Starting phenix.real_space_refine on Tue Mar 19 21:35:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8akr_15490/03_2024/8akr_15490_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8akr_15490/03_2024/8akr_15490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8akr_15490/03_2024/8akr_15490.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8akr_15490/03_2024/8akr_15490.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8akr_15490/03_2024/8akr_15490_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8akr_15490/03_2024/8akr_15490_updated.pdb" } resolution = 3.8 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= 0.002 sd= 0.019 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: 5 Type Number sf(0) Gaussians P 120 5.49 5 S 120 5.16 5 C 59280 2.51 5 N 17640 2.21 5 O 19080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 30": "OE1" <-> "OE2" Residue "H PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 62": "OD1" <-> "OD2" Residue "H TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 23": "OE1" <-> "OE2" Residue "A ASP 27": "OD1" <-> "OD2" Residue "A PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 62": "OD1" <-> "OD2" Residue "A TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B GLU 37": "OE1" <-> "OE2" Residue "B PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 179": "OE1" <-> "OE2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 37": "OE1" <-> "OE2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 37": "OE1" <-> "OE2" Residue "D PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 62": "OD1" <-> "OD2" Residue "D TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 80": "OD1" <-> "OD2" Residue "D TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "E GLU 37": "OE1" <-> "OE2" Residue "E PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 62": "OD1" <-> "OD2" Residue "E TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 201": "OE1" <-> "OE2" Residue "F GLU 37": "OE1" <-> "OE2" Residue "F PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 201": "OE1" <-> "OE2" Residue "G GLU 37": "OE1" <-> "OE2" Residue "G PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 62": "OD1" <-> "OD2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "G TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 200": "OE1" <-> "OE2" Residue "G GLU 201": "OE1" <-> "OE2" Residue "I GLU 23": "OE1" <-> "OE2" Residue "I GLU 35": "OE1" <-> "OE2" Residue "I GLU 37": "OE1" <-> "OE2" Residue "I PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 193": "OD1" <-> "OD2" Residue "I GLU 201": "OE1" <-> "OE2" Residue "J GLU 23": "OE1" <-> "OE2" Residue "J PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 80": "OD1" <-> "OD2" Residue "J TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 160": "OD1" <-> "OD2" Residue "J ASP 193": "OD1" <-> "OD2" Residue "J GLU 200": "OE1" <-> "OE2" Residue "J GLU 201": "OE1" <-> "OE2" Residue "J GLU 206": "OE1" <-> "OE2" Residue "K GLU 37": "OE1" <-> "OE2" Residue "K PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 62": "OD1" <-> "OD2" Residue "K ASP 80": "OD1" <-> "OD2" Residue "K TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 126": "OE1" <-> "OE2" Residue "K TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 193": "OD1" <-> "OD2" Residue "K GLU 201": "OE1" <-> "OE2" Residue "L GLU 37": "OE1" <-> "OE2" Residue "L PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 201": "OE1" <-> "OE2" Residue "M GLU 37": "OE1" <-> "OE2" Residue "M PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 62": "OD1" <-> "OD2" Residue "M GLU 73": "OE1" <-> "OE2" Residue "M ASP 80": "OD1" <-> "OD2" Residue "M GLU 126": "OE1" <-> "OE2" Residue "M TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 27": "OD1" <-> "OD2" Residue "N GLU 37": "OE1" <-> "OE2" Residue "N PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 62": "OD1" <-> "OD2" Residue "N ASP 80": "OD1" <-> "OD2" Residue "N TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 73": "OE1" <-> "OE2" Residue "O TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 62": "OD1" <-> "OD2" Residue "P ASP 80": "OD1" <-> "OD2" Residue "P TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 37": "OE1" <-> "OE2" Residue "Q PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 80": "OD1" <-> "OD2" Residue "Q TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 35": "OE1" <-> "OE2" Residue "R PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 73": "OE1" <-> "OE2" Residue "R TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 27": "OD1" <-> "OD2" Residue "S GLU 35": "OE1" <-> "OE2" Residue "S PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 62": "OD1" <-> "OD2" Residue "S TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 193": "OD1" <-> "OD2" Residue "T GLU 23": "OE1" <-> "OE2" Residue "T PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 193": "OD1" <-> "OD2" Residue "T GLU 206": "OE1" <-> "OE2" Residue "U GLU 23": "OE1" <-> "OE2" Residue "U PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 62": "OD1" <-> "OD2" Residue "U ASP 193": "OD1" <-> "OD2" Residue "U PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 193": "OD1" <-> "OD2" Residue "V GLU 200": "OE1" <-> "OE2" Residue "W GLU 35": "OE1" <-> "OE2" Residue "W GLU 42": "OE1" <-> "OE2" Residue "W PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 80": "OD1" <-> "OD2" Residue "W ASP 193": "OD1" <-> "OD2" Residue "X GLU 37": "OE1" <-> "OE2" Residue "X GLU 42": "OE1" <-> "OE2" Residue "X PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 80": "OD1" <-> "OD2" Residue "X GLU 126": "OE1" <-> "OE2" Residue "X TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 27": "OD1" <-> "OD2" Residue "Y GLU 37": "OE1" <-> "OE2" Residue "Y PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 62": "OD1" <-> "OD2" Residue "Z GLU 37": "OE1" <-> "OE2" Residue "Z PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 62": "OD1" <-> "OD2" Residue "Z ASP 80": "OD1" <-> "OD2" Residue "Z GLU 200": "OE1" <-> "OE2" Residue "a PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 62": "OD1" <-> "OD2" Residue "a ASP 193": "OD1" <-> "OD2" Residue "b GLU 35": "OE1" <-> "OE2" Residue "b GLU 37": "OE1" <-> "OE2" Residue "b PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 80": "OD1" <-> "OD2" Residue "b GLU 200": "OE1" <-> "OE2" Residue "c ASP 27": "OD1" <-> "OD2" Residue "c GLU 39": "OE1" <-> "OE2" Residue "c PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 126": "OE1" <-> "OE2" Residue "c ASP 193": "OD1" <-> "OD2" Residue "d GLU 35": "OE1" <-> "OE2" Residue "d PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 193": "OD1" <-> "OD2" Residue "d PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 30": "OE1" <-> "OE2" Residue "e PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 62": "OD1" <-> "OD2" Residue "e TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 23": "OE1" <-> "OE2" Residue "f GLU 35": "OE1" <-> "OE2" Residue "f PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 62": "OD1" <-> "OD2" Residue "f TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 197": "OE1" <-> "OE2" Residue "f GLU 200": "OE1" <-> "OE2" Residue "f GLU 201": "OE1" <-> "OE2" Residue "g GLU 23": "OE1" <-> "OE2" Residue "g ASP 27": "OD1" <-> "OD2" Residue "g PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 179": "OE1" <-> "OE2" Residue "g GLU 200": "OE1" <-> "OE2" Residue "g GLU 201": "OE1" <-> "OE2" Residue "h PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 62": "OD1" <-> "OD2" Residue "h TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 131": "OE1" <-> "OE2" Residue "h GLU 179": "OE1" <-> "OE2" Residue "h PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 200": "OE1" <-> "OE2" Residue "h GLU 201": "OE1" <-> "OE2" Residue "i GLU 23": "OE1" <-> "OE2" Residue "i PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 62": "OD1" <-> "OD2" Residue "i TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 110": "OE1" <-> "OE2" Residue "i TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 201": "OE1" <-> "OE2" Residue "j PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 62": "OD1" <-> "OD2" Residue "j GLU 73": "OE1" <-> "OE2" Residue "j ASP 80": "OD1" <-> "OD2" Residue "j TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 201": "OE1" <-> "OE2" Residue "k GLU 37": "OE1" <-> "OE2" Residue "k PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 62": "OD1" <-> "OD2" Residue "k TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 201": "OE1" <-> "OE2" Residue "l GLU 23": "OE1" <-> "OE2" Residue "l GLU 35": "OE1" <-> "OE2" Residue "l PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 131": "OE1" <-> "OE2" Residue "l GLU 201": "OE1" <-> "OE2" Residue "m GLU 23": "OE1" <-> "OE2" Residue "m GLU 37": "OE1" <-> "OE2" Residue "m PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 201": "OE1" <-> "OE2" Residue "m GLU 206": "OE1" <-> "OE2" Residue "n GLU 37": "OE1" <-> "OE2" Residue "n PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 62": "OD1" <-> "OD2" Residue "n ASP 80": "OD1" <-> "OD2" Residue "n TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 201": "OE1" <-> "OE2" Residue "n GLU 206": "OE1" <-> "OE2" Residue "o GLU 37": "OE1" <-> "OE2" Residue "o PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 80": "OD1" <-> "OD2" Residue "o TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 62": "OD1" <-> "OD2" Residue "p TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 193": "OD1" <-> "OD2" Residue "p GLU 201": "OE1" <-> "OE2" Residue "q GLU 35": "OE1" <-> "OE2" Residue "q GLU 37": "OE1" <-> "OE2" Residue "q GLU 42": "OE1" <-> "OE2" Residue "q PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 80": "OD1" <-> "OD2" Residue "q TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 193": "OD1" <-> "OD2" Residue "q GLU 201": "OE1" <-> "OE2" Residue "r GLU 35": "OE1" <-> "OE2" Residue "r GLU 37": "OE1" <-> "OE2" Residue "r PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 62": "OD1" <-> "OD2" Residue "r ASP 80": "OD1" <-> "OD2" Residue "r TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 193": "OD1" <-> "OD2" Residue "s PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 62": "OD1" <-> "OD2" Residue "s ASP 80": "OD1" <-> "OD2" Residue "s TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 126": "OE1" <-> "OE2" Residue "s TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 37": "OE1" <-> "OE2" Residue "t PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 62": "OD1" <-> "OD2" Residue "t GLU 73": "OE1" <-> "OE2" Residue "t TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 193": "OD1" <-> "OD2" Residue "t PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 197": "OE1" <-> "OE2" Residue "u GLU 35": "OE1" <-> "OE2" Residue "u GLU 37": "OE1" <-> "OE2" Residue "u PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 80": "OD1" <-> "OD2" Residue "u GLU 126": "OE1" <-> "OE2" Residue "u TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 193": "OD1" <-> "OD2" Residue "u GLU 197": "OE1" <-> "OE2" Residue "v GLU 35": "OE1" <-> "OE2" Residue "v PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 126": "OE1" <-> "OE2" Residue "v TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 197": "OE1" <-> "OE2" Residue "w ASP 27": "OD1" <-> "OD2" Residue "w GLU 37": "OE1" <-> "OE2" Residue "w PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 62": "OD1" <-> "OD2" Residue "w TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 206": "OE1" <-> "OE2" Residue "x GLU 23": "OE1" <-> "OE2" Residue "x GLU 35": "OE1" <-> "OE2" Residue "x GLU 37": "OE1" <-> "OE2" Residue "x PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 80": "OD1" <-> "OD2" Residue "x TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 37": "OE1" <-> "OE2" Residue "y PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 200": "OE1" <-> "OE2" Residue "y GLU 201": "OE1" <-> "OE2" Residue "z PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 62": "OD1" <-> "OD2" Residue "z GLU 126": "OE1" <-> "OE2" Residue "z ASP 193": "OD1" <-> "OD2" Residue "0 GLU 35": "OE1" <-> "OE2" Residue "0 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ASP 62": "OD1" <-> "OD2" Residue "0 GLU 126": "OE1" <-> "OE2" Residue "0 TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ASP 193": "OD1" <-> "OD2" Residue "1 GLU 35": "OE1" <-> "OE2" Residue "1 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 73": "OE1" <-> "OE2" Residue "1 ASP 80": "OD1" <-> "OD2" Residue "1 TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 35": "OE1" <-> "OE2" Residue "2 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 80": "OD1" <-> "OD2" Residue "2 GLU 126": "OE1" <-> "OE2" Residue "2 TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 37": "OE1" <-> "OE2" Residue "3 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 126": "OE1" <-> "OE2" Residue "3 TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 27": "OD1" <-> "OD2" Residue "4 GLU 35": "OE1" <-> "OE2" Residue "4 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 193": "OD1" <-> "OD2" Residue "4 PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 27": "OD1" <-> "OD2" Residue "5 GLU 35": "OE1" <-> "OE2" Residue "5 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 126": "OE1" <-> "OE2" Residue "5 ASP 193": "OD1" <-> "OD2" Residue "6 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 62": "OD1" <-> "OD2" Residue "6 TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 89": "OE1" <-> "OE2" Residue "6 GLU 116": "OE1" <-> "OE2" Residue "6 GLU 126": "OE1" <-> "OE2" Residue "6 PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 37": "OE1" <-> "OE2" Residue "7 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 200": "OE1" <-> "OE2" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 96240 Number of models: 1 Model: "" Number of chains: 119 Chain: "H" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "A" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "B" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "C" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "D" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "E" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "F" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "G" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "I" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "J" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "K" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "L" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "M" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "N" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "O" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "P" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "Q" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "R" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "S" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "T" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "U" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "V" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "W" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "X" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "Y" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "Z" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "a" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "b" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "c" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "d" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "e" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "f" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "g" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "h" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "i" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "j" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "k" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "l" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "m" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "n" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "o" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "p" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "q" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "r" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "s" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "t" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "u" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "v" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "w" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "x" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "y" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "z" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "0" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "1" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "2" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "3" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "4" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "5" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "6" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "7" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1577 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "s" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 35.56, per 1000 atoms: 0.37 Number of scatterers: 96240 At special positions: 0 Unit cell: (232.902, 232.902, 224.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 P 120 15.00 O 19080 8.00 N 17640 7.00 C 59280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 30.55 Conformation dependent library (CDL) restraints added in 12.7 seconds 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22680 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 253 helices and 0 sheets defined 88.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.90 Creating SS restraints... Processing helix chain 'H' and resid 25 through 81 removed outlier: 4.305A pdb=" N ASP H 80 " --> pdb=" O GLN H 76 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG H 81 " --> pdb=" O ALA H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 155 removed outlier: 3.624A pdb=" N GLN H 95 " --> pdb=" O LEU H 91 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER H 96 " --> pdb=" O GLY H 92 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TYR H 97 " --> pdb=" O GLN H 93 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU H 110 " --> pdb=" O LYS H 106 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU H 116 " --> pdb=" O ARG H 112 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN H 117 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG H 127 " --> pdb=" O GLN H 123 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN H 135 " --> pdb=" O GLU H 131 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASN H 137 " --> pdb=" O LYS H 133 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU H 138 " --> pdb=" O SER H 134 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU H 153 " --> pdb=" O ALA H 149 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLU H 154 " --> pdb=" O GLN H 150 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE H 155 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 185 Processing helix chain 'H' and resid 191 through 216 removed outlier: 4.163A pdb=" N ARG H 216 " --> pdb=" O MET H 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 81 removed outlier: 4.137A pdb=" N ASP A 80 " --> pdb=" O GLN A 76 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 155 removed outlier: 3.672A pdb=" N GLN A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN A 135 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 185 Processing helix chain 'A' and resid 191 through 216 removed outlier: 4.042A pdb=" N ARG A 216 " --> pdb=" O MET A 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 81 removed outlier: 4.086A pdb=" N ASP B 80 " --> pdb=" O GLN B 76 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 155 removed outlier: 3.631A pdb=" N GLN B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR B 97 " --> pdb=" O GLN B 93 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU B 116 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN B 135 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASN B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LEU B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU B 154 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE B 155 " --> pdb=" O LYS B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 185 Processing helix chain 'B' and resid 191 through 216 removed outlier: 3.924A pdb=" N ARG B 216 " --> pdb=" O MET B 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 81 removed outlier: 3.501A pdb=" N GLU C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP C 80 " --> pdb=" O GLN C 76 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ARG C 81 " --> pdb=" O ALA C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 155 removed outlier: 3.712A pdb=" N GLN C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER C 96 " --> pdb=" O GLY C 92 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR C 97 " --> pdb=" O GLN C 93 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU C 110 " --> pdb=" O LYS C 106 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA C 113 " --> pdb=" O GLY C 109 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 116 " --> pdb=" O ARG C 112 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C 127 " --> pdb=" O GLN C 123 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN C 135 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASN C 137 " --> pdb=" O LYS C 133 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEU C 138 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU C 154 " --> pdb=" O GLN C 150 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE C 155 " --> pdb=" O LYS C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 185 Processing helix chain 'C' and resid 191 through 216 removed outlier: 4.003A pdb=" N ARG C 216 " --> pdb=" O MET C 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 81 removed outlier: 4.082A pdb=" N ASP D 80 " --> pdb=" O GLN D 76 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 155 removed outlier: 3.645A pdb=" N GLN D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR D 97 " --> pdb=" O GLN D 93 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU D 116 " --> pdb=" O ARG D 112 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 127 " --> pdb=" O GLN D 123 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN D 135 " --> pdb=" O GLU D 131 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASN D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU D 138 " --> pdb=" O SER D 134 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU D 154 " --> pdb=" O GLN D 150 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE D 155 " --> pdb=" O LYS D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 185 Processing helix chain 'D' and resid 191 through 216 removed outlier: 3.978A pdb=" N ARG D 216 " --> pdb=" O MET D 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 81 removed outlier: 4.319A pdb=" N ASP E 80 " --> pdb=" O GLN E 76 