Starting phenix.real_space_refine on Tue Mar 12 05:08:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8b_10117/03_2024/6s8b_10117_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8b_10117/03_2024/6s8b_10117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8b_10117/03_2024/6s8b_10117.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8b_10117/03_2024/6s8b_10117.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8b_10117/03_2024/6s8b_10117_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8b_10117/03_2024/6s8b_10117_updated.pdb" } resolution = 2.41 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= 0.723 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 Mn 3 7.51 5 Zn 1 6.06 5 P 98 5.49 5 S 103 5.16 5 C 39583 2.51 5 N 10243 2.21 5 O 12120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 62": "OD1" <-> "OD2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "B TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B ARG 79": "NH1" <-> "NH2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B GLU 149": "OE1" <-> "OE2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "C ASP 6": "OD1" <-> "OD2" Residue "C GLU 12": "OE1" <-> "OE2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "E GLU 28": "OE1" <-> "OE2" Residue "E PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E ASP 102": "OD1" <-> "OD2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "E GLU 246": "OE1" <-> "OE2" Residue "E PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 29": "OE1" <-> "OE2" Residue "F PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 102": "OD1" <-> "OD2" Residue "F GLU 200": "OE1" <-> "OE2" Residue "F PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 28": "OE1" <-> "OE2" Residue "G ASP 37": "OD1" <-> "OD2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 79": "OE1" <-> "OE2" Residue "G GLU 100": "OE1" <-> "OE2" Residue "G ASP 102": "OD1" <-> "OD2" Residue "G PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 172": "OE1" <-> "OE2" Residue "G GLU 246": "OE1" <-> "OE2" Residue "G PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 15": "NH1" <-> "NH2" Residue "H TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "H ARG 113": "NH1" <-> "NH2" Residue "H ARG 114": "NH1" <-> "NH2" Residue "H ASP 136": "OD1" <-> "OD2" Residue "H ASP 243": "OD1" <-> "OD2" Residue "H GLU 280": "OE1" <-> "OE2" Residue "H ASP 284": "OD1" <-> "OD2" Residue "I GLU 70": "OE1" <-> "OE2" Residue "I GLU 117": "OE1" <-> "OE2" Residue "I GLU 176": "OE1" <-> "OE2" Residue "I GLU 182": "OE1" <-> "OE2" Residue "I TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 280": "OE1" <-> "OE2" Residue "J GLU 30": "OE1" <-> "OE2" Residue "J GLU 31": "OE1" <-> "OE2" Residue "J PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 65": "OE1" <-> "OE2" Residue "J GLU 78": "OE1" <-> "OE2" Residue "J ARG 97": "NH1" <-> "NH2" Residue "J ARG 113": "NH1" <-> "NH2" Residue "J PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 175": "OD1" <-> "OD2" Residue "J ASP 215": "OD1" <-> "OD2" Residue "J ARG 246": "NH1" <-> "NH2" Residue "J ASP 273": "OD1" <-> "OD2" Residue "J ASP 296": "OD1" <-> "OD2" Residue "J TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 317": "OD1" <-> "OD2" Residue "J ASP 329": "OD1" <-> "OD2" Residue "J GLU 332": "OE1" <-> "OE2" Residue "J ARG 335": "NH1" <-> "NH2" Residue "J GLU 353": "OE1" <-> "OE2" Residue "J PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 383": "OD1" <-> "OD2" Residue "J PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 433": "NH1" <-> "NH2" Residue "J ASP 439": "OD1" <-> "OD2" Residue "J TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 50": "OD1" <-> "OD2" Residue "L TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 104": "OD1" <-> "OD2" Residue "L ARG 118": "NH1" <-> "NH2" Residue "L PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 34": "OD1" <-> "OD2" Residue "M GLU 35": "OE1" <-> "OE2" Residue "M TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 104": "OD1" <-> "OD2" Residue "M TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 118": "NH1" <-> "NH2" Residue "M TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 152": "OE1" <-> "OE2" Residue "N ASP 50": "OD1" <-> "OD2" Residue "N ASP 105": "OD1" <-> "OD2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "N TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 173": "OE1" <-> "OE2" Residue "O ASP 19": "OD1" <-> "OD2" Residue "O TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 116": "OD1" <-> "OD2" Residue "O ARG 118": "NH1" <-> "NH2" Residue "O ASP 162": "OD1" <-> "OD2" Residue "O GLU 165": "OE1" <-> "OE2" Residue "P TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 50": "OD1" <-> "OD2" Residue "P TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 105": "OD1" <-> "OD2" Residue "P ARG 118": "NH1" <-> "NH2" Residue "Q GLU 6": "OE1" <-> "OE2" Residue "Q PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 34": "OD1" <-> "OD2" Residue "Q TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 82": "OD1" <-> "OD2" Residue "Q TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 116": "OD1" <-> "OD2" Residue "Q ARG 118": "NH1" <-> "NH2" Residue "Q PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 157": "OE1" <-> "OE2" Residue "R GLU 51": "OE1" <-> "OE2" Residue "R TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 116": "OD1" <-> "OD2" Residue "R ARG 118": "NH1" <-> "NH2" Residue "R ASP 130": "OD1" <-> "OD2" Residue "R PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 118": "NH1" <-> "NH2" Residue "S GLU 152": "OE1" <-> "OE2" Residue "T PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 50": "OD1" <-> "OD2" Residue "T TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 118": "NH1" <-> "NH2" Residue "T GLU 140": "OE1" <-> "OE2" Residue "T PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 173": "OE1" <-> "OE2" Residue "W TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 19": "OD1" <-> "OD2" Residue "W ASP 28": "OD1" <-> "OD2" Residue "W ASP 82": "OD1" <-> "OD2" Residue "W TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 118": "NH1" <-> "NH2" Residue "W PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 152": "OE1" <-> "OE2" Residue "W ASP 162": "OD1" <-> "OD2" Residue "X TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 34": "OD1" <-> "OD2" Residue "X ASP 64": "OD1" <-> "OD2" Residue "X TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X GLU 152": "OE1" <-> "OE2" Residue "l PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 118": "NH1" <-> "NH2" Residue "l ASP 130": "OD1" <-> "OD2" Residue "l ASP 131": "OD1" <-> "OD2" Residue "l TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 118": "NH1" <-> "NH2" Residue "m TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 161": "OE1" <-> "OE2" Residue "m ASP 162": "OD1" <-> "OD2" Residue "n ASP 34": "OD1" <-> "OD2" Residue "n ASP 64": "OD1" <-> "OD2" Residue "n TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 105": "OD1" <-> "OD2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "n PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 118": "NH1" <-> "NH2" Residue "o TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 118": "NH1" <-> "NH2" Residue "p GLU 161": "OE1" <-> "OE2" Residue "q TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 50": "OD1" <-> "OD2" Residue "q ARG 118": "NH1" <-> "NH2" Residue "q TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 173": "OE1" <-> "OE2" Residue "r PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 35": "OE1" <-> "OE2" Residue "r TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 118": "NH1" <-> "NH2" Residue "r ASP 130": "OD1" <-> "OD2" Residue "r ASP 131": "OD1" <-> "OD2" Residue "r PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 118": "NH1" <-> "NH2" Residue "s PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 162": "OD1" <-> "OD2" Residue "s TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 173": "OE1" <-> "OE2" Residue "t TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 61": "OD1" <-> "OD2" Residue "t ARG 118": "NH1" <-> "NH2" Residue "t TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 173": "OE1" <-> "OE2" Residue "w TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 34": "OD1" <-> "OD2" Residue "w ASP 50": "OD1" <-> "OD2" Residue "w TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 118": "NH1" <-> "NH2" Residue "w PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 35": "OE1" <-> "OE2" Residue "x ASP 61": "OD1" <-> "OD2" Residue "x TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 82": "OD1" <-> "OD2" Residue "x ASP 105": "OD1" <-> "OD2" Residue "x TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 118": "NH1" <-> "NH2" Residue "x ASP 130": "OD1" <-> "OD2" Residue "x PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 12": "OD1" <-> "OD2" Residue "K TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 70": "OD1" <-> "OD2" Residue "K ASP 80": "OD1" <-> "OD2" Residue "K TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 112": "OD1" <-> "OD2" Residue "K GLU 155": "OE1" <-> "OE2" Residue "K ASP 160": "OD1" <-> "OD2" Residue "K ARG 171": "NH1" <-> "NH2" Residue "K PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 212": "OD1" <-> "OD2" Residue "K ARG 218": "NH1" <-> "NH2" Residue "K GLU 276": "OE1" <-> "OE2" Residue "K PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 311": "NH1" <-> "NH2" Residue "K ARG 355": "NH1" <-> "NH2" Residue "K ARG 360": "NH1" <-> "NH2" Residue "K TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 424": "OE1" <-> "OE2" Residue "K ARG 510": "NH1" <-> "NH2" Residue "K ASP 535": "OD1" <-> "OD2" Residue "K ARG 549": "NH1" <-> "NH2" Residue "K GLU 572": "OE1" <-> "OE2" Residue "K PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 648": "NH1" <-> "NH2" Residue "K GLU 659": "OE1" <-> "OE2" Residue "K TYR 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 671": "OD1" <-> "OD2" Residue "K TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 684": "OE1" <-> "OE2" Residue "K TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 736": "NH1" <-> "NH2" Residue "K ARG 763": "NH1" <-> "NH2" Residue "K ARG 821": "NH1" <-> "NH2" Residue "K TYR 859": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 868": "OD1" <-> "OD2" Residue "K TYR 890": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 891": "NH1" <-> "NH2" Residue "K ASP 904": "OD1" <-> "OD2" Residue "K PHE 908": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 923": "NH1" <-> "NH2" Residue "K TYR 960": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 961": "OD1" <-> "OD2" Residue "K TYR 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 996": "OE1" <-> "OE2" Residue "K GLU 1001": "OE1" <-> "OE2" Time to flip residues: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 62151 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1253 Classifications: {'peptide': 153} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 150} Chain: "B" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1261 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "C" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1261 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "D" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2274 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain: "E" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2274 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain: "F" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2274 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain: "G" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2273 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 274} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2468 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 8, 'TRANS': 295} Chain breaks: 1 Chain: "I" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2282 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 12, 'TRANS': 271} Chain: "J" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3889 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 469} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "U" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 933 Classifications: {'RNA': 44} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 18, 'rna3p_pyr': 19} Link IDs: {'rna2p': 7, 'rna3p': 36} Chain: "V" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1045 Classifications: {'RNA': 49} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 7, 'rna3p_pur': 17, 'rna3p_pyr': 13} Link IDs: {'rna2p': 19, 'rna3p': 29} Chain: "L" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "M" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "N" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "O" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "P" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "Q" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "R" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "S" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "T" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "W" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "X" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "l" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "m" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "n" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "o" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "p" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "q" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "r" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "s" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "t" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "w" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "x" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "K" Number of atoms: 8348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 8348 Unusual residues: {' MN': 3, ' ZN': 1, 'ANP': 2} Inner-chain residues flagged as termini: ['pdbres="LYS K1037 "'] Classifications: {'peptide': 1009, 'undetermined': 6} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 973, None: 6} Not linked: pdbres="LYS K1037 " pdbres=" ZN K1101 " Not linked: pdbres=" ZN K1101 " pdbres="ANP K1102 " Not linked: pdbres="ANP K1102 " pdbres="ANP K1103 " Not linked: pdbres="ANP K1103 " pdbres=" MN K1104 " Not linked: pdbres=" MN K1104 " pdbres=" MN K1105 " Not linked: pdbres=" MN K1105 " pdbres=" MN K1106 " Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 57437 SG CYS K 464 65.143 99.839 40.875 1.00 51.25 S ATOM 57831 SG CYS K 515 60.911 99.070 40.929 1.00 57.32 S Time building chain proxies: 26.64, per 1000 atoms: 0.43 Number of scatterers: 62151 At special positions: 0 Unit cell: (150.592, 171.392, 248.768, 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 1 29.99 Mn 3 24.99 S 103 16.00 P 98 15.00 O 12120 8.00 N 10243 7.00 C 39583 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS R 63 " distance=2.03 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS Q 63 " distance=2.03 Simple disulfide: pdb=" SG CYS C 115 " - pdb=" SG CYS S 63 " distance=2.02 Simple disulfide: pdb=" SG CYS D 256 " - pdb=" SG CYS O 63 " distance=2.03 Simple disulfide: pdb=" SG CYS E 256 " - pdb=" SG CYS l 63 " distance=2.03 Simple disulfide: pdb=" SG CYS F 256 " - pdb=" SG CYS m 63 " distance=2.03 Simple disulfide: pdb=" SG CYS G 256 " - pdb=" SG CYS N 63 " distance=2.03 Simple disulfide: pdb=" SG CYS H 304 " - pdb=" SG CYS X 63 " distance=2.03 Simple disulfide: pdb=" SG CYS I 252 " - pdb=" SG CYS p 63 " distance=2.04 Simple disulfide: pdb=" SG CYS J 262 " - pdb=" SG CYS J 268 " distance=2.03 Simple disulfide: pdb=" SG CYS J 356 " - pdb=" SG CYS J 474 " distance=2.04 Simple disulfide: pdb=" SG CYS J 396 " - pdb=" SG CYS J 399 " distance=2.04 Simple disulfide: pdb=" SG CYS J 466 " - pdb=" SG CYS w 63 " distance=2.03 Simple disulfide: pdb=" SG CYS K 578 " - pdb=" SG CYS K 587 " distance=2.04 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=0, symmetry=0 Time building additional restraints: 21.62 Conformation dependent library (CDL) restraints added in 8.