REVERT: C 127 ARG cc_start: 0.6673 (mtt90) cc_final: 0.5871 (mtm110) REVERT: C 134 MET cc_start: 0.7801 (mtp) cc_final: 0.7285 (mtm) REVERT: C 161 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6402 (tp30) REVERT: C 183 ASP cc_start: 0.7670 (t0) cc_final: 0.7390 (t0) REVERT: D 44 ARG cc_start: 0.5652 (ptm160) cc_final: 0.4607 (mmt180) REVERT: D 47 ARG cc_start: 0.4781 (OUTLIER) cc_final: 0.4099 (ptp-170) REVERT: D 105 MET cc_start: 0.6810 (OUTLIER) cc_final: 0.6028 (mpp) REVERT: D 116 GLN cc_start: 0.6095 (OUTLIER) cc_final: 0.4566 (tp40) REVERT: D 138 SER cc_start: 0.6932 (OUTLIER) cc_final: 0.6385 (t) REVERT: D 160 GLU cc_start: 0.5125 (mp0) cc_final: 0.4545 (mt-10) REVERT: D 183 LYS cc_start: 0.5757 (mtmm) cc_final: 0.5120 (tmtm) REVERT: D 184 ARG cc_start: 0.4137 (ptt90) cc_final: 0.3331 (ppt170) REVERT: D 200 ILE cc_start: 0.6496 (OUTLIER) cc_final: 0.6242 (mm) REVERT: E 26 LYS cc_start: 0.7688 (ttmt) cc_final: 0.7219 (tttp) REVERT: E 74 VAL cc_start: 0.7776 (t) cc_final: 0.7491 (m) REVERT: E 93 ARG cc_start: 0.7531 (mtm-85) cc_final: 0.7116 (mtt-85) REVERT: E 146 ASN cc_start: 0.5702 (m-40) cc_final: 0.5442 (p0) REVERT: E 147 MET cc_start: 0.7772 (ttp) cc_final: 0.7372 (ttp) REVERT: F 2 ARG cc_start: 0.6860 (mtt180) cc_final: 0.6655 (mtm-85) REVERT: F 9 MET cc_start: 0.7617 (mtm) cc_final: 0.6992 (mtt) REVERT: F 37 HIS cc_start: 0.6769 (m-70) cc_final: 0.6467 (m-70) REVERT: F 62 MET cc_start: 0.7179 (mtp) cc_final: 0.6568 (mpp) REVERT: F 90 MET cc_start: 0.6513 (mpp) cc_final: 0.6057 (mtp) REVERT: G 11 LYS cc_start: 0.5388 (OUTLIER) cc_final: 0.5143 (mmpt) REVERT: G 144 MET cc_start: 0.6522 (OUTLIER) cc_final: 0.6203 (mtp) REVERT: H 96 MET cc_start: 0.7298 (ttm) cc_final: 0.6863 (ttm) REVERT: I 20 PHE cc_start: 0.7249 (m-80) cc_final: 0.6875 (m-80) REVERT: I 68 LYS cc_start: 0.7787 (mttp) cc_final: 0.7446 (mtpt) REVERT: I 98 LEU cc_start: 0.6946 (mt) cc_final: 0.6644 (mp) REVERT: J 11 LYS cc_start: 0.7851 (mttt) cc_final: 0.7455 (mttp) REVERT: J 66 GLU cc_start: 0.7774 (pt0) cc_final: 0.7115 (pp20) REVERT: J 73 LEU cc_start: 0.7579 (tp) cc_final: 0.7174 (tm) REVERT: J 88 MET cc_start: 0.4036 (mmt) cc_final: 0.3348 (mpt) REVERT: L 75 GLN cc_start: 0.6927 (pt0) cc_final: 0.6458 (pt0) REVERT: M 13 LYS cc_start: 0.6426 (mttt) cc_final: 0.5964 (mtmm) REVERT: M 31 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7615 (ttmm) REVERT: M 75 MET cc_start: 0.5987 (mmp) cc_final: 0.5559 (mtm) REVERT: M 93 ARG cc_start: 0.6516 (mmt90) cc_final: 0.5711 (mmt90) REVERT: M 95 LEU cc_start: 0.8008 (mt) cc_final: 0.7796 (mt) REVERT: N 6 MET cc_start: 0.7738 (mmm) cc_final: 0.7354 (mmm) REVERT: N 21 PHE cc_start: 0.6783 (t80) cc_final: 0.6526 (t80) REVERT: N 86 GLU cc_start: 0.6695 (mt-10) cc_final: 0.6363 (mt-10) REVERT: O 47 LYS cc_start: 0.7701 (mttp) cc_final: 0.7240 (mtmt) REVERT: O 48 LYS cc_start: 0.7727 (mmtm) cc_final: 0.7271 (mmtt) REVERT: O 62 GLN cc_start: 0.7829 (tt0) cc_final: 0.7606 (tt0) REVERT: O 71 LYS cc_start: 0.7592 (ttmm) cc_final: 0.7296 (tttm) REVERT: P 35 ARG cc_start: 0.6997 (ttp80) cc_final: 0.6378 (ttt90) REVERT: Q 30 LYS cc_start: 0.8292 (tttt) cc_final: 0.7771 (tttm) REVERT: Q 60 GLU cc_start: 0.7227 (tt0) cc_final: 0.6743 (tt0) REVERT: R 24 LYS cc_start: 0.6430 (mtmm) cc_final: 