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ARG E 81 " --> pdb=" O ALA E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 155 removed outlier: 3.654A pdb=" N GLN E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TYR E 97 " --> pdb=" O GLN E 93 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU E 110 " --> pdb=" O LYS E 106 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU E 116 " --> pdb=" O ARG E 112 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN E 135 " --> pdb=" O GLU E 131 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASN E 137 " --> pdb=" O LYS E 133 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU E 138 " --> pdb=" O SER E 134 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU E 153 " --> pdb=" O ALA E 149 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU E 154 " --> pdb=" O GLN E 150 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 185 Processing helix chain 'E' and resid 191 through 216 removed outlier: 4.132A pdb=" N ARG E 216 " --> pdb=" O MET E 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 81 removed outlier: 4.176A pdb=" N ASP F 80 " --> pdb=" O GLN F 76 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG F 81 " --> pdb=" O ALA F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 155 removed outlier: 3.655A pdb=" N GLN F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N SER F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TYR F 97 " --> pdb=" O GLN F 93 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA F 113 " --> pdb=" O GLY F 109 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU F 116 " --> pdb=" O ARG F 112 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN F 117 " --> pdb=" O ALA F 113 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG F 127 " --> pdb=" O GLN F 123 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN F 135 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASN F 137 " --> pdb=" O LYS F 133 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LEU F 138 " --> pdb=" O SER F 134 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU F 153 " --> pdb=" O ALA F 149 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU F 154 " --> pdb=" O GLN F 150 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE F 155 " --> pdb=" O LYS F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 185 Processing helix chain 'F' and resid 191 through 216 removed outlier: 4.111A pdb=" N ARG F 216 " --> pdb=" O MET F 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 81 removed outlier: 4.484A pdb=" N ASP G 80 " --> pdb=" O GLN G 76 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ARG G 81 " --> pdb=" O ALA G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 155 removed outlier: 3.670A pdb=" N GLN G 95 " --> pdb=" O LEU G 91 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR G 97 " --> pdb=" O GLN G 93 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU G 110 " --> pdb=" O LYS G 106 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU G 116 " --> pdb=" O ARG G 112 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ARG G 127 " --> pdb=" O GLN G 123 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN G 135 " --> pdb=" O GLU G 131 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASN G 137 " --> pdb=" O LYS G 133 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU G 138 " --> pdb=" O SER G 134 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU G 153 " --> pdb=" O ALA G 149 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU G 154 " --> pdb=" O GLN G 150 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE G 155 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 185 Processing helix chain 'G' and resid 191 through 216 removed outlier: 4.107A pdb=" N ARG G 216 " --> pdb=" O MET G 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 81 removed outlier: 4.209A pdb=" N ASP I 80 " --> pdb=" O GLN I 76 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG I 81 " --> pdb=" O ALA I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 153 removed outlier: 3.671A pdb=" N GLN I 95 " --> pdb=" O LEU I 91 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER I 96 " --> pdb=" O GLY I 92 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TYR I 97 " --> pdb=" O GLN I 93 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU I 110 " --> pdb=" O LYS I 106 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA I 113 " --> pdb=" O GLY I 109 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU I 116 " --> pdb=" O ARG I 112 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN I 117 " --> pdb=" O ALA I 113 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG I 127 " --> pdb=" O GLN I 123 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN I 135 " --> pdb=" O GLU I 131 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASN I 137 " --> pdb=" O LYS I 133 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LEU I 138 " --> pdb=" O SER I 134 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU I 153 " --> pdb=" O ALA I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 185 Processing helix chain 'I' and resid 191 through 216 removed outlier: 4.131A pdb=" N ARG I 216 " --> pdb=" O MET I 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 81 removed outlier: 4.404A pdb=" N ASP J 80 " --> pdb=" O GLN J 76 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG J 81 " --> pdb=" O ALA J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 155 removed outlier: 3.687A pdb=" N GLN J 95 " --> pdb=" O LEU J 91 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SER J 96 " --> pdb=" O GLY J 92 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR J 97 " --> pdb=" O GLN J 93 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY J 109 " --> pdb=" O GLY J 105 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU J 110 " --> pdb=" O LYS J 106 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA J 113 " --> pdb=" O GLY J 109 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU J 116 " --> pdb=" O ARG J 112 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN J 117 " --> pdb=" O ALA J 113 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG J 127 " --> pdb=" O GLN J 123 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN J 135 " --> pdb=" O GLU J 131 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ASN J 137 " --> pdb=" O LYS J 133 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU J 138 " --> pdb=" O SER J 134 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU J 153 " --> pdb=" O ALA J 149 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU J 154 " --> pdb=" O GLN J 150 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE J 155 " --> pdb=" O LYS J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 185 Processing helix chain 'J' and resid 191 through 216 removed outlier: 4.152A pdb=" N ARG J 216 " --> pdb=" O MET J 212 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 81 removed outlier: 4.142A pdb=" N ASP K 80 " --> pdb=" O GLN K 76 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ARG K 81 " --> pdb=" O ALA K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 153 removed outlier: 3.640A pdb=" N GLN K 95 " --> pdb=" O LEU K 91 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER K 96 " --> pdb=" O GLY K 92 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR K 97 " --> pdb=" O GLN K 93 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU K 110 " --> pdb=" O LYS K 106 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA K 113 " --> pdb=" O GLY K 109 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU K 116 " --> pdb=" O ARG K 112 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN K 117 " --> pdb=" O ALA K 113 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG K 127 " --> pdb=" O GLN K 123 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN K 135 " --> pdb=" O GLU K 131 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASN K 137 " --> pdb=" O LYS K 133 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LEU K 138 " --> pdb=" O SER K 134 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU K 153 " --> pdb=" O ALA K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 185 Processing helix chain 'K' and resid 191 through 216 removed outlier: 4.134A pdb=" N ARG K 216 " --> pdb=" O MET K 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 81 removed outlier: 4.390A pdb=" N ASP L 80 " --> pdb=" O GLN L 76 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG L 81 " --> pdb=" O ALA L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 155 removed outlier: 3.586A pdb=" N GLN L 95 " --> pdb=" O LEU L 91 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER L 96 " --> pdb=" O GLY L 92 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR L 97 " --> pdb=" O GLN L 93 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU L 110 " --> pdb=" O LYS L 106 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA L 113 " --> pdb=" O GLY L 109 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU L 116 " --> pdb=" O ARG L 112 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN L 117 " --> pdb=" O ALA L 113 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN L 135 " --> pdb=" O GLU L 131 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASN L 137 " --> pdb=" O LYS L 133 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU L 138 " --> pdb=" O SER L 134 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU L 153 " --> pdb=" O ALA L 149 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU L 154 " --> pdb=" O GLN L 150 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE L 155 " --> pdb=" O LYS L 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 185 Processing helix chain 'L' and resid 191 through 216 removed outlier: 4.079A pdb=" N ARG L 216 " --> pdb=" O MET L 212 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 81 removed outlier: 4.650A pdb=" N ASP M 80 " --> pdb=" O GLN M 76 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ARG M 81 " --> pdb=" O ALA M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 155 removed outlier: 3.713A pdb=" N GLN M 95 " --> pdb=" O LEU M 91 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER M 96 " --> pdb=" O GLY M 92 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR M 97 " --> pdb=" O GLN M 93 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU M 110 " --> pdb=" O LYS M 106 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU M 116 " --> pdb=" O ARG M 112 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN M 117 " --> pdb=" O ALA M 113 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN M 135 " --> pdb=" O GLU M 131 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN M 137 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU M 138 " --> pdb=" O SER M 134 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU M 154 " --> pdb=" O GLN M 150 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE M 155 " --> pdb=" O LYS M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 167 through 185 Processing helix chain 'M' and resid 191 through 215 Processing helix chain 'N' and resid 25 through 81 removed outlier: 4.288A pdb=" N ASP N 80 " --> pdb=" O GLN N 76 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ARG N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 153 removed outlier: 3.765A pdb=" N GLN N 95 " --> pdb=" O LEU N 91 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N SER N 96 " --> pdb=" O GLY N 92 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TYR N 97 " --> pdb=" O GLN N 93 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU N 110 " --> pdb=" O LYS N 106 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA N 113 " --> pdb=" O GLY N 109 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU N 116 " --> pdb=" O ARG N 112 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN N 117 " --> pdb=" O ALA N 113 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN N 135 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASN N 137 " --> pdb=" O LYS N 133 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LEU N 138 " --> pdb=" O SER N 134 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU N 153 " --> pdb=" O ALA N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 185 Processing helix chain 'N' and resid 191 through 216 removed outlier: 4.006A pdb=" N ARG N 216 " --> pdb=" O MET N 212 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 81 removed outlier: 4.355A pdb=" N ASP O 80 " --> pdb=" O GLN O 76 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG O 81 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 84 through 153 removed outlier: 3.707A pdb=" N GLN O 95 " --> pdb=" O LEU O 91 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER O 96 " --> pdb=" O GLY O 92 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR O 97 " --> pdb=" O GLN O 93 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU O 110 " --> pdb=" O LYS O 106 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA O 113 " --> pdb=" O GLY O 109 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU O 116 " --> pdb=" O ARG O 112 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN O 117 " --> pdb=" O ALA O 113 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG O 127 " --> pdb=" O GLN O 123 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN O 135 " --> pdb=" O GLU O 131 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASN O 137 " --> pdb=" O LYS O 133 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU O 138 " --> pdb=" O SER O 134 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU O 153 " --> pdb=" O ALA O 149 " (cutoff:3.500A) Processing helix chain 'O' and resid 167 through 185 Processing helix chain 'O' and resid 191 through 216 removed outlier: 4.037A pdb=" N ARG O 216 " --> pdb=" O MET O 212 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 81 removed outlier: 4.003A pdb=" N ASP P 80 " --> pdb=" O GLN P 76 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG P 81 " --> pdb=" O ALA P 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 155 removed outlier: 3.653A pdb=" N GLN P 95 " --> pdb=" O LEU P 91 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N SER P 96 " --> pdb=" O GLY P 92 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR P 97 " --> pdb=" O GLN P 93 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU P 110 " --> pdb=" O LYS P 106 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA P 113 " --> pdb=" O GLY P 109 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU P 116 " --> pdb=" O ARG P 112 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN P 117 " --> pdb=" O ALA P 113 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG P 127 " --> pdb=" O GLN P 123 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN P 135 " --> pdb=" O GLU P 131 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASN P 137 " --> pdb=" O LYS P 133 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LEU P 138 " --> pdb=" O SER P 134 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU P 153 " --> pdb=" O ALA P 149 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU P 154 " --> pdb=" O GLN P 150 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE P 155 " --> pdb=" O LYS P 151 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 185 Processing helix chain 'P' and resid 191 through 215 Processing helix chain 'Q' and resid 25 through 81 removed outlier: 4.603A pdb=" N ASP Q 80 " --> pdb=" O GLN Q 76 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ARG Q 81 " --> pdb=" O ALA Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 84 through 155 removed outlier: 3.607A pdb=" N GLN Q 95 " --> pdb=" O LEU Q 91 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER Q 96 " --> pdb=" O GLY Q 92 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TYR Q 97 " --> pdb=" O GLN Q 93 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU Q 110 " --> pdb=" O LYS Q 106 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA Q 113 " --> pdb=" O GLY Q 109 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU Q 116 " --> pdb=" O ARG Q 112 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG Q 127 " --> pdb=" O GLN Q 123 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN Q 135 " --> pdb=" O GLU Q 131 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASN Q 137 " --> pdb=" O LYS Q 133 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LEU Q 138 " --> pdb=" O SER Q 134 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU Q 153 " --> pdb=" O ALA Q 149 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU Q 154 " --> pdb=" O GLN Q 150 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE Q 155 " --> pdb=" O LYS Q 151 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 185 removed outlier: 3.503A pdb=" N LEU Q 185 " --> pdb=" O GLU Q 181 " (cutoff:3.500A) Processing helix chain 'Q' and resid 191 through 216 removed outlier: 3.830A pdb=" N ARG Q 216 " --> pdb=" O MET Q 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 81 removed outlier: 4.303A pdb=" N ASP R 80 " --> pdb=" O GLN R 76 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG R 81 " --> pdb=" O ALA R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 153 removed outlier: 3.679A pdb=" N GLN R 95 " --> pdb=" O LEU R 91 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER R 96 " --> pdb=" O GLY R 92 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR R 97 " --> pdb=" O GLN R 93 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU R 110 " --> pdb=" O LYS R 106 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA R 113 " --> pdb=" O GLY R 109 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU R 116 " --> pdb=" O ARG R 112 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN R 117 " --> pdb=" O ALA R 113 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN R 135 " --> pdb=" O GLU R 131 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASN R 137 " --> pdb=" O LYS R 133 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LEU R 138 " --> pdb=" O SER R 134 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU R 153 " --> pdb=" O ALA R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 185 Processing helix chain 'R' and resid 191 through 216 removed outlier: 3.771A pdb=" N ARG R 216 " --> pdb=" O MET R 212 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 81 removed outlier: 4.281A pdb=" N ASP S 80 " --> pdb=" O GLN S 76 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ARG S 81 " --> pdb=" O ALA S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 84 through 153 removed outlier: 3.657A pdb=" N GLN S 95 " --> pdb=" O LEU S 91 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER S 96 " --> pdb=" O GLY S 92 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR S 97 " --> pdb=" O GLN S 93 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU S 110 " --> pdb=" O LYS S 106 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA S 113 " --> pdb=" O GLY S 109 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU S 116 " --> pdb=" O ARG S 112 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN S 117 " --> pdb=" O ALA S 113 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN S 135 " --> pdb=" O GLU S 131 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASN S 137 " --> pdb=" O LYS S 133 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU S 138 " --> pdb=" O SER S 134 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU S 153 " --> pdb=" O ALA S 149 " (cutoff:3.500A) Processing helix chain 'S' and resid 167 through 185 Processing helix chain 'S' and resid 191 through 215 Processing helix chain 'T' and resid 25 through 81 removed outlier: 4.116A pdb=" N ASP T 80 " --> pdb=" O GLN T 76 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG T 81 " --> pdb=" O ALA T 77 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 153 removed outlier: 3.646A pdb=" N GLN T 95 " --> pdb=" O LEU T 91 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N SER T 96 " --> pdb=" O GLY T 92 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR T 97 " --> pdb=" O GLN T 93 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU T 110 " --> pdb=" O LYS T 106 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA T 113 " --> pdb=" O GLY T 109 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU T 116 " --> pdb=" O ARG T 112 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN T 117 " --> pdb=" O ALA T 113 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG T 127 " --> pdb=" O GLN T 123 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN T 135 " --> pdb=" O GLU T 131 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASN T 137 " --> pdb=" O LYS T 133 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LEU T 138 " --> pdb=" O SER T 134 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU T 153 " --> pdb=" O ALA T 149 " (cutoff:3.500A) Processing helix chain 'T' and resid 167 through 185 Processing helix chain 'T' and resid 191 through 216 removed outlier: 3.792A pdb=" N ARG T 216 " --> pdb=" O MET T 212 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 81 removed outlier: 3.890A pdb=" N ASP U 80 " --> pdb=" O GLN U 76 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG U 81 " --> pdb=" O ALA U 77 " (cutoff:3.500A) Processing helix chain 'U' and resid 84 through 155 removed outlier: 3.590A pdb=" N GLN U 95 " --> pdb=" O LEU U 91 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N SER U 96 " --> pdb=" O GLY U 92 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TYR U 97 " --> pdb=" O GLN U 93 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU U 110 " --> pdb=" O LYS U 106 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA U 113 " --> pdb=" O GLY U 109 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU U 116 " --> pdb=" O ARG U 112 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN U 117 " --> pdb=" O ALA U 113 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG U 127 " --> pdb=" O GLN U 123 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN U 135 " --> pdb=" O GLU U 131 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN U 137 " --> pdb=" O LYS U 133 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU U 138 " --> pdb=" O SER U 134 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU U 153 " --> pdb=" O ALA U 149 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU U 154 " --> pdb=" O GLN U 150 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE U 155 " --> pdb=" O LYS U 151 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 161 No H-bonds generated for 'chain 'U' and resid 159 through 161' Processing helix chain 'U' and resid 167 through 185 Processing helix chain 'U' and resid 191 through 216 removed outlier: 3.776A pdb=" N ARG U 216 " --> pdb=" O MET U 212 " (cutoff:3.500A) Processing helix chain 'V' and resid 25 through 81 removed outlier: 4.071A pdb=" N ASP V 80 " --> pdb=" O GLN V 76 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ARG V 81 " --> pdb=" O ALA V 77 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 154 removed outlier: 3.666A pdb=" N GLN V 95 " --> pdb=" O LEU V 91 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER V 96 " --> pdb=" O GLY V 92 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR V 97 " --> pdb=" O GLN V 93 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU V 110 " --> pdb=" O LYS V 106 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA V 113 " --> pdb=" O GLY V 109 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU V 116 " --> pdb=" O ARG V 112 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN V 117 " --> pdb=" O ALA V 113 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG V 127 " --> pdb=" O GLN V 123 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN V 135 " --> pdb=" O GLU V 131 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASN V 137 " --> pdb=" O LYS V 133 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LEU V 138 " --> pdb=" O SER V 134 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU V 153 " --> pdb=" O ALA V 149 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU V 154 " --> pdb=" O GLN V 150 " (cutoff:3.500A) Processing helix chain 'V' and resid 159 through 161 No H-bonds generated for 'chain 'V' and resid 159 through 161' Processing helix chain 'V' and resid 167 through 185 Processing helix chain 'V' and resid 191 through 216 removed outlier: 3.870A pdb=" N ARG V 216 " --> pdb=" O MET V 212 " (cutoff:3.500A) Processing helix chain 'W' and resid 25 through 81 removed outlier: 4.280A pdb=" N ASP W 80 " --> pdb=" O GLN W 76 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ARG W 81 " --> pdb=" O ALA W 77 " (cutoff:3.500A) Processing helix chain 'W' and resid 84 through 155 removed outlier: 4.553A pdb=" N SER W 96 " --> pdb=" O GLY W 92 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR W 97 " --> pdb=" O GLN W 93 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU W 110 " --> pdb=" O LYS W 106 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA W 113 " --> pdb=" O GLY W 109 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU W 116 " --> pdb=" O ARG W 112 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN W 117 " --> pdb=" O ALA W 113 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN W 135 " --> pdb=" O GLU W 131 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASN W 137 " --> pdb=" O LYS W 133 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU W 138 " --> pdb=" O SER W 134 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU W 153 " --> pdb=" O ALA W 149 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU W 154 " --> pdb=" O GLN W 150 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE W 155 " --> pdb=" O LYS W 151 " (cutoff:3.500A) Processing helix chain 'W' and resid 167 through 185 Processing helix chain 'W' and resid 191 through 216 removed outlier: 3.941A pdb=" N ARG W 216 " --> pdb=" O MET W 212 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 81 removed outlier: 4.019A pdb=" N ASP X 80 " --> pdb=" O GLN X 76 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG X 81 " --> pdb=" O ALA X 77 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 153 removed outlier: 3.599A pdb=" N GLN X 95 " --> pdb=" O LEU X 91 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER X 96 " --> pdb=" O GLY X 92 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR X 97 " --> pdb=" O GLN X 93 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU X 110 " --> pdb=" O LYS X 106 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA X 113 " --> pdb=" O GLY X 109 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU X 116 " --> pdb=" O ARG X 112 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN X 117 " --> pdb=" O ALA X 113 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN X 135 " --> pdb=" O GLU X 131 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASN X 137 " --> pdb=" O LYS X 133 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU X 138 " --> pdb=" O SER X 134 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU X 153 " --> pdb=" O ALA X 149 " (cutoff:3.500A) Processing helix chain 'X' and resid 159 through 161 No H-bonds generated for 'chain 'X' and resid 159 through 161' Processing helix chain 'X' and resid 167 through 185 removed outlier: 3.514A pdb=" N LEU X 185 " --> pdb=" O GLU X 181 " (cutoff:3.500A) Processing helix chain 'X' and resid 191 through 216 removed outlier: 4.112A pdb=" N ARG X 216 " --> pdb=" O MET X 212 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 81 removed outlier: 3.969A pdb=" N ASP Y 80 " --> pdb=" O GLN Y 76 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG Y 81 " --> pdb=" O ALA Y 77 " (cutoff:3.500A) Processing helix chain 'Y' and resid 84 through 153 removed outlier: 3.610A pdb=" N GLN Y 95 " --> pdb=" O LEU Y 91 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER Y 96 " --> pdb=" O GLY Y 92 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR Y 97 " --> pdb=" O GLN Y 93 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU Y 110 " --> pdb=" O LYS Y 106 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA Y 113 " --> pdb=" O GLY Y 109 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU Y 116 " --> pdb=" O ARG Y 112 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN Y 117 " --> pdb=" O ALA Y 113 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN Y 135 " --> pdb=" O GLU Y 131 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASN Y 137 " --> pdb=" O LYS Y 133 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LEU Y 138 " --> pdb=" O SER Y 134 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU Y 153 " --> pdb=" O ALA Y 149 " (cutoff:3.500A) Processing helix chain 'Y' and resid 159 through 161 No H-bonds generated for 'chain 'Y' and resid 159 through 161' Processing helix chain 'Y' and resid 167 through 185 Processing helix chain 'Y' and resid 191 through 216 removed outlier: 4.046A pdb=" N ARG Y 216 " --> pdb=" O MET Y 212 " (cutoff:3.500A) Processing helix chain 'Z' and resid 25 through 81 removed outlier: 4.210A pdb=" N ASP Z 80 " --> pdb=" O GLN Z 76 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG Z 81 " --> pdb=" O ALA Z 77 " (cutoff:3.500A) Processing helix chain 'Z' and resid 84 through 153 removed outlier: 3.583A pdb=" N GLN Z 95 " --> pdb=" O LEU Z 91 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N SER Z 96 " --> pdb=" O GLY Z 92 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR Z 97 " --> pdb=" O GLN Z 93 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU Z 110 " --> pdb=" O LYS Z 106 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA Z 113 " --> pdb=" O GLY Z 109 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU Z 116 " --> pdb=" O ARG Z 112 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN Z 117 " --> pdb=" O ALA Z 113 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN Z 135 " --> pdb=" O GLU Z 131 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ASN Z 137 " --> pdb=" O LYS Z 133 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LEU Z 138 " --> pdb=" O SER Z 134 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU Z 153 " --> pdb=" O ALA Z 149 " (cutoff:3.500A) Processing helix chain 'Z' and resid 159 through 161 No H-bonds generated for 'chain 'Z' and resid 159 through 161' Processing helix chain 'Z' and resid 167 through 185 Processing helix chain 'Z' and resid 191 through 215 Processing helix chain 'a' and resid 25 through 81 removed outlier: 4.288A pdb=" N ASP a 80 " --> pdb=" O GLN a 76 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG a 81 " --> pdb=" O ALA a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 153 removed outlier: 3.617A pdb=" N GLN a 95 " --> pdb=" O LEU a 91 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N SER a 96 " --> pdb=" O GLY a 92 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYR a 97 " --> pdb=" O GLN a 93 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU a 110 " --> pdb=" O LYS a 106 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA a 113 " --> pdb=" O GLY a 109 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU a 116 " --> pdb=" O ARG a 112 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN a 117 " --> pdb=" O ALA a 113 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN a 135 " --> pdb=" O GLU a 131 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASN a 137 " --> pdb=" O LYS a 133 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU a 138 " --> pdb=" O SER a 134 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU a 153 " --> pdb=" O ALA a 149 " (cutoff:3.500A) Processing helix chain 'a' and resid 159 through 161 No H-bonds generated for 'chain 'a' and resid 159 through 161' Processing helix chain 'a' and resid 167 through 185 Processing helix chain 'a' and resid 191 through 216 removed outlier: 4.236A pdb=" N ARG a 216 " --> pdb=" O MET a 212 " (cutoff:3.500A) Processing helix chain 'b' and resid 25 through 81 removed outlier: 4.505A pdb=" N ASP b 80 " --> pdb=" O GLN b 76 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ARG b 81 " --> pdb=" O ALA b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 155 removed outlier: 3.625A pdb=" N GLN b 95 " --> pdb=" O LEU b 91 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N SER b 96 " --> pdb=" O GLY b 92 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR b 97 " --> pdb=" O GLN b 93 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU b 110 " --> pdb=" O LYS b 106 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA b 113 " --> pdb=" O GLY b 109 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU b 116 " --> pdb=" O ARG b 112 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN b 117 " --> pdb=" O ALA b 113 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG b 127 " --> pdb=" O GLN b 123 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN b 135 " --> pdb=" O GLU b 131 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASN b 137 " --> pdb=" O LYS b 133 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU b 138 " --> pdb=" O SER b 134 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU b 153 " --> pdb=" O ALA b 149 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU b 154 " --> pdb=" O GLN b 150 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE b 155 " --> pdb=" O LYS b 151 " (cutoff:3.500A) Processing helix chain 'b' and resid 167 through 185 Processing helix chain 'b' and resid 191 through 215 Processing helix chain 'c' and resid 25 through 81 removed outlier: 4.724A pdb=" N ASP c 80 " --> pdb=" O GLN c 76 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ARG c 81 " --> pdb=" O ALA c 77 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 155 removed outlier: 3.574A pdb=" N GLN c 95 " --> pdb=" O LEU c 91 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER c 96 " --> pdb=" O GLY c 92 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N TYR c 97 " --> pdb=" O GLN c 93 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU c 110 " --> pdb=" O LYS c 106 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA c 113 " --> pdb=" O GLY c 109 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU c 116 " --> pdb=" O ARG c 112 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN c 117 " --> pdb=" O ALA c 113 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN c 135 " --> pdb=" O GLU c 131 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASN c 137 " --> pdb=" O LYS c 133 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU c 138 " --> pdb=" O SER c 134 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU c 153 " --> pdb=" O ALA c 149 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU c 154 " --> pdb=" O GLN c 150 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE c 155 " --> pdb=" O LYS c 151 " (cutoff:3.500A) Processing helix chain 'c' and resid 159 through 161 No H-bonds generated for 'chain 'c' and resid 159 through 161' Processing helix chain 'c' and resid 167 through 185 removed outlier: 3.504A pdb=" N LEU c 185 " --> pdb=" O GLU c 181 " (cutoff:3.500A) Processing helix chain 'c' and resid 191 through 215 Processing helix chain 'd' and resid 25 through 81 removed outlier: 4.319A pdb=" N ASP d 80 " --> pdb=" O GLN d 76 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG d 81 " --> pdb=" O ALA d 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 153 removed outlier: 3.684A pdb=" N GLN d 95 " --> pdb=" O LEU d 91 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N SER d 96 " --> pdb=" O GLY d 92 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TYR d 97 " --> pdb=" O GLN d 93 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU d 110 " --> pdb=" O LYS d 106 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA d 113 " --> pdb=" O GLY d 109 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU d 116 " --> pdb=" O ARG d 112 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN d 117 " --> pdb=" O ALA d 113 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN d 135 " --> pdb=" O GLU d 131 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASN d 137 " --> pdb=" O LYS d 133 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU d 138 " --> pdb=" O SER d 134 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU d 153 " --> pdb=" O ALA d 149 " (cutoff:3.500A) Processing helix chain 'd' and resid 167 through 185 Processing helix chain 'd' and resid 191 through 215 Processing helix chain 'e' and resid 25 through 81 removed outlier: 4.173A pdb=" N ASP e 80 " --> pdb=" O GLN e 76 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ARG e 81 " --> pdb=" O ALA e 77 " (cutoff:3.500A) Processing helix chain 'e' and resid 84 through 155 removed outlier: 3.652A pdb=" N GLN e 95 " --> pdb=" O LEU e 91 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER e 96 " --> pdb=" O GLY e 92 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TYR e 97 " --> pdb=" O GLN e 93 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU e 110 " --> pdb=" O LYS e 106 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA e 113 " --> pdb=" O GLY e 109 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU e 116 " --> pdb=" O ARG e 112 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN e 117 " --> pdb=" O ALA e 113 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN e 135 " --> pdb=" O GLU e 131 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASN e 137 " --> pdb=" O LYS e 133 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU e 138 " --> pdb=" O SER e 134 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU e 153 " --> pdb=" O ALA e 149 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU e 154 " --> pdb=" O GLN e 150 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE e 155 " --> pdb=" O LYS e 151 " (cutoff:3.500A) Processing helix chain 'e' and resid 167 through 185 Processing helix chain 'e' and resid 191 through 216 removed outlier: 3.933A pdb=" N ARG e 216 " --> pdb=" O MET e 212 " (cutoff:3.500A) Processing helix chain 'f' and resid 25 through 81 removed outlier: 4.175A pdb=" N ASP f 80 " --> pdb=" O GLN f 76 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ARG f 81 " --> pdb=" O ALA f 77 " (cutoff:3.500A) Processing helix chain 'f' and resid 84 through 155 removed outlier: 3.695A pdb=" N GLN f 95 " --> pdb=" O LEU f 91 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER f 96 " --> pdb=" O GLY f 92 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TYR f 97 " --> pdb=" O GLN f 93 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU f 110 " --> pdb=" O LYS f 106 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU f 116 " --> pdb=" O ARG f 112 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN f 117 " --> pdb=" O ALA f 113 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG f 127 " --> pdb=" O GLN f 123 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN f 135 " --> pdb=" O GLU f 131 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASN f 137 " --> pdb=" O LYS f 133 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU f 138 " --> pdb=" O SER f 134 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU f 153 " --> pdb=" O ALA f 149 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU f 154 " --> pdb=" O GLN f 150 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE f 155 " --> pdb=" O LYS f 151 " (cutoff:3.500A) Processing helix chain 'f' and resid 167 through 185 Processing helix chain 'f' and resid 191 through 216 removed outlier: 4.095A pdb=" N ARG f 216 " --> pdb=" O MET f 212 " (cutoff:3.500A) Processing helix chain 'g' and resid 25 through 81 removed outlier: 4.157A pdb=" N ASP g 80 " --> pdb=" O GLN g 76 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ARG g 81 " --> pdb=" O ALA g 77 " (cutoff:3.500A) Processing helix chain 'g' and resid 84 through 155 removed outlier: 3.653A pdb=" N GLN g 95 " --> pdb=" O LEU g 91 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N SER g 96 " --> pdb=" O GLY g 92 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR g 97 " --> pdb=" O GLN g 93 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU g 110 " --> pdb=" O LYS g 106 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA g 113 " --> pdb=" O GLY g 109 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU g 116 " --> pdb=" O ARG g 112 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN g 117 " --> pdb=" O ALA g 113 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG g 127 " --> pdb=" O GLN g 123 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN g 135 " --> pdb=" O GLU g 131 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASN g 137 " --> pdb=" O LYS g 133 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU g 138 " --> pdb=" O SER g 134 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU g 153 " --> pdb=" O ALA g 149 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU g 154 " --> pdb=" O GLN g 150 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE g 155 " --> pdb=" O LYS g 151 " (cutoff:3.500A) Processing helix chain 'g' and resid 167 through 185 Processing helix chain 'g' and resid 191 through 216 removed outlier: 4.075A pdb=" N ARG g 216 " --> pdb=" O MET g 212 " (cutoff:3.500A) Processing helix chain 'h' and resid 25 through 81 removed outlier: 3.502A pdb=" N ALA h 77 " --> pdb=" O GLU h 73 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASP h 80 " --> pdb=" O GLN h 76 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ARG h 81 " --> pdb=" O ALA h 77 " (cutoff:3.500A) Processing helix chain 'h' and resid 84 through 155 removed outlier: 3.564A pdb=" N GLN h 95 " --> pdb=" O LEU h 91 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N SER h 96 " --> pdb=" O GLY h 92 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR h 97 " --> pdb=" O GLN h 93 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU h 110 " --> pdb=" O LYS h 106 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA h 113 " --> pdb=" O GLY h 109 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU h 116 " --> pdb=" O ARG h 112 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLN h 117 " --> pdb=" O ALA h 113 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG h 127 " --> pdb=" O GLN h 123 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN h 135 " --> pdb=" O GLU h 131 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASN h 137 " --> pdb=" O LYS h 133 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU h 138 " --> pdb=" O SER h 134 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU h 153 " --> pdb=" O ALA h 149 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU h 154 " --> pdb=" O GLN h 150 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE h 155 " --> pdb=" O LYS h 151 " (cutoff:3.500A) Processing helix chain 'h' and resid 167 through 185 Processing helix chain 'h' and resid 191 through 216 removed outlier: 4.028A pdb=" N ARG h 216 " --> pdb=" O MET h 212 " (cutoff:3.500A) Processing helix chain 'i' and resid 25 through 81 removed outlier: 4.188A pdb=" N ASP i 80 " --> pdb=" O GLN i 76 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ARG i 81 " --> pdb=" O ALA i 77 " (cutoff:3.500A) Processing helix chain 'i' and resid 84 through 155 removed outlier: 3.716A pdb=" N GLN i 95 " --> pdb=" O LEU i 91 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER i 96 " --> pdb=" O GLY i 92 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR i 97 " --> pdb=" O GLN i 93 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU i 110 " --> pdb=" O LYS i 106 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA i 113 " --> pdb=" O GLY i 109 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU i 116 " --> pdb=" O ARG i 112 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN i 117 " --> pdb=" O ALA i 113 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG i 127 " --> pdb=" O GLN i 123 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN i 135 " --> pdb=" O GLU i 131 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN i 137 " --> pdb=" O LYS i 133 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU i 138 " --> pdb=" O SER i 134 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU i 153 " --> pdb=" O ALA i 149 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU i 154 " --> pdb=" O GLN i 150 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE i 155 " --> pdb=" O LYS i 151 " (cutoff:3.500A) Processing helix chain 'i' and resid 167 through 185 Processing helix chain 'i' and resid 191 through 216 removed outlier: 3.979A pdb=" N ARG i 216 " --> pdb=" O MET i 212 " (cutoff:3.500A) Processing helix chain 'j' and resid 25 through 81 removed outlier: 4.061A pdb=" N ASP j 80 " --> pdb=" O GLN j 76 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG j 81 " --> pdb=" O ALA j 77 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 155 removed outlier: 3.724A pdb=" N GLN j 95 " --> pdb=" O LEU j 91 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N SER j 96 " --> pdb=" O GLY j 92 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TYR j 97 " --> pdb=" O GLN j 93 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU j 110 " --> pdb=" O LYS j 106 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA j 113 " --> pdb=" O GLY j 109 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU j 116 " --> pdb=" O ARG j 112 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN j 117 " --> pdb=" O ALA j 113 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG j 127 " --> pdb=" O GLN j 123 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN j 135 " --> pdb=" O GLU j 131 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASN j 137 " --> pdb=" O LYS j 133 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU j 138 " --> pdb=" O SER j 134 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU j 153 " --> pdb=" O ALA j 149 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU j 154 " --> pdb=" O GLN j 150 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE j 155 " --> pdb=" O LYS j 151 " (cutoff:3.500A) Processing helix chain 'j' and resid 167 through 185 Processing helix chain 'j' and resid 191 through 216 removed outlier: 4.011A pdb=" N ARG j 216 " --> pdb=" O MET j 212 " (cutoff:3.500A) Processing helix chain 'k' and resid 25 through 81 removed outlier: 4.123A pdb=" N ASP k 80 " --> pdb=" O GLN k 76 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG k 81 " --> pdb=" O ALA k 77 " (cutoff:3.500A) Processing helix chain 'k' and resid 84 through 155 removed outlier: 3.645A pdb=" N