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K1101 " pdb="ZN ZN K1101 " - pdb=" SG CYS K 515 " pdb="ZN ZN K1101 " - pdb=" SG CYS K 464 " 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14250 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 182 helices and 100 sheets defined 25.7% alpha, 14.8% beta 29 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 20.73 Creating SS restraints... Processing helix chain 'A' and resid 5 through 20 Processing helix chain 'A' and resid 24 through 44 removed outlier: 4.017A pdb=" N VAL A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLU A 39 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 61 through 71 removed outlier: 3.614A pdb=" N PHE A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 102 removed outlier: 4.151A pdb=" N ARG A 101 " --> pdb=" O TYR A 97 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'A' and resid 116 through 151 removed outlier: 4.531A pdb=" N LEU A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ASP A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) Proline residue: A 131 - end of helix removed outlier: 3.687A pdb=" N ALA A 135 " --> pdb=" O PRO A 131 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N THR A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TYR A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 20 Processing helix chain 'B' and resid 24 through 44 removed outlier: 4.145A pdb=" N VAL B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLU B 39 " --> pdb=" O ARG B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 Processing helix chain 'B' and resid 61 through 72 Processing helix chain 'B' and resid 82 through 100 Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 117 through 128 removed outlier: 3.771A pdb=" N ASP B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 136 Processing helix chain 'B' and resid 138 through 151 Processing helix chain 'C' and resid 6 through 20 removed outlier: 3.672A pdb=" N LYS C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 44 removed outlier: 3.521A pdb=" N SER C 32 " --> pdb=" O GLN C 28 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLU C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 57 Processing helix chain 'C' and resid 63 through 72 removed outlier: 3.974A pdb=" N PHE C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 100 removed outlier: 4.278A pdb=" N TYR C 87 " --> pdb=" O GLU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 116 through 128 removed outlier: 4.009A pdb=" N LEU C 120 " --> pdb=" O GLU C 116 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 133 No H-bonds generated for 'chain 'C' and resid 130 through 133' Processing helix chain 'C' and resid 137 through 151 Processing helix chain 'D' and resid 46 through 60 Processing helix chain 'D' and resid 65 through 72 Processing helix chain 'D' and resid 115 through 130 Processing helix chain 'D' and resid 137 through 149 removed outlier: 4.171A pdb=" N LYS D 149 " --> pdb=" O THR D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 4.834A pdb=" N GLU D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 256 removed outlier: 3.670A pdb=" N ILE D 252 " --> pdb=" O LYS D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 260 No H-bonds generated for 'chain 'D' and resid 258 through 260' Processing helix chain 'D' and resid 270 through 272 No H-bonds generated for 'chain 'D' and resid 270 through 272' Processing helix chain 'D' and resid 282 through 284 No H-bonds generated for 'chain 'D' and resid 282 through 284' Processing helix chain 'E' and resid 46 through 60 Processing helix chain 'E' and resid 65 through 71 Processing helix chain 'E' and resid 115 through 130 removed outlier: 3.567A pdb=" N GLN E 130 " --> pdb=" O ASP E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 149 removed outlier: 4.180A pdb=" N LYS E 149 " --> pdb=" O THR E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 204 removed outlier: 3.641A pdb=" N GLU E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 255 Processing helix chain 'E' and resid 258 through 260 No H-bonds generated for 'chain 'E' and resid 258 through 260' Processing helix chain 'E' and resid 282 through 284 No H-bonds generated for 'chain 'E' and resid 282 through 284' Processing helix chain 'F' and resid 46 through 60 removed outlier: 3.742A pdb=" N LYS F 59 " --> pdb=" O SER F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 71 Processing helix chain 'F' and resid 115 through 130 removed outlier: 3.526A pdb=" N GLN F 130 " --> pdb=" O ASP F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 149 removed outlier: 4.184A pdb=" N LYS F 149 " --> pdb=" O THR F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 205 removed outlier: 3.785A pdb=" N GLU F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 255 Processing helix chain 'F' and resid 258 through 260 No H-bonds generated for 'chain 'F' and resid 258 through 260' Processing helix chain 'F' and resid 270 through 272 No H-bonds generated for 'chain 'F' and resid 270 through 272' Processing helix chain 'F' and resid 282 through 285 No H-bonds generated for 'chain 'F' and resid 282 through 285' Processing helix chain 'G' and resid 46 through 60 Processing helix chain 'G' and resid 65 through 72 Processing helix chain 'G' and resid 115 through 131 removed outlier: 3.574A pdb=" N ILE G 128 " --> pdb=" O TYR G 124 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLN G 130 " --> pdb=" O ASP G 126 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU G 131 " --> pdb=" O SER G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 149 removed outlier: 3.843A pdb=" N LYS G 149 " --> pdb=" O THR G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 205 removed outlier: 3.778A pdb=" N GLU G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 256 Processing helix chain 'G' and resid 270 through 272 No H-bonds generated for 'chain 'G' and resid 270 through 272' Processing helix chain 'H' and resid 39 through 49 Processing helix chain 'H' and resid 60 through 67 removed outlier: 3.573A pdb=" N LEU H 67 " --> pdb=" O ASP H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 99 No H-bonds generated for 'chain 'H' and resid 97 through 99' Processing helix chain 'H' and resid 101 through 107 Proline residue: H 104 - end of helix Processing helix chain 'H' and resid 111 through 121 Processing helix chain 'H' and resid 226 through 231 Processing helix chain 'H' and resid 271 through 279 Processing helix chain 'H' and resid 283 through 295 Processing helix chain 'I' and resid 3 through 16 removed outlier: 4.829A pdb=" N LEU I 10 " --> pdb=" O LEU I 6 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLU I 11 " --> pdb=" O VAL I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 39 removed outlier: 3.686A pdb=" N ILE I 31 " --> pdb=" O SER I 27 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLY I 37 " --> pdb=" O TYR I 33 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLU I 38 " --> pdb=" O ASN I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 57 No H-bonds generated for 'chain 'I' and resid 54 through 57' Processing helix chain 'I' and resid 65 through 87 Processing helix chain 'I' and resid 93 through 108 Processing helix chain 'I' and resid 134 through 137 No H-bonds generated for 'chain 'I' and resid 134 through 137' Processing helix chain 'I' and resid 154 through 178 removed outlier: 7.703A pdb=" N GLU I 171 " --> pdb=" O GLY I 167 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N GLN I 172 " --> pdb=" O LYS I 168 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU I 173 " --> pdb=" O LEU I 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 219 No H-bonds generated for 'chain 'I' and resid 217 through 219' Processing helix chain 'I' and resid 245 through 260 removed outlier: 5.711A pdb=" N LYS I 249 " --> pdb=" O ASP I 246 " (cutoff:3.500A) Proline residue: I 250 - end of helix removed outlier: 3.814A pdb=" N MET I 255 " --> pdb=" O CYS I 252 " (cutoff:3.500A) Proline residue: I 256 - end of helix removed outlier: 4.007A pdb=" N LEU I 259 " --> pdb=" O PRO I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 269 No H-bonds generated for 'chain 'I' and resid 267 through 269' Processing helix chain 'J' and resid 35 through 57 Processing helix chain 'J' and resid 64 through 70 Processing helix chain 'J' and resid 110 through 112 No H-bonds generated for 'chain 'J' and resid 110 through 112' Processing helix chain 'J' and resid 152 through 158 Processing helix chain 'J' and resid 162 through 165 No H-bonds generated for 'chain 'J' and resid 162 through 165' Processing helix chain 'J' and resid 167 through 169 No H-bonds generated for 'chain 'J' and resid 167 through 169' Processing helix chain 'J' and resid 182 through 200 removed outlier: 3.984A pdb=" N TYR J 199 " --> pdb=" O ASN J 195 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE J 200 " --> pdb=" O TYR J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 241 Processing helix chain 'J' and resid 248 through 250 No H-bonds generated for 'chain 'J' and resid 248 through 250' Processing helix chain 'J' and resid 265 through 278 removed outlier: 7.182A pdb=" N LYS J 270 " --> pdb=" O SER J 266 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE J 271 " --> pdb=" O ILE J 267 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP J 273 " --> pdb=" O LYS J 269 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU J 274 " --> pdb=" O LYS J 270 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N PHE J 278 " --> pdb=" O LEU J 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 284 through 299 Processing helix chain 'J' and resid 339 through 350 removed outlier: 4.240A pdb=" N TYR J 347 " --> pdb=" O LEU J 343 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS J 348 " --> pdb=" O ALA J 344 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 374 Processing helix chain 'J' and resid 390 through 395 Processing helix chain 'J' and resid 418 through 423 Processing helix chain 'J' and resid 463 through 474 Processing helix chain 'L' and resid 131 through 140 Processing helix chain 'L' and resid 156 through 166 removed outlier: 4.024A pdb=" N ASP L 162 " --> pdb=" O LYS L 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 145 removed outlier: 3.937A pdb=" N LYS M 139 " --> pdb=" O ASN M 135 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP M 143 " --> pdb=" O LYS M 139 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LYS M 144 " --> pdb=" O GLU M 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 164 removed outlier: 4.194A pdb=" N ILE M 163 " --> pdb=" O VAL M 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 144 removed outlier: 5.043A pdb=" N ASP N 143 " --> pdb=" O LYS N 139 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS N 144 " --> pdb=" O GLU N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 156 through 166 removed outlier: 3.532A pdb=" N LYS N 160 " --> pdb=" O ILE N 156 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLU N 161 " --> pdb=" O GLU N 157 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 145 removed outlier: 5.482A pdb=" N ASP O 143 " --> pdb=" O LYS O 139 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N LYS O 144 " --> pdb=" O GLU O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 156 through 166 Processing helix chain 'P' and resid 132 through 140 Processing helix chain 'P' and resid 156 through 166 removed outlier: 3.727A pdb=" N ILE P 163 " --> pdb=" O VAL P 159 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS P 164 " --> pdb=" O LYS P 160 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU P 165 " --> pdb=" O GLU P 161 " (cutoff:3.500A) Processing helix chain 'Q' and resid 131 through 140 removed outlier: 3.708A pdb=" N ASN Q 136 " --> pdb=" O THR Q 132 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS Q 139 " --> pdb=" O ASN Q 135 " (cutoff:3.500A) Processing helix chain 'Q' and resid 156 through 166 removed outlier: 4.004A pdb=" N GLU Q 161 " --> pdb=" O GLU Q 157 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP Q 162 " --> pdb=" O LYS Q 158 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE Q 163 " --> pdb=" O VAL Q 159 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU Q 165 " --> pdb=" O GLU Q 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 140 Processing helix chain 'R' and resid 156 through 166 removed outlier: 3.733A pdb=" N GLU R 161 " --> pdb=" O GLU R 157 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU R 165 " --> pdb=" O GLU R 161 " (cutoff:3.500A) Processing helix chain 'S' and resid 132 through 140 removed outlier: 3.690A pdb=" N LYS S 139 " --> pdb=" O ASN S 135 " (cutoff:3.500A) Processing helix chain 'S' and resid 156 through 165 removed outlier: 3.815A pdb=" N GLU S 161 " --> pdb=" O GLU S 157 " (cutoff:3.500A) Processing helix chain 'T' and resid 131 through 138 Processing helix chain 'T' and resid 142 through 145 No H-bonds generated for 'chain 'T' and resid 142 through 145' Processing helix chain 'T' and resid 156 through 166 Processing helix chain 'W' and resid 131 through 140 removed outlier: 3.630A pdb=" N ASN W 135 " --> pdb=" O THR W 132 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASN W 136 " --> pdb=" O ILE W 133 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU W 140 " --> pdb=" O ILE W 137 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 166 removed outlier: 3.935A pdb=" N ILE W 163 " --> pdb=" O VAL W 159 " (cutoff:3.500A) Processing helix chain 'X' and resid 131 through 140 removed outlier: 4.543A pdb=" N LYS X 139 " --> pdb=" O ASN X 135 " (cutoff:3.500A) Processing helix chain 'X' and resid 156 through 166 Processing helix chain 'l' and resid 131 through 144 removed outlier: 3.612A pdb=" N ASN l 135 " --> pdb=" O ASP l 131 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN l 136 " --> pdb=" O THR l 132 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASP l 143 " --> pdb=" O LYS l 139 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS l 144 " --> pdb=" O GLU l 140 " (cutoff:3.500A) Processing helix chain 'l' and resid 156 through 163 removed outlier: 3.500A pdb=" N ASP l 162 " --> pdb=" O LYS l 158 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE l 163 " --> pdb=" O VAL l 159 " (cutoff:3.500A) Processing helix chain 'm' and resid 131 through 140 Processing helix chain 'm' and resid 156 through 166 Processing helix chain 'n' and resid 132 through 144 removed outlier: 4.186A pdb=" N ILE n 137 " --> pdb=" O ILE n 133 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS n 139 " --> pdb=" O ASN n 135 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASP n 143 " --> pdb=" O LYS n 139 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS n 144 " --> pdb=" O GLU n 140 " (cutoff:3.500A) Processing helix chain 'n' and resid 156 through 160 Processing helix chain 'o' and resid 131 through 140 removed outlier: 3.622A pdb=" N ASN o 135 " --> pdb=" O ASP o 131 " (cutoff:3.500A) Processing helix chain 'o' and resid 156 through 163 removed outlier: 3.613A pdb=" N ASP o 162 " --> pdb=" O LYS o 158 " (cutoff:3.500A) Processing helix chain 'p' and resid 131 through 142 removed outlier: 3.766A pdb=" N LYS p 139 " --> pdb=" O ASN p 135 " (cutoff:3.500A) Processing helix chain 'p' and resid 157 through 163 removed outlier: 4.018A pdb=" N ASP p 162 " --> pdb=" O LYS p 158 " (cutoff:3.500A) Processing helix chain 'q' and resid 131 through 141 removed outlier: 4.121A pdb=" N LYS q 139 " --> pdb=" O ASN q 135 " (cutoff:3.500A) Processing helix chain 'q' and resid 157 through 166 removed outlier: 3.722A pdb=" N ASP q 162 " --> pdb=" O LYS q 158 " (cutoff:3.500A) Processing helix chain 'r' and resid 131 through 144 removed outlier: 3.886A pdb=" N PHE r 142 " --> pdb=" O ILE r 138 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP r 143 " --> pdb=" O LYS r 139 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS r 144 " --> pdb=" O GLU r 140 " (cutoff:3.500A) Processing helix chain 'r' and resid 156 through 165 Processing helix chain 's' and resid 132 through 140 removed outlier: 4.117A pdb=" N LYS s 139 " --> pdb=" O ASN s 135 " (cutoff:3.500A) Processing helix chain 's' and resid 142 through 145 No H-bonds generated for 'chain 's' and resid 142 through 145' Processing helix chain 's' and resid 157 through 166 removed outlier: 4.071A pdb=" N ASP s 162 " --> pdb=" O LYS s 158 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU s 165 " --> pdb=" O GLU s 161 " (cutoff:3.500A) Processing helix chain 't' and resid 131 through 140 removed outlier: 4.827A pdb=" N LYS t 139 " --> pdb=" O ASN t 135 " (cutoff:3.500A) Processing helix chain 't' and resid 158 through 166 removed outlier: 3.850A pdb=" N ASP t 162 " --> pdb=" O LYS t 158 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE t 163 " --> pdb=" O VAL t 159 " (cutoff:3.500A) Processing helix chain 'w' and resid 131 through 140 removed outlier: 4.081A pdb=" N LYS w 139 " --> pdb=" O ASN w 135 " (cutoff:3.500A) Processing helix chain 'w' and resid 158 through 161 No H-bonds generated for 'chain 'w' and resid 158 through 161' Processing helix chain 'x' and resid 131 through 140 removed outlier: 3.824A pdb=" N LYS x 139 " --> pdb=" O ASN x 135 " (cutoff:3.500A) Processing helix chain 'x' and resid 156 through 163 removed outlier: 4.007A pdb=" N ILE x 163 " --> pdb=" O VAL x 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 20 removed outlier: 3.798A pdb=" N LEU K 19 " --> pdb=" O ILE K 15 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS K 20 " --> pdb=" O ILE K 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 15 through 20' Processing helix chain 'K' and resid 70 through 76 removed outlier: 3.848A pdb=" N LEU K 75 " --> pdb=" O ASN K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 82 No H-bonds generated for 'chain 'K' and resid 79 through 82' Processing helix chain 'K' and resid 85 through 90 Processing helix chain 'K' and resid 121 through 129 removed outlier: 4.347A pdb=" N ASP K 125 " --> pdb=" O LYS K 121 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ASN K 126 " --> pdb=" O SER K 122 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU K 127 " --> pdb=" O LYS K 123 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 151 Processing helix chain 'K' and resid 153 through 156 No H-bonds generated for 'chain 'K' and resid 153 through 156' Processing helix chain 'K' and resid 158 through 161 No H-bonds generated for 'chain 'K' and resid 158 through 161' Processing helix chain 'K' and resid 