Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 30 04:50:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8akn_15488/08_2023/8akn_15488_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8akn_15488/08_2023/8akn_15488.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8akn_15488/08_2023/8akn_15488_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8akn_15488/08_2023/8akn_15488_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8akn_15488/08_2023/8akn_15488_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8akn_15488/08_2023/8akn_15488.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8akn_15488/08_2023/8akn_15488.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8akn_15488/08_2023/8akn_15488_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8akn_15488/08_2023/8akn_15488_updated.pdb" } resolution = 2.3 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= 0.002 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4551 5.49 5 Mg 305 5.21 5 S 160 5.16 5 C 72829 2.51 5 N 26952 2.21 5 O 41714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 7": "OE1" <-> "OE2" Residue "0 ARG 44": "NH1" <-> "NH2" Residue "1 ARG 3": "NH1" <-> "NH2" Residue "1 ARG 12": "NH1" <-> "NH2" Residue "1 ARG 14": "NH1" <-> "NH2" Residue "1 ARG 21": "NH1" <-> "NH2" Residue "1 ARG 33": "NH1" <-> "NH2" Residue "1 ARG 41": "NH1" <-> "NH2" Residue "2 ARG 13": "NH1" <-> "NH2" Residue "2 PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 30": "NH1" <-> "NH2" Residue "2 ARG 40": "NH1" <-> "NH2" Residue "3 ARG 24": "NH1" <-> "NH2" Residue "4 ASP 4": "OD1" <-> "OD2" Residue "4 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 4": "NH1" <-> "NH2" Residue "A TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C ASP 123": "OD1" <-> "OD2" Residue "C PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 127": "OD1" <-> "OD2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C ASP 188": "OD1" <-> "OD2" Residue "C ASP 197": "OD1" <-> "OD2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 205": "OD1" <-> "OD2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "D ASP 34": "OD1" <-> "OD2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D ASP 112": "OD1" <-> "OD2" Residue "D ASP 118": "OD1" <-> "OD2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D ASP 181": "OD1" <-> "OD2" Residue "D TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 15": "OE1" <-> "OE2" Residue "E ASP 18": "OD1" <-> "OD2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E GLU 88": "OE1" <-> "OE2" Residue "E GLU 95": "OE1" <-> "OE2" Residue "E GLU 113": "OE1" <-> "OE2" Residue "E ASP 141": "OD1" <-> "OD2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "F GLU 10": "OE1" <-> "OE2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "F GLU 65": "OE1" <-> "OE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F ASP 142": "OD1" <-> "OD2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "G GLU 5": "OE1" <-> "OE2" Residue "G GLU 16": "OE1" <-> "OE2" Residue "G GLU 33": "OE1" <-> "OE2" Residue "G GLU 73": "OE1" <-> "OE2" Residue "G ASP 82": "OD1" <-> "OD2" Residue "G GLU 98": "OE1" <-> "OE2" Residue "H ASP 15": "OD1" <-> "OD2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 63": "OE1" <-> "OE2" Residue "H GLU 67": "OE1" <-> "OE2" Residue "H TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 126": "OD1" <-> "OD2" Residue "H ASP 140": "OD1" <-> "OD2" Residue "H TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 43": "OE1" <-> "OE2" Residue "I GLU 47": "OE1" <-> "OE2" Residue "I GLU 58": "OE1" <-> "OE2" Residue "I GLU 60": "OE1" <-> "OE2" Residue "J TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 36": "OE1" <-> "OE2" Residue "J TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 42": "OE1" <-> "OE2" Residue "J GLU 53": "OE1" <-> "OE2" Residue "J ASP 62": "OD1" <-> "OD2" Residue "J GLU 89": "OE1" <-> "OE2" Residue "J TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J GLU 112": "OE1" <-> "OE2" Residue "J ARG 124": "NH1" <-> "NH2" Residue "K PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 63": "OD1" <-> "OD2" Residue "K ASP 75": "OD1" <-> "OD2" Residue "K GLU 78": "OE1" <-> "OE2" Residue "K GLU 81": "OE1" <-> "OE2" Residue "L ASP 18": "OD1" <-> "OD2" Residue "L PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 72": "OD1" <-> "OD2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "M ARG 14": "NH1" <-> "NH2" Residue "M GLU 25": "OE1" <-> "OE2" Residue "M ARG 56": "NH1" <-> "NH2" Residue "M GLU 70": "OE1" <-> "OE2" Residue "M ASP 109": "OD1" <-> "OD2" Residue "N ASP 11": "OD1" <-> "OD2" Residue "N ASP 58": "OD1" <-> "OD2" Residue "O ASP 18": "OD1" <-> "OD2" Residue "O TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 38": "OD1" <-> "OD2" Residue "O ASP 40": "OD1" <-> "OD2" Residue "O ARG 65": "NH1" <-> "NH2" Residue "P GLU 14": "OE1" <-> "OE2" Residue "P ASP 21": "OD1" <-> "OD2" Residue "P GLU 83": "OE1" <-> "OE2" Residue "Q ARG 28": "NH1" <-> "NH2" Residue "Q GLU 34": "OE1" <-> "OE2" Residue "Q PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 45": "OE1" <-> "OE2" Residue "Q GLU 47": "OE1" <-> "OE2" Residue "Q GLU 48": "OE1" <-> "OE2" Residue "R ASP 15": "OD1" <-> "OD2" Residue "R GLU 49": "OE1" <-> "OE2" Residue "R GLU 52": "OE1" <-> "OE2" Residue "R GLU 63": "OE1" <-> "OE2" Residue "R GLU 80": "OE1" <-> "OE2" Residue "S PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 20": "OE1" <-> "OE2" Residue "S ASP 22": "OD1" <-> "OD2" Residue "S TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 35": "OE1" <-> "OE2" Residue "T ARG 3": "NH1" <-> "NH2" Residue "T ARG 32": "NH1" <-> "NH2" Residue "T ARG 55": "NH1" <-> "NH2" Residue "T PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 64": "OD1" <-> "OD2" Residue "T GLU 65": "OE1" <-> "OE2" Residue "T ARG 81": "NH1" <-> "NH2" Residue "U TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 59": "OD1" <-> "OD2" Residue "V GLU 10": "OE1" <-> "OE2" Residue "V ASP 13": "OD1" <-> "OD2" Residue "V GLU 39": "OE1" <-> "OE2" Residue "V GLU 63": "OE1" <-> "OE2" Residue "V ARG 66": "NH1" <-> "NH2" Residue "W ARG 15": "NH1" <-> "NH2" Residue "W GLU 18": "OE1" <-> "OE2" Residue "W ASP 25": "OD1" <-> "OD2" Residue "W ASP 31": "OD1" <-> "OD2" Residue "W PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 36": "NH1" <-> "NH2" Residue "W ASP 47": "OD1" <-> "OD2" Residue "W ARG 50": "NH1" <-> "NH2" Residue "W PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 60": "OE1" <-> "OE2" Residue "W ASP 70": "OD1" <-> "OD2" Residue "W ASP 71": "OD1" <-> "OD2" Residue "W GLU 73": "OE1" <-> "OE2" Residue "W ARG 75": "NH1" <-> "NH2" Residue "W GLU 76": "OE1" <-> "OE2" Residue "W ARG 83": "NH1" <-> "NH2" Residue "W GLU 90": "OE1" <-> "OE2" Residue "W ASP 104": "OD1" <-> "OD2" Residue "W ASP 106": "OD1" <-> "OD2" Residue "W ASP 107": "OD1" <-> "OD2" Residue "W PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 114": "OE1" <-> "OE2" Residue "W ARG 116": "NH1" <-> "NH2" Residue "W PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 133": "NH1" <-> "NH2" Residue "W TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 142": "NH1" <-> "NH2" Residue "W ARG 143": "NH1" <-> "NH2" Residue "W GLU 147": "OE1" <-> "OE2" Residue "W ARG 174": "NH1" <-> "NH2" Residue "W ASP 211": "OD1" <-> "OD2" Residue "W ARG 228": "NH1" <-> "NH2" Residue "W ASP 241": "OD1" <-> "OD2" Residue "W GLU 256": "OE1" <-> "OE2" Residue "W ARG 277": "NH1" <-> "NH2" Residue "W ARG 286": "NH1" <-> "NH2" Residue "W GLU 290": "OE1" <-> "OE2" Residue "W ARG 295": "NH1" <-> "NH2" Residue "W ARG 303": "NH1" <-> "NH2" Residue "W TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 23": "OE1" <-> "OE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ARG 63": "NH1" <-> "NH2" Residue "c ARG 80": "NH1" <-> "NH2" Residue "c ASP 114": "OD1" <-> "OD2" Residue "c ARG 133": "NH1" <-> "NH2" Residue "c TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 167": "NH1" <-> "NH2" Residue "c ASP 168": "OD1" <-> "OD2" Residue "c TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 177": "NH1" <-> "NH2" Residue "c ARG 182": "NH1" <-> "NH2" Residue "c ARG 189": "NH1" <-> "NH2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c ARG 212": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ASP 39": "OD1" <-> "OD2" Residue "d ARG 59": "NH1" <-> "NH2" Residue "d GLU 74": "OE1" <-> "OE2" Residue "d GLU 81": "OE1" <-> "OE2" Residue "d ARG 83": "NH1" <-> "NH2" Residue "d GLU 99": "OE1" <-> "OE2" Residue "d ASP 103": "OD1" <-> "OD2" Residue "d ARG 169": "NH1" <-> "NH2" Residue "d GLU 183": "OE1" <-> "OE2" Residue "e PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e ARG 61": "NH1" <-> "NH2" Residue "e ARG 88": "NH1" <-> "NH2" Residue "e ARG 102": "NH1" <-> "NH2" Residue "e ASP 116": "OD1" <-> "OD2" Residue "e GLU 122": "OE1" <-> "OE2" Residue "e PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 155": "OE1" <-> "OE2" Residue "e ARG 162": "NH1" <-> "NH2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "e ASP 176": "OD1" <-> "OD2" Residue "e ASP 184": "OD1" <-> "OD2" Residue "f ASP 6": "OD1" <-> "OD2" Residue "f ASP 10": "OD1" <-> "OD2" Residue "f GLU 32": "OE1" <-> "OE2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f GLU 94": "OE1" <-> "OE2" Residue "f ARG 102": "NH1" <-> "NH2" Residue "f ARG 110": "NH1" <-> "NH2" Residue "f ARG 112": "NH1" <-> "NH2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f ARG 133": "NH1" <-> "NH2" Residue "f ASP 144": "OD1" <-> "OD2" Residue "f ASP 147": "OD1" <-> "OD2" Residue "f GLU 164": "OE1" <-> "OE2" Residue "f ASP 174": "OD1" <-> "OD2" Residue "f PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 3": "NH1" <-> "NH2" Residue "g ASP 39": "OD1" <-> "OD2" Residue "g GLU 42": "OE1" <-> "OE2" Residue "g PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 56": "OD1" <-> "OD2" Residue "g GLU 81": "OE1" <-> "OE2" Residue "g GLU 124": "OE1" <-> "OE2" Residue "g GLU 130": "OE1" <-> "OE2" Residue "g ASP 137": "OD1" <-> "OD2" Residue "g ASP 147": "OD1" <-> "OD2" Residue "g ARG 153": "NH1" <-> "NH2" Residue "g ARG 163": "NH1" <-> "NH2" Residue "g GLU 167": "OE1" <-> "OE2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "h ASP 7": "OD1" <-> "OD2" Residue "h ARG 27": "NH1" <-> "NH2" Residue "i PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 13": "NH1" <-> "NH2" Residue "i ASP 14": "OD1" <-> "OD2" Residue "i ARG 37": "NH1" <-> "NH2" Residue "i GLU 43": "OE1" <-> "OE2" Residue "i ASP 60": "OD1" <-> "OD2" Residue "i ASP 71": "OD1" <-> "OD2" Residue "i PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 96": "NH1" <-> "NH2" Residue "i ARG 120": "NH1" <-> "NH2" Residue "j ASP 56": "OD1" <-> "OD2" Residue "j PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 110": "OE1" <-> "OE2" Residue "k GLU 10": "OE1" <-> "OE2" Residue "k ARG 21": "NH1" <-> "NH2" Residue "k ARG 33": "NH1" <-> "NH2" Residue "k ARG 41": "NH1" <-> "NH2" Residue "k ARG 47": "NH1" <-> "NH2" Residue "k ARG 60": "NH1" <-> "NH2" Residue "k PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 78": "NH1" <-> "NH2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "k GLU 143": "OE1" <-> "OE2" Residue "l ARG 10": "NH1" <-> "NH2" Residue "l ARG 18": "NH1" <-> "NH2" Residue "l ASP 25": "OD1" <-> "OD2" Residue "l PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 40": "NH1" <-> "NH2" Residue "l ARG 44": "NH1" <-> "NH2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "l GLU 90": "OE1" <-> "OE2" Residue "l ARG 114": "NH1" <-> "NH2" Residue "m ARG 12": "NH1" <-> "NH2" Residue "m ARG 17": "NH1" <-> "NH2" Residue "m ARG 22": "NH1" <-> "NH2" Residue "m ARG 46": "NH1" <-> "NH2" Residue "m ARG 63": "NH1" <-> "NH2" Residue "m ARG 64": "NH1" <-> "NH2" Residue "m ARG 69": "NH1" <-> "NH2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "m GLU 82": "OE1" <-> "OE2" Residue "m ARG 96": "NH1" <-> "NH2" Residue "m ASP 117": "OD1" <-> "OD2" Residue "m ARG 118": "NH1" <-> "NH2" Residue "n ASP 2": "OD1" <-> "OD2" Residue "n ARG 10": "NH1" <-> "NH2" Residue "n ARG 16": "NH1" <-> "NH2" Residue "n ARG 25": "NH1" <-> "NH2" Residue "n TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 46": "OE1" <-> "OE2" Residue "n GLU 60": "OE1" <-> "OE2" Residue "n GLU 80": "OE1" <-> "OE2" Residue "n ARG 81": "NH1" <-> "NH2" Residue "n ASP 89": "OD1" <-> "OD2" Residue "n ARG 94": "NH1" <-> "NH2" Residue "n ARG 102": "NH1" <-> "NH2" Residue "n ARG 111": "NH1" <-> "NH2" Residue "n PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 21": "NH1" <-> "NH2" Residue "o ARG 39": "NH1" <-> "NH2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "o ARG 101": "NH1" <-> "NH2" Residue "o ARG 109": "NH1" <-> "NH2" Residue "p ARG 3": "NH1" <-> "NH2" Residue "p ARG 6": "NH1" <-> "NH2" Residue "p ARG 13": "NH1" <-> "NH2" Residue "p ARG 33": "NH1" <-> "NH2" Residue "p ARG 48": "NH1" <-> "NH2" Residue "p TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 97": "OD1" <-> "OD2" Residue "p GLU 111": "OE1" <-> "OE2" Residue "q GLU 16": "OE1" <-> "OE2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q ASP 26": "OD1" <-> "OD2" Residue "q GLU 34": "OE1" <-> "OE2" Residue "q GLU 45": "OE1" <-> "OE2" Residue "q ARG 68": "NH1" <-> "NH2" Residue "q GLU 70": "OE1" <-> "OE2" Residue "q ARG 79": "NH1" <-> "NH2" Residue "q ARG 84": "NH1" <-> "NH2" Residue "r ASP 34": "OD1" <-> "OD2" Residue "r GLU 59": "OE1" <-> "OE2" Residue "r ASP 62": "OD1" <-> "OD2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "r ARG 88": "NH1" <-> "NH2" Residue "r ARG 95": "NH1" <-> "NH2" Residue "r ASP 109": "OD1" <-> "OD2" Residue "r ARG 110": "NH1" <-> "NH2" Residue "s GLU 52": "OE1" <-> "OE2" Residue "s ARG 73": "NH1" <-> "NH2" Residue "s GLU 89": "OE1" <-> "OE2" Residue "t ARG 6": "NH1" <-> "NH2" Residue "t ARG 7": "NH1" <-> "NH2" Residue "t ASP 9": "OD1" <-> "OD2" Residue "t ARG 82": "NH1" <-> "NH2" Residue "t ARG 86": "NH1" <-> "NH2" Residue "t PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 89": "OD1" <-> "OD2" Residue "t ARG 94": "NH1" <-> "NH2" Residue "u PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 11": "OE1" <-> "OE2" Residue "u PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 41": "OE1" <-> "OE2" Residue "u ASP 43": "OD1" <-> "OD2" Residue "u PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 70": "OE1" <-> "OE2" Residue "v GLU 83": "OE1" <-> "OE2" Residue "w ARG 3": "NH1" <-> "NH2" Residue "w ARG 11": "NH1" <-> "NH2" Residue "w PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 37": "NH1" <-> "NH2" Residue "w GLU 41": "OE1" <-> "OE2" Residue "w GLU 43": "OE1" <-> "OE2" Residue "w ARG 50": "NH1" <-> "NH2" Residue "w ARG 57": "NH1" <-> "NH2" Residue "w ASP 65": "OD1" <-> "OD2" Residue "w ARG 74": "NH1" <-> "NH2" Residue "w GLU 76": "OE1" <-> "OE2" Residue "x GLU 12": "OE1" <-> "OE2" 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 ASP 49": "OD1" <-> "OD2" Residue "x ARG 52": "NH1" <-> "NH2" Residue "y ARG 11": "NH1" <-> "NH2" Residue "y ARG 30": "NH1" <-> "NH2" Residue "y GLU 37": "OE1" <-> "OE2" Residue "y ARG 45": "NH1" <-> "NH2" Residue "y GLU 58": "OE1" <-> "OE2" Residue "y GLU 59": "OE1" <-> "OE2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 16": "NH1" <-> "NH2" Residue "z GLU 36": "OE1" <-> "OE2" Residue "z ASP 46": "OD1" <-> "OD2" Residue "z ARG 52": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 146513 Number of models: 1 Model: "" Number of chains: 103 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: "A" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 155 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 6, 'TRANS': 12} Chain: "B" Number of atoms: 32608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32608 Classifications: {'RNA': 1519} Modifications used: {'rna2p': 1, 'rna2p_pur': 120, 'rna2p_pyr': 81, 'rna3p': 8, 'rna3p_pur': 744, 'rna3p_pyr': 565} Link IDs: {'rna2p': 202, 'rna3p': 1316} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 7 Chain: "C" 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: "D" 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: "E" 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: "F" 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: "G" 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: "H" 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: "I" 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: "J" 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: "K" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "L" 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: "M" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Chain: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2792 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 11, 'TRANS': 342} Chain: "X" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Classifications: {'RNA': 76} Modifications used: {'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p_pur': 32, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 65} Chain: "Y" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 188 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 7} Chain: "Z" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1616 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 32, 'rna3p_pyr': 32} Link IDs: {'rna2p': 11, 'rna3p': 64} Chain: "a" Number of atoms: 59128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2753, 59128 Classifications: {'RNA': 2753} Modifications used: {'rna2p': 6, 'rna2p_pur': 267, 'rna2p_pyr': 142, 'rna3p': 16, 'rna3p_pur': 1319, 'rna3p_pyr': 1003} Link IDs: {'rna2p': 414, 'rna3p': 2338} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 9 Chain: "b" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 56, 'rna3p_pyr': 49} Link IDs: {'rna2p': 14, 'rna3p': 104} 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: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "n" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "o" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "p" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "r" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "s" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "t" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "u" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "v" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 586 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "w" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "x" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "y" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "z" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'A2G': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 89 Unusual residues: {' MG': 89} Classifications: {'undetermined': 89} Link IDs: {None: 88} Chain: "a" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 222 Unusual residues: {' MG': 208, 'SPM': 1} Classifications: {'undetermined': 209} Link IDs: {None: 208} Chain: "b" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "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: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "1" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "3" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "B" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 189 Classifications: {'water': 189} Link IDs: {None: 188} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "W" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Y" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "a" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1331, 1331 Classifications: {'water': 1331} Link IDs: {None: 1330} Chain: "b" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "c" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "d" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "e" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "i" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "k" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "l" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "m" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "o" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "p" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "q" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "r" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "s" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "v" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "w" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1383 SG CYS 3 11 116.629 146.873 174.413 1.00 63.87 S ATOM 1408 SG CYS 3 14 114.958 150.142 172.610 1.00 55.03 S ATOM 1511 SG CYS 3 27 118.275 149.920 174.563 1.00 55.31 S ATOM 1730 SG CYS 4 16 58.167 67.645 123.829 1.00117.15 S ATOM 1742 SG CYS 4 18 57.095 65.529 126.712 1.00128.32 S ATOM 1884 SG CYS 4 37 57.245 69.317 127.024 1.00111.13 S ATOM 1905 SG CYS 4 40 60.518 67.360 126.958 1.00108.38 S Time building chain proxies: 53.23, per 1000 atoms: 0.36 Number of scatterers: 146513 At special positions: 0 Unit cell: (264.8, 276, 221.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 160 16.00 P 4551 15.00 Mg 305 11.99 O 41714 8.00 N 26952 7.00 C 72829 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 67.91 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" ND1 HIS 3 33 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 16 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 37 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 40 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 18 " Number of angles added : 9 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10960 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 185 helices and 73 sheets defined 39.9% alpha, 19.7% beta 1538 base pairs and 2387 stacking pairs defined. Time for finding SS restraints: 75.13 Creating SS restraints... Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.080A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LYS 1 25 " --> pdb=" O ARG 1 21 " (cutoff:3.500A) Processing helix chain '1' and resid 26 through 38 Processing helix chain '2' and resid 7 through 14 removed outlier: 3.521A pdb=" N ARG 2 13 " --> pdb=" O GLY 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 32 through 37 removed outlier: 4.574A pdb=" N LYS 2 36 " --> pdb=" O ILE 2 32 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ALA 2 37 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 32 through 37' Processing helix chain '2' and resid 38 through 46 Proline residue: 2 46 - end of helix Processing helix chain '2' and resid 51 through 63 removed outlier: 4.520A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 4.999A 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 64 Processing helix chain 'C' and resid 5 through 13 removed outlier: 3.926A pdb=" N MET C 9 " --> pdb=" O SER C 5 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS C 11 " --> pdb=" O ARG C 7 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ALA C 12 " --> pdb=" O ASP C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 32 removed outlier: 4.361A pdb=" N LYS C 28 " --> pdb=" O ASN C 24 " (cutoff:3.500A) Proline residue: C 29 - end of helix removed outlier: 5.473A pdb=" N PHE C 32 " --> pdb=" O LYS C 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 24 through 32' Processing helix chain 'C' and resid 42 through 64 Proline residue: C 48 - end of helix removed outlier: 4.260A pdb=" N LYS C 64 " --> pdb=" O ILE C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 88 Processing helix chain 'C' and resid 103 through 124 removed outlier: 4.072A pdb=" N GLN C 109 " --> pdb=" O LYS C 105 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR C 119 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.809A pdb=" N LEU C 129 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR C 130 " --> pdb=" O PHE C 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 125 through 130' Processing helix chain 'C' and resid 131 through 148 removed outlier: 3.623A pdb=" N LEU C 135 " --> pdb=" O LYS C 131 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER C 147 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 170 removed outlier: 3.670A pdb=" N GLU C 169 " --> pdb=" O ASP C 165 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N HIS C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 165 through 170' Processing helix chain 'C' and resid 171 through 180 Processing helix chain 'C' and resid 206 through 227 removed outlier: 3.638A pdb=" N LEU C 212 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 12 removed outlier: 4.374A pdb=" N ARG D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 48 removed outlier: 4.306A pdb=" N ALA D 30 " --> pdb=" O THR D 26 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ASP D 31 " --> pdb=" O LYS D 27 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA D 48 " --> pdb=" O THR D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 78 removed outlier: 3.804A pdb=" N VAL D 76 " --> pdb=" O ARG D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 96 removed outlier: 5.451A pdb=" N GLU D 85 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 127 Processing helix chain 'D' and resid 129 through 145 removed outlier: 3.977A pdb=" N ALA D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 16 removed outlier: 4.292A pdb=" N LEU E 11 " --> pdb=" O PRO E 7 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 32 removed outlier: 3.771A pdb=" N LYS E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 66 removed outlier: 3.712A pdb=" N TYR E 65 " --> pdb=" O VAL E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 83 removed outlier: 5.476A pdb=" N LYS E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 97 Processing helix chain 'E' and resid 98 through 106 Processing helix chain 'E' and resid 110 through 121 removed outlier: 3.514A pdb=" N ARG E 115 " --> pdb=" O ARG E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 152 removed outlier: 4.495A pdb=" N LYS E 151 " --> pdb=" O GLU E 147 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLN E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 166 removed outlier: 3.795A pdb=" N ALA E 158 " --> pdb=" O ARG E 154 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU E 159 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU E 160 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LEU E 161 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG E 165 " --> pdb=" O LEU E 161 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N GLU E 166 " --> pdb=" O ALA E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 192 removed outlier: 3.657A pdb=" N LEU E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N SER E 192 " --> pdb=" O ARG E 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 187 through 192' Processing helix chain 'E' and resid 196 through 206 removed outlier: 4.034A pdb=" N ILE E 200 " --> pdb=" O ASN E 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 71 removed outlier: 3.622A pdb=" N ARG F 69 " --> pdb=" O GLU F 65 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 119 removed outlier: 4.178A pdb=" N ALA F 113 " --> pdb=" O GLY F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 147 removed outlier: 3.959A pdb=" N MET F 147 " --> pdb=" O GLY F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 158 Processing helix chain 'F' and resid 160 through 165 removed outlier: 3.950A pdb=" N ILE F 164 " --> pdb=" O SER F 160 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU F 165 " --> pdb=" O VAL F 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 160 through 165' Processing helix chain 'G' and resid 11 through 16 removed outlier: 5.393A pdb=" N GLU G 16 " --> pdb=" O PRO G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 33 Processing helix chain 'G' and resid 67 through 81 removed outlier: 3.838A pdb=" N ILE G 71 " --> pdb=" O PRO G 67 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLU G 73 " --> pdb=" O GLU G 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 31 Processing helix chain 'H' and resid 35 through 55 Processing helix chain 'H' and resid 57 through 70 removed outlier: 3.617A pdb=" N ASN H 68 " --> pdb=" O VAL H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 111 removed outlier: 3.536A pdb=" N ASN H 97 " --> pdb=" O PRO H 93 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 130 Processing helix chain 'H' and resid 132 through 149 removed outlier: 4.598A pdb=" N GLU H 139 " --> pdb=" O VAL H 135 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA H 145 " --> pdb=" O VAL H 141 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN H 148 " --> pdb=" O MET H 144 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYS H 149 " --> pdb=" O ALA H 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 21 Processing helix chain 'I' and resid 30 through 44 Processing helix chain 'I' and resid 112 through 120 Processing helix chain 'J' and resid 34 through 39 Processing helix chain 'J' and resid 41 through 56 Proline residue: J 51 - end of helix Processing helix chain 'J' and resid 71 through 91 Processing helix chain 'J' and resid 92 through 102 removed outlier: 4.605A pdb=" N SER J 96 " --> pdb=" O GLU J 92 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLU J 97 " --> pdb=" O SER J 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 33 removed outlier: 4.290A pdb=" N ILE K 18 " --> pdb=" O ASP K 14 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG K 31 " --> pdb=" O GLU K 27 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR K 32 " --> pdb=" O THR K 28 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY K 33 " --> pdb=" O ALA K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 90 removed outlier: 3.799A pdb=" N ASP K 85 " --> pdb=" O GLU K 81 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET K 88 " --> pdb=" O VAL K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 51 removed outlier: 4.489A pdb=" N GLY L 51 " --> pdb=" O ALA L 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 54 through 59 removed outlier: 3.785A pdb=" N SER L 58 " --> pdb=" O GLY L 54 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR L 59 " --> pdb=" O SER L 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 54 through 59' Processing helix chain 'L' and resid 60 through 75 removed outlier: 3.657A pdb=" N LYS L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 104 removed outlier: 4.378A pdb=" N SER L 95 " --> pdb=" O PRO L 91 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ILE L 97 " --> pdb=" O ARG L 93 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG L 98 " --> pdb=" O GLU L 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 11 Proline residue: M 11 - end of helix Processing helix chain 'M' and resid 113 through 118 removed outlier: 3.647A pdb=" N TYR M 117 " --> pdb=" O ALA M 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 22 removed outlier: 4.536A pdb=" N THR N 20 " --> pdb=" O VAL N 16 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER N 21 " --> pdb=" O ILE N 17 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE N 22 " --> pdb=" O ALA N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 38 Processing helix chain 'N' and resid 44 through 49 removed outlier: 5.684A pdb=" N SER N 49 " --> pdb=" O ILE N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 64 removed outlier: 4.154A pdb=" N LYS N 62 " --> pdb=" O ASP N 58 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE N 63 " --> pdb=" O GLU N 59 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N VAL N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 84 removed outlier: 4.323A pdb=" N GLU N 72 " --> pdb=" O ASP N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 94 Processing helix chain 'N' and resid 106 through 111 Processing helix chain 'O' and resid 3 through 21 removed outlier: 3.614A pdb=" N GLU O 10 " --> pdb=" O MET O 6 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE O 21 " --> pdb=" O ALA O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 33 removed outlier: 4.035A pdb=" N ASP O 33 " --> pdb=" O ALA O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 51 removed outlier: 3.598A pdb=" N GLN O 49 " --> pdb=" O VAL O 45 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR O 50 " --> pdb=" O LEU O 46 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU O 51 " --> pdb=" O LYS O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 91 Processing helix chain 'O' and resid 52 through 57 Proline residue: O 57 - end of helix Processing helix chain 'P' and resid 4 through 16 removed outlier: 3.505A pdb=" N ILE P 11 " --> pdb=" O ALA P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 24 through 44 removed outlier: 3.612A pdb=" N ASN P 37 " --> pdb=" O THR P 33 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY P 41 " --> pdb=" O ASN P 37 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N HIS P 42 " --> pdb=" O HIS P 38 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA P 44 " --> pdb=" O GLN P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 74 removed outlier: 3.850A pdb=" N GLY P 55 " --> pdb=" O HIS P 51 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS P 73 " --> pdb=" O TYR P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 86 Processing helix chain 'Q' and resid 53 through 64 Processing helix chain 'Q' and resid 68 through 80 Processing helix chain 'S' and resid 11 through 17 Processing helix chain 'S' and resid 25 through 34 removed outlier: 4.255A pdb=" N ASN S 31 " --> pdb=" O ALA S 27 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR S 32 " --> pdb=" O THR S 28 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR S 34 " --> pdb=" O LYS S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 46 