GLN k 95 " --> pdb=" O LEU k 91 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER k 96 " --> pdb=" O GLY k 92 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TYR k 97 " --> pdb=" O GLN k 93 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU k 110 " --> pdb=" O LYS k 106 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU k 116 " --> pdb=" O ARG k 112 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN k 117 " --> pdb=" O ALA k 113 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG k 127 " --> pdb=" O GLN k 123 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN k 135 " --> pdb=" O GLU k 131 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASN k 137 " --> pdb=" O LYS k 133 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU k 138 " --> pdb=" O SER k 134 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU k 153 " --> pdb=" O ALA k 149 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU k 154 " --> pdb=" O GLN k 150 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE k 155 " --> pdb=" O LYS k 151 " (cutoff:3.500A) Processing helix chain 'k' and resid 167 through 185 Processing helix chain 'k' and resid 191 through 216 removed outlier: 4.128A pdb=" N ARG k 216 " --> pdb=" O MET k 212 " (cutoff:3.500A) Processing helix chain 'l' and resid 25 through 81 removed outlier: 4.379A pdb=" N ASP l 80 " --> pdb=" O GLN l 76 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ARG l 81 " --> pdb=" O ALA l 77 " (cutoff:3.500A) Processing helix chain 'l' and resid 84 through 155 removed outlier: 3.641A pdb=" N GLN l 95 " --> pdb=" O LEU l 91 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N SER l 96 " --> pdb=" O GLY l 92 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR l 97 " --> pdb=" O GLN l 93 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU l 110 " --> pdb=" O LYS l 106 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU l 116 " --> pdb=" O ARG l 112 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN l 117 " --> pdb=" O ALA l 113 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN l 135 " --> pdb=" O GLU l 131 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN l 137 " --> pdb=" O LYS l 133 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU l 138 " --> pdb=" O SER l 134 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU l 153 " --> pdb=" O ALA l 149 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU l 154 " --> pdb=" O GLN l 150 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE l 155 " --> pdb=" O LYS l 151 " (cutoff:3.500A) Processing helix chain 'l' and resid 167 through 185 Processing helix chain 'l' and resid 191 through 216 removed outlier: 4.111A pdb=" N ARG l 216 " --> pdb=" O MET l 212 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 81 removed outlier: 4.318A pdb=" N ASP m 80 " --> pdb=" O GLN m 76 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG m 81 " --> pdb=" O ALA m 77 " (cutoff:3.500A) Processing helix chain 'm' and resid 84 through 155 removed outlier: 3.628A pdb=" N GLN m 95 " --> pdb=" O LEU m 91 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER m 96 " --> pdb=" O GLY m 92 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N TYR m 97 " --> pdb=" O GLN m 93 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU m 110 " --> pdb=" O LYS m 106 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU m 116 " --> pdb=" O ARG m 112 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN m 117 " --> pdb=" O ALA m 113 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG m 127 " --> pdb=" O GLN m 123 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN m 135 " --> pdb=" O GLU m 131 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN m 137 " --> pdb=" O LYS m 133 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N LEU m 138 " --> pdb=" O SER m 134 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU m 153 " --> pdb=" O ALA m 149 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU m 154 " --> pdb=" O GLN m 150 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE m 155 " --> pdb=" O LYS m 151 " (cutoff:3.500A) Processing helix chain 'm' and resid 167 through 185 Processing helix chain 'm' and resid 191 through 215 Processing helix chain 'n' and resid 25 through 81 removed outlier: 4.196A pdb=" N ASP n 80 " --> pdb=" O GLN n 76 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG n 81 " --> pdb=" O ALA n 77 " (cutoff:3.500A) Processing helix chain 'n' and resid 84 through 155 removed outlier: 3.663A pdb=" N GLN n 95 " --> pdb=" O LEU n 91 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER n 96 " --> pdb=" O GLY n 92 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR n 97 " --> pdb=" O GLN n 93 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU n 110 " --> pdb=" O LYS n 106 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA n 113 " --> pdb=" O GLY n 109 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU n 116 " --> pdb=" O ARG n 112 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN n 117 " --> pdb=" O ALA n 113 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG n 127 " --> pdb=" O GLN n 123 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN n 135 " --> pdb=" O GLU n 131 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN n 137 " --> pdb=" O LYS n 133 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LEU n 138 " --> pdb=" O SER n 134 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU n 153 " --> pdb=" O ALA n 149 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU n 154 " --> pdb=" O GLN n 150 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE n 155 " --> pdb=" O LYS n 151 " (cutoff:3.500A) Processing helix chain 'n' and resid 167 through 185 Processing helix chain 'n' and resid 191 through 216 removed outlier: 4.037A pdb=" N ARG n 216 " --> pdb=" O MET n 212 " (cutoff:3.500A) Processing helix chain 'o' and resid 25 through 81 removed outlier: 4.186A pdb=" N ASP o 80 " --> pdb=" O GLN o 76 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ARG o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) Processing helix chain 'o' and resid 84 through 155 removed outlier: 3.616A pdb=" N GLN o 95 " --> pdb=" O LEU o 91 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER o 96 " --> pdb=" O GLY o 92 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR o 97 " --> pdb=" O GLN o 93 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU o 110 " --> pdb=" O LYS o 106 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA o 113 " --> pdb=" O GLY o 109 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU o 116 " --> pdb=" O ARG o 112 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN o 117 " --> pdb=" O ALA o 113 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG o 127 " --> pdb=" O GLN o 123 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN o 135 " --> pdb=" O GLU o 131 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASN o 137 " --> pdb=" O LYS o 133 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU o 138 " --> pdb=" O SER o 134 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU o 153 " --> pdb=" O ALA o 149 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU o 154 " --> pdb=" O GLN o 150 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE o 155 " --> pdb=" O LYS o 151 " (cutoff:3.500A) Processing helix chain 'o' and resid 167 through 185 Processing helix chain 'o' and resid 191 through 216 removed outlier: 4.054A pdb=" N ARG o 216 " --> pdb=" O MET o 212 " (cutoff:3.500A) Processing helix chain 'p' and resid 25 through 81 removed outlier: 4.394A pdb=" N ASP p 80 " --> pdb=" O GLN p 76 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ARG p 81 " --> pdb=" O ALA p 77 " (cutoff:3.500A) Processing helix chain 'p' and resid 84 through 155 removed outlier: 3.601A pdb=" N GLN p 95 " --> pdb=" O LEU p 91 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER p 96 " --> pdb=" O GLY p 92 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TYR p 97 " --> pdb=" O GLN p 93 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU p 110 " --> pdb=" O LYS p 106 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA p 113 " --> pdb=" O GLY p 109 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU p 116 " --> pdb=" O ARG p 112 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN p 117 " --> pdb=" O ALA p 113 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG p 127 " --> pdb=" O GLN p 123 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN p 135 " --> pdb=" O GLU p 131 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASN p 137 " --> pdb=" O LYS p 133 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU p 138 " --> pdb=" O SER p 134 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU p 153 " --> pdb=" O ALA p 149 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU p 154 " --> pdb=" O GLN p 150 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE p 155 " --> pdb=" O LYS p 151 " (cutoff:3.500A) Processing helix chain 'p' and resid 167 through 185 Processing helix chain 'p' and resid 191 through 216 removed outlier: 4.097A pdb=" N ARG p 216 " --> pdb=" O MET p 212 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 81 removed outlier: 4.228A pdb=" N ASP q 80 " --> pdb=" O GLN q 76 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ARG q 81 " --> pdb=" O ALA q 77 " (cutoff:3.500A) Processing helix chain 'q' and resid 84 through 155 removed outlier: 3.717A pdb=" N GLN q 95 " --> pdb=" O LEU q 91 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER q 96 " --> pdb=" O GLY q 92 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR q 97 " --> pdb=" O GLN q 93 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU q 110 " --> pdb=" O LYS q 106 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA q 113 " --> pdb=" O GLY q 109 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU q 116 " --> pdb=" O ARG q 112 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG q 127 " --> pdb=" O GLN q 123 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN q 135 " --> pdb=" O GLU q 131 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASN q 137 " --> pdb=" O LYS q 133 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU q 138 " --> pdb=" O SER q 134 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU q 153 " --> pdb=" O ALA q 149 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU q 154 " --> pdb=" O GLN q 150 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE q 155 " --> pdb=" O LYS q 151 " (cutoff:3.500A) Processing helix chain 'q' and resid 167 through 185 Processing helix chain 'q' and resid 191 through 216 removed outlier: 4.142A pdb=" N ARG q 216 " --> pdb=" O MET q 212 " (cutoff:3.500A) Processing helix chain 'r' and resid 25 through 81 removed outlier: 4.266A pdb=" N ASP r 80 " --> pdb=" O GLN r 76 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG r 81 " --> pdb=" O ALA r 77 " (cutoff:3.500A) Processing helix chain 'r' and resid 84 through 153 removed outlier: 3.717A pdb=" N GLN r 95 " --> pdb=" O LEU r 91 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N SER r 96 " --> pdb=" O GLY r 92 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR r 97 " --> pdb=" O GLN r 93 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU r 110 " --> pdb=" O LYS r 106 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA r 113 " --> pdb=" O GLY r 109 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU r 116 " --> pdb=" O ARG r 112 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN r 117 " --> pdb=" O ALA r 113 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN r 135 " --> pdb=" O GLU r 131 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASN r 137 " --> pdb=" O LYS r 133 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N LEU r 138 " --> pdb=" O SER r 134 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU r 153 " --> pdb=" O ALA r 149 " (cutoff:3.500A) Processing helix chain 'r' and resid 167 through 185 Processing helix chain 'r' and resid 191 through 215 Processing helix chain 's' and resid 25 through 81 removed outlier: 4.256A pdb=" N ASP s 80 " --> pdb=" O GLN s 76 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ARG s 81 " --> pdb=" O ALA s 77 " (cutoff:3.500A) Processing helix chain 's' and resid 84 through 153 removed outlier: 3.726A pdb=" N GLN s 95 " --> pdb=" O LEU s 91 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N SER s 96 " --> pdb=" O GLY s 92 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR s 97 " --> pdb=" O GLN s 93 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU s 110 " --> pdb=" O LYS s 106 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA s 113 " --> pdb=" O GLY s 109 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU s 116 " --> pdb=" O ARG s 112 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN s 117 " --> pdb=" O ALA s 113 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN s 135 " --> pdb=" O GLU s 131 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASN s 137 " --> pdb=" O LYS s 133 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LEU s 138 " --> pdb=" O SER s 134 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU s 153 " --> pdb=" O ALA s 149 " (cutoff:3.500A) Processing helix chain 's' and resid 167 through 185 Processing helix chain 's' and resid 191 through 216 removed outlier: 3.871A pdb=" N ARG s 216 " --> pdb=" O MET s 212 " (cutoff:3.500A) Processing helix chain 't' and resid 25 through 81 removed outlier: 4.402A pdb=" N ASP t 80 " --> pdb=" O GLN t 76 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ARG t 81 " --> pdb=" O ALA t 77 " (cutoff:3.500A) Processing helix chain 't' and resid 84 through 155 removed outlier: 3.648A pdb=" N GLN t 95 " --> pdb=" O LEU t 91 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N SER t 96 " --> pdb=" O GLY t 92 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR t 97 " --> pdb=" O GLN t 93 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU t 110 " --> pdb=" O LYS t 106 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA t 113 " --> pdb=" O GLY t 109 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU t 116 " --> pdb=" O ARG t 112 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN t 117 " --> pdb=" O ALA t 113 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG t 127 " --> pdb=" O GLN t 123 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN t 135 " --> pdb=" O GLU t 131 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN t 137 " --> pdb=" O LYS t 133 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N LEU t 138 " --> pdb=" O SER t 134 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU t 153 " --> pdb=" O ALA t 149 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU t 154 " --> pdb=" O GLN t 150 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE t 155 " --> pdb=" O LYS t 151 " (cutoff:3.500A) Processing helix chain 't' and resid 167 through 185 Processing helix chain 't' and resid 191 through 215 Processing helix chain 'u' and resid 25 through 81 removed outlier: 4.002A pdb=" N ASP u 80 " --> pdb=" O GLN u 76 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG u 81 " --> pdb=" O ALA u 77 " (cutoff:3.500A) Processing helix chain 'u' and resid 84 through 153 removed outlier: 3.931A pdb=" N GLN u 95 " --> pdb=" O LEU u 91 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER u 96 " --> pdb=" O GLY u 92 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TYR u 97 " --> pdb=" O GLN u 93 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU u 110 " --> pdb=" O LYS u 106 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA u 113 " --> pdb=" O GLY u 109 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU u 116 " --> pdb=" O ARG u 112 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN u 117 " --> pdb=" O ALA u 113 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG u 127 " --> pdb=" O GLN u 123 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN u 135 " --> pdb=" O GLU u 131 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN u 137 " --> pdb=" O LYS u 133 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU u 138 " --> pdb=" O SER u 134 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU u 153 " --> pdb=" O ALA u 149 " (cutoff:3.500A) Processing helix chain 'u' and resid 167 through 185 removed outlier: 3.515A pdb=" N LEU u 185 " --> pdb=" O GLU u 181 " (cutoff:3.500A) Processing helix chain 'u' and resid 191 through 216 removed outlier: 3.969A pdb=" N ARG u 216 " --> pdb=" O MET u 212 " (cutoff:3.500A) Processing helix chain 'v' and resid 25 through 81 removed outlier: 4.202A pdb=" N ASP v 80 " --> pdb=" O GLN v 76 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ARG v 81 " --> pdb=" O ALA v 77 " (cutoff:3.500A) Processing helix chain 'v' and resid 84 through 155 removed outlier: 3.766A pdb=" N GLN v 95 " --> pdb=" O LEU v 91 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N SER v 96 " --> pdb=" O GLY v 92 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N TYR v 97 " --> pdb=" O GLN v 93 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU v 110 " --> pdb=" O LYS v 106 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA v 113 " --> pdb=" O GLY v 109 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU v 116 " --> pdb=" O ARG v 112 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN v 117 " --> pdb=" O ALA v 113 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG v 127 " --> pdb=" O GLN v 123 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN v 135 " --> pdb=" O GLU v 131 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASN v 137 " --> pdb=" O LYS v 133 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU v 138 " --> pdb=" O SER v 134 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU v 153 " --> pdb=" O ALA v 149 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU v 154 " --> pdb=" O GLN v 150 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE v 155 " --> pdb=" O LYS v 151 " (cutoff:3.500A) Processing helix chain 'v' and resid 167 through 185 removed outlier: 3.518A pdb=" N LEU v 185 " --> pdb=" O GLU v 181 " (cutoff:3.500A) Processing helix chain 'v' and resid 191 through 216 removed outlier: 3.984A pdb=" N ARG v 216 " --> pdb=" O MET v 212 " (cutoff:3.500A) Processing helix chain 'w' and resid 25 through 81 removed outlier: 4.264A pdb=" N ASP w 80 " --> pdb=" O GLN w 76 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ARG w 81 " --> pdb=" O ALA w 77 " (cutoff:3.500A) Processing helix chain 'w' and resid 84 through 153 removed outlier: 3.757A pdb=" N GLN w 95 " --> pdb=" O LEU w 91 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER w 96 " --> pdb=" O GLY w 92 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR w 97 " --> pdb=" O GLN w 93 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU w 110 " --> pdb=" O LYS w 106 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA w 113 " --> pdb=" O GLY w 109 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU w 116 " --> pdb=" O ARG w 112 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN w 117 " --> pdb=" O ALA w 113 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN w 135 " --> pdb=" O GLU w 131 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASN w 137 " --> pdb=" O LYS w 133 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LEU w 138 " --> pdb=" O SER w 134 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU w 153 " --> pdb=" O ALA w 149 " (cutoff:3.500A) Processing helix chain 'w' and resid 159 through 161 No H-bonds generated for 'chain 'w' and resid 159 through 161' Processing helix chain 'w' and resid 167 through 185 removed outlier: 3.503A pdb=" N LEU w 178 " --> pdb=" O LYS w 174 " (cutoff:3.500A) Processing helix chain 'w' and resid 191 through 216 removed outlier: 4.118A pdb=" N ARG w 216 " --> pdb=" O MET w 212 " (cutoff:3.500A) Processing helix chain 'x' and resid 25 through 81 removed outlier: 4.008A pdb=" N ASP x 80 " --> pdb=" O GLN x 76 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ARG x 81 " --> pdb=" O ALA x 77 " (cutoff:3.500A) Processing helix chain 'x' and resid 84 through 153 removed outlier: 3.687A pdb=" N GLN x 95 " --> pdb=" O LEU x 91 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N SER x 96 " --> pdb=" O GLY x 92 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR x 97 " --> pdb=" O GLN x 93 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU x 110 " --> pdb=" O LYS x 106 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA x 113 " --> pdb=" O GLY x 109 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU x 116 " --> pdb=" O ARG x 112 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN x 117 " --> pdb=" O ALA x 113 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG x 127 " --> pdb=" O GLN x 123 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN x 135 " --> pdb=" O GLU x 131 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN x 137 " --> pdb=" O LYS x 133 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LEU x 138 " --> pdb=" O SER x 134 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU x 153 " --> pdb=" O ALA x 149 " (cutoff:3.500A) Processing helix chain 'x' and resid 159 through 161 No H-bonds generated for 'chain 'x' and resid 159 through 161' Processing helix chain 'x' and resid 167 through 185 Processing helix chain 'x' and resid 191 through 216 removed outlier: 4.094A pdb=" N ARG x 216 " --> pdb=" O MET x 212 " (cutoff:3.500A) Processing helix chain 'y' and resid 25 through 81 removed outlier: 4.041A pdb=" N ASP y 80 " --> pdb=" O GLN y 76 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG y 81 " --> pdb=" O ALA y 77 " (cutoff:3.500A) Processing helix chain 'y' and resid 84 through 153 removed outlier: 3.674A pdb=" N GLN y 95 " --> pdb=" O LEU y 91 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER y 96 " --> pdb=" O GLY y 92 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR y 97 " --> pdb=" O GLN y 93 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU y 110 " --> pdb=" O LYS y 106 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA y 113 " --> pdb=" O GLY y 109 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU y 116 " --> pdb=" O ARG y 112 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN y 117 " --> pdb=" O ALA y 113 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG y 127 " --> pdb=" O GLN y 123 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN y 135 " --> pdb=" O GLU y 131 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASN y 137 " --> pdb=" O LYS y 133 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU y 138 " --> pdb=" O SER y 134 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU y 153 " --> pdb=" O ALA y 149 " (cutoff:3.500A) Processing helix chain 'y' and resid 159 through 161 No H-bonds generated for 'chain 'y' and resid 159 through 161' Processing helix chain 'y' and resid 167 through 185 Processing helix chain 'y' and resid 191 through 216 removed outlier: 3.826A pdb=" N ARG y 216 " --> pdb=" O MET y 212 " (cutoff:3.500A) Processing helix chain 'z' and resid 25 through 81 removed outlier: 4.267A pdb=" N ASP z 80 " --> pdb=" O GLN z 76 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG z 81 " --> pdb=" O ALA z 77 " (cutoff:3.500A) Processing