177 through 195 removed outlier: 3.779A pdb=" N ALA K 183 " --> pdb=" O ASP K 179 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN K 189 " --> pdb=" O ALA K 185 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP K 190 " --> pdb=" O ALA K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 215 Processing helix chain 'K' and resid 221 through 244 removed outlier: 3.679A pdb=" N LEU K 234 " --> pdb=" O VAL K 230 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE K 238 " --> pdb=" O LEU K 234 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP K 240 " --> pdb=" O TYR K 236 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE K 241 " --> pdb=" O VAL K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 261 through 272 removed outlier: 3.591A pdb=" N LYS K 271 " --> pdb=" O GLU K 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 289 removed outlier: 3.854A pdb=" N LEU K 285 " --> pdb=" O GLU K 281 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS K 288 " --> pdb=" O GLU K 284 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR K 289 " --> pdb=" O LEU K 285 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 300 No H-bonds generated for 'chain 'K' and resid 297 through 300' Processing helix chain 'K' and resid 336 through 360 removed outlier: 3.580A pdb=" N TRP K 347 " --> pdb=" O TYR K 343 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 376 Processing helix chain 'K' and resid 410 through 412 No H-bonds generated for 'chain 'K' and resid 410 through 412' Processing helix chain 'K' and resid 414 through 430 removed outlier: 3.922A pdb=" N LEU K 430 " --> pdb=" O LYS K 426 " (cutoff:3.500A) Processing helix chain 'K' and resid 435 through 438 Processing helix chain 'K' and resid 442 through 446 Processing helix chain 'K' and resid 497 through 504 removed outlier: 4.049A pdb=" N MET K 504 " --> pdb=" O SER K 500 " (cutoff:3.500A) Processing helix chain 'K' and resid 513 through 523 Processing helix chain 'K' and resid 527 through 533 removed outlier: 3.881A pdb=" N LEU K 533 " --> pdb=" O ILE K 530 " (cutoff:3.500A) Processing helix chain 'K' and resid 539 through 548 removed outlier: 3.849A pdb=" N SER K 548 " --> pdb=" O ASN K 544 " (cutoff:3.500A) Processing helix chain 'K' and resid 558 through 572 removed outlier: 3.514A pdb=" N SER K 563 " --> pdb=" O SER K 559 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LYS K 565 " --> pdb=" O ILE K 561 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR K 566 " --> pdb=" O ALA K 562 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU K 572 " --> pdb=" O GLU K 568 " (cutoff:3.500A) Processing helix chain 'K' and resid 601 through 603 No H-bonds generated for 'chain 'K' and resid 601 through 603' Processing helix chain 'K' and resid 625 through 635 removed outlier: 3.549A pdb=" N SER K 630 " --> pdb=" O ARG K 626 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG K 634 " --> pdb=" O SER K 630 " (cutoff:3.500A) Processing helix chain 'K' and resid 654 through 658 Processing helix chain 'K' and resid 662 through 664 No H-bonds generated for 'chain 'K' and resid 662 through 664' Processing helix chain 'K' and resid 673 through 676 Processing helix chain 'K' and resid 678 through 696 removed outlier: 4.980A pdb=" N GLU K 683 " --> pdb=" O GLU K 680 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN K 686 " --> pdb=" O GLU K 683 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS K 687 " --> pdb=" O GLU K 684 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU K 689 " --> pdb=" O ASN K 686 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU K 690 " --> pdb=" O LYS K 687 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU K 693 " --> pdb=" O GLU K 690 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL K 694 " --> pdb=" O GLU K 691 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASN K 695 " --> pdb=" O TYR K 692 " (cutoff:3.500A) Processing helix chain 'K' and resid 700 through 708 removed outlier: 4.286A pdb=" N VAL K 705 " --> pdb=" O VAL K 702 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS K 706 " --> pdb=" O ASP K 703 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR K 707 " --> pdb=" O TYR K 704 " (cutoff:3.500A) Processing helix chain 'K' and resid 722 through 724 No H-bonds generated for 'chain 'K' and resid 722 through 724' Processing helix chain 'K' and resid 726 through 733 removed outlier: 3.802A pdb=" N LYS K 732 " --> pdb=" O ASN K 728 " (cutoff:3.500A) Processing helix chain 'K' and resid 747 through 760 removed outlier: 3.652A pdb=" N SER K 751 " --> pdb=" O GLU K 747 " (cutoff:3.500A) Processing helix chain 'K' and resid 768 through 791 Processing helix chain 'K' and resid 810 through 825 removed outlier: 3.788A pdb=" N VAL K 813 " --> pdb=" O VAL K 810 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU K 814 " --> pdb=" O ASP K 811 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASP K 815 " --> pdb=" O GLU K 812 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS K 818 " --> pdb=" O ASP K 815 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG K 821 " --> pdb=" O LYS K 818 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE K 824 " --> pdb=" O ARG K 821 " (cutoff:3.500A) Processing helix chain 'K' and resid 870 through 887 removed outlier: 3.717A pdb=" N LEU K 881 " --> pdb=" O SER K 877 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU K 886 " --> pdb=" O GLU K 882 " (cutoff:3.500A) Processing helix chain 'K' and resid 930 through 934 Processing helix chain 'K' and resid 937 through 950 removed outlier: 3.955A pdb=" N ARG K 948 " --> pdb=" O GLU K 944 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP K 950 " --> pdb=" O LYS K 946 " (cutoff:3.500A) Processing helix chain 'K' and resid 961 through 971 removed outlier: 3.809A pdb=" N LYS K 966 " --> pdb=" O GLU K 963 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N HIS K 967 " --> pdb=" O LYS K 964 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU K 968 " --> pdb=" O TYR K 965 " (cutoff:3.500A) Processing helix chain 'K' and resid 975 through 989 removed outlier: 4.154A pdb=" N ASN K 989 " --> pdb=" O TRP K 985 " (cutoff:3.500A) Processing helix chain 'K' and resid 1001 through 1003 No H-bonds generated for 'chain 'K' and resid 1001 through 1003' Processing helix chain 'K' and resid 1021 through 1036 removed outlier: 4.141A pdb=" N GLU K1036 " --> pdb=" O ILE K1032 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'D' and resid 263 through 265 Processing sheet with id= B, first strand: chain 'D' and resid 94 through 97 Processing sheet with id= C, first strand: chain 'D' and resid 162 through 165 Processing sheet with id= D, first strand: chain 'D' and resid 207 through 212 Processing sheet with id= E, first strand: chain 'D' and resid 90 through 93 removed outlier: 6.737A pdb=" N ILE D 237 " --> pdb=" O PHE D 92 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 263 through 265 Processing sheet with id= G, first strand: chain 'E' and resid 94 through 97 Processing sheet with id= H, first strand: chain 'E' and resid 98 through 100 Processing sheet with id= I, first strand: chain 'E' and resid 207 through 212 Processing sheet with id= J, first strand: chain 'E' and resid 90 through 93 removed outlier: 6.799A pdb=" N ILE E 237 " --> pdb=" O PHE E 92 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 6 through 11 Processing sheet with id= L, first strand: chain 'F' and resid 12 through 14 Processing sheet with id= M, first strand: chain 'F' and resid 94 through 97 Processing sheet with id= N, first strand: chain 'F' and resid 98 through 100 Processing sheet with id= O, first strand: chain 'F' and resid 207 through 212 Processing sheet with id= P, first strand: chain 'F' and resid 90 through 93 removed outlier: 6.807A pdb=" N ILE F 237 " --> pdb=" O PHE F 92 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 263 through 265 Processing sheet with id= R, first strand: chain 'G' and resid 94 through 97 Processing sheet with id= S, first strand: chain 'G' and resid 98 through 100 Processing sheet with id= T, first strand: chain 'G' and resid 207 through 212 Processing sheet with id= U, first strand: chain 'G' and resid 90 through 93 removed outlier: 6.738A pdb=" N ILE G 237 " --> pdb=" O PHE G 92 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 195 through 200 Processing sheet with id= W, first strand: chain 'H' and resid 83 through 87 Processing sheet with id= X, first strand: chain 'H' and resid 132 through 140 Processing sheet with id= Y, first strand: chain 'H' and resid 268 through 270 Processing sheet with id= Z, first strand: chain 'H' and resid 242 through 246 Processing sheet with id= AA, first strand: chain 'I' and resid 187 through 189 removed outlier: 6.268A pdb=" N THR I 119 " --> pdb=" O LEU I 276 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU I 276 " --> pdb=" O THR I 119 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'I' and resid 202 through 209 Processing sheet with id= AC, first strand: chain 'I' and resid 193 through 197 removed outlier: 6.978A pdb=" N THR I 235 " --> pdb=" O THR I 195 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 84 through 90 removed outlier: 5.930A pdb=" N LEU J 214 " --> pdb=" O LEU J 4 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU J 4 " --> pdb=" O LEU J 214 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LYS J 11 " --> pdb=" O ILE J 257 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE J 257 " --> pdb=" O LYS J 11 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU J 13 " --> pdb=" O LEU J 255 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU J 255 " --> pdb=" O LEU J 13 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'J' and resid 171 through 175 Processing sheet with id= AF, first strand: chain 'J' and resid 331 through 335 Processing sheet with id= AG, first strand: chain 'J' and resid 100 through 104 removed outlier: 6.826A pdb=" N LYS J 143 " --> pdb=" O SER J 101 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL J 103 " --> pdb=" O SER J 141 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N SER J 141 " --> pdb=" O VAL J 103 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 42 through 45 removed outlier: 5.731A pdb=" N LYS L 107 " --> pdb=" O ARG L 5 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N TYR L 7 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N TYR L 109 " --> pdb=" O TYR L 7 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N PHE L 9 " --> pdb=" O TYR L 109 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 47 through 49 Processing sheet with id= AJ, first strand: chain 'L' and resid 124 through 126 Processing sheet with id= AK, first strand: chain 'M' and resid 42 through 45 removed outlier: 5.539A pdb=" N LYS M 107 " --> pdb=" O ARG M 5 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TYR M 7 " --> pdb=" O LYS M 107 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR M 109 " --> pdb=" O TYR M 7 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N PHE M 9 " --> pdb=" O TYR M 109 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'M' and resid 124 through 126 Processing sheet with id= AM, first strand: chain 'N' and resid 84 through 88 removed outlier: 6.920A pdb=" N ARG N 5 " --> pdb=" O TYR N 109 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL N 41 " --> pdb=" O ILE N 96 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR N 94 " --> pdb=" O VAL N 43 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'N' and resid 124 through 127 Processing sheet with id= AO, first strand: chain 'O' and resid 42 through 45 removed outlier: 5.658A pdb=" N LYS O 107 " --> pdb=" O ARG O 5 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N TYR O 7 " --> pdb=" O LYS O 107 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR O 109 " --> pdb=" O TYR O 7 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N PHE O 9 " --> pdb=" O TYR O 109 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'O' and resid 47 through 49 Processing sheet with id= AQ, first strand: chain 'O' and resid 124 through 126 removed outlier: 3.536A pdb=" N TYR O 169 " --> pdb=" O VAL O 126 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'P' and resid 42 through 45 removed outlier: 5.977A pdb=" N LYS P 107 " --> pdb=" O ARG P 5 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N TYR P 7 " --> pdb=" O LYS P 107 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR P 109 " --> pdb=" O TYR P 7 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N PHE P 9 " --> pdb=" O TYR P 109 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'P' and resid 124 through 126 Processing sheet with id= AT, first strand: chain 'Q' and resid 108 through 110 removed outlier: 7.041A pdb=" N ARG Q 5 " --> pdb=" O TYR Q 109 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'Q' and resid 124 through 127 Processing sheet with id= AV, first strand: chain 'R' and resid 5 through 9 Processing sheet with id= AW, first strand: chain 'R' and resid 86 through 88 Processing sheet with id= AX, first strand: chain 'R' and resid 124 through 127 removed outlier: 3.761A pdb=" N TYR R 169 " --> pdb=" O VAL R 126 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'S' and resid 42 through 45 removed outlier: 6.238A pdb=" N LYS S 107 " --> pdb=" O ARG S 5 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N TYR S 7 " --> pdb=" O LYS S 107 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR S 109 " --> pdb=" O TYR S 7 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N PHE S 9 " --> pdb=" O TYR S 109 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'S' and resid 47 through 49 Processing sheet with id= BA, first strand: chain 'S' and resid 124 through 127 removed outlier: 4.142A pdb=" N TYR S 169 " --> pdb=" O VAL S 126 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'T' and resid 42 through 45 removed outlier: 3.712A pdb=" N LEU T 42 " --> pdb=" O GLY T 68 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LYS T 107 " --> pdb=" O ARG T 5 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N TYR T 7 " --> pdb=" O LYS T 107 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR T 109 " --> pdb=" O TYR T 7 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N PHE T 9 " --> pdb=" O TYR T 109 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU T 106 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE T 110 " --> pdb=" O LEU T 84 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'T' and resid 124 through 126 Processing sheet with id= BD, first strand: chain 'W' and resid 94 through 96 removed outlier: 4.145A pdb=" N TYR W 94 " --> pdb=" O VAL W 43 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LYS W 107 " --> pdb=" O ARG W 5 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N TYR W 7 " --> pdb=" O LYS W 107 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR W 109 " --> pdb=" O TYR W 7 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N PHE W 9 " --> pdb=" O TYR W 109 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'W' and resid 47 through 49 Processing sheet with id= BF, first strand: chain 'W' and resid 124 through 127 Processing sheet with id= BG, first strand: chain 'X' and resid 6 through 9 Processing sheet with id= BH, first strand: chain 'X' and resid 47 through 49 Processing sheet with id= BI, first strand: chain 'X' and resid 84 through 88 Processing sheet with id= BJ, first strand: chain 'X' and resid 124 through 127 Processing sheet with id= BK, first strand: chain 'l' and resid 42 through 45 removed outlier: 5.571A pdb=" N LYS l 107 " --> pdb=" O ARG l 5 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N TYR l 7 " --> pdb=" O LYS l 107 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N TYR l 109 " --> pdb=" O TYR l 7 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N PHE l 9 " --> pdb=" O TYR l 109 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'l' and resid 47 through 49 Processing sheet with id= BM, first strand: chain 'l' and resid 124 through 127 Processing sheet with id= BN, first strand: chain 'm' and resid 42 through 45 removed outlier: 6.049A pdb=" N LYS m 107 " --> pdb=" O ARG m 5 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N TYR m 7 " --> pdb=" O LYS m 107 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N TYR m 109 " --> pdb=" O TYR m 7 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N PHE m 9 " --> pdb=" O TYR m 109 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'm' and resid 47 through 49 Processing sheet with id= BP, first strand: chain 'm' and resid 124 through 127 Processing sheet with id= BQ, first strand: chain 'n' and resid 69 through 71 removed outlier: 5.845A pdb=" N LYS n 107 " --> pdb=" O ARG n 5 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N TYR n 7 " --> pdb=" O LYS n 107 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TYR n 109 " --> pdb=" O TYR n 7 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'n' and resid 42 through 45 Processing sheet with id= BS, first strand: chain 'n' and resid 124 through 126 Processing sheet with id= BT, first strand: chain 'o' and resid 42 through 45 removed outlier: 5.584A pdb=" N LYS o 107 " --> pdb=" O ARG o 5 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR o 7 " --> pdb=" O LYS o 107 