0.6115 (mtpt) REVERT: R 51 TYR cc_start: 0.7160 (m-80) cc_final: 0.6665 (m-80) REVERT: R 55 LEU cc_start: 0.7341 (tp) cc_final: 0.7005 (tp) REVERT: R 57 ARG cc_start: 0.7316 (mtm-85) cc_final: 0.6973 (mtp180) REVERT: S 44 MET cc_start: 0.5802 (mtp) cc_final: 0.5410 (ttm) REVERT: S 73 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6923 (mt-10) REVERT: T 16 LYS cc_start: 0.6551 (ttpp) cc_final: 0.6149 (mtpp) REVERT: T 53 GLU cc_start: 0.5901 (OUTLIER) cc_final: 0.5489 (tt0) REVERT: U 21 ARG cc_start: 0.5230 (ttt180) cc_final: 0.4624 (mmm160) REVERT: U 36 GLU cc_start: 0.6651 (tt0) cc_final: 0.5732 (mt-10) REVERT: U 56 HIS cc_start: 0.4552 (OUTLIER) cc_final: 0.4337 (t70) REVERT: c 5 LYS cc_start: 0.8012 (mtpp) cc_final: 0.7389 (mttm) REVERT: c 26 LYS cc_start: 0.8237 (mttm) cc_final: 0.7751 (mttt) REVERT: c 66 ASP cc_start: 0.8027 (t0) cc_final: 0.7804 (t0) REVERT: c 97 LYS cc_start: 0.7009 (ttmm) cc_final: 0.6635 (mttt) REVERT: c 102 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7897 (mtp85) REVERT: c 111 LYS cc_start: 0.7274 (pttm) cc_final: 0.6684 (ptpp) REVERT: c 167 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6339 (tpt90) REVERT: c 185 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6355 (tt0) REVERT: c 269 ARG cc_start: 0.7295 (ttm-80) cc_final: 0.6926 (ttt90) REVERT: d 1 MET cc_start: 0.4797 (tpt) cc_final: 0.4013 (tpp) REVERT: d 7 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.8061 (ptpt) REVERT: d 28 GLU cc_start: 0.7716 (pp20) cc_final: 0.7468 (tm-30) REVERT: d 185 ASN cc_start: 0.7814 (m110) cc_final: 0.7277 (m110) REVERT: e 25 GLU cc_start: 0.7284 (tt0) cc_final: 0.7081 (tt0) REVERT: e 134 LEU cc_start: 0.6328 (tp) cc_final: 0.6028 (tm) REVERT: e 136 GLN cc_start: 0.6514 (tp-100) cc_final: 0.5873 (mm-40) REVERT: e 139 LYS cc_start: 0.6664 (tttp) cc_final: 0.6224 (ttpm) REVERT: e 140 ASP cc_start: 0.5357 (m-30) cc_final: 0.4806 (m-30) REVERT: e 191 ASP cc_start: 0.5608 (OUTLIER) cc_final: 0.5241 (t70) REVERT: f 47 LYS cc_start: 0.6293 (mmtt) cc_final: 0.5986 (mtpm) REVERT: f 129 SER cc_start: 0.7929 (m) cc_final: 0.7622 (m) REVERT: f 133 ARG cc_start: 0.5598 (mtm-85) cc_final: 0.5394 (mtm180) REVERT: f 147 ASP cc_start: 0.5943 (OUTLIER) cc_final: 0.5412 (m-30) REVERT: f 164 GLU cc_start: 0.5853 (pm20) cc_final: 0.5559 (pt0) REVERT: g 139 GLN cc_start: 0.6421 (tm-30) cc_final: 0.5312 (tt0) REVERT: g 155 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6561 (pp20) REVERT: i 23 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7866 (mttp) REVERT: i 31 GLU cc_start: 0.7026 (tp30) cc_final: 0.6802 (tp30) REVERT: i 49 ASP cc_start: 0.8109 (t0) cc_final: 0.7801 (t0) REVERT: i 95 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6795 (mtp-110) REVERT: i 96 ARG cc_start: 0.6643 (mmm-85) cc_final: 0.6357 (ptt-90) REVERT: i 125 TYR cc_start: 0.7994 (m-80) cc_final: 0.7335 (m-80) REVERT: j 17 ARG cc_start: 0.7637 (mmt90) cc_final: 0.7290 (mmt90) REVERT: j 51 LYS cc_start: 0.7501 (mttp) cc_final: 0.7180 (mttm) REVERT: j 113 MET cc_start: 0.6315 (mmm) cc_final: 0.5977 (mmm) REVERT: k 123 ARG cc_start: 0.7094 (ttm170) cc_final: 0.6766 (ttp80) REVERT: k 129 LYS cc_start: 0.6919 (mppt) cc_final: 0.6596 (mmpt) REVERT: l 7 THR cc_start: 0.7941 (p) cc_final: 0.7545 (p) REVERT: l 55 ARG cc_start: 0.7649 (tpt170) cc_final: 0.6367 (ttm110) REVERT: l 127 LYS cc_start: 0.7719 (ttmt) cc_final: 0.7279 (tptm) REVERT: m 117 ASP cc_start: 0.7605 (p0) cc_final: 0.7225 (p0) REVERT: n 13 ARG cc_start: 0.6921 (ttm-80) cc_final: 0.6337 (ttm170) REVERT: n 16 ARG cc_start: 0.7285 (mmp80) cc_final: 0.6967 (mmp-170) REVERT: n 46 GLU cc_start: 0.6634 (pt0) cc_final: 0.6420 (tm-30) REVERT: n 58 ILE cc_start: 0.6275 (OUTLIER) cc_final: 0.6021 (mm) REVERT: n 76 LYS cc_start: 0.6545 (tttt) cc_final: 0.6154 (tptt) REVERT: o 111 LYS cc_start: 0.7639 (ttpt) cc_final: 0.7078 (tttp) REVERT: p 59 GLN cc_start: 0.8274 (tt0) cc_final: 0.8017 (tt0) REVERT: q 15 SER cc_start: 0.8399 (p) cc_final: 0.7751 (m) REVERT: q 48 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.7219 (mttp) REVERT: q 73 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7745 (mttp) REVERT: r 33 LEU cc_start: 0.7961 (mt) cc_final: 0.7734 (mt) REVERT: r 86 MET cc_start: 0.7601 (ttm) cc_final: 0.7162 (ttp) REVERT: s 51 PHE cc_start: 0.7628 (m-10) cc_final: 0.7346 (m-10) REVERT: t 47 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6750 (mptm) REVERT: u 25 LYS cc_start: 0.7631 (mtpp) cc_final: 0.7329 (mtmp) REVERT: u 34 LYS cc_start: 0.5429 (tppt) cc_final: 0.5225 (tptm) REVERT: u 45 ASP cc_start: 0.7142 (m-30) cc_final: 0.6802 (m-30) REVERT: u 73 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.7311 (tttm) REVERT: v 3 HIS cc_start: 0.7223 (m90) cc_final: 0.6866 (m-70) REVERT: v 25 ARG cc_start: 0.7970 (mmt90) cc_final: 0.7635 (mmt90) REVERT: v 64 ASP cc_start: 0.7984 (m-30) cc_final: 0.7457 (m-30) REVERT: v 72 LYS cc_start: 0.7780 (ptpp) cc_final: 0.7169 (ptmm) REVERT: w 11 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.6187 (mtp85) REVERT: w 45 ARG cc_start: 0.6779 (ptt90) cc_final: 0.5960 (ptt-90) REVERT: x 8 GLU cc_start: 0.5613 (mm-30) cc_final: 0.4893 (tp30) REVERT: x 39 GLN cc_start: 0.6887 (mt0) cc_final: 0.6301 (mt0) REVERT: x 45 GLN cc_start: 0.6643 (mt0) cc_final: 0.5846 (mt0) REVERT: y 56 LYS cc_start: 0.8078 (ttpt) cc_final: 0.7476 (ttmp) REVERT: z 31 ASP cc_start: 0.8035 (t70) cc_final: 0.7783 (t70) REVERT: 0 45 GLN cc_start: 0.7669 (mm110) cc_final: 0.7401 (mm110) REVERT: 1 1 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.7116 (mpp) REVERT: 3 17 VAL cc_start: 0.8367 (p) cc_final: 0.8155 (m) REVERT: 3 24 ARG cc_start: 0.7897 (ptm160) cc_final: 0.7627 (mtt-85) outliers start: 170 outliers final: 120 residues processed: 967 average time/residue: 2.3013 time to fit residues: 3114.5718 Evaluate side-chains 994 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 847 time to evaluate : 5.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain G residue 11 LYS Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 99 ARG Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 97 LYS Chi-restraints excluded: chain O residue 72 ARG Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 83 GLU Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain S residue 3 ARG Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 56 HIS Chi-restraints excluded: chain c residue 102 ARG Chi-restraints excluded: chain c residue 167 ARG Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 169 VAL Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain e residue 199 MET Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 147 ASP Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 14 ASP Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain i residue 95 ARG Chi-restraints excluded: chain i residue 131 ASN Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain l residue 24 THR Chi-restraints excluded: chain m residue 35 LYS Chi-restraints excluded: chain m residue 36 THR Chi-restraints excluded: chain m residue 57 THR Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 91 SER Chi-restraints excluded: chain n residue 103 VAL Chi-restraints excluded: chain o residue 115 ASN Chi-restraints excluded: chain p residue 87 SER Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 48 LYS Chi-restraints excluded: chain q residue 73 LYS Chi-restraints excluded: chain r residue 22 ASP Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain s residue 55 VAL Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain t residue 103 ILE Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 64 VAL Chi-restraints excluded: chain u residue 73 LYS Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain w residue 11 ARG Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 55 VAL Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 30 VAL Chi-restraints excluded: chain 0 residue 42 VAL Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 2 residue 52 LYS Chi-restraints excluded: chain 3 residue 19 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 886 optimal weight: 6.9990 chunk 583 optimal weight: 9.9990 chunk 940 optimal weight: 10.0000 chunk 573 optimal weight: 9.9990 chunk 446 optimal weight: 10.0000 chunk 653 optimal weight: 10.0000 chunk 986 optimal weight: 10.0000 chunk 907 optimal weight: 3.9990 chunk 785 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 606 optimal weight: 10.0000 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 54 GLN D 71 GLN D 198 HIS E 19 ASN E 78 ASN E 97 GLN E 148 ASN G 142 HIS H 18 GLN J 64 GLN L 73 ASN L 112 GLN N 60 GLN O 37 ASN O 80 GLN ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 ASN d 36 GLN ** f 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 27 GLN g 38 ASN ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 18 GLN n 98 GLN q 6 GLN q 18 GLN t 46 GLN x 20 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 153976 Z= 0.341 Angle : 0.801 18.254 230432 Z= 0.428 Chirality : 0.043 0.405 29298 Planarity : 0.008 0.150 12266 Dihedral : 23.193 176.668 77213 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 3.63 % Allowed : 18.97 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.11), residues: 5480 helix: 0.72 (0.12), residues: 1848 sheet: -0.16 (0.15), residues: 1087 loop : -0.85 (0.12), residues: 2545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP c 248 HIS 0.007 0.002 HIS k 35 PHE 0.026 0.002 PHE S 10 TYR 0.022 0.002 TYR p 32 ARG 0.012 0.001 ARG s 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 850 time to evaluate : 6.021 Fit side-chains revert: symmetry clash REVERT: B 49 MET cc_start: 0.2071 (OUTLIER) cc_final: 0.1676 (mpm) REVERT: B 100 MET cc_start: 0.3831 (OUTLIER) cc_final: 0.3555 (mmm) REVERT: C 49 LYS cc_start: 0.6703 (mmmm) cc_final: 0.6025 (mmtm) REVERT: C 110 