helix chain 'z' and resid 84 through 154 removed outlier: 3.569A pdb=" N GLN z 95 " --> pdb=" O LEU z 91 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER z 96 " --> pdb=" O GLY z 92 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TYR z 97 " --> pdb=" O GLN z 93 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU z 110 " --> pdb=" O LYS z 106 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA z 113 " --> pdb=" O GLY z 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU z 116 " --> pdb=" O ARG z 112 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN z 117 " --> pdb=" O ALA z 113 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG z 127 " --> pdb=" O GLN z 123 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN z 135 " --> pdb=" O GLU z 131 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASN z 137 " --> pdb=" O LYS z 133 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU z 138 " --> pdb=" O SER z 134 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU z 153 " --> pdb=" O ALA z 149 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU z 154 " --> pdb=" O GLN z 150 " (cutoff:3.500A) Processing helix chain 'z' and resid 159 through 161 No H-bonds generated for 'chain 'z' and resid 159 through 161' Processing helix chain 'z' and resid 167 through 185 Processing helix chain 'z' and resid 191 through 216 removed outlier: 3.823A pdb=" N ARG z 216 " --> pdb=" O MET z 212 " (cutoff:3.500A) Processing helix chain '0' and resid 25 through 81 removed outlier: 4.316A pdb=" N ASP 0 80 " --> pdb=" O GLN 0 76 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ARG 0 81 " --> pdb=" O ALA 0 77 " (cutoff:3.500A) Processing helix chain '0' and resid 84 through 153 removed outlier: 3.645A pdb=" N GLN 0 95 " --> pdb=" O LEU 0 91 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER 0 96 " --> pdb=" O GLY 0 92 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR 0 97 " --> pdb=" O GLN 0 93 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU 0 110 " --> pdb=" O LYS 0 106 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA 0 113 " --> pdb=" O GLY 0 109 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU 0 116 " --> pdb=" O ARG 0 112 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN 0 117 " --> pdb=" O ALA 0 113 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN 0 135 " --> pdb=" O GLU 0 131 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASN 0 137 " --> pdb=" O LYS 0 133 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU 0 138 " --> pdb=" O SER 0 134 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU 0 153 " --> pdb=" O ALA 0 149 " (cutoff:3.500A) Processing helix chain '0' and resid 159 through 161 No H-bonds generated for 'chain '0' and resid 159 through 161' Processing helix chain '0' and resid 167 through 185 Processing helix chain '0' and resid 191 through 216 removed outlier: 3.999A pdb=" N ARG 0 216 " --> pdb=" O MET 0 212 " (cutoff:3.500A) Processing helix chain '1' and resid 25 through 81 removed outlier: 4.386A pdb=" N ASP 1 80 " --> pdb=" O GLN 1 76 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ARG 1 81 " --> pdb=" O ALA 1 77 " (cutoff:3.500A) Processing helix chain '1' and resid 84 through 153 removed outlier: 3.573A pdb=" N GLN 1 95 " --> pdb=" O LEU 1 91 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N SER 1 96 " --> pdb=" O GLY 1 92 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N TYR 1 97 " --> pdb=" O GLN 1 93 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU 1 110 " --> pdb=" O LYS 1 106 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA 1 113 " --> pdb=" O GLY 1 109 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU 1 116 " --> pdb=" O ARG 1 112 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN 1 117 " --> pdb=" O ALA 1 113 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN 1 135 " --> pdb=" O GLU 1 131 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASN 1 137 " --> pdb=" O LYS 1 133 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LEU 1 138 " --> pdb=" O SER 1 134 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU 1 153 " --> pdb=" O ALA 1 149 " (cutoff:3.500A) Processing helix chain '1' and resid 167 through 185 Processing helix chain '1' and resid 191 through 216 removed outlier: 4.203A pdb=" N ARG 1 216 " --> pdb=" O MET 1 212 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 81 removed outlier: 4.131A pdb=" N ASP 2 80 " --> pdb=" O GLN 2 76 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG 2 81 " --> pdb=" O ALA 2 77 " (cutoff:3.500A) Processing helix chain '2' and resid 84 through 153 removed outlier: 3.534A pdb=" N GLN 2 95 " --> pdb=" O LEU 2 91 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER 2 96 " --> pdb=" O GLY 2 92 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TYR 2 97 " --> pdb=" O GLN 2 93 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU 2 110 " --> pdb=" O LYS 2 106 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA 2 113 " --> pdb=" O GLY 2 109 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU 2 116 " --> pdb=" O ARG 2 112 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN 2 117 " --> pdb=" O ALA 2 113 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN 2 135 " --> pdb=" O GLU 2 131 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASN 2 137 " --> pdb=" O LYS 2 133 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU 2 138 " --> pdb=" O SER 2 134 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU 2 153 " --> pdb=" O ALA 2 149 " (cutoff:3.500A) Processing helix chain '2' and resid 167 through 185 Processing helix chain '2' and resid 191 through 216 removed outlier: 4.098A pdb=" N ARG 2 216 " --> pdb=" O MET 2 212 " (cutoff:3.500A) Processing helix chain '3' and resid 25 through 81 removed outlier: 4.063A pdb=" N ASP 3 80 " --> pdb=" O GLN 3 76 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG 3 81 " --> pdb=" O ALA 3 77 " (cutoff:3.500A) Processing helix chain '3' and resid 84 through 153 removed outlier: 3.544A pdb=" N GLN 3 95 " --> pdb=" O LEU 3 91 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER 3 96 " --> pdb=" O GLY 3 92 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N TYR 3 97 " --> pdb=" O GLN 3 93 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU 3 110 " --> pdb=" O LYS 3 106 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA 3 113 " --> pdb=" O GLY 3 109 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU 3 116 " --> pdb=" O ARG 3 112 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN 3 117 " --> pdb=" O ALA 3 113 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN 3 135 " --> pdb=" O GLU 3 131 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASN 3 137 " --> pdb=" O LYS 3 133 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LEU 3 138 " --> pdb=" O SER 3 134 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU 3 153 " --> pdb=" O ALA 3 149 " (cutoff:3.500A) Processing helix chain '3' and resid 159 through 161 No H-bonds generated for 'chain '3' and resid 159 through 161' Processing helix chain '3' and resid 167 through 185 Processing helix chain '3' and resid 191 through 215 Processing helix chain '4' and resid 25 through 81 removed outlier: 4.506A pdb=" N ASP 4 80 " --> pdb=" O GLN 4 76 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ARG 4 81 " --> pdb=" O ALA 4 77 " (cutoff:3.500A) Processing helix chain '4' and resid 84 through 155 removed outlier: 3.715A pdb=" N GLN 4 95 " --> pdb=" O LEU 4 91 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER 4 96 " --> pdb=" O GLY 4 92 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR 4 97 " --> pdb=" O GLN 4 93 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU 4 110 " --> pdb=" O LYS 4 106 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA 4 113 " --> pdb=" O GLY 4 109 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU 4 116 " --> pdb=" O ARG 4 112 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN 4 117 " --> pdb=" O ALA 4 113 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG 4 127 " --> pdb=" O GLN 4 123 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN 4 135 " --> pdb=" O GLU 4 131 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ASN 4 137 " --> pdb=" O LYS 4 133 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU 4 138 " --> pdb=" O SER 4 134 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU 4 153 " --> pdb=" O ALA 4 149 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU 4 154 " --> pdb=" O GLN 4 150 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE 4 155 " --> pdb=" O LYS 4 151 " (cutoff:3.500A) Processing helix chain '4' and resid 167 through 185 Processing helix chain '4' and resid 191 through 216 removed outlier: 4.262A pdb=" N ARG 4 216 " --> pdb=" O MET 4 212 " (cutoff:3.500A) Processing helix chain '5' and resid 25 through 81 removed outlier: 4.352A pdb=" N ASP 5 80 " --> pdb=" O GLN 5 76 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ARG 5 81 " --> pdb=" O ALA 5 77 " (cutoff:3.500A) Processing helix chain '5' and resid 84 through 153 removed outlier: 3.666A pdb=" N GLN 5 95 " --> pdb=" O LEU 5 91 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER 5 96 " --> pdb=" O GLY 5 92 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TYR 5 97 " --> pdb=" O GLN 5 93 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU 5 110 " --> pdb=" O LYS 5 106 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA 5 113 " --> pdb=" O GLY 5 109 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU 5 116 " --> pdb=" O ARG 5 112 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN 5 117 " --> pdb=" O ALA 5 113 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN 5 135 " --> pdb=" O GLU 5 131 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN 5 137 " --> pdb=" O LYS 5 133 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LEU 5 138 " --> pdb=" O SER 5 134 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU 5 153 " --> pdb=" O ALA 5 149 " (cutoff:3.500A) Processing helix chain '5' and resid 167 through 185 Processing helix chain '5' and resid 191 through 215 Processing helix chain '6' and resid 25 through 81 removed outlier: 4.233A pdb=" N ASP 6 80 " --> pdb=" O GLN 6 76 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG 6 81 " --> pdb=" O ALA 6 77 " (cutoff:3.500A) Processing helix chain '6' and resid 84 through 155 removed outlier: 3.557A pdb=" N GLN 6 95 " --> pdb=" O LEU 6 91 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N SER 6 96 " --> pdb=" O GLY 6 92 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR 6 97 " --> pdb=" O GLN 6 93 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU 6 110 " --> pdb=" O LYS 6 106 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA 6 113 " --> pdb=" O GLY 6 109 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU 6 116 " --> pdb=" O ARG 6 112 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN 6 117 " --> pdb=" O ALA 6 113 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN 6 135 " --> pdb=" O GLU 6 131 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ASN 6 137 " --> pdb=" O LYS 6 133 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU 6 138 " --> pdb=" O SER 6 134 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU 6 153 " --> pdb=" O ALA 6 149 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU 6 154 " --> pdb=" O GLN 6 150 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE 6 155 " --> pdb=" O LYS 6 151 " (cutoff:3.500A) Processing helix chain '6' and resid 167 through 185 removed outlier: 3.539A pdb=" N LEU 6 185 " --> pdb=" O GLU 6 181 " (cutoff:3.500A) Processing helix chain '6' and resid 191 through 215 Processing helix chain '7' and resid 25 through 81 removed outlier: 4.459A pdb=" N ASP 7 80 " --> pdb=" O GLN 7 76 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ARG 7 81 " --> pdb=" O ALA 7 77 " (cutoff:3.500A) Processing helix chain '7' and resid 84 through 153 removed outlier: 3.680A pdb=" N GLN 7 95 " --> pdb=" O LEU 7 91 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N SER 7 96 " --> pdb=" O GLY 7 92 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR 7 97 " --> pdb=" O GLN 7 93 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU 7 110 " --> pdb=" O LYS 7 106 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA 7 113 " --> pdb=" O GLY 7 109 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU 7 116 " --> pdb=" O ARG 7 112 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN 7 117 " --> pdb=" O ALA 7 113 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN 7 135 " --> pdb=" O GLU 7 131 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASN 7 137 " --> pdb=" O LYS 7 133 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LEU 7 138 " --> pdb=" O SER 7 134 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU 7 153 " --> pdb=" O ALA 7 149 " (cutoff:3.500A) Processing helix chain '7' and resid 167 through 185 Processing helix chain '7' and resid 191 through 215 8485 hydrogen bonds defined for protein. 25455 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 30.26 Time building geometry restraints manager: 33.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 33677 1.34 - 1.46: 14479 1.46 - 1.58: 48744 1.58 - 1.69: 180 1.69 - 1.81: 240 Bond restraints: 97320 Sorted by residual: bond pdb=" CG1 ILE c 152 " pdb=" CD1 ILE c 152 " ideal model delta sigma weight residual 1.513 1.449 0.064 3.90e-02 6.57e+02 2.69e+00 bond pdb=" CG1 ILE o 152 " pdb=" CD1 ILE o 152 " ideal model delta sigma weight residual 1.513 1.451 0.062 3.90e-02 6.57e+02 2.51e+00 bond pdb=" CG1 ILE e 147 " pdb=" CD1 ILE e 147 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.08e+00 bond pdb=" CB ARG 6 70 " pdb=" CG ARG 6 70 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.95e+00 bond pdb=" SD MET v 36 " pdb=" CE MET v 36 " ideal model delta sigma weight residual 1.791 1.760 0.031 2.50e-02 1.60e+03 1.53e+00 ... (remaining 97315 not shown) Histogram of bond angle deviations from ideal: 95.03 - 103.38: 642 103.38 - 111.73: 45437 111.73 - 120.08: 45905 120.08 - 128.43: 38518 128.43 - 136.78: 478 Bond angle restraints: 130980 Sorted by residual: angle pdb=" CA ARG 6 70 " pdb=" CB ARG 6 70 " pdb=" CG ARG 6 70 " ideal model delta sigma weight residual 114.10 122.77 -8.67 2.00e+00 2.50e-01 1.88e+01 angle pdb=" CA MET 3 212 " pdb=" CB MET 3 212 " pdb=" CG MET 3 212 " ideal model delta sigma weight residual 114.10 122.45 -8.35 2.00e+00 2.50e-01 1.74e+01 angle pdb=" CB MET S 36 " pdb=" CG MET S 36 " pdb=" SD MET S 36 " ideal model delta sigma weight residual 112.70 125.05 -12.35 3.00e+00 1.11e-01 1.69e+01 angle pdb=" CA GLU T 197 " pdb=" CB GLU T 197 " pdb=" CG GLU T 197 " ideal model delta sigma weight residual 114.10 122.18 -8.08 2.00e+00 2.50e-01 1.63e+01 angle pdb=" CB MET 3 212 " pdb=" CG MET 3 212 " pdb=" SD MET 3 212 " ideal model delta sigma weight residual 112.70 124.36 -11.66 3.00e+00 1.11e-01 1.51e+01 ... (remaining 130975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.12: 59197 31.12 - 62.23: 2199 62.23 - 93.35: 163 93.35 - 124.46: 0 124.46 - 155.58: 1 Dihedral angle restraints: 61560 sinusoidal: 26940 harmonic: 34620 Sorted by residual: dihedral pdb=" C5' ADP S 301 " pdb=" O5' ADP S 301 " pdb=" PA ADP S 301 " pdb=" O2A ADP S 301 " ideal model delta sinusoidal sigma weight residual -60.00 95.58 -155.58 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" C5' ADP 0 301 " pdb=" O5' ADP 0 301 " pdb=" PA ADP 0 301 " pdb=" O2A ADP 0 301 " ideal model delta sinusoidal sigma weight residual -60.00 -148.71 88.71 1 2.00e+01 2.50e-03 2.35e+01 dihedral pdb=" C5' ADP d 301 " pdb=" O5' ADP d 301 " pdb=" PA ADP d 301 " pdb=" O2A ADP d 301 " ideal model delta sinusoidal sigma weight residual -60.00 -145.54 85.54 1 2.00e+01 2.50e-03 2.21e+01 ... (remaining 61557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 11459 0.041 - 0.082: 2546 0.082 - 0.123: 321 0.123 - 0.164: 70 0.164 - 0.205: 4 Chirality restraints: 14400 Sorted by residual: chirality pdb=" CB THR O 208 " pdb=" CA THR O 208 " pdb=" OG1 THR O 208 " pdb=" CG2 THR O 208 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CG LEU R 32 " pdb=" CB LEU R 32 " pdb=" CD1 LEU R 32 " pdb=" CD2 LEU R 32 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.92e-01 chirality pdb=" CB THR S 208 " pdb=" CA THR S 208 " pdb=" OG1 THR S 208 " pdb=" CG2 THR S 208 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.84e-01 ... (remaining 14397 not shown) Planarity restraints: 17160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP y 199 " 0.026 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP y 199 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP y 199 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP y 199 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP y 199 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP y 199 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP y 199 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP y 199 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP y 199 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP y 199 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 199 " -0.023 2.00e-02 2.50e+03 1.89e-02 8.95e+00 pdb=" CG TRP K 199 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP K 199 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP K 199 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP K 199 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP K 199 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP K 199 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 199 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 199 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP K 199 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP Z 199 " 0.023 2.00e-02 2.50e+03 1.69e-02 7.14e+00 pdb=" CG TRP Z 199 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP Z 199 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP Z 199 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP Z 199 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP Z 199 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP Z 199 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP Z 199 " 0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP Z 199 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP Z 199 " 0.000 2.00e-02 2.50e+03 ... (remaining 17157 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1266 2.69 - 3.25: 102317 3.25 - 3.80: 153813 3.80 - 4.35: 173930 4.35 - 4.90: 286378 Nonbonded interactions: 717704 Sorted by model distance: nonbonded pdb=" OG SER H 145 " pdb=" OE1 GLN A 121 " model vdw 2.143 2.440 nonbonded pdb=" OG SER z 165 " pdb=" O2A ADP z 301 " model vdw 2.213 2.440 nonbonded pdb=" O ASN O 161 " pdb=" O2' ADP O 301 " model vdw 2.223 2.440 nonbonded pdb=" O ASN q 161 " pdb=" O2' ADP q 301 " model vdw 2.227 2.440 nonbonded pdb=" OD1 ASP A 27 " pdb=" N LEU A 28 " model vdw 2.234 2.520 ... (remaining 717699 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 '0' and resid 22 through 217) selection = (chain '1' and resid 22 through 217) selection = (chain '2' and resid 22 through 217) selection = (chain '3' and resid 22 through 217) selection = (chain '4' and resid 22 through 217) selection = (chain '5' and resid 22 through 217) selection = (chain '6' and resid 22 through 217) selection = (chain '7' and resid 22 through 217) selection = (chain 'A' and resid 22 through 217) selection = (chain 'B' and resid 22 through 217) selection = (chain 'C' and resid 22 through 217) selection = (chain 'D' and resid 22 through 217) selection = (chain 'E' and resid 22 through 217) selection = (chain 'F' and resid 22 through 217) selection = (chain 'G' and resid 22 through 217) selection = (chain 'H' and resid 22 through 217) selection = (chain 'I' and resid 22 through 217) selection = (chain 'J' and resid 22 through 217) selection = (chain 'K' and resid 22 through 217) selection = (chain 'L' and resid 22 through 217) selection = (chain 'M' and resid 22 through 217) selection = (chain 'N' and resid 22 through 217) selection = (chain 'O' and resid 22 through 217) selection = (chain 'P' and resid 22 through 217) selection = (chain 'Q' and resid 22 through 217) selection = (chain 'R' and resid 22 through 217) selection = (chain 'S' and resid 22 through 217) selection = (chain 'T' and resid 22 through 217) selection = (chain 'U' and resid 22 through 217) selection = (chain 'V' and resid 22 through 217) selection = (chain 'W' and resid 22 through 217) selection = (chain 'X' and resid 22 through 217) selection = (chain 'Y' and resid 22 through 217) selection = (chain 'Z' and resid 22 through 217) selection = (chain 'a' and resid 22 through 217) selection = (chain 'b' and resid 22 through 217) selection = (chain 'c' and resid 22 through 217) selection = (chain 'd' and resid 22 through 217) selection = (chain 'e' and resid 22 through 217) selection = (chain 'f' and resid 22 through 217) selection = (chain 'g' and resid 22 through 217) selection = (chain 'h' and resid 22 through 217) selection = (chain 'i' and resid 22 through 217) selection = (chain 'j' and resid 22 through 217) selection = (chain 'k' and resid 22 through 217) selection = (chain 'l' and resid 22 through 217) selection = (chain 'm' and resid 22 through 217) selection = (chain 'n' and resid 22 through 217) selection = (chain 'o' and resid 22 through 217) selection = (chain 'p' and resid 22 through 217) selection = (chain 'q' and resid 22 through 217) selection = (chain 'r' and resid 22 through 217) selection = (chain 's' and resid 22 through 217) selection = (chain 't' and resid 22 through 217) selection = (chain 'u' and resid 22 through 217) selection = (chain 'v' and resid 22 through 217) selection = (chain 'w' and resid 22 through 217) selection = chain 'x' selection = (chain 'y' and resid 22 through 217) selection = (chain 'z' and resid 22 through 217) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 15.960 Check model and map are aligned: 1.040 Set scattering table: 0.650 Process input model: 185.020 Find NCS groups from input model: 6.180 Set up NCS constraints: 1.270 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 216.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 0.003 0.064 97320 Z= 0.213 Angle : 0.748 13.085 130980 Z= 0.368 Chirality : 0.034 0.205 14400 Planarity : 0.003 0.069 17160 Dihedral : 15.163 155.578 38880 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.17 % Allowed : 14.84 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.80 (0.08), residues: 11640 helix: 2.68 (0.05), residues: 10260 sheet: None (None), residues: 0 loop : 1.21 (0.20), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP y 199 HIS 0.002 0.000 HIS A 100 PHE 0.009 0.001 PHE S 196 TYR 0.031 0.001 TYR S 129 ARG 0.014 0.000 ARG G 70 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 9780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 449 time to evaluate : 9.