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TYR o 109 " --> pdb=" O TYR o 7 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE o 9 " --> pdb=" O TYR o 109 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'o' and resid 124 through 126 Processing sheet with id= BV, first strand: chain 'p' and resid 94 through 96 removed outlier: 4.540A pdb=" N TYR p 94 " --> pdb=" O VAL p 43 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS p 107 " --> pdb=" O ARG p 5 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N TYR p 7 " --> pdb=" O LYS p 107 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR p 109 " --> pdb=" O TYR p 7 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N PHE p 9 " --> pdb=" O TYR p 109 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'p' and resid 47 through 49 Processing sheet with id= BX, first strand: chain 'p' and resid 124 through 126 Processing sheet with id= BY, first strand: chain 'q' and resid 42 through 45 removed outlier: 5.752A pdb=" N LYS q 107 " --> pdb=" O ARG q 5 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TYR q 7 " --> pdb=" O LYS q 107 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N TYR q 109 " --> pdb=" O TYR q 7 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N PHE q 9 " --> pdb=" O TYR q 109 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'q' and resid 47 through 49 Processing sheet with id= CA, first strand: chain 'q' and resid 124 through 127 Processing sheet with id= CB, first strand: chain 'r' and resid 42 through 45 removed outlier: 6.197A pdb=" N LYS r 107 " --> pdb=" O ARG r 5 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N TYR r 7 " --> pdb=" O LYS r 107 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N TYR r 109 " --> pdb=" O TYR r 7 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N PHE r 9 " --> pdb=" O TYR r 109 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'r' and resid 124 through 126 Processing sheet with id= CD, first strand: chain 's' and resid 5 through 8 Processing sheet with id= CE, first strand: chain 's' and resid 42 through 45 Processing sheet with id= CF, first strand: chain 's' and resid 47 through 49 Processing sheet with id= CG, first strand: chain 's' and resid 86 through 88 removed outlier: 3.739A pdb=" N LEU s 86 " --> pdb=" O ILE s 108 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE s 108 " --> pdb=" O LEU s 86 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU s 88 " --> pdb=" O LEU s 106 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU s 106 " --> pdb=" O LEU s 88 " (cutoff:3.500A) No H-bonds generated for sheet with id= CG Processing sheet with id= CH, first strand: chain 's' and resid 124 through 127 Processing sheet with id= CI, first strand: chain 't' and resid 6 through 9 Processing sheet with id= CJ, first strand: chain 't' and resid 84 through 88 Processing sheet with id= CK, first strand: chain 't' and resid 124 through 127 Processing sheet with id= CL, first strand: chain 'w' and resid 42 through 45 removed outlier: 5.649A pdb=" N LYS w 107 " --> pdb=" O ARG w 5 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TYR w 7 " --> pdb=" O LYS w 107 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N TYR w 109 " --> pdb=" O TYR w 7 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE w 9 " --> pdb=" O TYR w 109 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'w' and resid 47 through 49 Processing sheet with id= CN, first strand: chain 'w' and resid 124 through 127 Processing sheet with id= CO, first strand: chain 'x' and resid 5 through 9 Processing sheet with id= CP, first strand: chain 'x' and resid 47 through 49 Processing sheet with id= CQ, first strand: chain 'x' and resid 84 through 88 removed outlier: 3.747A pdb=" N ILE x 110 " --> pdb=" O LEU x 84 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'x' and resid 124 through 127 Processing sheet with id= CS, first strand: chain 'K' and resid 311 through 316 Processing sheet with id= CT, first strand: chain 'K' and resid 803 through 809 removed outlier: 5.144A pdb=" N VAL K 905 " --> pdb=" O ARG K 857 " (cutoff:3.500A) Processing sheet with id= CU, first strand: chain 'K' and resid 841 through 844 removed outlier: 3.519A pdb=" N ALA K 847 " --> pdb=" O ILE K 844 " (cutoff:3.500A) Processing sheet with id= CV, first strand: chain 'K' and resid 1008 through 1010 1732 hydrogen bonds defined for protein. 4707 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 26.34 Time building geometry restraints manager: 23.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 16782 1.33 - 1.46: 14997 1.46 - 1.58: 31346 1.58 - 1.71: 160 1.71 - 1.84: 150 Bond restraints: 63435 Sorted by residual: bond pdb=" N3B ANP K1102 " pdb=" PG ANP K1102 " ideal model delta sigma weight residual 1.795 1.623 0.172 2.00e-02 2.50e+03 7.36e+01 bond pdb=" O3A ANP K1103 " pdb=" PB ANP K1103 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.46e+01 bond pdb=" O3A ANP K1102 " pdb=" PB ANP K1102 " ideal model delta sigma weight residual 1.700 1.563 0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" N3B ANP K1103 " pdb=" PG ANP K1103 " ideal model delta sigma weight residual 1.795 1.686 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" O5' ANP K1103 " pdb=" PA ANP K1103 " ideal model delta sigma weight residual 1.655 1.564 0.091 2.00e-02 2.50e+03 2.07e+01 ... (remaining 63430 not shown) Histogram of bond angle deviations from ideal: 97.28 - 104.63: 1225 104.63 - 111.97: 31196 111.97 - 119.32: 21809 119.32 - 126.67: 31271 126.67 - 134.01: 758 Bond angle restraints: 86259 Sorted by residual: angle pdb=" N VAL M 154 " pdb=" CA VAL M 154 " pdb=" C VAL M 154 " ideal model delta sigma weight residual 112.80 104.17 8.63 1.15e+00 7.56e-01 5.64e+01 angle pdb=" N VAL D 285 " pdb=" CA VAL D 285 " pdb=" C VAL D 285 " ideal model delta sigma weight residual 113.71 107.86 5.85 9.50e-01 1.11e+00 3.80e+01 angle pdb=" PB ANP K1103 " pdb=" N3B ANP K1103 " pdb=" PG ANP K1103 " ideal model delta sigma weight residual 126.95 108.87 18.08 3.00e+00 1.11e-01 3.63e+01 angle pdb=" N ILE J 271 " pdb=" CA ILE J 271 " pdb=" C ILE J 271 " ideal model delta sigma weight residual 111.90 107.05 4.85 8.10e-01 1.52e+00 3.59e+01 angle pdb=" N ILE K 208 " pdb=" CA ILE K 208 " pdb=" C ILE K 208 " ideal model delta sigma weight residual 111.00 116.97 -5.97 1.09e+00 8.42e-01 3.00e+01 ... (remaining 86254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 38171 35.40 - 70.79: 792 70.79 - 106.19: 88 106.19 - 141.59: 3 141.59 - 176.98: 5 Dihedral angle restraints: 39059 sinusoidal: 16972 harmonic: 22087 Sorted by residual: dihedral pdb=" CB CYS J 262 " pdb=" SG CYS J 262 " pdb=" SG CYS J 268 " pdb=" CB CYS J 268 " ideal model delta sinusoidal sigma weight residual 93.00 -177.85 -89.15 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CA CYS J 302 " pdb=" C CYS J 302 " pdb=" N ILE J 303 " pdb=" CA ILE J 303 " ideal model delta harmonic sigma weight residual 180.00 -132.54 -47.46 0 5.00e+00 4.00e-02 9.01e+01 dihedral pdb=" O4' U V 3 " pdb=" C1' U V 3 " pdb=" N1 U V 3 " pdb=" C2 U V 3 " ideal model delta sinusoidal sigma weight residual -160.00 15.34 -175.34 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 39056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 9254 0.092 - 0.185: 823 0.185 - 0.277: 9 0.277 - 0.370: 0 0.370 - 0.462: 1 Chirality restraints: 10087 Sorted by residual: chirality pdb=" C3' ANP K1102 " pdb=" C2' ANP K1102 " pdb=" C4' ANP K1102 " pdb=" O3' ANP K1102 " both_signs ideal model delta sigma weight residual False -2.36 -2.82 0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" C3' ANP K1103 " pdb=" C2' ANP K1103 " pdb=" C4' ANP K1103 " pdb=" O3' ANP K1103 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C1' A V 21 " pdb=" O4' A V 21 " pdb=" C2' A V 21 " pdb=" N9 A V 21 " both_signs ideal model delta sigma weight residual False 2.44 2.21 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 10084 not shown) Planarity restraints: 10532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 19 " 0.060 2.00e-02 2.50e+03 2.66e-02 1.95e+01 pdb=" N9 A V 19 " -0.060 2.00e-02 2.50e+03 pdb=" C8 A V 19 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A V 19 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 19 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A V 19 " 0.010 2.00e-02 2.50e+03 pdb=" N6 A V 19 " 0.016 2.00e-02 2.50e+03 pdb=" N1 A V 19 " 0.005 2.00e-02 2.50e+03 pdb=" C2 A V 19 " -0.006 2.00e-02 2.50e+03 pdb=" N3 A V 19 " -0.009 2.00e-02 2.50e+03 pdb=" C4 A V 19 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A V 13 " -0.051 2.00e-02 2.50e+03 2.18e-02 1.31e+01 pdb=" N9 A V 13 " 0.044 2.00e-02 2.50e+03 pdb=" C8 A V 13 " 0.006 2.00e-02 2.50e+03 pdb=" N7 A V 13 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A V 13 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A V 13 " -0.009 2.00e-02 2.50e+03 pdb=" N6 A V 13 " -0.013 2.00e-02 2.50e+03 pdb=" N1 A V 13 " -0.006 2.00e-02 2.50e+03 pdb=" C2 A V 13 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A V 13 " 0.009 2.00e-02 2.50e+03 pdb=" C4 A V 13 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS J 364 " -0.016 2.00e-02 2.50e+03 3.12e-02 9.72e+00 pdb=" C LYS J 364 " 0.054 2.00e-02 2.50e+03 pdb=" O LYS J 364 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR J 365 " -0.018 2.00e-02 2.50e+03 ... (remaining 10529 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 161 2.34 - 2.98: 33559 2.98 - 3.62: 94995 3.62 - 4.26: 153928 4.26 - 4.90: 247906 Nonbonded interactions: 530549 Sorted by model distance: nonbonded pdb=" O2A ANP K1103 " pdb="MN MN K1105 " model vdw 1.698 2.320 nonbonded pdb=" O1G ANP K1103 " pdb="MN MN K1104 " model vdw 1.728 2.320 nonbonded pdb=" O2B ANP K1103 " pdb="MN MN K1104 " model vdw 1.733 2.320 nonbonded pdb=" O1A ANP K1103 " pdb="MN MN K1104 " model vdw 1.900 2.320 nonbonded pdb=" O3A ANP K1102 " pdb="MN MN K1106 " model vdw 1.996 2.320 ... (remaining 530544 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 3 through 155) selection = (chain 'C' and resid 3 through 155) } ncs_group { reference = (chain 'D' and (resid 2 through 157 or (resid 158 and (name N or name CA or name \ C or name O or name CB )) or resid 159 through 286)) selection = (chain 'E' and (resid 2 through 157 or (resid 158 and (name N or name CA or name \ C or name O or name CB )) or resid 159 through 286)) selection = (chain 'F' and (resid 2 through 157 or (resid 158 and (name N or name CA or name \ C or name O or name CB )) or resid 159 through 286)) selection = chain 'G' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'w' selection = chain 'x' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.660 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: 0.070 Extract box with map and model: 27.520 Check model and map are aligned: 0.930 Set scattering table: 0.540 Process input model: 162.300 Find NCS groups from input model: 2.960 Set up NCS constraints: 0.550 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: 0.010 Load rotamer database and sin/cos tables:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 214.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 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 : 0.006 0.172 63435 Z= 0.393 Angle : 0.790 18.080 86259 Z= 0.435 Chirality : 0.051 0.462 10087 Planarity : 0.004 0.045 10532 Dihedral : 15.092 176.983 24767 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.45 % Allowed : 15.00 % Favored : 84.56 % Rotamer: Outliers : 0.19 % Allowed : 6.06 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -4.57 (0.08), residues: 7409 helix: -2.64 (0.09), residues: 2048 sheet: -1.91 (0.12), residues: 1555 loop : -3.86 (0.08), residues: 3806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 158 HIS 0.008 0.001 HIS D 19 PHE 0.023 0.002 PHE D 136 TYR 0.032 0.002 TYR B 42 ARG 0.017 0.001 ARG K 256 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1583 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1570 time to evaluate : 5.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 8 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6732 (mm-30) REVERT: G 286 ILE cc_start: 0.6244 (OUTLIER) cc_final: 0.5868 (tt) REVERT: J 226 ASP cc_start: 0.7215 (p0) cc_final: 0.7007 (p0) REVERT: O 136 ASN cc_start: 0.7624 (p0) cc_final: 0.7287 (p0) REVERT: S 30 ILE cc_start: 0.7714 (mp) cc_final: 0.7307 (tt) REVERT: S 104 ASP cc_start: 0.7658 (t70) cc_final: 0.7445 (p0) REVERT: T 13 THR cc_start: 0.6639 (p) cc_final: 0.6318 (p) REVERT: W 116 ASP cc_start: 0.6961 (t0) cc_final: 0.6652 (t0) REVERT: X 121 MET cc_start: 0.5656 (ptt) cc_final: 0.5394 (pmt) REVERT: l 102 ILE cc_start: 0.7593 (mm) cc_final: 0.7326 (mm) REVERT: p 52 LYS cc_start: 0.8184 (ttmm) cc_final: 0.7804 (mmmt) REVERT: s 95 LEU cc_start: 0.8334 (mt) cc_final: 0.8085 (mt) REVERT: s 121 MET cc_start: 0.6459 (mmp) cc_final: 0.5255 (mmp) REVERT: s 172 LEU cc_start: 0.7308 (pp) cc_final: 0.7093 (pp) REVERT: x 98 LYS cc_start: 0.8071 (ptmt) cc_final: 0.7552 (tptm) REVERT: K 121 LYS cc_start: 0.4615 (tttp) cc_final: 0.4371 (mptt) REVERT: K 158 TRP cc_start: 0.3648 (m100) cc_final: 0.2640 (m100) REVERT: K 187 MET cc_start: 0.6630 (ppp) cc_final: 0.6287 (tmm) REVERT: K 240 TRP cc_start: 0.7894 (t60) cc_final: 0.7013 (t60) REVERT: K 759 LEU cc_start: 0.8918 (pp) cc_final: 0.8703 (pp) REVERT: K 1013 TYR cc_start: 0.6526 (t80) cc_final: 0.6215 (t80) outliers start: 13 outliers final: 6 residues processed: 1579 average time/residue: 1.2784 time to fit residues: 2652.4197 Evaluate side-chains 1013 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1006 time to evaluate : 5.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain M residue 128 ILE Chi-restraints excluded: chain S residue 137 ILE Chi-restraints excluded: chain K residue 212 ASP Chi-restraints excluded: chain K residue 448 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 629 optimal weight: 6.9990 chunk 564 optimal weight: 0.0170 chunk 313 optimal weight: 0.1980 chunk 192 optimal weight: 0.9980 chunk 380 optimal weight: 0.7980 chunk 301 optimal weight: 10.0000 chunk 583 optimal weight: 0.0470 chunk 225 optimal weight: 3.9990 chunk 355 optimal weight: 10.0000 chunk 434 optimal weight: 9.9990 chunk 676 optimal weight: 0.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN B 75 ASN B 84 ASN C 60 ASN C 84 ASN C 128 ASN D 17 HIS D 141 ASN D 153 ASN D 178 ASN ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 ASN F 166 ASN F 178 ASN G 13 HIS G 133 ASN G 141 ASN H 32 GLN H 79 ASN H 130 GLN H 133 ASN H 182 ASN H 298 ASN I 19 ASN I 61 ASN I 74 ASN I 87 ASN I 97 ASN J 23 HIS J 46 ASN J 158 ASN J 337 ASN J 345 ASN J 424 GLN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 135 ASN ** M 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 GLN N 135 ASN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 ASN ** P 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN P 119 ASN ** Q 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 135 ASN S 77 GLN X 29 HIS X 40 ASN X 135 ASN l 32 ASN l 40 ASN l 174 GLN m 4 GLN m 101 ASN m 174 GLN o 135 ASN p 40 ASN p 135 ASN p 174 GLN q 14 ASN q 147 ASN s 39 HIS s 77 GLN s 91 ASN t 4 GLN t 29 HIS t 79 GLN ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 135 ASN x 32 ASN ** x 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 259 GLN ** K 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 344 ASN K 387 ASN K 392 GLN K 604 ASN K 695 ASN K 846 ASN Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 63435 Z= 0.195 Angle : 0.705 17.847 86259 Z= 0.366 Chirality : 0.048 0.229 10087 Planarity : 0.004 0.067 10532 Dihedral : 12.389 179.728 9631 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.63 % Favored : 87.19 % Rotamer: Outliers : 3.06 % Allowed : 16.56 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.09), residues: 7409 helix: -1.58 (0.10), residues: 2073 sheet: -1.51 (0.12), residues: 1565 loop : -3.42 (0.08), residues: 3771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 985 HIS 0.007 0.001 HIS O 39 PHE 0.015 0.001 PHE R 83 TYR 0.024 0.001 TYR W 112 ARG 0.009 0.000 ARG H 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1459 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1251 time to evaluate : 5.