GLU cc_start: 0.6616 (mp0) cc_final: 0.6367 (mp0) REVERT: C 127 ARG cc_start: 0.6726 (mtt90) cc_final: 0.5901 (mtm110) REVERT: C 129 MET cc_start: 0.5831 (mmm) cc_final: 0.5630 (mmt) REVERT: C 134 MET cc_start: 0.7838 (mtp) cc_final: 0.7349 (mtm) REVERT: C 161 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6400 (tp30) REVERT: C 183 ASP cc_start: 0.7666 (t0) cc_final: 0.7373 (t0) REVERT: D 44 ARG cc_start: 0.5701 (ptm160) cc_final: 0.4448 (ttt90) REVERT: D 47 ARG cc_start: 0.4832 (OUTLIER) cc_final: 0.4120 (ptp-170) REVERT: D 105 MET cc_start: 0.6819 (OUTLIER) cc_final: 0.6049 (mpp) REVERT: D 116 GLN cc_start: 0.6126 (OUTLIER) cc_final: 0.4618 (tp40) REVERT: D 138 SER cc_start: 0.6796 (OUTLIER) cc_final: 0.6258 (t) REVERT: D 160 GLU cc_start: 0.5107 (OUTLIER) cc_final: 0.4528 (mt-10) REVERT: D 183 LYS cc_start: 0.5716 (mtmm) cc_final: 0.5063 (tmtm) REVERT: D 184 ARG cc_start: 0.4146 (ptt90) cc_final: 0.3442 (ppt170) REVERT: D 200 ILE cc_start: 0.6503 (OUTLIER) cc_final: 0.6245 (mm) REVERT: E 26 LYS cc_start: 0.7697 (ttmt) cc_final: 0.7223 (tttp) REVERT: E 93 ARG cc_start: 0.7555 (mtm-85) cc_final: 0.7137 (mtt-85) REVERT: E 146 ASN cc_start: 0.5675 (m-40) cc_final: 0.5414 (p0) REVERT: E 147 MET cc_start: 0.7784 (ttp) cc_final: 0.7408 (ttp) REVERT: F 2 ARG cc_start: 0.6911 (mtt180) cc_final: 0.6636 (mtm-85) REVERT: F 9 MET cc_start: 0.7606 (mtm) cc_final: 0.6990 (mtt) REVERT: F 37 HIS cc_start: 0.6767 (m-70) cc_final: 0.6463 (m-70) REVERT: F 62 MET cc_start: 0.7184 (mtp) cc_final: 0.6555 (mpp) REVERT: F 90 MET cc_start: 0.6595 (mpp) cc_final: 0.6077 (mtp) REVERT: G 11 LYS cc_start: 0.5392 (OUTLIER) cc_final: 0.5146 (mmpt) REVERT: G 144 MET cc_start: 0.6477 (OUTLIER) cc_final: 0.6161 (mtp) REVERT: H 96 MET cc_start: 0.7307 (ttm) cc_final: 0.6862 (ttm) REVERT: I 20 PHE cc_start: 0.7238 (m-80) cc_final: 0.6870 (m-80) REVERT: I 68 LYS cc_start: 0.7779 (mttp) cc_final: 0.7442 (mtpt) REVERT: I 98 LEU cc_start: 0.6968 (mt) cc_final: 0.6679 (mp) REVERT: J 11 LYS cc_start: 0.7853 (mttt) cc_final: 0.7459 (mttp) REVERT: J 66 GLU cc_start: 0.7773 (pt0) cc_final: 0.7115 (pp20) REVERT: J 73 LEU cc_start: 0.7577 (tp) cc_final: 0.7189 (tm) REVERT: L 75 GLN cc_start: 0.6900 (pt0) cc_final: 0.6440 (pt0) REVERT: M 13 LYS cc_start: 0.6442 (mttt) cc_final: 0.5972 (mtmm) REVERT: M 31 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7617 (ttmm) REVERT: M 75 MET cc_start: 0.5994 (mmp) cc_final: 0.5560 (mtm) REVERT: M 93 ARG cc_start: 0.6554 (mmt90) cc_final: 0.5728 (mmt90) REVERT: N 6 MET cc_start: 0.7742 (mmm) cc_final: 0.7439 (mmm) REVERT: N 21 PHE cc_start: 0.6764 (t80) cc_final: 0.6517 (t80) REVERT: N 86 GLU cc_start: 0.6671 (mt-10) cc_final: 0.6304 (mt-10) REVERT: O 47 LYS cc_start: 0.7738 (mttp) cc_final: 0.7271 (mtmt) REVERT: O 48 LYS cc_start: 0.7733 (mmtm) cc_final: 0.7286 (mmtt) REVERT: O 62 GLN cc_start: 0.7832 (tt0) cc_final: 0.7605 (tt0) REVERT: O 71 LYS cc_start: 0.7514 (ttmm) cc_final: 0.7213 (tttm) REVERT: P 35 ARG cc_start: 0.7000 (ttp80) cc_final: 0.6381 (ttt90) REVERT: Q 30 LYS cc_start: 0.8308 (tttt) cc_final: 0.7784 (tttm) REVERT: Q 60 GLU cc_start: 0.7250 (tt0) cc_final: 0.6758 (tt0) REVERT: R 24 LYS cc_start: 0.6454 (mtmm) cc_final: 0.6119 (mtpt) REVERT: R 51 TYR cc_start: 0.7133 (m-80) cc_final: 