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8065 (m-30) cc_final: 0.7535 (m-30) REVERT: A 83 ASN cc_start: 0.7452 (t0) cc_final: 0.6864 (p0) REVERT: C 62 ASP cc_start: 0.8453 (m-30) cc_final: 0.8131 (t0) REVERT: I 212 MET cc_start: 0.7624 (tpt) cc_final: 0.7404 (tpt) REVERT: J 200 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8577 (mm-30) REVERT: P 80 ASP cc_start: 0.7797 (t0) cc_final: 0.7477 (m-30) REVERT: S 197 GLU cc_start: 0.8013 (pp20) cc_final: 0.7785 (pp20) REVERT: a 212 MET cc_start: 0.6370 (tpt) cc_final: 0.6075 (tpt) REVERT: c 62 ASP cc_start: 0.8802 (m-30) cc_final: 0.8272 (m-30) REVERT: d 212 MET cc_start: 0.6659 (ptt) cc_final: 0.5548 (tmm) REVERT: 4 41 ILE cc_start: 0.9129 (pt) cc_final: 0.8738 (mm) outliers start: 17 outliers final: 8 residues processed: 457 average time/residue: 0.7659 time to fit residues: 633.4482 Evaluate side-chains 401 residues out of total 9780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 393 time to evaluate : 8.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain b residue 147 ILE Chi-restraints excluded: chain i residue 193 ASP Chi-restraints excluded: chain l residue 152 ILE Chi-restraints excluded: chain s residue 40 LEU Chi-restraints excluded: chain t residue 101 THR Chi-restraints excluded: chain y residue 100 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 962 optimal weight: 1.9990 chunk 864 optimal weight: 0.8980 chunk 479 optimal weight: 10.0000 chunk 295 optimal weight: 0.9980 chunk 582 optimal weight: 2.9990 chunk 461 optimal weight: 1.9990 chunk 893 optimal weight: 0.0270 chunk 345 optimal weight: 1.9990 chunk 543 optimal weight: 4.9990 chunk 665 optimal weight: 3.9990 chunk 1035 optimal weight: 0.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 95 GLN b 203 GLN ** h 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 137 ASN v 203 GLN ** 6 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 97320 Z= 0.180 Angle : 0.636 10.836 130980 Z= 0.283 Chirality : 0.032 0.145 14400 Planarity : 0.003 0.041 17160 Dihedral : 6.217 143.473 13634 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.36 % Allowed : 13.79 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.77 (0.08), residues: 11640 helix: 3.38 (0.05), residues: 10200 sheet: None (None), residues: 0 loop : 1.11 (0.19), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 199 HIS 0.001 0.000 HIS A 100 PHE 0.006 0.001 PHE 2 54 TYR 0.017 0.001 TYR e 72 ARG 0.007 0.000 ARG n 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 9780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 472 time to evaluate : 8.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 81 ARG cc_start: 0.6857 (mtt-85) cc_final: 0.6613 (mtt-85) REVERT: A 62 ASP cc_start: 0.8047 (m-30) cc_final: 0.7474 (m-30) REVERT: A 83 ASN cc_start: 0.7434 (t0) cc_final: 0.6792 (p0) REVERT: B 199 TRP cc_start: 0.8616 (t60) cc_final: 0.8136 (t60) REVERT: C 62 ASP cc_start: 0.8367 (m-30) cc_final: 0.8067 (t0) REVERT: I 212 MET cc_start: 0.7618 (tpt) cc_final: 0.7245 (tpt) REVERT: J 200 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8538 (mm-30) REVERT: S 36 MET cc_start: 0.8234 (tmm) cc_final: 0.7971 (tmm) REVERT: S 197 GLU cc_start: 0.8046 (pp20) cc_final: 0.7814 (pp20) REVERT: V 36 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7628 (ttt) REVERT: Y 206 GLU cc_start: 0.8351 (pp20) cc_final: 0.8002 (pp20) REVERT: a 212 MET cc_start: 0.6581 (tpt) cc_final: 0.6075 (tpt) REVERT: c 62 ASP cc_start: 0.8834 (m-30) cc_final: 0.8326 (m-30) REVERT: d 212 MET cc_start: 0.6523 (ptt) cc_final: 0.5359 (tmm) REVERT: h 62 ASP cc_start: 0.8172 (m-30) cc_final: 0.7927 (t0) REVERT: p 62 ASP cc_start: 0.8065 (m-30) cc_final: 0.7824 (m-30) REVERT: q 40 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8507 (tp) REVERT: s 196 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.7645 (m-80) REVERT: t 196 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.7187 (t80) REVERT: t 197 GLU cc_start: 0.8214 (pp20) cc_final: 0.7944 (pp20) REVERT: y 212 MET cc_start: 0.7423 (tpt) cc_final: 0.7039 (tpp) REVERT: 1 212 MET cc_start: 0.6305 (tpt) cc_final: 0.5941 (tpt) REVERT: 3 212 MET cc_start: 0.8289 (ppp) cc_final: 0.7908 (ppp) REVERT: 4 41 ILE cc_start: 0.9098 (pt) cc_final: 0.8754 (mm) REVERT: 4 137 ASN cc_start: 0.7883 (p0) cc_final: 0.7670 (p0) REVERT: 6 67 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8435 (tt) REVERT: 6 196 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7996 (m-80) REVERT: 6 206 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8828 (pt0) outliers start: 231 outliers final: 93 residues processed: 664 average time/residue: 0.7682 time to fit residues: 926.8562 Evaluate side-chains 510 residues out of total 9780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 411 time to evaluate : 8.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain I residue 193 ASP Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain K residue 193 ASP Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 80 ASP Chi-restraints excluded: chain T residue 152 ILE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 176 LEU Chi-restraints excluded: chain V residue 36 MET Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 193 ASP Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain X residue 67 ILE Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 152 ILE Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain c residue 27 ASP Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 80 ASP Chi-restraints excluded: chain d residue 137 ASN Chi-restraints excluded: chain d residue 196 PHE Chi-restraints excluded: chain e residue 27 ASP Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 73 GLU Chi-restraints excluded: chain e residue 165 SER Chi-restraints excluded: chain e residue 193 ASP Chi-restraints excluded: chain f residue 185 LEU Chi-restraints excluded: chain f residue 193 ASP Chi-restraints excluded: chain g residue 152 ILE Chi-restraints excluded: chain g residue 176 LEU Chi-restraints excluded: chain g residue 193 ASP Chi-restraints excluded: chain h residue 176 LEU Chi-restraints excluded: chain i residue 79 LEU Chi-restraints excluded: chain i residue 176 LEU Chi-restraints excluded: chain i residue 193 ASP Chi-restraints excluded: chain j residue 193 ASP Chi-restraints excluded: chain k residue 36 MET Chi-restraints excluded: chain l residue 40 LEU Chi-restraints excluded: chain m residue 193 ASP Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain o residue 185 LEU Chi-restraints excluded: chain q residue 40 LEU Chi-restraints excluded: chain q residue 176 LEU Chi-restraints excluded: chain s residue 38 LEU Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain s residue 152 ILE Chi-restraints excluded: chain s residue 196 PHE Chi-restraints excluded: chain t residue 196 PHE Chi-restraints excluded: chain u residue 80 ASP Chi-restraints excluded: chain u residue 108 LEU Chi-restraints excluded: chain u residue 176 LEU Chi-restraints excluded: chain v residue 33 LEU Chi-restraints excluded: chain x residue 36 MET Chi-restraints excluded: chain x residue 67 ILE Chi-restraints excluded: chain x residue 152 ILE Chi-restraints excluded: chain x residue 193 ASP Chi-restraints excluded: chain y residue 28 LEU Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain y residue 100 HIS Chi-restraints excluded: chain y residue 165 SER Chi-restraints excluded: chain y residue 176 LEU Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain z residue 67 ILE Chi-restraints excluded: chain z residue 193 ASP Chi-restraints excluded: chain 2 residue 67 ILE Chi-restraints excluded: chain 2 residue 152 ILE Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 50 THR Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 165 SER Chi-restraints excluded: chain 6 residue 27 ASP Chi-restraints excluded: chain 6 residue 38 LEU Chi-restraints excluded: chain 6 residue 67 ILE Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 196 PHE Chi-restraints excluded: chain 7 residue 79 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 575 optimal weight: 6.9990 chunk 321 optimal weight: 3.9990 chunk 861 optimal weight: 5.9990 chunk 704 optimal weight: 4.9990 chunk 285 optimal weight: 4.9990 chunk 1037 optimal weight: 4.9990 chunk 1120 optimal weight: 9.9990 chunk 923 optimal weight: 1.9990 chunk 1028 optimal weight: 5.9990 chunk 353 optimal weight: 3.9990 chunk 832 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN C 60 GLN D 60 GLN E 60 GLN F 60 GLN F 98 GLN I 60 GLN J 60 GLN K 98 GLN L 60 GLN M 60 GLN N 60 GLN O 60 GLN ** O 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 60 GLN Q 60 GLN S 60 GLN T 60 GLN T 100 HIS V 60 GLN W 60 GLN W 95 GLN X 60 GLN Y 60 GLN Z 60 GLN Z 137 ASN Z 161 ASN a 60 GLN d 98 GLN ** e 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 186 ASN g 60 GLN ** g 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 60 GLN ** h 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 60 GLN k 60 GLN m 137 ASN n 203 GLN p 60 GLN q 60 GLN q 203 GLN r 60 GLN s 60 GLN s 203 GLN u 60 GLN u 203 GLN v 60 GLN w 60 GLN x 60 GLN x 161 ASN 0 203 GLN 1 60 GLN 2 60 GLN 3 60 GLN 3 161 ASN 4 60 GLN ** 6 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 203 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 97320 Z= 0.360 Angle : 0.776 11.457 130980 Z= 0.361 Chirality : 0.038 0.166 14400 Planarity : 0.003 0.054 17160 Dihedral : 6.167 128.601 13624 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 4.38 % Allowed : 15.58 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.06 (0.07), residues: 11640 helix: 2.88 (0.05), residues: 10200 sheet: None (None), residues: 0 loop : 1.07 (0.19), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP j 199 HIS 0.003 0.001 HIS a 100 PHE 0.010 0.001 PHE V 196 TYR 0.019 0.002 TYR f 72 ARG 0.006 0.001 ARG z 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 9780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 428 poor density : 439 time to evaluate : 8.678 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: B 184 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7870 (mp) REVERT: C 62 ASP cc_start: 0.8370 (m-30) cc_final: 0.8092 (t0) REVERT: D 176 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9128 (mp) REVERT: I 33 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7435 (mp) REVERT: I 212 MET cc_start: 0.7645 (tpt) cc_final: 0.7130 (tpt) REVERT: M 40 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8662 (tp) REVERT: Q 45 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8175 (ttp-110) REVERT: S 36 MET cc_start: 0.8577 (tmm) cc_final: 0.8336 (tmm) REVERT: T 66 LEU cc_start: 0.9343 (tp) cc_final: 0.9096 (tt) REVERT: U 28 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6534 (tt) REVERT: U 117 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7513 (tt0) REVERT: V 36 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8080 (ttt) REVERT: X 154 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8230 (pp20) REVERT: Y 154 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8361 (pp20) REVERT: Y 206 GLU cc_start: 0.8489 (pp20) cc_final: 0.8149 (pp20) REVERT: Y 212 MET cc_start: 0.8092 (tpt) cc_final: 0.7656 (tpt) REVERT: Z 40 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.6947 (tp) REVERT: d 33 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6849 (mp) REVERT: d 70 ARG cc_start: 0.8756 (tmm-80) cc_final: 0.8314 (tmm-80) REVERT: d 212 MET cc_start: 0.6624 (ptt) cc_final: 0.5308 (tmm) REVERT: f 108 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9090 (mp) REVERT: h 62 ASP cc_start: 0.8308 (m-30) cc_final: 0.8076 (t0) REVERT: j 36 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8230 (ttp) REVERT: k 212 MET cc_start: 0.7959 (tpp) cc_final: 0.7277 (tpt) REVERT: l 81 ARG cc_start: 0.8943 (mtp180) cc_final: 0.8678 (mmp80) REVERT: l 185 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7482 (tt) REVERT: m 33 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.6990 (mp) REVERT: p 62 ASP cc_start: 0.8148 (m-30) cc_final: 0.7941 (m-30) REVERT: q 40 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8778 (tp) REVERT: s 36 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8081 (tpp) REVERT: s 196 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.8109 (m-80) REVERT: t 33 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6116 (mp) REVERT: t 196 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7325 (t80) REVERT: t 197 GLU cc_start: 0.8273 (pp20) cc_final: 0.7951 (pp20) REVERT: x 81 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7368 (ptp-110) REVERT: y 28 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7228 (tt) REVERT: y 126 GLU cc_start: 0.7379 (tp30) cc_final: 0.7134 (tp30) REVERT: y 212 MET cc_start: 0.7655 (tpt) cc_final: 0.7192 (tpp) REVERT: z 45 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7233 (ttm-80) REVERT: 0 70 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8749 (ttp80) REVERT: 1 42 GLU cc_start: 0.8442 (mm-30) cc_final: 0.7713 (mm-30) REVERT: 1 45 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8307 (ttp-110) REVERT: 2 154 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8220 (pp20) REVERT: 3 117 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7625 (tm130) REVERT: 3 212 MET cc_start: 0.8352 (ppp) cc_final: 0.7898 (ppp) REVERT: 4 137 ASN cc_start: 0.7970 (p0) cc_final: 0.7690 (p0) REVERT: 5 37 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7715 (tm-30) REVERT: 6 196 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8343 (m-80) REVERT: 6 206 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8924 (pt0) REVERT: 7 117 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7688 (tm130) REVERT: 7 212 MET cc_start: 0.8374 (tpt) cc_final: 0.8090 (tpt) outliers start: 428 outliers final: 224 residues processed: 812 average time/residue: 0.7547 time to fit residues: 1104.5529 Evaluate side-chains 641 residues out of total 9780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 387 time to evaluate : 8.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 193 ASP Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 193 ASP Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 193 ASP Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 100 HIS Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 193 ASP Chi-restraints excluded: chain N residue 196 PHE Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain O residue 152 ILE Chi-restraints excluded: chain O residue 193 ASP Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 101 THR Chi-restraints excluded: chain P residue 193 ASP Chi-restraints excluded: chain Q residue 45 ARG Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 67 ILE Chi-restraints excluded: chain S residue 147 ILE Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 80 ASP Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 152 ILE Chi-restraints excluded: chain T residue 193 ASP Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 117 GLN Chi-restraints excluded: chain U residue 176 LEU Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 36 MET Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 193 ASP Chi-restraints excluded: chain W residue 41 ILE Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 67 ILE Chi-restraints excluded: chain X residue 147 ILE Chi-restraints excluded: chain X residue 154 GLU Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 40 LEU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 152 ILE Chi-restraints excluded: chain Y residue 154 GLU Chi-restraints excluded: chain Y residue 193 ASP Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain Z residue 62 ASP Chi-restraints excluded: chain Z residue 67 ILE Chi-restraints excluded: chain Z residue 80 ASP Chi-restraints excluded: chain Z residue 165 SER Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 67 ILE Chi-restraints excluded: chain a residue 137 ASN Chi-restraints excluded: chain a residue 165 SER Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain b residue 29 LEU Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain d residue 33 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 137 ASN Chi-restraints excluded: chain d residue 196 PHE Chi-restraints excluded: chain e residue 27 ASP Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 165 SER Chi-restraints excluded: chain e residue 178 LEU Chi-restraints excluded: chain e residue 193 ASP Chi-restraints excluded: chain f residue 36 MET Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 108 LEU Chi-restraints excluded: chain f residue 185 LEU Chi-restraints excluded: chain f residue 193 ASP Chi-restraints excluded: chain g residue 40 LEU Chi-restraints excluded: chain g residue 173 THR Chi-restraints excluded: chain g residue 176 LEU Chi-restraints excluded: chain g residue 193 ASP Chi-restraints excluded: chain h residue 101 THR Chi-restraints excluded: chain h residue 176 LEU Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 176 LEU Chi-restraints excluded: chain i residue 193 ASP Chi-restraints excluded: chain j residue 36 MET Chi-restraints excluded: chain j residue 176 LEU Chi-restraints excluded: chain j residue 193 ASP Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain k residue 36 MET Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain k residue 193 ASP Chi-restraints excluded: chain l residue 40 LEU Chi-restraints excluded: chain l residue 185 LEU Chi-restraints excluded: chain l residue 193 ASP Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 50 THR Chi-restraints excluded: chain m residue 83 ASN Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 184 LEU Chi-restraints excluded: chain m residue 193 ASP Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 193 ASP Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain o residue 67 ILE Chi-restraints excluded: chain o residue 176 LEU Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain p residue 101 THR Chi-restraints excluded: chain p residue 165 SER Chi-restraints excluded: chain p residue 193 ASP Chi-restraints excluded: chain q residue 40 LEU Chi-restraints excluded: chain q residue 67 ILE Chi-restraints excluded: chain q residue 101 THR Chi-restraints excluded: chain q residue 176 LEU Chi-restraints excluded: chain r residue 33 LEU Chi-restraints excluded: chain r residue 101 THR Chi-restraints excluded: chain r residue 108 LEU Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 36 MET Chi-restraints excluded: chain s residue 67 ILE Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain s residue 101 THR Chi-restraints excluded: chain s residue 147 ILE Chi-restraints excluded: chain s residue 152 ILE Chi-restraints excluded: chain s residue 196 PHE Chi-restraints excluded: chain t residue 33 LEU Chi-restraints excluded: chain t residue 36 MET Chi-restraints excluded: chain t residue 50 THR Chi-restraints excluded: chain t residue 67 ILE Chi-restraints excluded: chain t residue 147 ILE Chi-restraints excluded: chain t residue 165 SER Chi-restraints excluded: chain t residue 196 PHE Chi-restraints excluded: chain u residue 80 ASP Chi-restraints excluded: chain u residue 101 THR Chi-restraints excluded: chain u residue 108 LEU Chi-restraints excluded: chain u residue 193 ASP Chi-restraints excluded: chain v residue 33 LEU Chi-restraints excluded: chain v residue 50 THR Chi-restraints excluded: chain v residue 67 ILE Chi-restraints excluded: chain v residue 147 ILE Chi-restraints excluded: chain v residue 193 ASP Chi-restraints excluded: chain w residue 147 ILE Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain x residue 33 LEU Chi-restraints excluded: chain x residue 36 MET Chi-restraints excluded: chain x residue 50 THR Chi-restraints excluded: chain x residue 67 ILE Chi-restraints excluded: chain x residue 81 ARG Chi-restraints excluded: chain x residue 147 ILE Chi-restraints excluded: chain x residue 152 ILE Chi-restraints excluded: chain x residue 193 ASP Chi-restraints excluded: chain y residue 28 LEU Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain y residue 100 HIS Chi-restraints excluded: chain y residue 165 SER Chi-restraints excluded: chain y residue 176 LEU Chi-restraints excluded: chain y residue 193 ASP Chi-restraints excluded: chain z residue 33 LEU Chi-restraints excluded: chain z residue 45 ARG Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain z residue 67 ILE Chi-restraints excluded: chain z residue 193 ASP Chi-restraints excluded: chain 0 residue 36 MET Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 0 residue 67 ILE Chi-restraints excluded: chain 0 residue 70 ARG Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 1 residue 45 ARG Chi-restraints excluded: chain 1 residue 147 ILE Chi-restraints excluded: chain 1 residue 212 MET Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 2 residue 67 ILE Chi-restraints excluded: chain 2 residue 152 ILE Chi-restraints excluded: chain 2 residue 154 GLU Chi-restraints excluded: chain 3 residue 50 THR Chi-restraints excluded: chain 3 residue 67 ILE Chi-restraints excluded: chain 3 residue 117 GLN Chi-restraints excluded: chain 3 residue 165 SER Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 67 ILE Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 165 SER Chi-restraints excluded: chain 5 residue 41 ILE Chi-restraints excluded: chain 5 residue 79 LEU Chi-restraints excluded: chain 6 residue 29 LEU Chi-restraints excluded: chain 6 residue 38 LEU Chi-restraints excluded: chain 6 residue 40 LEU Chi-restraints excluded: chain 6 residue 50 THR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 196 PHE Chi-restraints excluded: chain 7 residue 50 THR Chi-restraints excluded: chain 7 residue 79 LEU Chi-restraints excluded: chain 7 residue 117 GLN Chi-restraints excluded: chain 7 residue 193 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 1024 optimal weight: 2.9990 chunk 779 optimal weight: 8.9990 chunk 538 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 494 optimal weight: 0.9990 chunk 696 optimal weight: 0.9980 chunk 1040 optimal weight: 0.6980 chunk 1101 optimal weight: 5.9990 chunk 543 optimal weight: 4.9990 chunk 986 optimal weight: 4.9990 chunk 296 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 ASN N 203 GLN Z 137 ASN ** d 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 158 ASN h 161 ASN l 137 ASN p 203 GLN t 161 ASN v 100 HIS ** 6 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 97320 Z= 0.184 Angle : 0.634 10.174 130980 Z= 0.282 Chirality : 0.032 0.163 14400 Planarity : 0.003 0.035 17160 Dihedral : 5.948 111.629 13624 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.67 % Allowed : 18.10 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.93 (0.07), residues: 11640 helix: 3.49 (0.05), residues: 10200 sheet: None (None), residues: 0 loop : 1.15 (0.19), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP e 199 HIS 0.002 0.000 HIS a 100 PHE 0.007 0.001 PHE 2 54 TYR 0.019 0.001 TYR A 72 ARG 0.007 0.000 ARG i 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 9780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 459 time to evaluate : 8.