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7956 (tt0) REVERT: D 138 ASN cc_start: 0.7109 (OUTLIER) cc_final: 0.6829 (m110) REVERT: D 195 ASP cc_start: 0.6524 (m-30) cc_final: 0.6117 (m-30) REVERT: G 136 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7369 (p90) REVERT: H 144 LYS cc_start: 0.7490 (mmtm) cc_final: 0.6805 (mtmp) REVERT: H 163 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7912 (mmmm) REVERT: H 271 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.6840 (ttm-80) REVERT: J 65 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7094 (mt-10) REVERT: J 426 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7282 (mp0) REVERT: O 136 ASN cc_start: 0.7537 (p0) cc_final: 0.7331 (p0) REVERT: P 144 LYS cc_start: 0.6929 (mptt) cc_final: 0.6029 (tppt) REVERT: S 88 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7458 (mm) REVERT: T 13 THR cc_start: 0.6468 (p) cc_final: 0.6256 (p) REVERT: W 169 TYR cc_start: 0.7201 (p90) cc_final: 0.6826 (p90) REVERT: X 121 MET cc_start: 0.5560 (ptt) cc_final: 0.5212 (pmt) REVERT: l 102 ILE cc_start: 0.7428 (mm) cc_final: 0.7120 (mm) REVERT: n 30 ILE cc_start: 0.6214 (OUTLIER) cc_final: 0.5876 (tp) REVERT: n 172 LEU cc_start: 0.4431 (mt) cc_final: 0.4216 (mt) REVERT: p 52 LYS cc_start: 0.7864 (ttmm) cc_final: 0.7614 (mmmt) REVERT: s 95 LEU cc_start: 0.8399 (mt) cc_final: 0.8120 (mt) REVERT: s 110 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8296 (tp) REVERT: s 121 MET cc_start: 0.6555 (mmp) cc_final: 0.5230 (mmp) REVERT: s 163 ILE cc_start: 0.7830 (mp) cc_final: 0.7620 (mp) REVERT: s 164 LYS cc_start: 0.7004 (tmtt) cc_final: 0.6755 (tptp) REVERT: s 172 LEU cc_start: 0.7252 (pp) cc_final: 0.7023 (pp) REVERT: t 166 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7671 (tt) REVERT: K 121 LYS cc_start: 0.4630 (tttp) cc_final: 0.4420 (mptt) REVERT: K 150 PHE cc_start: 0.6375 (t80) cc_final: 0.6079 (t80) REVERT: K 187 MET cc_start: 0.6192 (ppp) cc_final: 0.5884 (tmm) REVERT: K 188 MET cc_start: 0.7220 (mmm) cc_final: 0.6850 (mmm) REVERT: K 216 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7796 (mttm) REVERT: K 528 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7724 (mpp) REVERT: K 656 ASP cc_start: 0.7307 (p0) cc_final: 0.7036 (p0) REVERT: K 831 LYS cc_start: 0.8582 (tttt) cc_final: 0.8378 (tttt) REVERT: K 846 ASN cc_start: 0.6629 (OUTLIER) cc_final: 0.6394 (m-40) REVERT: K 910 TYR cc_start: 0.7409 (t80) cc_final: 0.7111 (t80) REVERT: K 1002 LYS cc_start: 0.7811 (mmtm) cc_final: 0.7609 (mmtm) outliers start: 208 outliers final: 67 residues processed: 1367 average time/residue: 1.1658 time to fit residues: 2146.1679 Evaluate side-chains 1079 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 999 time to evaluate : 5.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LYS Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain G residue 136 PHE Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 90 ASN Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 271 ARG Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 363 ASP Chi-restraints excluded: chain J residue 399 CYS Chi-restraints excluded: chain J residue 426 GLU Chi-restraints excluded: chain J residue 459 ILE Chi-restraints excluded: chain L residue 127 SER Chi-restraints excluded: chain L residue 131 ASP Chi-restraints excluded: chain N residue 34 ASP Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 16 ILE Chi-restraints excluded: chain O residue 130 ASP Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain Q residue 148 ILE Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 137 ILE Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 34 ASP Chi-restraints excluded: chain m residue 6 GLU Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 132 THR Chi-restraints excluded: chain r residue 16 ILE Chi-restraints excluded: chain r residue 141 VAL Chi-restraints excluded: chain r residue 166 LEU Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain s residue 110 ILE Chi-restraints excluded: chain t residue 34 ASP Chi-restraints excluded: chain t residue 166 LEU Chi-restraints excluded: chain w residue 104 ASP Chi-restraints excluded: chain w residue 105 ASP Chi-restraints excluded: chain w residue 141 VAL Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 148 ILE Chi-restraints excluded: chain K residue 108 ASN Chi-restraints excluded: chain K residue 212 ASP Chi-restraints excluded: chain K residue 216 LYS Chi-restraints excluded: chain K residue 528 MET Chi-restraints excluded: chain K residue 531 LEU Chi-restraints excluded: chain K residue 819 GLU Chi-restraints excluded: chain K residue 846 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 375 optimal weight: 7.9990 chunk 209 optimal weight: 5.9990 chunk 563 optimal weight: 1.9990 chunk 460 optimal weight: 8.9990 chunk 186 optimal weight: 4.9990 chunk 677 optimal weight: 6.9990 chunk 732 optimal weight: 1.9990 chunk 603 optimal weight: 7.9990 chunk 672 optimal weight: 0.8980 chunk 231 optimal weight: 4.9990 chunk 543 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN C 60 ASN E 19 HIS E 178 ASN F 141 ASN F 260 ASN G 19 HIS G 133 ASN H 79 ASN H 91 HIS H 130 GLN H 279 ASN I 61 ASN L 53 ASN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 135 ASN ** M 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 ASN P 32 ASN P 135 ASN ** Q 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 HIS m 4 GLN m 14 ASN m 40 ASN o 4 GLN p 40 ASN q 14 ASN t 101 ASN ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 259 GLN K 695 ASN ** K 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 911 GLN K1024 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 63435 Z= 0.387 Angle : 0.742 19.480 86259 Z= 0.384 Chirality : 0.050 0.239 10087 Planarity : 0.005 0.074 10532 Dihedral : 12.101 179.115 9624 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.58 % Favored : 86.22 % Rotamer: Outliers : 4.63 % Allowed : 18.93 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.09), residues: 7409 helix: -1.37 (0.11), residues: 2083 sheet: -1.38 (0.12), residues: 1591 loop : -3.33 (0.08), residues: 3735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 411 HIS 0.006 0.001 HIS R 39 PHE 0.022 0.002 PHE D 136 TYR 0.028 0.002 TYR O 112 ARG 0.010 0.001 ARG m 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1365 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 1050 time to evaluate : 5.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 138 ASN cc_start: 0.7181 (OUTLIER) cc_final: 0.6882 (m110) REVERT: G 136 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.7452 (p90) REVERT: H 163 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8001 (mmmm) REVERT: H 210 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6538 (mt-10) REVERT: H 271 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.6772 (ttm-80) REVERT: I 245 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7699 (pm20) REVERT: J 426 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: J 465 ARG cc_start: 0.7487 (ttp80) cc_final: 0.7215 (tmm-80) REVERT: P 144 LYS cc_start: 0.7053 (mptt) cc_final: 0.6079 (tppt) REVERT: Q 69 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7382 (pt) REVERT: S 110 ILE cc_start: 0.8220 (pp) cc_final: 0.8013 (pt) REVERT: T 13 THR cc_start: 0.6447 (p) cc_final: 0.6244 (p) REVERT: W 64 ASP cc_start: 0.6964 (m-30) cc_final: 0.6755 (m-30) REVERT: X 121 MET cc_start: 0.5078 (ptt) cc_final: 0.4859 (pmt) REVERT: l 102 ILE cc_start: 0.7597 (mm) cc_final: 0.7304 (mm) REVERT: m 14 ASN cc_start: 0.5163 (OUTLIER) cc_final: 0.4656 (m-40) REVERT: o 121 MET cc_start: 0.7884 (pmm) cc_final: 0.7569 (ptp) REVERT: p 52 LYS cc_start: 0.7816 (ttmm) cc_final: 0.7312 (pptt) REVERT: r 55 ARG cc_start: 0.4332 (OUTLIER) cc_final: 0.4091 (tpp-160) REVERT: s 88 LEU cc_start: 0.8264 (mt) cc_final: 0.8004 (mt) REVERT: s 110 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8373 (tp) REVERT: s 121 MET cc_start: 0.6654 (mmp) cc_final: 0.5371 (mmp) REVERT: s 172 LEU cc_start: 0.7266 (pp) cc_final: 0.6982 (pp) REVERT: K 121 LYS cc_start: 0.4785 (tttp) cc_final: 0.4518 (mttt) REVERT: K 158 TRP cc_start: 0.3563 (m100) cc_final: 0.2585 (m100) REVERT: K 187 MET cc_start: 0.6184 (ppp) cc_final: 0.5940 (tmm) REVERT: K 188 MET cc_start: 0.7257 (mmm) cc_final: 0.6783 (mmm) REVERT: K 216 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7914 (mttm) REVERT: K 319 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6440 (mm) REVERT: K 528 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.8003 (mpp) REVERT: K 656 ASP cc_start: 0.7385 (p0) cc_final: 0.7119 (p0) REVERT: K 910 TYR cc_start: 0.7635 (t80) cc_final: 0.7304 (t80) REVERT: K 1019 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7403 (p0) outliers start: 315 outliers final: 150 residues processed: 1250 average time/residue: 1.2314 time to fit residues: 2105.2050 Evaluate side-chains 1097 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 933 time to evaluate : 5.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 133 ASN Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain G residue 136 PHE Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 90 ASN Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 265 GLU Chi-restraints excluded: chain H residue 271 ARG Chi-restraints excluded: chain H residue 304 CYS Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 245 GLU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 307 TYR Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 363 ASP Chi-restraints excluded: chain J residue 399 CYS Chi-restraints excluded: chain J residue 426 GLU Chi-restraints excluded: chain J residue 459 ILE Chi-restraints excluded: chain L residue 127 SER Chi-restraints excluded: chain L residue 131 ASP Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 129 SER Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 34 ASP Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 96 ILE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 16 ILE Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 130 ASP Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 99 LYS Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 108 ILE Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 137 ILE Chi-restraints excluded: chain T residue 45 THR Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 108 ILE Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 34 ASP Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 98 LYS Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain l residue 137 ILE Chi-restraints excluded: chain l residue 156 ILE Chi-restraints excluded: chain m residue 14 ASN Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 81 ASN Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 103 SER Chi-restraints excluded: chain n residue 41 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 93 LEU Chi-restraints excluded: chain o residue 131 ASP Chi-restraints excluded: chain o residue 132 THR Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain p residue 42 LEU Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain p residue 51 GLU Chi-restraints excluded: chain q residue 74 THR Chi-restraints excluded: chain q residue 123 THR Chi-restraints excluded: chain q residue 132 THR Chi-restraints excluded: chain r residue 16 ILE Chi-restraints excluded: chain r residue 36 ARG Chi-restraints excluded: chain r residue 55 ARG Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 141 VAL Chi-restraints excluded: chain r residue 166 LEU Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain s residue 110 ILE Chi-restraints excluded: chain s residue 141 VAL Chi-restraints excluded: chain s residue 166 LEU Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain t residue 32 ASN Chi-restraints excluded: chain t residue 34 ASP Chi-restraints excluded: chain w residue 141 VAL Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 17 THR Chi-restraints excluded: chain x residue 38 ILE Chi-restraints excluded: chain x residue 108 ILE Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 148 ILE Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 108 ASN Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 212 ASP Chi-restraints excluded: chain K residue 216 LYS Chi-restraints excluded: chain K residue 227 SER Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain K residue 328 LYS Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 396 THR Chi-restraints excluded: chain K residue 469 VAL Chi-restraints excluded: chain K residue 528 MET Chi-restraints excluded: chain K residue 531 LEU Chi-restraints excluded: chain K residue 666 LEU Chi-restraints excluded: chain K residue 694 VAL Chi-restraints excluded: chain K residue 744 VAL Chi-restraints excluded: chain K residue 758 ILE Chi-restraints excluded: chain K residue 788 LEU Chi-restraints excluded: chain K residue 820 SER Chi-restraints excluded: chain K residue 858 SER Chi-restraints excluded: chain K residue 1019 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 669 optimal weight: 10.0000 chunk 509 optimal weight: 10.0000 chunk 351 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 323 optimal weight: 4.9990 chunk 455 optimal weight: 9.9990 chunk 680 optimal weight: 5.9990 chunk 720 optimal weight: 0.7980 chunk 355 optimal weight: 6.9990 chunk 644 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN C 60 ASN E 130 GLN G 133 ASN H 79 ASN H 130 GLN I 61 ASN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 150 GLN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 ASN ** R 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 HIS ** l 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 4 GLN o 4 GLN t 29 HIS ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 39 HIS K 259 GLN K 846 ASN K 911 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 63435 Z= 0.342 Angle : 0.720 24.550 86259 Z= 0.372 Chirality : 0.049 0.206 10087 Planarity : 0.004 0.080 10532 Dihedral : 11.967 179.648 9624 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.29 % Favored : 86.54 % Rotamer: Outliers : 5.07 % Allowed : 20.55 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.26 (0.09), residues: 7409 helix: -1.18 (0.11), residues: 2074 sheet: -1.27 (0.13), residues: 1591 loop : -3.25 (0.08), residues: 3744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 411 HIS 0.004 0.001 HIS X 39 PHE 0.022 0.002 PHE D 136 TYR 0.030 0.002 TYR P 169 ARG 0.009 0.000 ARG H 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1372 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 345 poor density : 1027 time to evaluate : 5.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 138 ASN cc_start: 0.7181 (OUTLIER) cc_final: 0.6873 (m110) REVERT: D 216 ARG cc_start: 0.6690 (OUTLIER) cc_final: 0.6375 (ttm-80) REVERT: D 266 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8030 (mp) REVERT: E 99 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8550 (mp) REVERT: G 136 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7543 (p90) REVERT: G 222 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.7076 (mt-10) REVERT: H 163 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7974 (mmmm) REVERT: H 210 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6570 (mt-10) REVERT: H 271 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.6833 (ttm-80) REVERT: I 215 LYS cc_start: 0.8123 (mmtt) cc_final: 0.7904 (mmmt) REVERT: I 245 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7686 (pm20) REVERT: J 426 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: P 77 GLN cc_start: 0.5997 (OUTLIER) cc_final: 0.5442 (mm110) REVERT: P 144 LYS cc_start: 0.7036 (mptt) cc_final: 0.6057 (tppt) REVERT: Q 69 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7299 (pt) REVERT: Q 131 ASP cc_start: 0.6664 (OUTLIER) cc_final: 0.6378 (t70) REVERT: R 102 ILE cc_start: 0.6034 (OUTLIER) cc_final: 0.5697 (pp) REVERT: X 98 LYS cc_start: 0.4725 (OUTLIER) cc_final: 0.4429 (ptpp) REVERT: X 121 MET cc_start: 0.4790 (ptt) cc_final: 0.4512 (pmt) REVERT: l 102 ILE cc_start: 0.7512 (mm) cc_final: 0.7247 (mm) REVERT: n 142 PHE cc_start: 0.6933 (OUTLIER) cc_final: 0.6644 (m-80) REVERT: n 172 LEU cc_start: 0.4549 (mt) cc_final: 0.4340 (mt) REVERT: p 52 LYS cc_start: 0.7769 (ttmm) cc_final: 0.7290 (pptt) REVERT: s 95 LEU cc_start: 0.8678 (mt) cc_final: 0.8439 (mt) REVERT: s 110 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8398 (tp) REVERT: s 121 MET cc_start: 0.6721 (mmp) cc_final: 0.5491 (mmp) REVERT: s 172 LEU cc_start: 0.7245 (pp) cc_final: 0.6948 (pp) REVERT: x 65 TYR cc_start: 0.8204 (p90) cc_final: 0.7647 (p90) REVERT: K 121 LYS cc_start: 0.4925 (tttp) cc_final: 0.4646 (mttt) REVERT: K 158 TRP cc_start: 0.3527 (m100) cc_final: 0.2537 (m100) REVERT: K 188 MET cc_start: 0.7326 (mmm) cc_final: 0.6898 (mmm) REVERT: K 319 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6486 (mm) REVERT: K 528 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.8075 (mpp) REVERT: K 656 ASP cc_start: 0.7425 (p0) cc_final: 0.7148 (p0) REVERT: K 846 ASN cc_start: 0.6923 (OUTLIER) cc_final: 0.6622 (m-40) outliers start: 345 outliers final: 162 residues processed: 1263 average time/residue: 1.1475 time to fit residues: 1958.8524 Evaluate side-chains 1111 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 929 time to evaluate : 5.