0.6627 (m-80) REVERT: R 55 LEU cc_start: 0.7377 (tp) cc_final: 0.7064 (tp) REVERT: R 57 ARG cc_start: 0.7348 (mtm-85) cc_final: 0.7127 (mtp180) REVERT: S 44 MET cc_start: 0.5771 (mtp) cc_final: 0.5355 (ttm) REVERT: S 73 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6864 (mt-10) REVERT: T 16 LYS cc_start: 0.6555 (ttpp) cc_final: 0.6138 (mtpp) REVERT: T 53 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.5524 (tt0) REVERT: T 80 THR cc_start: 0.6533 (m) cc_final: 0.6132 (t) REVERT: U 36 GLU cc_start: 0.6661 (tt0) cc_final: 0.5737 (mt-10) REVERT: U 56 HIS cc_start: 0.4555 (OUTLIER) cc_final: 0.4355 (t70) REVERT: c 5 LYS cc_start: 0.8027 (mtpp) cc_final: 0.7402 (mttm) REVERT: c 26 LYS cc_start: 0.8245 (mttm) cc_final: 0.7758 (mttt) REVERT: c 66 ASP cc_start: 0.8033 (t0) cc_final: 0.7819 (t0) REVERT: c 97 LYS cc_start: 0.7022 (ttmm) cc_final: 0.6467 (ttmt) REVERT: c 102 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7839 (mtp85) REVERT: c 111 LYS cc_start: 0.7294 (pttm) cc_final: 0.6694 (ptpp) REVERT: c 167 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6344 (tpt90) REVERT: c 185 GLU cc_start: 0.6780 (mt-10) cc_final: 0.6274 (tt0) REVERT: c 269 ARG cc_start: 0.7292 (ttm-80) cc_final: 0.6889 (ttt90) REVERT: d 1 MET cc_start: 0.4813 (tpt) cc_final: 0.4034 (tpp) REVERT: d 7 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8061 (ptpt) REVERT: d 28 GLU cc_start: 0.7729 (pp20) cc_final: 0.7479 (tm-30) REVERT: d 185 ASN cc_start: 0.7812 (m110) cc_final: 0.7270 (m-40) REVERT: e 25 GLU cc_start: 0.7288 (tt0) cc_final: 0.7084 (tt0) REVERT: e 134 LEU cc_start: 0.6355 (tp) cc_final: 0.6059 (tm) REVERT: e 136 GLN cc_start: 0.6577 (tp-100) cc_final: 0.5941 (mm-40) REVERT: e 139 LYS cc_start: 0.6681 (tttp) cc_final: 0.6244 (ttpm) REVERT: e 140 ASP cc_start: 0.5386 (m-30) cc_final: 0.4852 (m-30) REVERT: e 191 ASP cc_start: 0.5528 (OUTLIER) cc_final: 0.5160 (t70) REVERT: f 47 LYS cc_start: 0.6236 (mmtt) cc_final: 0.6001 (mtpm) REVERT: f 129 SER cc_start: 0.7948 (m) cc_final: 0.7640 (m) REVERT: f 133 ARG cc_start: 0.5562 (mtm-85) cc_final: 0.5321 (mtm180) REVERT: f 147 ASP cc_start: 0.5948 (OUTLIER) cc_final: 0.5416 (m-30) REVERT: f 164 GLU cc_start: 0.5810 (pm20) cc_final: 0.5524 (pt0) REVERT: g 139 GLN cc_start: 0.6408 (tm-30) cc_final: 0.6120 (tm-30) REVERT: g 155 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6623 (pp20) REVERT: i 23 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7860 (mttp) REVERT: i 49 ASP cc_start: 0.8118 (t0) cc_final: 0.7806 (t0) REVERT: i 95 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6795 (mtp-110) REVERT: i 96 ARG cc_start: 0.6647 (mmm-85) cc_final: 0.6364 (ptt-90) REVERT: i 125 TYR cc_start: 0.8030 (m-80) cc_final: 0.7371 (m-80) REVERT: j 17 ARG cc_start: 0.7640 (mmt90) cc_final: 0.7289 (mmt90) REVERT: j 51 LYS cc_start: 0.7464 (mttp) cc_final: 0.7141 (mttm) REVERT: j 113 MET cc_start: 0.6294 (mmm) cc_final: 0.5914 (mmm) REVERT: k 123 ARG cc_start: 0.7150 (ttm170) cc_final: 0.6806 (ttp80) REVERT: k 129 LYS cc_start: 0.6899 (mppt) cc_final: 0.6570 (mmpt) REVERT: l 7 THR cc_start: 0.7925 (p) cc_final: 0.7534 (p) REVERT: l 55 ARG cc_start: 0.7665 (tpt170) cc_final: 0.6386 (ttm110) REVERT: l 127 LYS cc_start: 0.7729 (ttmt) cc_final: 0.7285 (tptm) REVERT: m 