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASN cc_start: 0.7556 (t0) cc_final: 0.6531 (p0) REVERT: C 62 ASP cc_start: 0.8274 (m-30) cc_final: 0.8058 (t0) REVERT: G 79 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7412 (tp) REVERT: I 212 MET cc_start: 0.7571 (tpt) cc_final: 0.7012 (tpt) REVERT: N 81 ARG cc_start: 0.7993 (mmt-90) cc_final: 0.7648 (mmp80) REVERT: V 36 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7764 (ttt) REVERT: X 154 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8257 (pp20) REVERT: Y 154 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8494 (pp20) REVERT: Y 163 SER cc_start: 0.6424 (m) cc_final: 0.5857 (p) REVERT: Y 206 GLU cc_start: 0.8477 (pp20) cc_final: 0.8160 (pp20) REVERT: b 152 ILE cc_start: 0.8752 (tp) cc_final: 0.8224 (tp) REVERT: c 62 ASP cc_start: 0.8704 (m-30) cc_final: 0.8200 (m-30) REVERT: d 117 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7576 (tm-30) REVERT: d 212 MET cc_start: 0.6637 (ptt) cc_final: 0.5411 (tmm) REVERT: l 81 ARG cc_start: 0.8894 (mtp180) cc_final: 0.8654 (mmp80) REVERT: n 199 TRP cc_start: 0.8857 (t60) cc_final: 0.8581 (t60) REVERT: p 62 ASP cc_start: 0.8027 (m-30) cc_final: 0.7800 (m-30) REVERT: q 40 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8667 (tp) REVERT: q 50 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8698 (p) REVERT: s 196 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7690 (m-80) REVERT: t 196 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.7199 (t80) REVERT: t 197 GLU cc_start: 0.8304 (pp20) cc_final: 0.7950 (pp20) REVERT: u 36 MET cc_start: 0.8370 (tpp) cc_final: 0.7691 (tpp) REVERT: x 81 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7640 (ptp-110) REVERT: y 212 MET cc_start: 0.7640 (tpt) cc_final: 0.7238 (tpp) REVERT: z 45 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7193 (ttm-80) REVERT: 0 70 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8802 (ttp80) REVERT: 1 42 GLU cc_start: 0.8557 (mm-30) cc_final: 0.7758 (mm-30) REVERT: 1 45 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8180 (ttp-110) REVERT: 2 154 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8399 (pp20) REVERT: 3 154 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8571 (pp20) REVERT: 3 212 MET cc_start: 0.8364 (ppp) cc_final: 0.7925 (ppp) REVERT: 4 137 ASN cc_start: 0.7957 (p0) cc_final: 0.7686 (p0) REVERT: 5 37 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7564 (tm-30) REVERT: 6 196 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.7852 (m-80) REVERT: 7 212 MET cc_start: 0.8439 (tpt) cc_final: 0.8184 (tpt) outliers start: 261 outliers final: 148 residues processed: 670 average time/residue: 0.8222 time to fit residues: 994.6490 Evaluate side-chains 565 residues out of total 9780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 401 time to evaluate : 8.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 193 ASP Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 193 ASP Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 196 PHE Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 193 ASP Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 196 PHE Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 36 MET Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 152 ILE Chi-restraints excluded: chain T residue 193 ASP Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 36 MET Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 193 ASP Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain X residue 154 GLU Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Y residue 40 LEU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 152 ILE Chi-restraints excluded: chain Y residue 154 GLU Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 137 ASN Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain b residue 79 LEU Chi-restraints excluded: chain b residue 147 ILE Chi-restraints excluded: chain c residue 27 ASP Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 80 ASP Chi-restraints excluded: chain d residue 117 GLN Chi-restraints excluded: chain d residue 137 ASN Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 193 ASP Chi-restraints excluded: chain f residue 36 MET Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 185 LEU Chi-restraints excluded: chain f residue 193 ASP Chi-restraints excluded: chain g residue 193 ASP Chi-restraints excluded: chain h residue 176 LEU Chi-restraints excluded: chain i residue 147 ILE Chi-restraints excluded: chain i residue 176 LEU Chi-restraints excluded: chain i residue 193 ASP Chi-restraints excluded: chain j residue 176 LEU Chi-restraints excluded: chain j residue 185 LEU Chi-restraints excluded: chain j residue 193 ASP Chi-restraints excluded: chain k residue 36 MET Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain k residue 193 ASP Chi-restraints excluded: chain k residue 196 PHE Chi-restraints excluded: chain m residue 50 THR Chi-restraints excluded: chain m residue 193 ASP Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 147 ILE Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 101 THR Chi-restraints excluded: chain o residue 185 LEU Chi-restraints excluded: chain o residue 193 ASP Chi-restraints excluded: chain p residue 108 LEU Chi-restraints excluded: chain p residue 193 ASP Chi-restraints excluded: chain q residue 40 LEU Chi-restraints excluded: chain q residue 50 THR Chi-restraints excluded: chain q residue 176 LEU Chi-restraints excluded: chain r residue 108 LEU Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain s residue 152 ILE Chi-restraints excluded: chain s residue 185 LEU Chi-restraints excluded: chain s residue 196 PHE Chi-restraints excluded: chain t residue 36 MET Chi-restraints excluded: chain t residue 50 THR Chi-restraints excluded: chain t residue 196 PHE Chi-restraints excluded: chain u residue 80 ASP Chi-restraints excluded: chain u residue 108 LEU Chi-restraints excluded: chain u residue 193 ASP Chi-restraints excluded: chain v residue 100 HIS Chi-restraints excluded: chain w residue 196 PHE Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 36 MET Chi-restraints excluded: chain x residue 67 ILE Chi-restraints excluded: chain x residue 81 ARG Chi-restraints excluded: chain x residue 152 ILE Chi-restraints excluded: chain x residue 176 LEU Chi-restraints excluded: chain x residue 185 LEU Chi-restraints excluded: chain x residue 193 ASP Chi-restraints excluded: chain y residue 28 LEU Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain y residue 80 ASP Chi-restraints excluded: chain y residue 100 HIS Chi-restraints excluded: chain y residue 176 LEU Chi-restraints excluded: chain z residue 33 LEU Chi-restraints excluded: chain z residue 45 ARG Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain z residue 193 ASP Chi-restraints excluded: chain 0 residue 36 MET Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 0 residue 70 ARG Chi-restraints excluded: chain 1 residue 45 ARG Chi-restraints excluded: chain 1 residue 212 MET Chi-restraints excluded: chain 2 residue 40 LEU Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 2 residue 80 ASP Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 152 ILE Chi-restraints excluded: chain 2 residue 154 GLU Chi-restraints excluded: chain 2 residue 176 LEU Chi-restraints excluded: chain 3 residue 50 THR Chi-restraints excluded: chain 3 residue 154 GLU Chi-restraints excluded: chain 3 residue 176 LEU Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 5 residue 29 LEU Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 5 residue 79 LEU Chi-restraints excluded: chain 6 residue 27 ASP Chi-restraints excluded: chain 6 residue 38 LEU Chi-restraints excluded: chain 6 residue 40 LEU Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 196 PHE Chi-restraints excluded: chain 7 residue 79 LEU Chi-restraints excluded: chain 7 residue 91 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 917 optimal weight: 2.9990 chunk 625 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 820 optimal weight: 3.9990 chunk 454 optimal weight: 4.9990 chunk 940 optimal weight: 0.8980 chunk 761 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 562 optimal weight: 0.9990 chunk 989 optimal weight: 0.7980 chunk 278 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 137 ASN P 203 GLN R 203 GLN ** d 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 186 ASN g 161 ASN l 137 ASN p 137 ASN q 137 ASN u 137 ASN v 137 ASN y 137 ASN z 203 GLN 5 137 ASN ** 6 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 97320 Z= 0.167 Angle : 0.620 9.651 130980 Z= 0.273 Chirality : 0.031 0.176 14400 Planarity : 0.002 0.033 17160 Dihedral : 5.679 90.567 13624 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.97 % Allowed : 18.56 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 5.36 (0.07), residues: 11640 helix: 3.79 (0.05), residues: 10200 sheet: None (None), residues: 0 loop : 1.11 (0.19), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP 7 199 HIS 0.002 0.000 HIS v 100 PHE 0.007 0.001 PHE 2 54 TYR 0.011 0.001 TYR v 97 ARG 0.013 0.000 ARG b 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 9780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 478 time to evaluate : 8.633 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: A 62 ASP cc_start: 0.8058 (m-30) cc_final: 0.7530 (m-30) REVERT: B 199 TRP cc_start: 0.8593 (t60) cc_final: 0.8287 (t60) REVERT: E 66 LEU cc_start: 0.9086 (tp) cc_final: 0.8810 (tt) REVERT: G 79 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6809 (tp) REVERT: I 29 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6620 (tt) REVERT: I 212 MET cc_start: 0.7452 (tpt) cc_final: 0.6754 (tpt) REVERT: J 152 ILE cc_start: 0.7704 (tp) cc_final: 0.7484 (tp) REVERT: L 29 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7371 (tt) REVERT: M 40 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8269 (tt) REVERT: X 154 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8373 (pp20) REVERT: Y 206 GLU cc_start: 0.8426 (pp20) cc_final: 0.8085 (pp20) REVERT: Z 40 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6931 (tp) REVERT: c 38 LEU cc_start: 0.8977 (pp) cc_final: 0.8635 (pp) REVERT: c 62 ASP cc_start: 0.8738 (m-30) cc_final: 0.8239 (m-30) REVERT: d 117 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7529 (tm-30) REVERT: d 154 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8092 (pp20) REVERT: d 212 MET cc_start: 0.6635 (ptt) cc_final: 0.5396 (tmm) REVERT: f 45 ARG cc_start: 0.8324 (ttp80) cc_final: 0.7943 (ttp80) REVERT: h 40 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6975 (tp) REVERT: l 81 ARG cc_start: 0.8864 (mtp180) cc_final: 0.8613 (mmp80) REVERT: l 108 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8542 (mt) REVERT: n 199 TRP cc_start: 0.8861 (t60) cc_final: 0.8630 (t60) REVERT: n 212 MET cc_start: 0.8605 (tmm) cc_final: 0.8271 (ppp) REVERT: p 62 ASP cc_start: 0.8081 (m-30) cc_final: 0.7736 (m-30) REVERT: q 40 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8591 (tp) REVERT: s 196 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.7383 (m-80) REVERT: t 196 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7239 (t80) REVERT: t 197 GLU cc_start: 0.8538 (pp20) cc_final: 0.8298 (pp20) REVERT: u 36 MET cc_start: 0.7895 (tpp) cc_final: 0.7579 (tpp) REVERT: x 81 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7672 (ttp80) REVERT: y 212 MET cc_start: 0.7601 (tpt) cc_final: 0.7339 (tpp) REVERT: 2 154 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8315 (pp20) REVERT: 3 154 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8551 (pp20) REVERT: 3 212 MET cc_start: 0.8502 (ppp) cc_final: 0.7983 (ppp) REVERT: 4 137 ASN cc_start: 0.7663 (p0) cc_final: 0.7415 (p0) REVERT: 5 37 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7506 (tm-30) REVERT: 6 154 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8233 (tm-30) REVERT: 6 196 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.8078 (m-80) REVERT: 6 206 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8886 (pt0) REVERT: 7 117 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: 7 212 MET cc_start: 0.8425 (tpt) cc_final: 0.8173 (tpt) outliers start: 290 outliers final: 158 residues processed: 721 average time/residue: 0.7383 time to fit residues: 963.8507 Evaluate side-chains 603 residues out of total 9780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 426 time to evaluate : 8.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 193 ASP Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 193 ASP Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain O residue 152 ILE Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain P residue 193 ASP Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 196 PHE Chi-restraints excluded: chain T residue 29 LEU Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 152 ILE Chi-restraints excluded: chain T residue 193 ASP Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 176 LEU Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 80 ASP Chi-restraints excluded: chain V residue 193 ASP Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain X residue 154 GLU Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 152 ILE Chi-restraints excluded: chain Y residue 176 LEU Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain Z residue 80 ASP Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain b residue 79 LEU Chi-restraints excluded: chain c residue 27 ASP Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 80 ASP Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 117 GLN Chi-restraints excluded: chain d residue 154 GLU Chi-restraints excluded: chain d residue 196 PHE Chi-restraints excluded: chain e residue 158 ASN Chi-restraints excluded: chain e residue 165 SER Chi-restraints excluded: chain e residue 193 ASP Chi-restraints excluded: chain f residue 36 MET Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 185 LEU Chi-restraints excluded: chain f residue 193 ASP Chi-restraints excluded: chain g residue 176 LEU Chi-restraints excluded: chain g residue 193 ASP Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 176 LEU Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 161 ASN Chi-restraints excluded: chain i residue 176 LEU Chi-restraints excluded: chain i residue 193 ASP Chi-restraints excluded: chain j residue 185 LEU Chi-restraints excluded: chain j residue 193 ASP Chi-restraints excluded: chain k residue 36 MET Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain k residue 185 LEU Chi-restraints excluded: chain k residue 193 ASP Chi-restraints excluded: chain l residue 108 LEU Chi-restraints excluded: chain l residue 176 LEU Chi-restraints excluded: chain m residue 50 THR Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 193 ASP Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 147 ILE Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 185 LEU Chi-restraints excluded: chain o residue 193 ASP Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain p residue 193 ASP Chi-restraints excluded: chain q residue 40 LEU Chi-restraints excluded: chain q residue 176 LEU Chi-restraints excluded: chain q residue 185 LEU Chi-restraints excluded: chain r residue 108 LEU Chi-restraints excluded: chain s residue 38 LEU Chi-restraints excluded: chain s residue 67 ILE Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain s residue 152 ILE Chi-restraints excluded: chain s residue 185 LEU Chi-restraints excluded: chain s residue 196 PHE Chi-restraints excluded: chain t residue 50 THR Chi-restraints excluded: chain t residue 196 PHE Chi-restraints excluded: chain u residue 80 ASP Chi-restraints excluded: chain u residue 108 LEU Chi-restraints excluded: chain u residue 196 PHE Chi-restraints excluded: chain v residue 33 LEU Chi-restraints excluded: chain v residue 101 THR Chi-restraints excluded: chain w residue 196 PHE Chi-restraints excluded: chain x residue 36 MET Chi-restraints excluded: chain x residue 67 ILE Chi-restraints excluded: chain x residue 81 ARG Chi-restraints excluded: chain x residue 147 ILE Chi-restraints excluded: chain x residue 152 ILE Chi-restraints excluded: chain x residue 193 ASP Chi-restraints excluded: chain y residue 28 LEU Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain y residue 100 HIS Chi-restraints excluded: chain y residue 176 LEU Chi-restraints excluded: chain y residue 193 ASP Chi-restraints excluded: chain z residue 33 LEU Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain z residue 67 ILE Chi-restraints excluded: chain z residue 193 ASP Chi-restraints excluded: chain 0 residue 36 MET Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 1 residue 209 LEU Chi-restraints excluded: chain 1 residue 212 MET Chi-restraints excluded: chain 2 residue 40 LEU Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 152 ILE Chi-restraints excluded: chain 2 residue 154 GLU Chi-restraints excluded: chain 3 residue 38 LEU Chi-restraints excluded: chain 3 residue 50 THR Chi-restraints excluded: chain 3 residue 154 GLU Chi-restraints excluded: chain 3 residue 176 LEU Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 5 residue 29 LEU Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 5 residue 79 LEU Chi-restraints excluded: chain 6 residue 27 ASP Chi-restraints excluded: chain 6 residue 40 LEU Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 154 GLU Chi-restraints excluded: chain 6 residue 196 PHE Chi-restraints excluded: chain 7 residue 91 LEU Chi-restraints excluded: chain 7 residue 117 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 370 optimal weight: 0.9990 chunk 992 optimal weight: 3.9990 chunk 217 optimal weight: 0.9980 chunk 646 optimal weight: 0.0470 chunk 272 optimal weight: 6.9990 chunk 1102 optimal weight: 0.9980 chunk 915 optimal weight: 0.7980 chunk 510 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 364 optimal weight: 0.8980 chunk 579 optimal weight: 6.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 137 ASN M 203 GLN N 137 ASN T 203 GLN d 161 ASN ** e 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 161 ASN m 137 ASN r 137 ASN y 137 ASN ** 6 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 97320 Z= 0.157 Angle : 0.612 11.046 130980 Z= 0.267 Chirality : 0.030 0.175 14400 Planarity : 0.002 0.034 17160 Dihedral : 5.493 86.036 13624 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.56 % Allowed : 19.15 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 5.55 (0.07), residues: 11640 helix: 3.93 (0.05), residues: 10200 sheet: None (None), residues: 0 loop : 1.09 (0.19), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 199 HIS 0.001 0.000 HIS v 100 PHE 0.006 0.000 PHE 2 54 TYR 0.016 0.001 TYR W 129 ARG 0.006 0.000 ARG c 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 9780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 487 time to evaluate : 9.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 126 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6976 (tp30) REVERT: A 62 ASP cc_start: 0.8062 (m-30) cc_final: 0.7522 (m-30) REVERT: A 83 ASN cc_start: 0.7526 (t0) cc_final: 0.6464 (p0) REVERT: B 199 TRP cc_start: 0.8576 (t60) cc_final: 0.8309 (t60) REVERT: E 66 LEU cc_start: 0.9028 (tp) cc_final: 0.8737 (tt) REVERT: F 185 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7636 (mt) REVERT: G 126 GLU cc_start: 0.8500 (pm20) cc_final: 0.8162 (pm20) REVERT: I 29 LEU cc_start: 0.6831 (OUTLIER) cc_final: 0.6511 (tt) REVERT: I 40 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7843 (tt) REVERT: J 152 ILE cc_start: 0.7792 (tp) cc_final: 0.7542 (tp) REVERT: M 40 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8211 (tt) REVERT: N 81 ARG cc_start: 0.8060 (mpt180) cc_final: 0.6762 (tmm-80) REVERT: U 126 GLU cc_start: 0.7509 (tp30) cc_final: 0.7300 (tp30) REVERT: Y 206 GLU cc_start: 0.8415 (pp20) cc_final: 0.8080 (pp20) REVERT: Z 40 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6898 (tp) REVERT: b 79 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8242 (pp) REVERT: c 62 ASP cc_start: 0.8731 (m-30) cc_final: 0.8246 (m-30) REVERT: d 212 MET cc_start: 0.6637 (ptt) cc_final: 0.5469 (tmm) REVERT: f 45 ARG cc_start: 0.8383 (ttp80) cc_final: 0.8038 (ttp80) REVERT: f 62 ASP cc_start: 0.7870 (m-30) cc_final: 0.7554 (m-30) REVERT: h 40 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6975 (tp) REVERT: h 199 TRP cc_start: 0.8611 (t60) cc_final: 0.8401 (t60) REVERT: i 185 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8170 (tt) REVERT: k 62 ASP cc_start: 0.8549 (m-30) cc_final: 0.8018 (m-30) REVERT: k 176 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8287 (mp) REVERT: l 62 ASP cc_start: 0.8621 (m-30) cc_final: 0.8055 (m-30) REVERT: l 81 ARG cc_start: 0.8825 (mtp180) cc_final: 0.8585 (mmp80) REVERT: p 62 ASP cc_start: 0.8069 (m-30) cc_final: 0.7707 (m-30) REVERT: r 62 ASP cc_start: 0.8455 (m-30) cc_final: 0.7962 (m-30) REVERT: s 196 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.7350 (m-80) REVERT: t 196 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7163 (t80) REVERT: t 197 GLU cc_start: 0.8546 (pp20) cc_final: 0.8293 (pp20) REVERT: v 40 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8114 (tt) REVERT: z 45 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7170 (ttm-80) REVERT: 0 70 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8841 (ttp80) REVERT: 1 42 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7287 (mm-30) REVERT: 1 45 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7991 (ttp-110) REVERT: 2 154 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8444 (pp20) REVERT: 3 40 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6751 (tp) REVERT: 3 212 MET cc_start: 0.8398 (ppp) cc_final: 0.7867 (ppp) REVERT: 4 137 ASN cc_start: 0.7686 (p0) cc_final: 0.7419 (p0) REVERT: 5 37 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7451 (tm-30) REVERT: 6 40 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8206 (tt) REVERT: 6 196 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.8220 (m-80) REVERT: 7 212 MET cc_start: 0.8425 (tpt) cc_final: 0.8170 (tpt) outliers start: 250 outliers final: 157 residues processed: 695 average time/residue: 0.7463 time to fit residues: 940.9308 Evaluate side-chains 606 residues out of total 9780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 429 time to evaluate : 8.