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 133 ASN Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain G residue 136 PHE Chi-restraints excluded: chain G residue 218 LYS Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 222 GLU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 90 ASN Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 265 GLU Chi-restraints excluded: chain H residue 271 ARG Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 221 GLU Chi-restraints excluded: chain I residue 245 GLU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 125 ASP Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 363 ASP Chi-restraints excluded: chain J residue 399 CYS Chi-restraints excluded: chain J residue 426 GLU Chi-restraints excluded: chain J residue 459 ILE Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 127 SER Chi-restraints excluded: chain L residue 131 ASP Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 129 SER Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 34 ASP Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 96 ILE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 149 THR Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 16 ILE Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 130 ASP Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain P residue 99 LYS Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 131 ASP Chi-restraints excluded: chain Q residue 135 ASN Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 137 ILE Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain X residue 98 LYS Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 156 ILE Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 81 ASN Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 103 SER Chi-restraints excluded: chain n residue 41 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 59 THR Chi-restraints excluded: chain n residue 120 SER Chi-restraints excluded: chain n residue 142 PHE Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain o residue 17 THR Chi-restraints excluded: chain o residue 131 ASP Chi-restraints excluded: chain o residue 136 ASN Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain p residue 42 LEU Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain p residue 51 GLU Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 74 THR Chi-restraints excluded: chain q residue 88 LEU Chi-restraints excluded: chain q residue 123 THR Chi-restraints excluded: chain q residue 132 THR Chi-restraints excluded: chain r residue 16 ILE Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 141 VAL Chi-restraints excluded: chain r residue 166 LEU Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain s residue 110 ILE Chi-restraints excluded: chain s residue 141 VAL Chi-restraints excluded: chain s residue 166 LEU Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain t residue 34 ASP Chi-restraints excluded: chain w residue 141 VAL Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 17 THR Chi-restraints excluded: chain x residue 38 ILE Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain x residue 108 ILE Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 148 ILE Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 108 ASN Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 227 SER Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain K residue 328 LYS Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 469 VAL Chi-restraints excluded: chain K residue 528 MET Chi-restraints excluded: chain K residue 531 LEU Chi-restraints excluded: chain K residue 631 VAL Chi-restraints excluded: chain K residue 666 LEU Chi-restraints excluded: chain K residue 694 VAL Chi-restraints excluded: chain K residue 744 VAL Chi-restraints excluded: chain K residue 788 LEU Chi-restraints excluded: chain K residue 820 SER Chi-restraints excluded: chain K residue 846 ASN Chi-restraints excluded: chain K residue 858 SER Chi-restraints excluded: chain K residue 925 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 599 optimal weight: 10.0000 chunk 408 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 536 optimal weight: 0.0050 chunk 297 optimal weight: 0.0050 chunk 614 optimal weight: 6.9990 chunk 497 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 367 optimal weight: 0.9990 chunk 646 optimal weight: 0.0770 chunk 181 optimal weight: 5.9990 overall best weight: 0.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN C 60 ASN D 178 ASN E 130 GLN G 133 ASN H 79 ASN H 130 GLN I 61 ASN I 227 HIS ** J 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN L 135 ASN N 77 GLN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 ASN ** Q 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 GLN T 136 ASN W 53 ASN l 79 GLN m 4 GLN m 40 ASN ** m 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 4 GLN t 101 ASN ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 259 GLN K 875 ASN K 911 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 63435 Z= 0.174 Angle : 0.675 25.196 86259 Z= 0.347 Chirality : 0.047 0.251 10087 Planarity : 0.004 0.068 10532 Dihedral : 11.718 179.005 9622 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.16 % Favored : 87.72 % Rotamer: Outliers : 4.00 % Allowed : 22.77 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.09), residues: 7409 helix: -0.88 (0.11), residues: 2078 sheet: -1.20 (0.12), residues: 1679 loop : -3.05 (0.09), residues: 3652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP K 411 HIS 0.005 0.001 HIS I 210 PHE 0.016 0.001 PHE N 83 TYR 0.029 0.001 TYR O 112 ARG 0.010 0.000 ARG H 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1388 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1116 time to evaluate : 5.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7886 (tt0) REVERT: D 138 ASN cc_start: 0.7195 (OUTLIER) cc_final: 0.6923 (m110) REVERT: E 99 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8546 (mp) REVERT: F 152 LYS cc_start: 0.7720 (pttm) cc_final: 0.7492 (ptpt) REVERT: G 136 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7456 (p90) REVERT: G 246 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6264 (mp0) REVERT: H 144 LYS cc_start: 0.7466 (mmtm) cc_final: 0.6716 (mtmp) REVERT: H 163 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7825 (mmmm) REVERT: M 16 ILE cc_start: 0.2900 (OUTLIER) cc_final: 0.1718 (mm) REVERT: M 79 GLN cc_start: 0.4954 (OUTLIER) cc_final: 0.4578 (mm-40) REVERT: P 144 LYS cc_start: 0.6777 (mptt) cc_final: 0.6014 (tppt) REVERT: Q 69 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7278 (pt) REVERT: S 131 ASP cc_start: 0.6136 (p0) cc_final: 0.5908 (p0) REVERT: S 160 LYS cc_start: 0.4661 (tptt) cc_final: 0.2995 (ptpp) REVERT: W 13 THR cc_start: 0.7169 (p) cc_final: 0.6962 (t) REVERT: X 98 LYS cc_start: 0.4680 (OUTLIER) cc_final: 0.4456 (ptpp) REVERT: X 121 MET cc_start: 0.4608 (ptt) cc_final: 0.4236 (pmt) REVERT: l 102 ILE cc_start: 0.7334 (mm) cc_final: 0.7019 (mm) REVERT: s 110 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8334 (tp) REVERT: s 121 MET cc_start: 0.6243 (mmp) cc_final: 0.4743 (mmp) REVERT: s 172 LEU cc_start: 0.7250 (pp) cc_final: 0.6846 (pp) REVERT: x 65 TYR cc_start: 0.8125 (p90) cc_final: 0.7637 (p90) REVERT: x 98 LYS cc_start: 0.8191 (ptmt) cc_final: 0.7621 (tptm) REVERT: K 14 LYS cc_start: 0.8279 (mttp) cc_final: 0.7982 (mttt) REVERT: K 121 LYS cc_start: 0.4835 (tttp) cc_final: 0.4614 (mptt) REVERT: K 156 LEU cc_start: 0.8411 (mm) cc_final: 0.7909 (mm) REVERT: K 158 TRP cc_start: 0.3390 (m100) cc_final: 0.2421 (m100) REVERT: K 188 MET cc_start: 0.7156 (mmm) cc_final: 0.6841 (mmm) REVERT: K 528 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7855 (mpp) REVERT: K 656 ASP cc_start: 0.7135 (p0) cc_final: 0.6903 (p0) REVERT: K 666 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8751 (mm) REVERT: K 719 CYS cc_start: 0.5310 (OUTLIER) cc_final: 0.5077 (t) REVERT: K 846 ASN cc_start: 0.6640 (t0) cc_final: 0.6413 (m-40) outliers start: 272 outliers final: 117 residues processed: 1284 average time/residue: 1.1903 time to fit residues: 2051.6056 Evaluate side-chains 1093 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 962 time to evaluate : 5.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 136 PHE Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 90 ASN Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 308 LEU Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 399 CYS Chi-restraints excluded: chain J residue 459 ILE Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 127 SER Chi-restraints excluded: chain L residue 131 ASP Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 129 SER Chi-restraints excluded: chain N residue 34 ASP Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 149 THR Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 97 ARG Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 32 ASN Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 79 GLN Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain X residue 98 LYS Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain n residue 41 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 93 LEU Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 17 THR Chi-restraints excluded: chain o residue 83 PHE Chi-restraints excluded: chain o residue 136 ASN Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain p residue 42 LEU Chi-restraints excluded: chain q residue 74 THR Chi-restraints excluded: chain q residue 123 THR Chi-restraints excluded: chain r residue 36 ARG Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 141 VAL Chi-restraints excluded: chain r residue 166 LEU Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain s residue 110 ILE Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain t residue 22 ILE Chi-restraints excluded: chain t residue 121 MET Chi-restraints excluded: chain w residue 24 ILE Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 17 THR Chi-restraints excluded: chain x residue 50 ASP Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain x residue 108 ILE Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 148 ILE Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 108 ASN Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 396 THR Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 528 MET Chi-restraints excluded: chain K residue 631 VAL Chi-restraints excluded: chain K residue 666 LEU Chi-restraints excluded: chain K residue 719 CYS Chi-restraints excluded: chain K residue 744 VAL Chi-restraints excluded: chain K residue 783 LEU Chi-restraints excluded: chain K residue 883 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 242 optimal weight: 4.9990 chunk 648 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 chunk 422 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 720 optimal weight: 10.0000 chunk 598 optimal weight: 8.9990 chunk 333 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 378 optimal weight: 0.4980 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 75 ASN C 60 ASN ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 133 ASN H 130 GLN I 61 ASN ** J 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 GLN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 ASN ** Q 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 GLN T 136 ASN ** W 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 4 GLN ** m 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 174 GLN o 4 GLN ** p 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 147 ASN ** q 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 29 HIS ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 259 GLN K 695 ASN K 846 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 63435 Z= 0.283 Angle : 0.706 23.286 86259 Z= 0.361 Chirality : 0.048 0.206 10087 Planarity : 0.004 0.071 10532 Dihedral : 11.643 179.277 9620 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.71 % Favored : 87.16 % Rotamer: Outliers : 4.13 % Allowed : 24.02 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.09), residues: 7409 helix: -0.81 (0.11), residues: 2068 sheet: -1.14 (0.12), residues: 1692 loop : -2.98 (0.09), residues: 3649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K 411 HIS 0.004 0.001 HIS s 29 PHE 0.018 0.002 PHE D 136 TYR 0.037 0.002 TYR r 112 ARG 0.012 0.000 ARG K 419 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1261 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 980 time to evaluate : 6.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7234 (pp20) REVERT: D 138 ASN cc_start: 0.7212 (OUTLIER) cc_final: 0.6902 (m110) REVERT: E 99 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8549 (mp) REVERT: G 136 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7631 (p90) REVERT: G 222 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6571 (mm-30) REVERT: G 246 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6188 (mp0) REVERT: G 286 ILE cc_start: 0.5709 (OUTLIER) cc_final: 0.5130 (tt) REVERT: H 144 LYS cc_start: 0.7509 (mmtm) cc_final: 0.6764 (mtmp) REVERT: H 163 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7898 (mmmm) REVERT: P 144 LYS cc_start: 0.6857 (mptt) cc_final: 0.6063 (tppt) REVERT: Q 69 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7245 (pt) REVERT: R 102 ILE cc_start: 0.5898 (OUTLIER) cc_final: 0.5650 (pp) REVERT: S 121 MET cc_start: 0.6647 (mtm) cc_final: 0.6414 (mpm) REVERT: S 138 ILE cc_start: 0.5317 (OUTLIER) cc_final: 0.5045 (pt) REVERT: S 160 LYS cc_start: 0.4094 (tptt) cc_final: 0.2939 (ptpp) REVERT: W 13 THR cc_start: 0.7152 (p) cc_final: 0.6927 (t) REVERT: X 98 LYS cc_start: 0.4726 (OUTLIER) cc_final: 0.4450 (ptpp) REVERT: X 121 MET cc_start: 0.4555 (ptt) cc_final: 0.4106 (pmt) REVERT: l 102 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.7184 (mm) REVERT: m 14 ASN cc_start: 0.5322 (OUTLIER) cc_final: 0.4647 (m-40) REVERT: n 86 LEU cc_start: 0.7086 (tm) cc_final: 0.6601 (tp) REVERT: n 142 PHE cc_start: 0.6858 (OUTLIER) cc_final: 0.6492 (m-80) REVERT: s 95 LEU cc_start: 0.8541 (mt) cc_final: 0.8281 (tp) REVERT: s 110 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8399 (tp) REVERT: s 121 MET cc_start: 0.5965 (mmp) cc_final: 0.4510 (mmp) REVERT: s 156 ILE cc_start: 0.6454 (tp) cc_final: 0.6235 (pp) REVERT: s 172 LEU cc_start: 0.7326 (pp) cc_final: 0.7094 (pt) REVERT: t 38 ILE cc_start: 0.8403 (mp) cc_final: 0.7984 (tt) REVERT: x 38 ILE cc_start: 0.4316 (OUTLIER) cc_final: 0.3928 (pt) REVERT: x 65 TYR cc_start: 0.8109 (p90) cc_final: 0.7688 (p90) REVERT: x 98 LYS cc_start: 0.8131 (ptmt) cc_final: 0.7558 (tptm) REVERT: K 121 LYS cc_start: 0.4883 (tttp) cc_final: 0.4659 (mptt) REVERT: K 158 TRP cc_start: 0.3523 (m100) cc_final: 0.2426 (m100) REVERT: K 188 MET cc_start: 0.7160 (mmm) cc_final: 0.6852 (mmm) REVERT: K 287 THR cc_start: 0.7945 (OUTLIER) cc_final: 0.7712 (m) REVERT: K 528 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7988 (mpp) REVERT: K 656 ASP cc_start: 0.7343 (p0) cc_final: 0.7096 (p0) REVERT: K 719 CYS cc_start: 0.5342 (OUTLIER) cc_final: 0.5123 (t) REVERT: K 753 GLU cc_start: 0.7562 (pp20) cc_final: 0.7340 (pp20) outliers start: 281 outliers final: 151 residues processed: 1167 average time/residue: 1.1383 time to fit residues: 1800.5747 Evaluate side-chains 1096 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 925 time to evaluate : 5.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain F residue 133 ASN Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 136 PHE Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 222 GLU Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 90 ASN Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 221 GLU Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 363 ASP Chi-restraints excluded: chain J residue 391 ILE Chi-restraints excluded: chain J residue 399 CYS Chi-restraints excluded: chain J residue 459 ILE Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 127 SER Chi-restraints excluded: chain L residue 131 ASP Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 129 SER Chi-restraints excluded: chain M residue 131 ASP Chi-restraints excluded: chain N residue 34 ASP Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 96 ILE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 149 THR Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 99 LYS Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 32 ASN Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 87 LYS Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 74 THR Chi-restraints excluded: chain T residue 79 GLN Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain X residue 98 LYS Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 98 LYS Chi-restraints excluded: chain l residue 102 ILE Chi-restraints excluded: chain m residue 14 ASN Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 103 SER Chi-restraints excluded: chain m residue 172 LEU Chi-restraints excluded: chain n residue 41 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 59 THR Chi-restraints excluded: chain n residue 93 LEU Chi-restraints excluded: chain n residue 142 PHE Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 17 THR Chi-restraints excluded: chain o residue 83 PHE Chi-restraints excluded: chain o residue 136 ASN Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain p residue 42 LEU Chi-restraints excluded: chain q residue 59 THR Chi-restraints excluded: chain q residue 74 THR Chi-restraints excluded: chain q residue 123 THR Chi-restraints excluded: chain q residue 153 LYS Chi-restraints excluded: chain r residue 30 ILE Chi-restraints excluded: chain r residue 55 ARG Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 141 VAL Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain s residue 110 ILE Chi-restraints excluded: chain s residue 141 VAL Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain w residue 24 ILE Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 17 THR Chi-restraints excluded: chain x residue 38 ILE Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain x residue 108 ILE Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 148 ILE Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 108 ASN Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 212 ASP Chi-restraints excluded: chain K residue 227 SER Chi-restraints excluded: chain K residue 287 THR Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 396 THR Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 504 MET Chi-restraints excluded: chain K residue 528 MET Chi-restraints excluded: chain K residue 531 LEU Chi-restraints excluded: chain K residue 631 VAL Chi-restraints excluded: chain K residue 719 CYS Chi-restraints excluded: chain K residue 744 VAL Chi-restraints excluded: chain K residue 764 ILE Chi-restraints excluded: chain K residue 783 LEU Chi-restraints excluded: chain K residue 788 LEU Chi-restraints excluded: chain K residue 858 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 694 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 410 optimal weight: 5.9990 chunk 526 optimal weight: 20.0000 chunk 407 optimal weight: 6.9990 chunk 606 optimal weight: 0.9990 chunk 402 optimal weight: 2.9990 chunk 718 optimal weight: 0.6980 chunk 449 optimal weight: 9.9990 chunk 437 optimal weight: 8.9990 chunk 331 optimal weight: 9.