117 ASP cc_start: 0.7620 (p0) cc_final: 0.7230 (p0) REVERT: n 13 ARG cc_start: 0.6937 (ttm-80) cc_final: 0.6364 (ttm170) REVERT: n 16 ARG cc_start: 0.7291 (mmp80) cc_final: 0.6968 (mmp-170) REVERT: n 46 GLU cc_start: 0.6602 (pt0) cc_final: 0.6397 (tm-30) REVERT: n 58 ILE cc_start: 0.6260 (OUTLIER) cc_final: 0.6011 (mm) REVERT: n 76 LYS cc_start: 0.6545 (tttt) cc_final: 0.6130 (tmtm) REVERT: n 98 GLN cc_start: 0.7269 (tp40) cc_final: 0.7068 (tp-100) REVERT: o 111 LYS cc_start: 0.7644 (ttpt) cc_final: 0.7078 (tttp) REVERT: p 59 GLN cc_start: 0.8287 (tt0) cc_final: 0.8027 (tt0) REVERT: q 15 SER cc_start: 0.8425 (p) cc_final: 0.7748 (m) REVERT: q 48 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.7216 (mttp) REVERT: q 73 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7778 (mttp) REVERT: r 33 LEU cc_start: 0.7973 (mt) cc_final: 0.7753 (mt) REVERT: r 86 MET cc_start: 0.7642 (ttm) cc_final: 0.7213 (ttp) REVERT: s 51 PHE cc_start: 0.7609 (m-10) cc_final: 0.7328 (m-10) REVERT: t 47 LYS cc_start: 0.7075 (OUTLIER) cc_final: 0.6661 (mptm) REVERT: u 25 LYS cc_start: 0.7613 (mtpp) cc_final: 0.7307 (mtmp) REVERT: u 34 LYS cc_start: 0.5408 (tppt) cc_final: 0.5207 (tptm) REVERT: u 45 ASP cc_start: 0.7155 (m-30) cc_final: 0.6815 (m-30) REVERT: u 73 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7302 (tttm) REVERT: v 3 HIS cc_start: 0.7227 (m90) cc_final: 0.6883 (m170) REVERT: v 25 ARG cc_start: 0.7980 (mmt90) cc_final: 0.7658 (mmt90) REVERT: v 64 ASP cc_start: 0.7981 (m-30) cc_final: 0.7451 (m-30) REVERT: v 72 LYS cc_start: 0.7778 (ptpp) cc_final: 0.7012 (pptt) REVERT: w 11 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.6541 (mtp85) REVERT: w 45 ARG cc_start: 0.6814 (ptt90) cc_final: 0.5971 (ptt-90) REVERT: x 8 GLU cc_start: 0.5551 (mm-30) cc_final: 0.4862 (tp30) REVERT: x 39 GLN cc_start: 0.6893 (mt0) cc_final: 0.6303 (mt0) REVERT: x 45 GLN cc_start: 0.6662 (mt0) cc_final: 0.5862 (mt0) REVERT: y 56 LYS cc_start: 0.8149 (ttpt) cc_final: 0.7539 (ttmp) REVERT: z 31 ASP cc_start: 0.8032 (t70) cc_final: 0.7775 (t70) REVERT: 0 45 GLN cc_start: 0.7668 (mm110) cc_final: 0.7393 (mm110) REVERT: 1 1 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.7117 (mpp) REVERT: 3 17 VAL cc_start: 0.8362 (p) cc_final: 0.8145 (m) outliers start: 166 outliers final: 126 residues processed: 954 average time/residue: 2.3743 time to fit residues: 3161.7758 Evaluate side-chains 996 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 842 time to evaluate : 5.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain G residue 11 LYS Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 99 ARG Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 97 LYS Chi-restraints excluded: chain O residue 72 ARG Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 83 GLU Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain S residue 3 ARG Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 56 HIS Chi-restraints excluded: chain c residue 102 ARG Chi-restraints excluded: chain c residue 167 ARG Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 144 GLU Chi-restraints excluded: chain e residue 169 VAL Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain e residue 199 MET Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 147 