Processing helix chain 'S' and resid 48 through 66 removed outlier: 3.515A pdb=" N GLN S 54 " --> pdb=" O LYS S 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 12 through 26 removed outlier: 3.501A pdb=" N GLU T 24 " --> pdb=" O GLU T 20 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER T 25 " --> pdb=" O LYS T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 70 through 76 removed outlier: 4.403A pdb=" N PHE T 74 " --> pdb=" O LYS T 70 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA T 75 " --> pdb=" O LEU T 71 " (cutoff:3.500A) Proline residue: T 76 - end of helix No H-bonds generated for 'chain 'T' and resid 70 through 76' Processing helix chain 'U' and resid 4 through 41 removed outlier: 3.602A pdb=" N VAL U 35 " --> pdb=" O PHE U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 43 through 65 Proline residue: U 56 - end of helix Processing helix chain 'U' and resid 68 through 87 removed outlier: 3.568A pdb=" N ALA U 87 " --> pdb=" O ILE U 83 " (cutoff:3.500A) Processing helix chain 'V' and resid 11 through 27 Processing helix chain 'V' and resid 28 through 37 removed outlier: 4.780A pdb=" N PHE V 37 " --> pdb=" O ARG V 33 " (cutoff:3.500A) Processing helix chain 'V' and resid 40 through 68 removed outlier: 3.666A pdb=" N LYS V 59 " --> pdb=" O ARG V 55 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU V 60 " --> pdb=" O HIS V 56 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU V 63 " --> pdb=" O LYS V 59 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN V 64 " --> pdb=" O LEU V 60 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ALA V 65 " --> pdb=" O ALA V 61 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG V 66 " --> pdb=" O ARG V 62 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N THR V 68 " --> pdb=" O ASN V 64 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 21 removed outlier: 3.899A pdb=" N HIS W 13 " --> pdb=" O LEU W 9 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU W 17 " --> pdb=" O HIS W 13 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU W 18 " --> pdb=" O GLU W 14 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N VAL W 19 " --> pdb=" O ARG W 15 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN W 20 " --> pdb=" O HIS W 16 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA W 21 " --> pdb=" O GLU W 17 " (cutoff:3.500A) Processing helix chain 'W' and resid 35 through 57 removed outlier: 3.854A pdb=" N ARG W 40 " --> pdb=" O ARG W 36 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLU W 41 " --> pdb=" O ALA W 37 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN W 44 " --> pdb=" O ARG W 40 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP W 47 " --> pdb=" O ALA W 43 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL W 48 " --> pdb=" O GLN W 44 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS W 51 " --> pdb=" O ASP W 47 " (cutoff:3.500A) Processing helix chain 'W' and resid 59 through 66 removed outlier: 4.092A pdb=" N GLU W 63 " --> pdb=" O GLN W 59 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR W 64 " --> pdb=" O GLU W 60 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN W 66 " --> pdb=" O ILE W 62 " (cutoff:3.500A) Processing helix chain 'W' and resid 77 through 101 removed outlier: 4.387A pdb=" N GLU W 81 " --> pdb=" O MET W 77 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU W 82 " --> pdb=" O ALA W 78 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL W 98 " --> pdb=" O GLN W 94 " (cutoff:3.500A) Processing helix chain 'W' and resid 104 through 109 removed outlier: 4.113A pdb=" N GLU W 108 " --> pdb=" O ASP W 104 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG W 109 " --> pdb=" O PRO W 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 104 through 109' Processing helix chain 'W' and resid 121 through 143 removed outlier: 3.711A pdb=" N ARG W 142 " --> pdb=" O TYR W 138 " (cutoff:3.500A) Processing helix chain 'W' and resid 170 through 176 removed outlier: 3.878A pdb=" N ARG W 174 " --> pdb=" O GLY W 170 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS W 176 " --> pdb=" O TYR W 172 " (cutoff:3.500A) Processing helix chain 'W' and resid 218 through 223 removed outlier: 3.750A pdb=" N LEU W 222 " --> pdb=" O ASN W 218 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ARG W 223 " --> pdb=" O PRO W 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 218 through 223' Processing helix chain 'W' and resid 234 through 240 Processing helix chain 'W' and resid 262 through 299 Processing helix chain 'W' and resid 328 through 335 Processing helix chain 'W' and resid 338 through 356 removed outlier: 4.186A pdb=" N GLU W 342 " --> pdb=" O ASP W 338 " (cutoff:3.500A) Proline residue: W 343 - end of helix removed outlier: 3.517A pdb=" N ASP W 351 " --> pdb=" O GLU W 347 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA W 354 " --> pdb=" O ALA W 350 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU W 356 " --> pdb=" O GLN W 352 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 15 removed outlier: 4.953A pdb=" N HIS c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 35 removed outlier: 3.892A pdb=" N LEU c 34 " --> pdb=" O PHE c 30 " (cutoff:3.500A) removed outlier: 5.688A 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: 3.550A 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: 3.938A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 226 removed outlier: 3.819A pdb=" N MET c 225 " --> pdb=" O ARG c 221 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN c 226 " --> pdb=" O GLY c 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 221 through 226' Processing helix chain 'c' and resid 260 through 268 removed outlier: 4.680A pdb=" N LYS c 265 " --> pdb=" O LYS c 261 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N PHE c 266 " --> pdb=" O ARG c 262 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE c 267 " --> pdb=" O THR c 263 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL c 268 " --> pdb=" O ASP c 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 56 through 61 removed outlier: 5.293A pdb=" N THR d 61 " --> pdb=" O ALA d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 72 removed outlier: 3.512A pdb=" N ALA d 71 " --> pdb=" O HIS d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 103 removed outlier: 4.167A pdb=" N ALA d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) removed outlier: 5.231A 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 24 through 40 removed outlier: 3.572A pdb=" N ARG e 40 " --> pdb=" O ALA e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 97 through 116 removed outlier: 3.755A pdb=" N ASP e 116 " --> pdb=" O LEU e 112 " (cutoff:3.500A) Processing helix chain 'e' and resid 130 through 142 removed outlier: 3.627A pdb=" N LEU e 134 " --> pdb=" O LYS e 130 " (cutoff:3.500A) Processing helix chain 'e' and resid 154 through 163 removed outlier: 4.486A 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: 5.866A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 47 removed outlier: 3.644A pdb=" N ASP f 46 " --> pdb=" O GLU f 42 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS f 47 " --> pdb=" O ALA f 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 42 through 47' Processing helix chain 'f' and resid 48 through 62 Processing helix chain 'f' and resid 93 through 111 removed outlier: 3.724A pdb=" N ILE f 106 " --> pdb=" O ARG f 102 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA f 107 " --> pdb=" O LEU f 103 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL f 108 " --> pdb=" O ILE f 104 " (cutoff:3.500A) Proline residue: f 109 - end of helix Processing helix chain 'f' and resid 162 through 174 removed outlier: 3.708A pdb=" N PHE f 173 " --> pdb=" O LEU f 169 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP f 174 " --> pdb=" O LEU f 170 " (cutoff:3.500A) Processing helix chain 'f' and resid 134 through 139 removed outlier: 3.636A pdb=" N ILE f 137 " --> pdb=" O GLU f 134 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE f 138 " --> pdb=" O GLN f 135 " (cutoff:3.500A) Proline residue: f 139 - end of helix No H-bonds generated for 'chain 'f' and resid 134 through 139' 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 Processing helix chain 'g' and resid 137 through 153 removed outlier: 3.606A pdb=" N TYR g 151 " --> pdb=" O ASP g 147 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG g 152 " --> pdb=" O LEU g 148 " (cutoff:3.500A) Processing helix chain 'h' and resid 22 through 28 Processing helix chain 'h' and resid 29 through 34 Processing helix chain 'i' and resid 24 through 38 removed outlier: 3.770A 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: 4.254A pdb=" N ILE i 101 " --> pdb=" O PRO i 97 " (cutoff:3.500A) removed outlier: 3.711A 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 123 removed outlier: 3.961A pdb=" N LYS i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU i 122 " --> pdb=" O MET i 118 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LYS i 123 " --> pdb=" O PHE i 119 " (cutoff:3.500A) Processing helix chain 'i' and resid 67 through 72 removed outlier: 4.296A pdb=" N LYS i 72 " --> pdb=" O ASN i 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 67 through 72' Processing helix chain 'j' and resid 112 through 119 Processing helix chain 'k' and resid 37 through 42 removed outlier: 3.984A pdb=" N ARG k 41 " --> pdb=" O GLY k 37 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N SER k 42 " --> pdb=" O GLN k 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 37 through 42' Processing helix chain 'k' and resid 56 through 62 Proline residue: k 62 - end of helix Processing helix chain 'k' and resid 68 through 75 removed outlier: 3.933A pdb=" N ALA k 72 " --> pdb=" O SER k 68 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE k 73 " --> pdb=" O ARG k 69 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ALA k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 78 through 85 removed outlier: 3.775A pdb=" N LEU k 82 " --> pdb=" O ARG k 78 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA k 83 " --> pdb=" O LEU k 79 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS k 84 " --> pdb=" O SER k 80 " (cutoff:3.500A) removed outlier: 3.592A 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 removed outlier: 3.661A pdb=" N LEU k 95 " --> pdb=" O ASP k 91 " (cutoff:3.500A) 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: 4.058A pdb=" N LYS l 123 " --> pdb=" O LEU l 119 " (cutoff:3.500A) removed outlier: 3.685A 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 37 through 58 removed outlier: 3.524A pdb=" N ARG m 45 " --> pdb=" O ALA m 41 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL m 47 " --> pdb=" O GLU m 43 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU m 49 " --> pdb=" O ARG m 45 " (cutoff:3.500A) Proline residue: m 50 - end of helix removed outlier: 4.506A pdb=" N THR m 57 " --> pdb=" O THR m 53 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASP m 58 " --> pdb=" O LEU m 54 " (cutoff:3.500A) Processing helix chain 'm' and resid 59 through 71 removed outlier: 3.855A pdb=" N THR m 70 " --> pdb=" O ALA