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 75 ASN C 60 ASN ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 133 ASN H 130 GLN I 61 ASN ** J 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 ASN ** Q 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 53 ASN T 76 GLN ** W 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 79 GLN m 4 GLN ** m 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 4 GLN ** p 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 29 HIS ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 259 GLN ** K 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 911 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 63435 Z= 0.322 Angle : 0.718 22.420 86259 Z= 0.368 Chirality : 0.049 0.240 10087 Planarity : 0.004 0.069 10532 Dihedral : 11.661 179.216 9620 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.88 % Favored : 87.00 % Rotamer: Outliers : 4.54 % Allowed : 24.53 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.09), residues: 7409 helix: -0.84 (0.11), residues: 2075 sheet: -1.01 (0.13), residues: 1620 loop : -3.02 (0.09), residues: 3714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 411 HIS 0.006 0.001 HIS J 157 PHE 0.021 0.002 PHE D 136 TYR 0.037 0.002 TYR r 112 ARG 0.009 0.000 ARG H 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1271 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 309 poor density : 962 time to evaluate : 5.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7260 (pp20) REVERT: D 138 ASN cc_start: 0.7239 (OUTLIER) cc_final: 0.6914 (m110) REVERT: D 210 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7338 (mtt180) REVERT: D 266 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.7994 (mp) REVERT: E 99 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8544 (mp) REVERT: G 136 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7651 (p90) REVERT: G 246 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6237 (mp0) REVERT: G 283 LYS cc_start: 0.7463 (pttt) cc_final: 0.7158 (pttt) REVERT: G 286 ILE cc_start: 0.5577 (OUTLIER) cc_final: 0.5008 (tt) REVERT: H 17 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.7180 (pp30) REVERT: H 144 LYS cc_start: 0.7512 (mmtm) cc_final: 0.6779 (mtmp) REVERT: H 163 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7922 (mmmm) REVERT: I 245 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7711 (pm20) REVERT: O 140 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7495 (mp0) REVERT: P 144 LYS cc_start: 0.6924 (mptt) cc_final: 0.6116 (tppt) REVERT: Q 69 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7219 (pt) REVERT: R 51 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6783 (pm20) REVERT: R 102 ILE cc_start: 0.5908 (OUTLIER) cc_final: 0.5619 (pp) REVERT: S 121 MET cc_start: 0.6652 (mtm) cc_final: 0.6397 (mpm) REVERT: S 138 ILE cc_start: 0.5379 (OUTLIER) cc_final: 0.5125 (pt) REVERT: S 160 LYS cc_start: 0.4231 (mptt) cc_final: 0.3308 (ptpp) REVERT: W 13 THR cc_start: 0.7153 (p) cc_final: 0.6923 (t) REVERT: W 169 TYR cc_start: 0.7275 (p90) cc_final: 0.7071 (p90) REVERT: X 98 LYS cc_start: 0.4715 (OUTLIER) cc_final: 0.4498 (ptpp) REVERT: X 121 MET cc_start: 0.4546 (ptt) cc_final: 0.4258 (pmt) REVERT: l 102 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7252 (mm) REVERT: m 14 ASN cc_start: 0.5394 (OUTLIER) cc_final: 0.4690 (m-40) REVERT: s 95 LEU cc_start: 0.8547 (mt) cc_final: 0.8301 (tp) REVERT: s 110 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8408 (OUTLIER) REVERT: s 121 MET cc_start: 0.5887 (mmp) cc_final: 0.4539 (mmp) REVERT: s 156 ILE cc_start: 0.6438 (tp) cc_final: 0.6226 (pp) REVERT: t 38 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7972 (tt) REVERT: x 38 ILE cc_start: 0.4310 (OUTLIER) cc_final: 0.3949 (pt) REVERT: x 65 TYR cc_start: 0.8104 (p90) cc_final: 0.7731 (p90) REVERT: x 98 LYS cc_start: 0.8113 (ptmt) cc_final: 0.7489 (tptp) REVERT: K 121 LYS cc_start: 0.4902 (tttp) cc_final: 0.4673 (mptt) REVERT: K 158 TRP cc_start: 0.3531 (m100) cc_final: 0.2432 (m100) REVERT: K 188 MET cc_start: 0.7203 (mmm) cc_final: 0.6892 (mmm) REVERT: K 287 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7701 (m) REVERT: K 328 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7259 (ptmm) REVERT: K 528 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7831 (mpp) REVERT: K 656 ASP cc_start: 0.7373 (p0) cc_final: 0.7069 (p0) REVERT: K 719 CYS cc_start: 0.5412 (OUTLIER) cc_final: 0.5212 (t) REVERT: K 753 GLU cc_start: 0.7668 (pp20) cc_final: 0.7424 (pp20) REVERT: K 835 MET cc_start: 0.6409 (pmm) cc_final: 0.5905 (ptt) REVERT: K 846 ASN cc_start: 0.6807 (m-40) cc_final: 0.6573 (m-40) outliers start: 309 outliers final: 176 residues processed: 1167 average time/residue: 1.1797 time to fit residues: 1862.0091 Evaluate side-chains 1098 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 898 time to evaluate : 5.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 133 ASN Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 136 PHE Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 221 GLU Chi-restraints excluded: chain I residue 245 GLU Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 363 ASP Chi-restraints excluded: chain J residue 399 CYS Chi-restraints excluded: chain J residue 459 ILE Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 131 ASP Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 129 SER Chi-restraints excluded: chain M residue 131 ASP Chi-restraints excluded: chain N residue 34 ASP Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 81 ASN Chi-restraints excluded: chain N residue 96 ILE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 149 THR Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 16 ILE Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 101 ASN Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 130 ASP Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 99 LYS Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 32 ASN Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 87 LYS Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 79 GLN Chi-restraints excluded: chain T residue 108 ILE Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain W residue 136 ASN Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain X residue 98 LYS Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 98 LYS Chi-restraints excluded: chain l residue 102 ILE Chi-restraints excluded: chain l residue 156 ILE Chi-restraints excluded: chain m residue 14 ASN Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 103 SER Chi-restraints excluded: chain n residue 41 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 59 THR Chi-restraints excluded: chain n residue 70 LEU Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 17 THR Chi-restraints excluded: chain o residue 83 PHE Chi-restraints excluded: chain o residue 136 ASN Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain p residue 42 LEU Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 59 THR Chi-restraints excluded: chain q residue 74 THR Chi-restraints excluded: chain q residue 123 THR Chi-restraints excluded: chain q residue 132 THR Chi-restraints excluded: chain q residue 134 VAL Chi-restraints excluded: chain q residue 153 LYS Chi-restraints excluded: chain q residue 163 ILE Chi-restraints excluded: chain r residue 36 ARG Chi-restraints excluded: chain r residue 51 GLU Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 141 VAL Chi-restraints excluded: chain r residue 166 LEU Chi-restraints excluded: chain s residue 43 VAL Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain s residue 59 THR Chi-restraints excluded: chain s residue 110 ILE Chi-restraints excluded: chain s residue 141 VAL Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain t residue 38 ILE Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain w residue 24 ILE Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 17 THR Chi-restraints excluded: chain x residue 38 ILE Chi-restraints excluded: chain x residue 45 THR Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain x residue 108 ILE Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 148 ILE Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 108 ASN Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 212 ASP Chi-restraints excluded: chain K residue 227 SER Chi-restraints excluded: chain K residue 287 THR Chi-restraints excluded: chain K residue 328 LYS Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 396 THR Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 469 VAL Chi-restraints excluded: chain K residue 504 MET Chi-restraints excluded: chain K residue 528 MET Chi-restraints excluded: chain K residue 531 LEU Chi-restraints excluded: chain K residue 631 VAL Chi-restraints excluded: chain K residue 719 CYS Chi-restraints excluded: chain K residue 744 VAL Chi-restraints excluded: chain K residue 754 TYR Chi-restraints excluded: chain K residue 764 ILE Chi-restraints excluded: chain K residue 788 LEU Chi-restraints excluded: chain K residue 819 GLU Chi-restraints excluded: chain K residue 858 SER Chi-restraints excluded: chain K residue 1019 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 444 optimal weight: 6.9990 chunk 286 optimal weight: 3.9990 chunk 428 optimal weight: 8.9990 chunk 216 optimal weight: 0.0470 chunk 141 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 chunk 456 optimal weight: 6.9990 chunk 489 optimal weight: 0.7980 chunk 355 optimal weight: 3.9990 chunk 66 optimal weight: 0.3980 chunk 564 optimal weight: 5.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN B 75 ASN D 178 ASN ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 HIS G 133 ASN H 90 ASN H 130 GLN ** J 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 53 ASN T 76 GLN T 136 ASN W 14 ASN l 79 GLN m 4 GLN ** m 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 4 GLN ** p 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 14 ASN ** q 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 875 ASN K 911 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 63435 Z= 0.187 Angle : 0.686 19.235 86259 Z= 0.351 Chirality : 0.047 0.237 10087 Planarity : 0.004 0.072 10532 Dihedral : 11.508 179.290 9620 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.94 % Favored : 87.99 % Rotamer: Outliers : 3.49 % Allowed : 26.03 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.09), residues: 7409 helix: -0.65 (0.11), residues: 2075 sheet: -1.07 (0.12), residues: 1719 loop : -2.89 (0.09), residues: 3615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP K 411 HIS 0.004 0.001 HIS J 157 PHE 0.018 0.001 PHE T 83 TYR 0.030 0.001 TYR r 112 ARG 0.009 0.000 ARG H 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1232 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 995 time to evaluate : 5.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8458 (mtpp) cc_final: 0.8091 (mtpm) REVERT: D 100 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7302 (pp20) REVERT: D 138 ASN cc_start: 0.7175 (OUTLIER) cc_final: 0.6887 (m110) REVERT: E 99 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8545 (mp) REVERT: G 136 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7484 (p90) REVERT: G 246 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6090 (mp0) REVERT: H 17 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.7112 (pp30) REVERT: H 163 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7788 (mmmm) REVERT: I 223 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7292 (mtm-85) REVERT: I 245 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7657 (pm20) REVERT: M 16 ILE cc_start: 0.2957 (OUTLIER) cc_final: 0.1830 (mm) REVERT: M 79 GLN cc_start: 0.4705 (OUTLIER) cc_final: 0.4452 (mm-40) REVERT: P 144 LYS cc_start: 0.6682 (mptt) cc_final: 0.6012 (tppt) REVERT: Q 5 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.7146 (tpp-160) REVERT: Q 69 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7198 (pt) REVERT: R 51 GLU cc_start: 0.6997 (pt0) cc_final: 0.6671 (pm20) REVERT: R 102 ILE cc_start: 0.5785 (OUTLIER) cc_final: 0.5521 (pp) REVERT: S 116 ASP cc_start: 0.5982 (t0) cc_final: 0.5189 (t0) REVERT: S 138 ILE cc_start: 0.5410 (OUTLIER) cc_final: 0.5150 (pt) REVERT: S 160 LYS cc_start: 0.4251 (mptt) cc_final: 0.3316 (ptpp) REVERT: T 76 GLN cc_start: 0.1083 (OUTLIER) cc_final: 0.0169 (mm-40) REVERT: T 93 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7440 (mt) REVERT: W 169 TYR cc_start: 0.7221 (p90) cc_final: 0.6989 (p90) REVERT: X 121 MET cc_start: 0.4533 (ptt) cc_final: 0.4201 (pmt) REVERT: l 102 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.7018 (mm) REVERT: l 163 ILE cc_start: 0.6942 (mp) cc_final: 0.6710 (mp) REVERT: m 4 GLN cc_start: 0.6980 (OUTLIER) cc_final: 0.6744 (mt0) REVERT: m 14 ASN cc_start: 0.5266 (OUTLIER) cc_final: 0.4614 (m-40) REVERT: s 95 LEU cc_start: 0.8564 (mt) cc_final: 0.8339 (tp) REVERT: x 38 ILE cc_start: 0.4227 (OUTLIER) cc_final: 0.3905 (pt) REVERT: x 64 ASP cc_start: 0.6167 (m-30) cc_final: 0.5850 (m-30) REVERT: x 65 TYR cc_start: 0.8109 (p90) cc_final: 0.7671 (p90) REVERT: x 98 LYS cc_start: 0.8083 (ptmt) cc_final: 0.7476 (tptp) REVERT: K 156 LEU cc_start: 0.8490 (mm) cc_final: 0.8051 (tp) REVERT: K 158 TRP cc_start: 0.3557 (m100) cc_final: 0.2482 (m100) REVERT: K 188 MET cc_start: 0.7178 (mmm) cc_final: 0.6903 (mmm) REVERT: K 287 THR cc_start: 0.7909 (OUTLIER) cc_final: 0.7689 (m) REVERT: K 528 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7659 (mpp) REVERT: K 599 GLN cc_start: 0.8133 (tt0) cc_final: 0.7878 (tp-100) REVERT: K 666 LEU cc_start: 0.8948 (mm) cc_final: 0.8535 (mm) REVERT: K 719 CYS cc_start: 0.5478 (OUTLIER) cc_final: 0.5221 (t) REVERT: K 753 GLU cc_start: 0.7657 (pp20) cc_final: 0.7440 (pp20) REVERT: K 835 MET cc_start: 0.6349 (pmm) cc_final: 0.5689 (ptt) outliers start: 237 outliers final: 128 residues processed: 1149 average time/residue: 1.1649 time to fit residues: 1809.8186 Evaluate side-chains 1088 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 936 time to evaluate : 5.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 136 PHE Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 221 GLU Chi-restraints excluded: chain I residue 223 ARG Chi-restraints excluded: chain I residue 245 GLU Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 363 ASP Chi-restraints excluded: chain J residue 399 CYS Chi-restraints excluded: chain J residue 459 ILE Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 127 SER Chi-restraints excluded: chain L residue 131 ASP Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 129 SER Chi-restraints excluded: chain N residue 34 ASP Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 45 THR Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 149 THR Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 87 LYS Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 76 GLN Chi-restraints excluded: chain T residue 79 GLN Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain W residue 136 ASN Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 102 ILE Chi-restraints excluded: chain l residue 140 GLU Chi-restraints excluded: chain m residue 4 GLN Chi-restraints excluded: chain m residue 14 ASN Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 103 SER Chi-restraints excluded: chain n residue 41 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 70 LEU Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 17 THR Chi-restraints excluded: chain o residue 136 ASN Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain p residue 38 ILE Chi-restraints excluded: chain p residue 42 LEU Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain q residue 59 THR Chi-restraints excluded: chain q residue 74 THR Chi-restraints excluded: chain q residue 123 THR Chi-restraints excluded: chain q residue 132 THR Chi-restraints excluded: chain q residue 134 VAL Chi-restraints excluded: chain q residue 153 LYS Chi-restraints excluded: chain r residue 51 GLU Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain s residue 8 VAL Chi-restraints excluded: chain s residue 43 VAL Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain s residue 59 THR Chi-restraints excluded: chain s residue 141 VAL Chi-restraints excluded: chain t residue 60 LEU Chi-restraints excluded: chain w residue 24 ILE Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 17 THR Chi-restraints excluded: chain x residue 38 ILE Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain x residue 108 ILE Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 148 ILE Chi-restraints excluded: chain K residue 108 ASN Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 212 ASP Chi-restraints excluded: chain K residue 287 THR Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 396 THR Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 469 VAL Chi-restraints excluded: chain K residue 528 MET Chi-restraints excluded: chain K residue 531 LEU Chi-restraints excluded: chain K residue 631 VAL Chi-restraints excluded: chain K residue 719 CYS Chi-restraints excluded: chain K residue 744 VAL Chi-restraints excluded: chain K residue 788 LEU Chi-restraints excluded: chain K residue 819 GLU Chi-restraints excluded: chain K residue 1019 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 653 optimal weight: 3.9990 chunk 687 optimal weight: 5.9990 chunk 627 optimal weight: 6.9990 chunk 669 optimal weight: 1.9990 chunk 402 optimal weight: 20.0000 chunk 291 optimal weight: 4.9990 chunk 525 optimal weight: 0.8980 chunk 205 optimal weight: 4.9990 chunk 604 optimal weight: 0.0040 chunk 632 optimal weight: 1.9990 chunk 666 optimal weight: 2.