ASP Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 14 ASP Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain i residue 95 ARG Chi-restraints excluded: chain i residue 131 ASN Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain l residue 24 THR Chi-restraints excluded: chain m residue 35 LYS Chi-restraints excluded: chain m residue 36 THR Chi-restraints excluded: chain m residue 57 THR Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 91 SER Chi-restraints excluded: chain n residue 103 VAL Chi-restraints excluded: chain o residue 115 ASN Chi-restraints excluded: chain p residue 87 SER Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 48 LYS Chi-restraints excluded: chain q residue 73 LYS Chi-restraints excluded: chain r residue 22 ASP Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain s residue 55 VAL Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain t residue 103 ILE Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 64 VAL Chi-restraints excluded: chain u residue 73 LYS Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain w residue 11 ARG Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 55 VAL Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 30 VAL Chi-restraints excluded: chain z residue 53 LYS Chi-restraints excluded: chain 0 residue 42 VAL Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 52 LYS Chi-restraints excluded: chain 3 residue 19 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 481 optimal weight: 9.9990 chunk 623 optimal weight: 10.0000 chunk 836 optimal weight: 0.9980 chunk 240 optimal weight: 20.0000 chunk 724 optimal weight: 4.9990 chunk 115 optimal weight: 20.0000 chunk 218 optimal weight: 4.9990 chunk 786 optimal weight: 0.8980 chunk 329 optimal weight: 1.9990 chunk 807 optimal weight: 7.9990 chunk 99 optimal weight: 30.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 54 GLN D 71 GLN D 198 HIS E 19 ASN E 78 ASN E 97 GLN G 142 HIS H 18 GLN L 73 ASN L 112 GLN N 49 GLN N 60 GLN O 37 ASN O 80 GLN ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 ASN c 163 GLN d 36 GLN ** f 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 27 GLN g 38 ASN ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 18 GLN q 6 GLN q 18 GLN t 46 GLN x 20 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.151908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.131068 restraints weight = 132634.761| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 0.26 r_work: 0.3226 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 153976 Z= 0.199 Angle : 0.691 14.540 230432 Z= 0.383 Chirality : 0.037 0.399 29298 Planarity : 0.007 0.138 12266 Dihedral : 23.153 177.389 77213 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.96 % Favored : 95.97 % Rotamer: Outliers : 3.13 % Allowed : 19.50 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.11), residues: 5480 helix: 1.01 (0.12), residues: 1846 sheet: -0.10 (0.16), residues: 1049 loop : -0.74 (0.12), residues: 2585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP c 248 HIS 0.006 0.001 HIS k 35 PHE 0.023 0.002 PHE F 8 TYR 0.017 0.002 TYR R 51 ARG 0.009 0.001 ARG t 7 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 43093.90 seconds wall clock time: 747 minutes 21.16 seconds (44841.16 seconds total)