m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 72 through 88 removed outlier: 3.861A pdb=" N LEU m 83 " --> pdb=" O LEU m 79 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLY m 84 " --> pdb=" O PHE m 80 " (cutoff:3.500A) Proline residue: m 85 - end of helix Processing helix chain 'n' and resid 2 through 22 removed outlier: 4.290A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 63 removed outlier: 4.218A pdb=" N GLU n 60 " --> pdb=" O LYS n 56 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLN n 61 " --> pdb=" O ALA n 57 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU n 62 " --> pdb=" O ILE n 58 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LYS n 63 " --> pdb=" O ALA n 59 " (cutoff:3.500A) Processing helix chain 'n' and resid 67 through 86 removed outlier: 3.815A pdb=" N LYS n 85 " --> pdb=" O ARG n 81 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 114 Processing helix chain 'o' and resid 2 through 13 removed outlier: 4.016A pdb=" N GLN o 12 " --> pdb=" O LEU o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 104 removed outlier: 4.453A pdb=" N ARG o 101 " --> pdb=" O LEU o 97 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU o 102 " --> pdb=" O TYR o 98 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG o 103 " --> pdb=" O TYR o 99 " (cutoff:3.500A) removed outlier: 5.083A 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: 3.509A pdb=" N LYS p 22 " --> pdb=" O LEU p 18 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 31 removed outlier: 3.625A pdb=" N ARG p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) Processing helix chain 'p' and resid 32 through 37 removed outlier: 3.821A pdb=" N GLN p 37 " --> pdb=" O ARG p 33 " (cutoff:3.500A) Processing helix chain 'p' and resid 39 through 73 removed outlier: 3.911A pdb=" N ARG p 51 " --> pdb=" O TYR p 47 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (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: 4.076A pdb=" N VAL r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) Processing helix chain 'r' and resid 28 through 39 Processing helix chain 'r' and resid 41 through 61 removed outlier: 3.659A pdb=" N VAL r 45 " --> pdb=" O LYS r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 65 through 70 removed outlier: 3.575A pdb=" N LEU r 69 " --> pdb=" O ASP r 65 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LYS r 70 " --> pdb=" O ILE r 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 65 through 70' Processing helix chain 's' and resid 3 through 11 removed outlier: 4.011A pdb=" N LYS s 9 " --> pdb=" O GLU s 5 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL s 10 " --> pdb=" O ARG s 6 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU s 11 " --> pdb=" O LEU s 7 " (cutoff:3.500A) Processing helix chain 's' and resid 17 through 26 Processing helix chain 's' and resid 39 through 51 Processing helix chain 't' and resid 66 through 71 removed outlier: 3.883A pdb=" N VAL t 70 " --> pdb=" O GLN t 66 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ALA t 71 " --> pdb=" O VAL t 67 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 66 through 71' Processing helix chain 'u' and resid 13 through 24 Processing helix chain 'u' and resid 43 through 53 removed outlier: 3.647A pdb=" N ALA u 52 " --> pdb=" O MET u 48 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LYS u 53 " --> pdb=" O ASN u 49 " (cutoff:3.500A) Processing helix chain 'u' and resid 54 through 59 removed outlier: 4.003A pdb=" N SER u 58 " --> pdb=" O ALA u 54 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU u 59 " --> pdb=" O GLU u 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 54 through 59' 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: 3.734A pdb=" N GLU x 8 " --> pdb=" O LYS x 4 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS x 9 " --> pdb=" O GLU x 5 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N SER x 10 " --> pdb=" O LEU x 6 " (cutoff:3.500A) Processing helix chain 'x' and resid 11 through 35 removed outlier: 3.634A pdb=" N THR x 16 " --> pdb=" O GLU x 12 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU x 17 " --> pdb=" O GLU x 13 " (cutoff:3.500A) Processing helix chain 'x' and resid 39 through 62 removed outlier: 4.732A pdb=" N LEU x 43 " --> pdb=" O GLN x 39 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS x 44 " --> pdb=" O SER x 40 " (cutoff:3.500A) Processing helix chain 'y' and resid 17 through 28 Processing helix chain 'y' and resid 41 through 52 Processing helix chain 'z' and resid 9 through 19 removed outlier: 4.848A pdb=" N HIS z 19 " --> pdb=" O MET z 15 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '0' and resid 19 through 25 removed outlier: 5.933A pdb=" N HIS 0 19 " --> pdb=" O SER 0 13 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU 0 34 " --> pdb=" O GLU 0 51 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '2' and resid 22 through 25 removed outlier: 5.627A pdb=" N PHE 2 22 " --> pdb=" O VAL 2 50 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '3' and resid 1 through 5 removed outlier: 7.068A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER 3 28 " --> pdb=" O ASN 3 13 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ASN 3 13 " --> pdb=" O SER 3 28 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '4' and resid 20 through 25 removed outlier: 4.528A pdb=" N ASN 4 20 " --> pdb=" O CYS 4 16 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 15 through 18 removed outlier: 4.931A pdb=" N HIS C 15 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N HIS C 39 " --> pdb=" O GLY C 17 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 89 through 93 Processing sheet with id= 7, first strand: chain 'D' and resid 53 through 59 removed outlier: 3.567A pdb=" N ARG D 54 " --> pdb=" O HIS D 69 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 164 through 169 removed outlier: 4.863A pdb=" N GLY D 194 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR D 191 " --> pdb=" O GLY D 194 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASP D 181 " --> pdb=" O LYS D 204 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'E' and resid 141 through 145 removed outlier: 3.733A pdb=" N ASP E 141 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N MET E 178 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU E 179 " --> pdb=" O ASP E 174 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 11 through 16 removed outlier: 6.774A pdb=" N LEU F 36 " --> pdb=" O ILE F 16 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'F' and resid 84 through 88 removed outlier: 3.724A pdb=" N ALA F 99 " --> pdb=" O ASN F 122 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ASN F 122 " --> pdb=" O ALA F 99 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'F' and resid 33 through 41 removed outlier: 6.923A pdb=" N ARG F 45 " --> pdb=" O ASP F 41 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'G' and resid 38 through 43 removed outlier: 4.244A pdb=" N ARG G 38 " --> pdb=" O ASN G 63 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N TYR G 59 " --> pdb=" O TRP G 42 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N HIS G 3 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG G 86 " --> pdb=" O MET G 9 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 44 through 47 removed outlier: 6.740A pdb=" N HIS G 55 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'H' and resid 72 through 77 removed outlier: 6.439A pdb=" N THR H 72 " --> pdb=" O VAL H 91 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'I' and resid 23 through 29 removed outlier: 5.864A pdb=" N ALA I 23 " --> pdb=" O LEU I 63 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP I 48 " --> pdb=" O THR I 62 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'I' and resid 74 through 77 removed outlier: 6.746A pdb=" N VAL I 103 " --> pdb=" O ILE I 126 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'J' and resid 5 through 11 removed outlier: 4.529A pdb=" N LYS J 27 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU J 63 " --> pdb=" O LYS J 27 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'K' and resid 39 through 42 removed outlier: 4.455A pdb=" N LEU K 71 " --> pdb=" O LEU K 42 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'K' and resid 44 through 52 Processing sheet with id= 21, first strand: chain 'L' and resid 29 through 36 removed outlier: 3.598A pdb=" N ASN L 29 " --> pdb=" O SER L 26 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'M' and resid 29 through 32 removed outlier: 5.019A pdb=" N LEU M 81 " --> pdb=" O VAL M 98 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'M' and resid 36 through 41 removed outlier: 3.730A pdb=" N ARG M 36 " --> pdb=" O ARG M 54 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LYS M 51 " --> pdb=" O ILE M 67 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'Q' and resid 4 through 10 removed outlier: 3.830A pdb=" N GLY Q 37 " --> pdb=" O VAL Q 19 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLY Q 49 " --> pdb=" O ASN Q 40 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'R' and resid 7 through 11 removed outlier: 6.973A pdb=" N GLU R 60 " --> pdb=" O VAL R 76 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'R' and resid 19 through 30 No H-bonds generated for sheet with id= 26 Processing sheet with id= 27, first strand: chain 'T' and resid 30 through 34 removed outlier: 4.750A pdb=" N LEU T 47 " --> pdb=" O VAL T 62 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'W' and resid 144 through 149 removed outlier: 6.964A pdb=" N ILE W 163 " --> pdb=" O MET W 149 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LYS W 160 " --> pdb=" O ALA W 117 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ASN W 110 " --> pdb=" O GLU W 208 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG W 308 " --> pdb=" O GLY W 181 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL W 187 " --> pdb=" O PHE W 312 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'W' and resid 224 through 228 Processing sheet with id= 30, first strand: chain 'W' and resid 150 through 153 Processing sheet with id= 31, first strand: chain 'c' and resid 2 through 6 removed outlier: 5.729A pdb=" N VAL c 16 " --> pdb=" O CYS c 6 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'c' and resid 73 through 78 removed outlier: 4.990A pdb=" N ILE c 74 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N SER c 118 " --> pdb=" O ILE c 74 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASP c 114 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLY c 127 " --> pdb=" O GLN c 115 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N GLN c 117 " --> pdb=" O GLY c 127 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'c' and resid 80 through 83 removed outlier: 5.324A pdb=" N ASN c 90 " --> pdb=" O ALA c 106 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'c' and resid 138 through 142 removed outlier: 4.187A pdb=" N SER c 139 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR c 173 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU c 180 " --> pdb=" O LEU c 176 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'd' and resid 3 through 6 removed