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 75 ASN ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 HIS G 133 ASN H 66 ASN H 130 GLN I 61 ASN ** J 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 440 ASN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 32 ASN ** R 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 GLN S 91 ASN T 53 ASN T 76 GLN T 136 ASN ** l 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 4 GLN ** m 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 4 GLN ** p 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 14 ASN t 39 HIS ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 63435 Z= 0.257 Angle : 0.720 17.771 86259 Z= 0.368 Chirality : 0.048 0.244 10087 Planarity : 0.004 0.076 10532 Dihedral : 11.465 179.316 9619 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.01 % Favored : 87.88 % Rotamer: Outliers : 3.16 % Allowed : 27.08 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.09), residues: 7409 helix: -0.63 (0.11), residues: 2083 sheet: -0.97 (0.12), residues: 1688 loop : -2.85 (0.09), residues: 3638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP K 411 HIS 0.009 0.001 HIS R 39 PHE 0.023 0.002 PHE O 83 TYR 0.042 0.002 TYR r 112 ARG 0.010 0.000 ARG K 419 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1171 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 956 time to evaluate : 6.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7314 (pp20) REVERT: D 138 ASN cc_start: 0.7193 (OUTLIER) cc_final: 0.6870 (m110) REVERT: D 266 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7962 (mp) REVERT: E 99 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8543 (mp) REVERT: G 136 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.7629 (p90) REVERT: G 246 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6122 (mp0) REVERT: H 17 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.7140 (pp30) REVERT: H 163 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7841 (mmmm) REVERT: I 245 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7706 (pm20) REVERT: M 79 GLN cc_start: 0.4739 (OUTLIER) cc_final: 0.4493 (mm-40) REVERT: N 95 LEU cc_start: 0.7976 (mm) cc_final: 0.7774 (mm) REVERT: N 129 SER cc_start: 0.8028 (m) cc_final: 0.7560 (p) REVERT: P 105 ASP cc_start: 0.6762 (t0) cc_final: 0.6295 (t70) REVERT: P 144 LYS cc_start: 0.6717 (mptt) cc_final: 0.6026 (tppt) REVERT: Q 5 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.7210 (ttm110) REVERT: Q 69 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7388 (pt) REVERT: R 51 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6668 (pm20) REVERT: R 102 ILE cc_start: 0.5940 (OUTLIER) cc_final: 0.5578 (pp) REVERT: T 76 GLN cc_start: 0.0964 (OUTLIER) cc_final: 0.0136 (mm-40) REVERT: W 169 TYR cc_start: 0.7287 (p90) cc_final: 0.7067 (p90) REVERT: X 121 MET cc_start: 0.4566 (ptt) cc_final: 0.4271 (pmt) REVERT: l 102 ILE cc_start: 0.7431 (OUTLIER) cc_final: 0.7187 (mm) REVERT: m 14 ASN cc_start: 0.5290 (OUTLIER) cc_final: 0.4614 (m-40) REVERT: s 95 LEU cc_start: 0.8539 (mt) cc_final: 0.8313 (tp) REVERT: w 115 PRO cc_start: 0.7060 (Cg_exo) cc_final: 0.6663 (Cg_endo) REVERT: x 38 ILE cc_start: 0.4164 (OUTLIER) cc_final: 0.3829 (pt) REVERT: x 64 ASP cc_start: 0.6160 (m-30) cc_final: 0.5830 (m-30) REVERT: x 65 TYR cc_start: 0.8097 (p90) cc_final: 0.7689 (p90) REVERT: x 98 LYS cc_start: 0.8044 (ptmt) cc_final: 0.7509 (tptm) REVERT: K 156 LEU cc_start: 0.8485 (mm) cc_final: 0.8030 (tp) REVERT: K 158 TRP cc_start: 0.3715 (m100) cc_final: 0.2600 (m100) REVERT: K 181 LEU cc_start: 0.7712 (mt) cc_final: 0.7465 (pp) REVERT: K 188 MET cc_start: 0.7232 (mmm) cc_final: 0.6958 (mmm) REVERT: K 287 THR cc_start: 0.7923 (OUTLIER) cc_final: 0.7703 (m) REVERT: K 528 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7614 (mpp) REVERT: K 599 GLN cc_start: 0.8094 (tt0) cc_final: 0.7824 (tp-100) REVERT: K 835 MET cc_start: 0.6455 (pmm) cc_final: 0.5753 (ptt) outliers start: 215 outliers final: 142 residues processed: 1098 average time/residue: 1.1639 time to fit residues: 1734.6727 Evaluate side-chains 1083 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 921 time to evaluate : 5.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 136 PHE Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 221 GLU Chi-restraints excluded: chain I residue 245 GLU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 399 CYS Chi-restraints excluded: chain J residue 459 ILE Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 131 ASP Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 129 SER Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 45 THR Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 96 ILE Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain N residue 149 THR Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 101 ASN Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 99 LYS Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 32 ASN Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 76 GLN Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain W residue 136 ASN Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 102 ILE Chi-restraints excluded: chain l residue 140 GLU Chi-restraints excluded: chain m residue 14 ASN Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain n residue 41 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 70 LEU Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 17 THR Chi-restraints excluded: chain o residue 60 LEU Chi-restraints excluded: chain o residue 136 ASN Chi-restraints excluded: chain p residue 38 ILE Chi-restraints excluded: chain p residue 42 LEU Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain q residue 59 THR Chi-restraints excluded: chain q residue 123 THR Chi-restraints excluded: chain q residue 132 THR Chi-restraints excluded: chain q residue 134 VAL Chi-restraints excluded: chain q residue 153 LYS Chi-restraints excluded: chain r residue 51 GLU Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain s residue 8 VAL Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 43 VAL Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain s residue 59 THR Chi-restraints excluded: chain s residue 141 VAL Chi-restraints excluded: chain s residue 156 ILE Chi-restraints excluded: chain t residue 38 ILE Chi-restraints excluded: chain t residue 60 LEU Chi-restraints excluded: chain w residue 24 ILE Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 17 THR Chi-restraints excluded: chain x residue 38 ILE Chi-restraints excluded: chain x residue 45 THR Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain x residue 108 ILE Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 148 ILE Chi-restraints excluded: chain K residue 108 ASN Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 212 ASP Chi-restraints excluded: chain K residue 287 THR Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 396 THR Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 469 VAL Chi-restraints excluded: chain K residue 528 MET Chi-restraints excluded: chain K residue 531 LEU Chi-restraints excluded: chain K residue 631 VAL Chi-restraints excluded: chain K residue 744 VAL Chi-restraints excluded: chain K residue 788 LEU Chi-restraints excluded: chain K residue 813 VAL Chi-restraints excluded: chain K residue 858 SER Chi-restraints excluded: chain K residue 1019 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 439 optimal weight: 0.9990 chunk 707 optimal weight: 7.9990 chunk 431 optimal weight: 0.0470 chunk 335 optimal weight: 0.3980 chunk 491 optimal weight: 3.9990 chunk 742 optimal weight: 0.8980 chunk 683 optimal weight: 3.9990 chunk 591 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 456 optimal weight: 20.0000 chunk 362 optimal weight: 8.9990 overall best weight: 0.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 43 ASN B 75 ASN G 133 ASN H 130 GLN ** J 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 ASN S 91 ASN T 53 ASN T 76 GLN T 91 ASN T 136 ASN W 14 ASN ** l 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 101 ASN ** m 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 4 GLN ** p 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 63435 Z= 0.197 Angle : 0.715 18.015 86259 Z= 0.364 Chirality : 0.048 0.433 10087 Planarity : 0.004 0.078 10532 Dihedral : 11.436 179.923 9619 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.74 % Favored : 88.19 % Rotamer: Outliers : 2.65 % Allowed : 27.81 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % 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: -2.54 (0.09), residues: 7409 helix: -0.56 (0.11), residues: 2077 sheet: -0.94 (0.12), residues: 1685 loop : -2.80 (0.09), residues: 3647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP K 411 HIS 0.006 0.001 HIS R 39 PHE 0.025 0.001 PHE T 83 TYR 0.035 0.001 TYR K 910 ARG 0.009 0.000 ARG K 419 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1132 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 952 time to evaluate : 5.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7314 (pp20) REVERT: D 138 ASN cc_start: 0.7138 (OUTLIER) cc_final: 0.6820 (m110) REVERT: E 99 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8543 (mp) REVERT: G 136 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7607 (p90) REVERT: H 17 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.7089 (pp30) REVERT: H 163 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7773 (mmmm) REVERT: I 245 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7690 (pm20) REVERT: M 16 ILE cc_start: 0.3064 (OUTLIER) cc_final: 0.1938 (mm) REVERT: N 95 LEU cc_start: 0.7928 (mm) cc_final: 0.7715 (mm) REVERT: N 129 SER cc_start: 0.8220 (m) cc_final: 0.7752 (p) REVERT: P 105 ASP cc_start: 0.6715 (t0) cc_final: 0.6307 (t70) REVERT: P 143 ASP cc_start: 0.6913 (t0) cc_final: 0.6241 (m-30) REVERT: P 144 LYS cc_start: 0.6685 (mptt) cc_final: 0.6019 (tppt) REVERT: Q 5 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6968 (tpp-160) REVERT: Q 69 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7431 (pt) REVERT: R 51 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6674 (pm20) REVERT: R 102 ILE cc_start: 0.5770 (OUTLIER) cc_final: 0.5390 (pp) REVERT: S 116 ASP cc_start: 0.5792 (t0) cc_final: 0.5297 (t0) REVERT: S 160 LYS cc_start: 0.4112 (mptt) cc_final: 0.3464 (ptpp) REVERT: W 169 TYR cc_start: 0.7259 (p90) cc_final: 0.7043 (p90) REVERT: X 121 MET cc_start: 0.4518 (ptt) cc_final: 0.4233 (pmt) REVERT: l 102 ILE cc_start: 0.7344 (OUTLIER) cc_final: 0.7103 (mm) REVERT: m 14 ASN cc_start: 0.5228 (OUTLIER) cc_final: 0.4552 (m-40) REVERT: s 95 LEU cc_start: 0.8530 (mt) cc_final: 0.8305 (tp) REVERT: w 115 PRO cc_start: 0.7013 (Cg_exo) cc_final: 0.6666 (Cg_endo) REVERT: x 38 ILE cc_start: 0.4119 (OUTLIER) cc_final: 0.3797 (pt) REVERT: x 65 TYR cc_start: 0.8115 (p90) cc_final: 0.7680 (p90) REVERT: x 98 LYS cc_start: 0.8066 (ptmt) cc_final: 0.7507 (tptm) REVERT: K 156 LEU cc_start: 0.8447 (mm) cc_final: 0.7524 (mt) REVERT: K 158 TRP cc_start: 0.3742 (m100) cc_final: 0.2593 (m100) REVERT: K 181 LEU cc_start: 0.7725 (mt) cc_final: 0.7500 (pp) REVERT: K 188 MET cc_start: 0.7244 (mmm) cc_final: 0.6988 (mmm) REVERT: K 287 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7687 (m) REVERT: K 528 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7543 (mpp) REVERT: K 599 GLN cc_start: 0.8043 (tt0) cc_final: 0.7751 (tp-100) REVERT: K 835 MET cc_start: 0.6296 (pmm) cc_final: 0.5486 (ptt) outliers start: 180 outliers final: 135 residues processed: 1072 average time/residue: 1.1860 time to fit residues: 1719.7196 Evaluate side-chains 1062 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 910 time to evaluate : 5.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 136 PHE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 245 GLU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 399 CYS Chi-restraints excluded: chain J residue 459 ILE Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 45 THR Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 149 THR Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 99 LYS Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 32 ASN Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 74 THR Chi-restraints excluded: chain T residue 76 GLN Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 16 ILE Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain W residue 136 ASN Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 162 ASP Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 102 ILE Chi-restraints excluded: chain l residue 140 GLU Chi-restraints excluded: chain m residue 14 ASN Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 103 SER Chi-restraints excluded: chain n residue 41 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 70 LEU Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 17 THR Chi-restraints excluded: chain o residue 136 ASN Chi-restraints excluded: chain p residue 38 ILE Chi-restraints excluded: chain p residue 42 LEU Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 20 VAL Chi-restraints excluded: chain q residue 59 THR Chi-restraints excluded: chain q residue 123 THR Chi-restraints excluded: chain q residue 132 THR Chi-restraints excluded: chain q residue 134 VAL Chi-restraints excluded: chain q residue 153 LYS Chi-restraints excluded: chain r residue 51 GLU Chi-restraints excluded: chain r residue 55 ARG Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain s residue 8 VAL Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain s residue 59 THR Chi-restraints excluded: chain s residue 141 VAL Chi-restraints excluded: chain s residue 156 ILE Chi-restraints excluded: chain t residue 38 ILE Chi-restraints excluded: chain t residue 60 LEU Chi-restraints excluded: chain w residue 24 ILE Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 17 THR Chi-restraints excluded: chain x residue 38 ILE Chi-restraints excluded: chain x residue 45 THR Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain x residue 108 ILE Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 148 ILE Chi-restraints excluded: chain K residue 108 ASN Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 287 THR Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 396 THR Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 469 VAL Chi-restraints excluded: chain K residue 528 MET Chi-restraints excluded: chain K residue 531 LEU Chi-restraints excluded: chain K residue 631 VAL Chi-restraints excluded: chain K residue 744 VAL Chi-restraints excluded: chain K residue 788 LEU Chi-restraints excluded: chain K residue 813 VAL Chi-restraints excluded: chain K residue 1019 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 469 optimal weight: 1.9990 chunk 629 optimal weight: 0.9990 chunk 181 optimal weight: 0.9980 chunk 544 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 591 optimal weight: 0.7980 chunk 247 optimal weight: 6.9990 chunk 607 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 75 ASN B 111 GLN G 133 ASN H 130 GLN I 61 ASN ** Q 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 ASN S 91 ASN T 76 GLN T 91 ASN W 14 ASN ** l 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 101 ASN ** m 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 4 GLN ** p 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.190465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.117597 restraints weight = 85088.261| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.59 r_work: 0.3321 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 63435 Z= 0.208 Angle : 0.714 16.928 86259 Z= 0.363 Chirality : 0.047 0.251 10087 Planarity : 0.004 0.076 10532 Dihedral : 11.382 179.797 9619 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.80 % Favored : 88.12 % Rotamer: Outliers : 2.63 % Allowed : 28.36 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % 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: -2.50 (0.09), residues: 7409 helix: -0.54 (0.12), residues: 2080 sheet: -0.88 (0.13), residues: 1669 loop : -2.79 (0.09), residues: 3660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP K 411 HIS 0.005 0.001 HIS G 13 PHE 0.030 0.001 PHE T 83 TYR 0.033 0.001 TYR K 910 ARG 0.013 0.000 ARG p 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29789.45 seconds wall clock time: 515 minutes 45.78 seconds (30945.78 seconds total)