outlier: 4.099A pdb=" N GLU d 168 " --> pdb=" O SER d 113 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'd' and resid 10 through 16 removed outlier: 3.646A pdb=" N GLY d 10 " --> pdb=" O VAL d 26 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL d 20 " --> pdb=" O THR d 16 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'd' and resid 79 through 84 removed outlier: 5.623A pdb=" N ARG d 46 " --> pdb=" O LEU d 84 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLN d 94 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'd' and resid 105 through 108 removed outlier: 6.346A pdb=" N LYS d 105 " --> pdb=" O VAL d 177 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'e' and resid 1 through 6 removed outlier: 3.691A pdb=" N MET e 1 " --> pdb=" O VAL e 14 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU e 5 " --> pdb=" O SER e 10 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER e 10 " --> pdb=" O LEU e 5 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'e' and resid 117 through 120 removed outlier: 5.692A pdb=" N ARG e 117 " --> pdb=" O ASP e 184 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'f' and resid 65 through 69 removed outlier: 4.864A pdb=" N ILE f 85 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS f 33 " --> pdb=" O THR f 157 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLY f 39 " --> pdb=" O GLY f 151 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N GLY f 151 " --> pdb=" O GLY f 39 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N THR f 158 " --> pdb=" O GLY f 126 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLY f 126 " --> pdb=" O THR f 158 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'g' and resid 16 through 19 removed outlier: 3.554A pdb=" N LYS g 18 " --> pdb=" O THR g 25 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'g' and resid 41 through 45 Processing sheet with id= 44, first strand: chain 'g' and resid 82 through 89 removed outlier: 5.757A pdb=" N THR g 129 " --> pdb=" O LEU g 89 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'g' and resid 94 through 99 removed outlier: 6.349A pdb=" N ASN g 101 " --> pdb=" O LEU g 117 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'h' and resid 17 through 21 removed outlier: 4.605A pdb=" N ASP h 17 " --> pdb=" O LEU h 5 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLN h 2 " --> pdb=" O ALA h 39 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LYS h 35 " --> pdb=" O LEU h 6 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'i' and resid 52 through 57 removed outlier: 4.861A pdb=" N ASP i 19 " --> pdb=" O LEU i 140 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'i' and resid 74 through 78 removed outlier: 7.603A pdb=" N GLY i 83 " --> pdb=" O THR i 78 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'j' and resid 6 through 9 removed outlier: 4.334A pdb=" N THR j 6 " --> pdb=" O CYS j 21 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'j' and resid 39 through 42 Processing sheet with id= 51, first strand: chain 'j' and resid 63 through 66 removed outlier: 4.198A pdb=" N LYS j 66 " --> pdb=" O GLY j 81 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLY j 81 " --> pdb=" O LYS j 66 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'j' and resid 68 through 71 removed outlier: 3.749A pdb=" N SER j 75 " --> pdb=" O ARG j 71 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'l' and resid 62 through 65 removed outlier: 3.516A pdb=" N TYR l 103 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU l 33 " --> pdb=" O LEU l 102 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS l 100 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'l' and resid 30 through 36 removed outlier: 7.782A pdb=" N SER l 30 " --> pdb=" O LYS l 133 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS l 127 " --> pdb=" O VAL l 36 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'm' and resid 33 through 36 removed outlier: 4.993A pdb=" N ARG m 103 " --> pdb=" O ASN m 107 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLY m 101 " --> pdb=" O PRO m 109 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA m 111 " --> pdb=" O LYS m 99 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS m 99 " --> pdb=" O ALA m 111 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE m 113 " --> pdb=" O ILE m 97 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE m 97 " --> pdb=" O ILE m 113 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU m 115 " --> pdb=" O THR m 95 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR m 95 " --> pdb=" O LEU m 115 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'n' and resid 49 through 53 removed outlier: 6.551A pdb=" N ILE n 35 " --> pdb=" O THR n 53 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'o' and resid 49 through 53 removed outlier: 3.565A pdb=" N ALA o 49 " --> pdb=" O THR o 60 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ARG o 53 " --> pdb=" O HIS o 56 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR o 60 " --> pdb=" O ILE o 48 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'o' and resid 58 through 64 Processing sheet with id= 59, first strand: chain 'q' and resid 11 through 15 Processing sheet with id= 60, first strand: chain 'q' and resid 18 through 21 removed outlier: 4.288A pdb=" N GLN q 18 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASP q 95 " --> pdb=" O VAL q 64 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS q 60 " --> pdb=" O THR q 99 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'q' and resid 57 through 60 Processing sheet with id= 62, first strand: chain 'q' and resid 65 through 68 Processing sheet with id= 63, first strand: chain 'q' and resid 71 through 78 removed outlier: 4.197A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'r' and resid 2 through 8 Processing sheet with id= 65, first strand: chain 's' and resid 12 through 15 removed outlier: 5.149A pdb=" N VAL s 31 " --> pdb=" O HIS s 15 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS s 81 " --> pdb=" O VAL s 34 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS s 66 " --> pdb=" O ARG s 77 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ASP s 79 " --> pdb=" O LYS s 64 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LYS s 64 " --> pdb=" O ASP s 79 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS s 81 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL s 62 " --> pdb=" O LYS s 81 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA s 83 " --> pdb=" O THR s 60 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR s 60 " --> pdb=" O ALA s 83 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL s 85 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL s 58 " --> pdb=" O VAL s 85 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 't' and resid 82 through 87 removed outlier: 4.316A pdb=" N ARG t 82 " --> pdb=" O LYS t 97 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ARG t 94 " --> pdb=" O ILE t 103 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU t 101 " --> pdb=" O PHE t 96 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'u' and resid 69 through 72 removed outlier: 6.701A pdb=" N ALA u 39 " --> pdb=" O ARG u 9 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE u 89 " --> pdb=" O PRO u 27 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'v' and resid 51 through 54 removed outlier: 3.902A pdb=" N THR v 58 " --> pdb=" O GLY v 54 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'v' and resid 65 through 71 Processing sheet with id= 70, first strand: chain 'w' and resid 12 through 19 removed outlier: 4.478A pdb=" N ASN w 23 " --> pdb=" O SER w 19 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'w' and resid 35 through 41 removed outlier: 3.758A pdb=" N ARG w 45 " --> pdb=" O VAL w 40 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'y' and resid 33 through 39 removed outlier: 4.457A pdb=" N HIS y 34 " --> pdb=" O GLN y 9 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N MET y 54 " --> pdb=" O THR y 10 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'z' and resid 29 through 32 removed outlier: 4.375A pdb=" N GLU z 36 " --> pdb=" O ASP z 31 " (cutoff:3.500A) 2010 hydrogen bonds defined for protein. 5934 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3833 hydrogen bonds 5966 hydrogen bond angles 0 basepair planarities 1538 basepair parallelities 2387 stacking parallelities Total time for adding SS restraints: 377.81 Time building geometry restraints manager: 72.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 17278 1.33 - 1.45: 68697 1.45 - 1.58: 61451 1.58 - 1.70: 9101 1.70 - 1.83: 285 Bond restraints: 156812 Sorted by residual: bond pdb=" C4 5MU a 747 " pdb=" C5 5MU a 747 " ideal model delta sigma weight residual 1.802 1.444 0.358 2.00e-02 2.50e+03 3.20e+02 bond pdb=" C4 5MU a1939 " pdb=" C5 5MU a1939 " ideal model delta sigma weight residual 1.802 1.445 0.357 2.00e-02 2.50e+03 3.19e+02 bond pdb=" N1 5MU a1939 " pdb=" C6 5MU a1939 " ideal model delta sigma weight residual 1.635 1.381 0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" N1 5MU a 747 " pdb=" C6 5MU a 747 " ideal model delta sigma weight residual 1.635 1.387 0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" N6 6MZ a1618 " pdb=" C9 6MZ a1618 " ideal model delta sigma weight residual 1.464 1.681 -0.217 2.00e-02 2.50e+03 1.17e+02 ... (remaining 156807 not shown) Histogram of bond angle deviations from ideal: 78.17 - 89.47: 2 89.47 - 100.76: 6000 100.76 - 112.06: 95666 112.06 - 123.36: 99423 123.36 - 134.65: 33135 Bond angle restraints: 234226 Sorted by residual: angle pdb=" C1' G7M a2069 " pdb=" N9 G7M a2069 " pdb=" C8 G7M a2069 " ideal model delta sigma weight residual 94.96 126.69 -31.73 3.00e+00 1.11e-01 1.12e+02 angle pdb=" C1' G7M B 527 " pdb=" N9 G7M B 527 " pdb=" C8 G7M B 527 " ideal model delta sigma weight residual 94.96 126.45 -31.49 3.00e+00 1.11e-01 1.10e+02 angle pdb=" O3' C a1617 " pdb=" P 6MZ a1618 " pdb=" O2P 6MZ a1618 " ideal model delta sigma weight residual 108.00 78.17 29.83 3.00e+00 1.11e-01 9.89e+01 angle pdb=" O3' C a1617 " pdb=" P 6MZ a1618 " pdb=" O1P 6MZ a1618 " ideal model delta sigma weight residual 108.00 80.50 27.50 3.00e+00 1.11e-01 8.40e+01 angle pdb=" O3' G a 329 " pdb=" P A a 330 " pdb=" O5' A a 330 " ideal model delta sigma weight residual 104.00 90.74 13.26 1.50e+00 4.44e-01 7.81e+01 ... (remaining 234221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.36: 81130 35.36 - 70.73: 2506 70.73 - 106.09: 238 106.09 - 141.46: 12 141.46 - 176.82: 16 Dihedral angle restraints: 83902 sinusoidal: 66915 harmonic: 16987 Sorted by residual: dihedral pdb=" O4' U B 365 " pdb=" C1' U B 365 " pdb=" N1 U B 365 " pdb=" C2 U B 365 " ideal model delta sinusoidal sigma weight residual 200.00 53.79 146.21 1 1.50e+01 4.44e-03 7.81e+01 dihedral pdb=" O4' U X 20 " pdb=" C1' U X 20 " pdb=" N1 U X 20 " pdb=" C2 U X 20 " ideal model delta sinusoidal sigma weight residual 200.00 55.57 144.43 1 1.50e+01 4.44e-03 7.74e+01 dihedral pdb=" O4' U a1779 " pdb=" C1' U a1779 " pdb=" N1 U a1779 " pdb=" C2 U a1779 " ideal model delta sinusoidal sigma weight residual 200.00 57.84 142.16 1 1.50e+01 4.44e-03 7.64e+01 ... (remaining 83899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 20280 0.130 - 0.259: 6397 0.259 - 0.389: 642 0.389 - 0.519: 2335 0.519 - 0.649: 115 Chirality restraints: 29769 Sorted by residual: chirality pdb=" P C a1170 " pdb=" OP1 C a1170 " pdb=" OP2 C a1170 " pdb=" O5' C a1170 " both_signs ideal model delta sigma weight residual True 2.41 -3.06 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" P C a2824 " pdb=" OP1 C a2824 " pdb=" OP2 C a2824 " pdb=" O5' C a2824 " both_signs ideal model delta sigma weight residual True 2.41 -3.05 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" P G a1107 " pdb=" OP1 G a1107 " pdb=" OP2 G a1107 " pdb=" O5' G a1107 " both_signs ideal model delta sigma weight residual True 2.41 -3.04 -0.63 2.00e-01 2.50e+01 9.91e+00 ... (remaining 29766 not shown) Planarity restraints: 12793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG B1207 " -0.096 2.00e-02 2.50e+03 6.25e-01 8.79e+03 pdb=" C4' 2MG B1207 " -0.446 2.00e-02 2.50e+03 pdb=" O4' 2MG B1207 " -0.693 2.00e-02 2.50e+03 pdb=" C3' 2MG B1207 " 0.629 2.00e-02 2.50e+03 pdb=" O3' 2MG B1207 " 0.673 2.00e-02 2.50e+03 pdb=" C2' 2MG B1207 " 0.147 2.00e-02 2.50e+03 pdb=" O2' 2MG B1207 " -0.992 2.00e-02 2.50e+03 pdb=" C1' 2MG B1207 " -0.190 2.00e-02 2.50e+03 pdb=" N9 2MG B1207 " 0.967 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a2445 " -0.070 2.00e-02 2.50e+03 6.12e-01 8.43e+03 pdb=" C4' 2MG a2445 " -0.427 2.00e-02 2.50e+03 pdb=" O4' 2MG a2445 " -0.680 2.00e-02 2.50e+03 pdb=" C3' 2MG a2445 " 0.657 2.00e-02 2.50e+03 pdb=" O3' 2MG a2445 " 0.657 2.00e-02 2.50e+03 pdb=" C2' 2MG a2445 " 0.149 2.00e-02 2.50e+03 pdb=" O2' 2MG a2445 " -0.980 2.00e-02 2.50e+03 pdb=" C1' 2MG a2445 " -0.216 2.00e-02 2.50e+03 pdb=" N9 2MG a2445 " 0.911 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC B1407 " -0.093 2.00e-02 2.50e+03 5.98e-01 8.04e+03 pdb=" C4' 5MC B1407 " -0.438 2.00e-02 2.50e+03 pdb=" O4' 5MC B1407 " -0.610 2.00e-02 2.50e+03 pdb=" C3' 5MC B1407 " 0.626 2.00e-02 2.50e+03 pdb=" O3' 5MC B1407 " 0.636 2.00e-02 2.50e+03 pdb=" C2' 5MC B1407 " 0.161 2.00e-02 2.50e+03 pdb=" O2' 5MC B1407 " -0.968 2.00e-02 2.50e+03 pdb=" C1' 5MC B1407 " -0.226 2.00e-02 2.50e+03 pdb=" N1 5MC B1407 " 0.913 2.00e-02 2.50e+03 ... (remaining 12790 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 630 2.20 - 2.88: 45320 2.88 - 3.55: 231531 3.55 - 4.23: 486149 4.23 - 4.90: 634780 Nonbonded interactions: 1398410 Sorted by model distance: nonbonded pdb=" C5 G B 324 " pdb="MG MG B1649 " model vdw 1.528 2.390 nonbonded pdb=" C4 G B 324 " pdb="MG MG B1649 " model vdw 1.570 2.390 nonbonded pdb=" C5 G B 774 " pdb="MG MG B1665 " model vdw 1.742 2.390 nonbonded pdb=" C6 G B 774 " pdb="MG MG B1665 " model vdw 1.767 2.390 nonbonded pdb="MG MG a6017 " pdb=" O HOH a6947 " model vdw 1.817 2.170 ... (remaining 1398405 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: 11.850 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: 0.110 Extract box with map and model: 50.680 Check model and map are aligned: 1.550 Set scattering table: 1.000 Process input model: 697.420 Find NCS groups from input model: 2.950 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:15.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 781.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 : 0.013 0.358 156812 Z= 0.796 Angle : 1.776 31.728 234226 Z= 1.061 Chirality : 0.169 0.649 29769 Planarity : 0.021 0.625 12793 Dihedral : 14.476 176.821 72942 Min Nonbonded Distance : 1.528 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.89 % Allowed : 5.93 % Favored : 93.18 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.31 (0.09), residues: 5853 helix: -2.85 (0.08), residues: 1995 sheet: -1.66 (0.14), residues: 1077 loop : -1.77 (0.10), residues: 2781 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1319 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1212 time to evaluate : 6.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 16 residues processed: 1288 average time/residue: 2.4919 time to fit residues: 4464.7306 Evaluate side-chains 895 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 879 time to evaluate : 6.492 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 3 average time/residue: 1.3386 time to fit residues: 13.5951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 863 optimal weight: 0.9990 chunk 775 optimal weight: 0.6980 chunk 430 optimal weight: 0.9990 chunk 264 optimal weight: 6.9990 chunk 523 optimal weight: 0.7980 chunk 414 optimal weight: 1.9990 chunk 801 optimal weight: 6.9990 chunk 310 optimal weight: 0.9990 chunk 487 optimal weight: 7.9990 chunk 596 optimal weight: 7.9990 chunk 928 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN 4 41 HIS C 51 ASN ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 ASN E 198 HIS F 19 ASN F 97 GLN F 132 ASN G 3 HIS H 68 ASN H 122 ASN J 110 GLN K 15 HIS P 37 ASN Q 26 ASN R 45 HIS S 31 ASN T 14 HIS T 43 ASN T 52 HIS U 3 ASN U 55 GLN U 78 ASN W 248 HIS W 288 GLN W 307 ASN W 314 GLN W 346 GLN e 165 HIS e 195 GLN i 58 ASN i 128 ASN i 136 GLN k 104 GLN ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 18 GLN ** q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 86 GLN s 48 GLN s 59 ASN t 40 ASN t 74 ASN x 58 ASN z 6 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 156812 Z= 0.154 Angle : 0.642 15.513 234226 Z= 0.350 Chirality : 0.035 0.342 29769 Planarity : 0.006 0.133 12793 Dihedral : 13.384 179.790 61155 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.24 % Favored : 97.59 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.67 (0.10), residues: 5853 helix: 0.28 (0.11), residues: 2042 sheet: -0.93 (0.14), residues: 1121 loop : -0.66 (0.11), residues: 2690 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 978 time to evaluate : 6.612 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 120 outliers final: 36 residues processed: 1041 average time/residue: 2.5089 time to fit residues: 3658.7267 Evaluate side-chains 921 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 885 time to evaluate : 6.566 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 21 residues processed: 15 average time/residue: 1.5846 time to fit residues: 45.4284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 516 optimal weight: 8.9990 chunk 288 optimal weight: 9.9990 chunk 773 optimal weight: 5.9990 chunk 632 optimal weight: 7.9990 chunk 256 optimal weight: 8.9990 chunk 930 optimal weight: 10.0000 chunk 1005 optimal weight: 5.9990 chunk 828 optimal weight: 0.9980 chunk 922 optimal weight: 3.9990 chunk 317 optimal weight: 0.8980 chunk 746 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: 1 29 GLN C 18 HIS C 51 ASN C 58 ASN C 177 ASN ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 GLN E 198 HIS F 19 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN ** G 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 HIS H 68 ASN J 110 GLN K 56 HIS L 15 GLN L 22 HIS P 28 GLN P 37 ASN P 46 HIS T 83 HIS U 21 ASN U 48 GLN U 68 HIS U 75 HIS W 248 HIS W 349 GLN g 64 GLN k 104 GLN n 98 GLN n 100 HIS q 18 GLN q 43 ASN s 59 ASN t 54 GLN x 27 ASN x 58 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.086 156812 Z= 0.299 Angle : 0.769 15.924 234226 Z= 0.404 Chirality : 0.041 0.354 29769 Planarity : 0.007 0.153 12793 Dihedral : 13.487 176.370 61155 Min Nonbonded Distance : 1.658 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.60 % Favored : 97.25 % Rotamer Outliers : 3.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 5853 helix: 0.85 (0.11), residues: 2049 sheet: -0.54 (0.14), residues: 1166 loop : -0.31 (0.12), residues: 2638 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 923 time to evaluate : 6.809 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 172 outliers final: 67 residues processed: 1022 average time/residue: 2.4963 time to fit residues: 3578.7134 Evaluate side-chains 938 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 871 time to evaluate : 6.631 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 43 residues processed: 24 average time/residue: 1.7502 time to fit residues: 73.8823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 919 optimal weight: 0.3980 chunk 699 optimal weight: 6.9990 chunk 483 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 444 optimal weight: 9.9990 chunk 624 optimal weight: 9.9990 chunk 934 optimal weight: 5.9990 chunk 988 optimal weight: 6.9990 chunk 487 optimal weight: 9.9990 chunk 885 optimal weight: 10.0000 chunk 266 optimal weight: 9.9990 overall best weight: 5.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN 4 61 ASN C 18 HIS ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 HIS F 19 ASN F 77 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN H 153 HIS J 31 ASN J 110 GLN L 118 HIS ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 ASN P 46 HIS U 68 HIS W 16 HIS W 59 GLN W 248 HIS g 64 GLN g 73 ASN h 2 GLN h 11 ASN i 136 GLN k 104 GLN n 104 GLN q 18 GLN q 43 ASN ** t 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 12 GLN x 27 ASN x 58 ASN z 42 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.110 156812 Z= 0.487 Angle : 0.977 19.632 234226 Z= 0.492 Chirality : 0.051 0.374 29769 Planarity : 0.009 0.161 12793 Dihedral : 13.890 177.058 61155 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.90 % Favored : 96.94 % Rotamer Outliers : 4.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.10), residues: 5853 helix: 0.31 (0.11), residues: 2049 sheet: -0.47 (0.14), residues: 1155 loop : -0.40 (0.11), residues: 2649 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1099 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 895 time to evaluate : 6.585 Fit side-chains outliers start: 204 outliers final: 94 residues processed: 1021 average time/residue: 2.4686 time to fit residues: 3534.7533 Evaluate side-chains 940 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 846 time to evaluate : 6.590 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 66 residues processed: 29 average time/residue: 1.5537 time to fit residues: 80.6585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 823 optimal weight: 0.0170 chunk 561 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 736 optimal weight: 10.0000 chunk 407 optimal weight: 9.9990 chunk 843 optimal weight: 0.0770 chunk 683 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 504 optimal weight: 6.9990 chunk 887 optimal weight: 0.0970 chunk 249 optimal weight: 0.9980 overall best weight: 0.4374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 18 HIS C 177 ASN ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 ASN F 77 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN G 3 HIS G 11 HIS ** G 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 GLN P 37 ASN P 46 HIS U 3 ASN U 61 GLN U 68 HIS W 44 GLN W 248 HIS W 348 HIS g 64 GLN g 73 ASN i 128 ASN i 136 GLN j 88 ASN k 104 GLN q 43 ASN r 40 ASN s 48 GLN t 53 ASN u 12 GLN x 58 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.105 156812 Z= 0.122 Angle : 0.596 14.656 234226 Z= 0.327 Chirality : 0.034 0.345 29769 Planarity : 0.005 0.126 12793 Dihedral : 13.430 179.028 61155 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.85 % Favored : 98.02 % Rotamer Outliers : 2.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.56 (0.11), residues: 5853 helix: 1.37 (0.11), residues: 2047 sheet: -0.10 (0.15), residues: 1156 loop : -0.09 (0.12), residues: 2650 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1055 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 910 time to evaluate : 6.734 Fit side-chains outliers start: 145 outliers final: 58 residues processed: 999 average time/residue: 2.5383 time to fit residues: 3545.4951 Evaluate side-chains 909 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 851 time to evaluate : 6.527 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 46 residues processed: 12 average time/residue: 1.5209 time to fit residues: 37.0605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 332 optimal weight: 9.9990 chunk 890 optimal weight: 0.9990 chunk 195 optimal weight: 9.9990 chunk 580 optimal weight: 8.9990 chunk 244 optimal weight: 10.0000 chunk 989 optimal weight: 0.9990 chunk 821 optimal weight: 9.9990 chunk 458 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 327 optimal weight: 10.0000 chunk 519 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 18 HIS C 177 ASN ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN ** G 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 HIS H 68 ASN H 130 ASN I 118 GLN J 110 GLN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 GLN P 46 HIS Q 63 GLN ** S 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 HIS U 68 HIS W 248 HIS g 64 GLN g 73 ASN h 20 ASN i 136 GLN j 29 HIS j 88 ASN n 98 GLN q 18 GLN q 86 GLN u 12 GLN x 27 ASN x 58 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.090 156812 Z= 0.483 Angle : 0.956 18.734 234226 Z= 0.481 Chirality : 0.050 0.387 29769 Planarity : 0.009 0.162 12793 Dihedral : 13.761 177.167 61155 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.94 % Favored : 96.91 % Rotamer Outliers : 3.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.10), residues: 5853 helix: 0.62 (0.11), residues: 2055 sheet: -0.31 (0.14), residues: 1163 loop : -0.29 (0.11), residues: 2635 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1054 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 874 time to evaluate : 6.667 Fit side-chains revert: symmetry clash outliers start: 180 outliers final: 97 residues processed: 992 average time/residue: 2.5899 time to fit residues: 3600.1315 Evaluate side-chains 950 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 853 time to evaluate : 6.813 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 73 residues processed: 24 average time/residue: 1.3030 time to fit residues: 61.4818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 954 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 563 optimal weight: 5.9990 chunk 722 optimal weight: 5.9990 chunk 560 optimal weight: 9.9990 chunk 833 optimal weight: 7.9990 chunk 552 optimal weight: 2.9990 chunk 986 optimal weight: 5.9990 chunk 617 optimal weight: 4.9990 chunk 601 optimal weight: 9.9990 chunk 455 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 18 HIS ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 GLN F 77 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 HIS J 110 GLN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 GLN P 37 ASN P 46 HIS S 54 GLN U 20 HIS U 61 GLN U 68 HIS W 97 GLN W 248 HIS g 64 GLN g 73 ASN i 136 GLN j 29 HIS j 88 ASN s 48 GLN u 12 GLN x 27 ASN x 58 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.094 156812 Z= 0.434 Angle : 0.909 18.270 234226 Z= 0.462 Chirality : 0.048 0.370 29769 Planarity : 0.008 0.158 12793 Dihedral : 13.829 177.067 61155 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.89 % Favored : 96.98 % Rotamer Outliers : 3.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.10), residues: 5853 helix: 0.44 (0.11), residues: 2053 sheet: -0.38 (0.14), residues: 1161 loop : -0.42 (0.11), residues: 2639 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 872 time to evaluate : 6.732 Fit side-chains revert: symmetry clash outliers start: 170 outliers final: 102 residues processed: 985 average time/residue: 2.4217 time to fit residues: 3365.4513 Evaluate side-chains 954 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 852 time to evaluate : 6.654 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 80 residues processed: 22 average time/residue: 1.6612 time to fit residues: 65.7543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 610 optimal weight: 5.9990 chunk 393 optimal weight: 5.9990 chunk 588 optimal weight: 6.9990 chunk 297 optimal weight: 10.0000 chunk 193 optimal weight: 7.9990 chunk 191 optimal weight: 4.9990 chunk 626 optimal weight: 6.9990 chunk 671 optimal weight: 9.9990 chunk 487 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 775 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 18 HIS ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 HIS ** G 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 14 HIS P 37 ASN P 46 HIS Q 63 GLN S 54 GLN U 20 HIS U 61 GLN U 68 HIS W 248 HIS c 117 GLN g 64 GLN i 128 ASN i 136 GLN j 29 HIS j 88 ASN u 12 GLN x 58 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.088 156812 Z= 0.452 Angle : 0.936 18.829 234226 Z= 0.475 Chirality : 0.049 0.372 29769 Planarity : 0.009 0.159 12793 Dihedral : 13.890 176.836 61155 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.09 % Favored : 96.77 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.10), residues: 5853 helix: 0.31 (0.11), residues: 2055 sheet: -0.42 (0.14), residues: 1164 loop : -0.50 (0.11), residues: 2634 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1020 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 866 time to evaluate : 6.879 Fit side-chains revert: symmetry clash outliers start: 154 outliers final: 105 residues processed: 979 average time/residue: 2.5206 time to fit residues: 3462.4214 Evaluate side-chains 964 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 859 time to evaluate : 6.593 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 87 residues processed: 18 average time/residue: 1.3941 time to fit residues: 50.2353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 896 optimal weight: 5.9990 chunk 944 optimal weight: 4.9990 chunk 861 optimal weight: 4.9990 chunk 918 optimal weight: 6.9990 chunk 553 optimal weight: 4.9990 chunk 400 optimal weight: 8.9990 chunk 721 optimal weight: 10.0000 chunk 281 optimal weight: 0.9980 chunk 830 optimal weight: 5.9990 chunk 869 optimal weight: 0.7980 chunk 915 optimal weight: 0.7980 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 18 HIS ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 HIS ** G 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 GLN P 37 ASN P 46 HIS Q 63 GLN S 54 GLN ** U 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 HIS W 248 HIS W 346 GLN c 117 GLN g 64 GLN i 128 ASN i 136 GLN j 29 HIS j 88 ASN s 48 GLN u 12 GLN x 58 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 156812 Z= 0.244 Angle : 0.711 15.469 234226 Z= 0.379 Chirality : 0.039 0.350 29769 Planarity : 0.007 0.145 12793 Dihedral : 13.600 177.379 61155 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.39 % Favored : 97.49 % Rotamer Outliers : 2.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.08 (0.11), residues: 5853 helix: 0.86 (0.11), residues: 2057 sheet: -0.26 (0.14), residues: 1174 loop : -0.32 (0.12), residues: 2622 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 862 time to evaluate : 6.636 Fit side-chains revert: symmetry clash outliers start: 130 outliers final: 92 residues processed: 962 average time/residue: 2.5276 time to fit residues: 3410.3390 Evaluate side-chains 933 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 841 time to evaluate : 6.595 Switching outliers to nearest non-outliers outliers start: 92 outliers final: 81 residues processed: 11 average time/residue: 1.3130 time to fit residues: 32.5130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 603 optimal weight: 10.0000 chunk 971 optimal weight: 8.9990 chunk 593 optimal weight: 7.9990 chunk 460 optimal weight: 9.9990 chunk 675 optimal weight: 8.9990 chunk 1019 optimal weight: 3.9990 chunk 938 optimal weight: 3.9990 chunk 811 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 626 optimal weight: 7.9990 chunk 497 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 18 HIS ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 GLN F 77 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 HIS ** G 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 GLN P 46 HIS S 54 GLN ** U 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 HIS W 248 HIS c 117 GLN g 64 GLN i 128 ASN j 29 HIS j 88 ASN u 12 GLN x 27 ASN x 58 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.092 156812 Z= 0.426 Angle : 0.904 18.877 234226 Z= 0.460 Chirality : 0.048 0.363 29769 Planarity : 0.008 0.159 12793 Dihedral : 13.804 176.820 61155 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.21 % Favored : 96.69 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.10), residues: 5853 helix: 0.51 (0.11), residues: 2055 sheet: -0.35 (0.14), residues: 1161 loop : -0.42 (0.11), residues: 2637 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 963 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 848 time to evaluate : 6.801 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 87 residues processed: 939 average time/residue: 2.5187 time to fit residues: 3316.7405 Evaluate side-chains 926 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 839 time to evaluate : 6.641 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 79 residues processed: 8 average time/residue: 1.1843 time to fit residues: 24.6293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 644 optimal weight: 5.9990 chunk 864 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 748 optimal weight: 0.6980 chunk 119 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 812 optimal weight: 4.9990 chunk 340 optimal weight: 8.9990 chunk 834 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 18 HIS ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 GLN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 HIS ** G 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 46 HIS S 54 GLN U 20 HIS U 68 HIS c 117 GLN i 128 ASN i 136 GLN j 29 HIS j 88 ASN s 48 GLN u 12 GLN x 58 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.165822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.146139 restraints weight = 127473.942| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 0.52 r_work: 0.3338 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 156812 Z= 0.301 Angle : 0.769 16.050 234226 Z= 0.403 Chirality : 0.042 0.361 29769 Planarity : 0.007 0.150 12793 Dihedral : 13.659 176.869 61155 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.63 % Favored : 97.27 % Rotamer Outliers : 2.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.10), residues: 5853 helix: 0.75 (0.11), residues: 2057 sheet: -0.29 (0.15), residues: 1165 loop : -0.35 (0.11), residues: 2631 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 51098.85 seconds wall clock time: 887 minutes 27.47 seconds (53247.47 seconds total)