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 193 ASP Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain N residue 196 PHE Chi-restraints excluded: chain O residue 152 ILE Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 193 ASP Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 196 PHE Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 152 ILE Chi-restraints excluded: chain T residue 185 LEU Chi-restraints excluded: chain T residue 193 ASP Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 176 LEU Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 80 ASP Chi-restraints excluded: chain V residue 193 ASP Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 152 ILE Chi-restraints excluded: chain Y residue 176 LEU Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain b residue 79 LEU Chi-restraints excluded: chain c residue 27 ASP Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 80 ASP Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 196 PHE Chi-restraints excluded: chain e residue 27 ASP Chi-restraints excluded: chain e residue 158 ASN Chi-restraints excluded: chain e residue 193 ASP Chi-restraints excluded: chain f residue 36 MET Chi-restraints excluded: chain f residue 165 SER Chi-restraints excluded: chain f residue 176 LEU Chi-restraints excluded: chain f residue 185 LEU Chi-restraints excluded: chain f residue 193 ASP Chi-restraints excluded: chain g residue 173 THR Chi-restraints excluded: chain g residue 176 LEU Chi-restraints excluded: chain g residue 193 ASP Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 176 LEU Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 176 LEU Chi-restraints excluded: chain i residue 185 LEU Chi-restraints excluded: chain i residue 193 ASP Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain j residue 185 LEU Chi-restraints excluded: chain j residue 193 ASP Chi-restraints excluded: chain k residue 36 MET Chi-restraints excluded: chain k residue 176 LEU Chi-restraints excluded: chain k residue 185 LEU Chi-restraints excluded: chain k residue 193 ASP Chi-restraints excluded: chain k residue 196 PHE Chi-restraints excluded: chain l residue 40 LEU Chi-restraints excluded: chain l residue 176 LEU Chi-restraints excluded: chain l residue 193 ASP Chi-restraints excluded: chain m residue 50 THR Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 193 ASP Chi-restraints excluded: chain n residue 29 LEU Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 185 LEU Chi-restraints excluded: chain o residue 193 ASP Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 185 LEU Chi-restraints excluded: chain p residue 193 ASP Chi-restraints excluded: chain q residue 176 LEU Chi-restraints excluded: chain q residue 185 LEU Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 108 LEU Chi-restraints excluded: chain s residue 67 ILE Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain s residue 185 LEU Chi-restraints excluded: chain s residue 196 PHE Chi-restraints excluded: chain t residue 50 THR Chi-restraints excluded: chain t residue 196 PHE Chi-restraints excluded: chain u residue 80 ASP Chi-restraints excluded: chain u residue 108 LEU Chi-restraints excluded: chain u residue 193 ASP Chi-restraints excluded: chain u residue 196 PHE Chi-restraints excluded: chain v residue 33 LEU Chi-restraints excluded: chain v residue 40 LEU Chi-restraints excluded: chain w residue 196 PHE Chi-restraints excluded: chain x residue 36 MET Chi-restraints excluded: chain x residue 152 ILE Chi-restraints excluded: chain x residue 185 LEU Chi-restraints excluded: chain x residue 193 ASP Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain y residue 100 HIS Chi-restraints excluded: chain y residue 176 LEU Chi-restraints excluded: chain z residue 33 LEU Chi-restraints excluded: chain z residue 45 ARG Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain z residue 193 ASP Chi-restraints excluded: chain 0 residue 36 MET Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 0 residue 70 ARG Chi-restraints excluded: chain 1 residue 45 ARG Chi-restraints excluded: chain 1 residue 212 MET Chi-restraints excluded: chain 2 residue 40 LEU Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 2 residue 67 ILE Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 152 ILE Chi-restraints excluded: chain 2 residue 154 GLU Chi-restraints excluded: chain 2 residue 176 LEU Chi-restraints excluded: chain 3 residue 40 LEU Chi-restraints excluded: chain 3 residue 50 THR Chi-restraints excluded: chain 3 residue 176 LEU Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 5 residue 79 LEU Chi-restraints excluded: chain 6 residue 27 ASP Chi-restraints excluded: chain 6 residue 38 LEU Chi-restraints excluded: chain 6 residue 40 LEU Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 176 LEU Chi-restraints excluded: chain 6 residue 196 PHE Chi-restraints excluded: chain 7 residue 91 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 1063 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 628 optimal weight: 0.8980 chunk 805 optimal weight: 0.8980 chunk 624 optimal weight: 3.9990 chunk 928 optimal weight: 1.9990 chunk 615 optimal weight: 5.9990 chunk 1098 optimal weight: 0.8980 chunk 687 optimal weight: 0.9990 chunk 669 optimal weight: 5.9990 chunk 507 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN M 137 ASN N 137 ASN ** e 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 137 ASN r 137 ASN v 100 HIS x 100 HIS y 137 ASN ** 6 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 97320 Z= 0.179 Angle : 0.624 13.498 130980 Z= 0.274 Chirality : 0.031 0.185 14400 Planarity : 0.002 0.041 17160 Dihedral : 5.377 83.519 13624 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.77 % Allowed : 19.29 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 5.48 (0.07), residues: 11640 helix: 3.89 (0.05), residues: 10200 sheet: None (None), residues: 0 loop : 1.05 (0.19), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP H 199 HIS 0.002 0.000 HIS a 100 PHE 0.006 0.000 PHE 2 54 TYR 0.012 0.001 TYR W 129 ARG 0.008 0.000 ARG 6 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 9780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 454 time to evaluate : 8.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 72 TYR cc_start: 0.8551 (t80) cc_final: 0.8270 (t80) REVERT: A 62 ASP cc_start: 0.8115 (m-30) cc_final: 0.7783 (m-30) REVERT: A 212 MET cc_start: 0.7563 (tpt) cc_final: 0.7315 (tpt) REVERT: B 199 TRP cc_start: 0.8576 (t60) cc_final: 0.8328 (t60) REVERT: E 66 LEU cc_start: 0.9075 (tp) cc_final: 0.8786 (tt) REVERT: F 50 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8588 (p) REVERT: I 29 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6532 (tt) REVERT: I 40 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7899 (tt) REVERT: L 29 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7236 (tt) REVERT: M 29 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7669 (tt) REVERT: M 40 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8231 (tt) REVERT: N 81 ARG cc_start: 0.8132 (mpt180) cc_final: 0.7031 (tmm-80) REVERT: U 126 GLU cc_start: 0.7571 (tp30) cc_final: 0.7355 (tp30) REVERT: Y 206 GLU cc_start: 0.8437 (pp20) cc_final: 0.8101 (pp20) REVERT: Z 40 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6900 (tp) REVERT: b 79 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8158 (pp) REVERT: c 36 MET cc_start: 0.7812 (tmm) cc_final: 0.7348 (tmm) REVERT: c 62 ASP cc_start: 0.8729 (m-30) cc_final: 0.8254 (m-30) REVERT: d 154 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8188 (pp20) REVERT: d 212 MET cc_start: 0.6643 (ptt) cc_final: 0.5472 (tmm) REVERT: f 45 ARG cc_start: 0.8391 (ttp80) cc_final: 0.8149 (ttp80) REVERT: f 62 ASP cc_start: 0.7896 (m-30) cc_final: 0.7572 (m-30) REVERT: h 199 TRP cc_start: 0.8651 (t60) cc_final: 0.8429 (t60) REVERT: i 185 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8169 (tt) REVERT: k 176 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8314 (mp) REVERT: l 81 ARG cc_start: 0.8817 (mtp180) cc_final: 0.8597 (mmp80) REVERT: p 62 ASP cc_start: 0.8095 (m-30) cc_final: 0.7732 (m-30) REVERT: q 29 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7699 (tt) REVERT: q 40 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8587 (tp) REVERT: r 36 MET cc_start: 0.7749 (tmm) cc_final: 0.7327 (tmm) REVERT: r 62 ASP cc_start: 0.8500 (m-30) cc_final: 0.8029 (m-30) REVERT: s 196 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7331 (m-80) REVERT: t 147 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8034 (tt) REVERT: t 196 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.7187 (t80) REVERT: t 197 GLU cc_start: 0.8564 (pp20) cc_final: 0.8303 (pp20) REVERT: v 40 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8197 (tt) REVERT: x 81 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7558 (ttp80) REVERT: z 45 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7177 (ttm-80) REVERT: z 79 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8155 (pp) REVERT: 1 42 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7523 (mm-30) REVERT: 1 45 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8111 (ttp-110) REVERT: 2 154 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8751 (pp20) REVERT: 2 196 PHE cc_start: 0.9112 (OUTLIER) cc_final: 0.8705 (m-80) REVERT: 3 40 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6898 (tp) REVERT: 3 212 MET cc_start: 0.8411 (ppp) cc_final: 0.7857 (ppp) REVERT: 4 137 ASN cc_start: 0.7725 (p0) cc_final: 0.7454 (p0) REVERT: 5 37 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7403 (tm-30) REVERT: 6 154 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7703 (tm-30) REVERT: 6 196 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.7701 (m-80) REVERT: 7 212 MET cc_start: 0.8438 (tpt) cc_final: 0.8158 (tpt) outliers start: 271 outliers final: 192 residues processed: 678 average time/residue: 0.7224 time to fit residues: 898.5741 Evaluate side-chains 647 residues out of total 9780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 429 time to evaluate : 8.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 193 ASP Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 193 ASP Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 196 PHE Chi-restraints excluded: chain O residue 152 ILE Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 193 ASP Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain S residue 193 ASP Chi-restraints excluded: chain S residue 196 PHE Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 152 ILE Chi-restraints excluded: chain T residue 193 ASP Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 176 LEU Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 80 ASP Chi-restraints excluded: chain V residue 193 ASP Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain Y residue 40 LEU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 152 ILE Chi-restraints excluded: chain Y residue 193 ASP Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain Z residue 62 ASP Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain b residue 27 ASP Chi-restraints excluded: chain b residue 79 LEU Chi-restraints excluded: chain c residue 27 ASP Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 80 ASP Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 154 GLU Chi-restraints excluded: chain d residue 196 PHE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 152 ILE Chi-restraints excluded: chain e residue 158 ASN Chi-restraints excluded: chain e residue 193 ASP Chi-restraints excluded: chain f residue 36 MET Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 165 SER Chi-restraints excluded: chain f residue 176 LEU Chi-restraints excluded: chain f residue 185 LEU Chi-restraints excluded: chain f residue 193 ASP Chi-restraints excluded: chain g residue 173 THR Chi-restraints excluded: chain g residue 176 LEU Chi-restraints excluded: chain g residue 193 ASP Chi-restraints excluded: chain h residue 176 LEU Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 176 LEU Chi-restraints excluded: chain i residue 185 LEU Chi-restraints excluded: chain i residue 193 ASP Chi-restraints excluded: chain j residue 185 LEU Chi-restraints excluded: chain j residue 193 ASP Chi-restraints excluded: chain k residue 36 MET Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain k residue 126 GLU Chi-restraints excluded: chain k residue 176 LEU Chi-restraints excluded: chain k residue 185 LEU Chi-restraints excluded: chain k residue 193 ASP Chi-restraints excluded: chain k residue 196 PHE Chi-restraints excluded: chain l residue 40 LEU Chi-restraints excluded: chain l residue 176 LEU Chi-restraints excluded: chain l residue 193 ASP Chi-restraints excluded: chain m residue 50 THR Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 193 ASP Chi-restraints excluded: chain n residue 29 LEU Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 147 ILE Chi-restraints excluded: chain n residue 193 ASP Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 101 THR Chi-restraints excluded: chain o residue 185 LEU Chi-restraints excluded: chain o residue 193 ASP Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 185 LEU Chi-restraints excluded: chain p residue 193 ASP Chi-restraints excluded: chain q residue 29 LEU Chi-restraints excluded: chain q residue 40 LEU Chi-restraints excluded: chain q residue 176 LEU Chi-restraints excluded: chain q residue 185 LEU Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 108 LEU Chi-restraints excluded: chain s residue 67 ILE Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain s residue 185 LEU Chi-restraints excluded: chain s residue 196 PHE Chi-restraints excluded: chain t residue 50 THR Chi-restraints excluded: chain t residue 67 ILE Chi-restraints excluded: chain t residue 147 ILE Chi-restraints excluded: chain t residue 196 PHE Chi-restraints excluded: chain u residue 80 ASP Chi-restraints excluded: chain u residue 108 LEU Chi-restraints excluded: chain u residue 193 ASP Chi-restraints excluded: chain u residue 196 PHE Chi-restraints excluded: chain v residue 33 LEU Chi-restraints excluded: chain v residue 40 LEU Chi-restraints excluded: chain v residue 117 GLN Chi-restraints excluded: chain w residue 196 PHE Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 36 MET Chi-restraints excluded: chain x residue 81 ARG Chi-restraints excluded: chain x residue 147 ILE Chi-restraints excluded: chain x residue 152 ILE Chi-restraints excluded: chain x residue 176 LEU Chi-restraints excluded: chain x residue 193 ASP Chi-restraints excluded: chain y residue 28 LEU Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain y residue 100 HIS Chi-restraints excluded: chain y residue 165 SER Chi-restraints excluded: chain y residue 176 LEU Chi-restraints excluded: chain y residue 193 ASP Chi-restraints excluded: chain z residue 33 LEU Chi-restraints excluded: chain z residue 45 ARG Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain z residue 67 ILE Chi-restraints excluded: chain z residue 79 LEU Chi-restraints excluded: chain z residue 193 ASP Chi-restraints excluded: chain 0 residue 36 MET Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 0 residue 67 ILE Chi-restraints excluded: chain 1 residue 45 ARG Chi-restraints excluded: chain 1 residue 212 MET Chi-restraints excluded: chain 2 residue 40 LEU Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 2 residue 67 ILE Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 152 ILE Chi-restraints excluded: chain 2 residue 154 GLU Chi-restraints excluded: chain 2 residue 176 LEU Chi-restraints excluded: chain 2 residue 196 PHE Chi-restraints excluded: chain 3 residue 40 LEU Chi-restraints excluded: chain 3 residue 50 THR Chi-restraints excluded: chain 3 residue 176 LEU Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 165 SER Chi-restraints excluded: chain 5 residue 29 LEU Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 5 residue 167 LEU Chi-restraints excluded: chain 6 residue 27 ASP Chi-restraints excluded: chain 6 residue 29 LEU Chi-restraints excluded: chain 6 residue 38 LEU Chi-restraints excluded: chain 6 residue 40 LEU Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 154 GLU Chi-restraints excluded: chain 6 residue 176 LEU Chi-restraints excluded: chain 6 residue 196 PHE Chi-restraints excluded: chain 7 residue 91 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 679 optimal weight: 6.9990 chunk 438 optimal weight: 0.5980 chunk 656 optimal weight: 0.9990 chunk 330 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 212 optimal weight: 0.6980 chunk 698 optimal weight: 0.9980 chunk 748 optimal weight: 3.9990 chunk 543 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 863 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100 HIS E 161 ASN K 137 ASN S 137 ASN ** e 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 137 ASN r 137 ASN y 137 ASN ** 6 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 97320 Z= 0.163 Angle : 0.614 12.257 130980 Z= 0.267 Chirality : 0.030 0.182 14400 Planarity : 0.002 0.033 17160 Dihedral : 5.265 81.971 13624 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.63 % Allowed : 19.75 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 5.60 (0.07), residues: 11640 helix: 3.98 (0.05), residues: 10200 sheet: None (None), residues: 0 loop : 0.97 (0.19), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP i 199 HIS 0.001 0.000 HIS a 100 PHE 0.006 0.000 PHE 2 54 TYR 0.015 0.001 TYR B 72 ARG 0.008 0.000 ARG c 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 9780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 471 time to evaluate : 8.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 72 TYR cc_start: 0.8502 (t80) cc_final: 0.8169 (t80) REVERT: A 62 ASP cc_start: 0.8095 (m-30) cc_final: 0.7768 (m-30) REVERT: A 212 MET cc_start: 0.7392 (tpt) cc_final: 0.7118 (tpt) REVERT: C 200 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8250 (mm-30) REVERT: E 36 MET cc_start: 0.7737 (ttp) cc_final: 0.7465 (tmm) REVERT: E 66 LEU cc_start: 0.9025 (tp) cc_final: 0.8724 (tt) REVERT: F 79 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7893 (pp) REVERT: F 185 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7656 (mt) REVERT: G 126 GLU cc_start: 0.8318 (pm20) cc_final: 0.8032 (pm20) REVERT: I 29 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6475 (tt) REVERT: I 40 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7811 (tt) REVERT: J 200 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8314 (mm-30) REVERT: L 29 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.7017 (tt) REVERT: M 29 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7585 (tt) REVERT: M 40 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8217 (tt) REVERT: N 81 ARG cc_start: 0.8034 (mpt180) cc_final: 0.7084 (tmm-80) REVERT: S 36 MET cc_start: 0.8069 (tmm) cc_final: 0.7449 (tmm) REVERT: W 126 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7416 (tm-30) REVERT: Y 206 GLU cc_start: 0.8419 (pp20) cc_final: 0.8085 (pp20) REVERT: Z 40 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6950 (tp) REVERT: b 79 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8140 (pp) REVERT: c 36 MET cc_start: 0.7743 (tmm) cc_final: 0.7324 (tmm) REVERT: c 62 ASP cc_start: 0.8715 (m-30) cc_final: 0.8240 (m-30) REVERT: d 62 ASP cc_start: 0.8592 (m-30) cc_final: 0.8350 (t0) REVERT: d 212 MET cc_start: 0.6638 (ptt) cc_final: 0.5458 (tmm) REVERT: f 45 ARG cc_start: 0.8396 (ttp80) cc_final: 0.8136 (ttp80) REVERT: f 62 ASP cc_start: 0.7938 (m-30) cc_final: 0.7589 (m-30) REVERT: h 199 TRP cc_start: 0.8649 (t60) cc_final: 0.8425 (t60) REVERT: i 185 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8134 (tt) REVERT: j 114 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8096 (mp) REVERT: k 176 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8295 (mp) REVERT: l 62 ASP cc_start: 0.8606 (m-30) cc_final: 0.8038 (m-30) REVERT: l 81 ARG cc_start: 0.8845 (mtp180) cc_final: 0.8616 (mmp80) REVERT: n 212 MET cc_start: 0.9078 (ttp) cc_final: 0.8703 (tpt) REVERT: p 62 ASP cc_start: 0.8077 (m-30) cc_final: 0.7698 (m-30) REVERT: q 40 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8535 (tp) REVERT: r 36 MET cc_start: 0.7755 (tmm) cc_final: 0.7533 (tmm) REVERT: r 62 ASP cc_start: 0.8494 (m-30) cc_final: 0.8021 (m-30) REVERT: s 196 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7420 (m-80) REVERT: t 196 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7131 (t80) REVERT: t 197 GLU cc_start: 0.8565 (pp20) cc_final: 0.8295 (pp20) REVERT: v 40 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8131 (tt) REVERT: w 212 MET cc_start: 0.9367 (tmm) cc_final: 0.9108 (tpp) REVERT: x 81 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7583 (ttp80) REVERT: y 80 ASP cc_start: 0.6452 (p0) cc_final: 0.6246 (p0) REVERT: z 45 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7161 (ttm-80) REVERT: 1 42 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7554 (mm-30) REVERT: 1 45 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7973 (ttp-110) REVERT: 2 154 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8745 (pp20) REVERT: 2 196 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8687 (m-80) REVERT: 3 40 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6916 (tp) REVERT: 3 212 MET cc_start: 0.8412 (ppp) cc_final: 0.7883 (ppp) REVERT: 4 137 ASN cc_start: 0.7706 (p0) cc_final: 0.7438 (p0) REVERT: 5 37 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7359 (tm-30) REVERT: 6 126 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8148 (tm-30) REVERT: 6 154 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7735 (tm-30) REVERT: 6 196 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.8182 (m-80) REVERT: 6 206 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8926 (pt0) REVERT: 7 212 MET cc_start: 0.8435 (tpt) cc_final: 0.8158 (tpt) outliers start: 257 outliers final: 187 residues processed: 680 average time/residue: 0.7269 time to fit residues: 903.2767 Evaluate side-chains 642 residues out of total 9780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 431 time to evaluate : 8.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 193 ASP Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain K residue 193 ASP Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 193 ASP Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain N residue 29 LEU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 196 PHE Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 152 ILE Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 193 ASP Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 193 ASP Chi-restraints excluded: chain S residue 196 PHE Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 152 ILE Chi-restraints excluded: chain T residue 193 ASP Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 176 LEU Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 80 ASP Chi-restraints excluded: chain V residue 193 ASP Chi-restraints excluded: chain W residue 36 MET Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 67 ILE Chi-restraints excluded: chain Y residue 40 LEU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 152 ILE Chi-restraints excluded: chain Y residue 176 LEU Chi-restraints excluded: chain Y residue 193 ASP Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain b residue 27 ASP Chi-restraints excluded: chain b residue 79 LEU Chi-restraints excluded: chain c residue 27 ASP Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 196 PHE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 152 ILE Chi-restraints excluded: chain e residue 158 ASN Chi-restraints excluded: chain e residue 193 ASP Chi-restraints excluded: chain f residue 36 MET Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 165 SER Chi-restraints excluded: chain f residue 176 LEU Chi-restraints excluded: chain f residue 185 LEU Chi-restraints excluded: chain f residue 193 ASP Chi-restraints excluded: chain g residue 152 ILE Chi-restraints excluded: chain g residue 173 THR Chi-restraints excluded: chain g residue 176 LEU Chi-restraints excluded: chain g residue 193 ASP Chi-restraints excluded: chain h residue 176 LEU Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 176 LEU Chi-restraints excluded: chain i residue 185 LEU Chi-restraints excluded: chain i residue 193 ASP Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain j residue 114 LEU Chi-restraints excluded: chain j residue 185 LEU Chi-restraints excluded: chain j residue 193 ASP Chi-restraints excluded: chain k residue 36 MET Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain k residue 126 GLU Chi-restraints excluded: chain k residue 176 LEU Chi-restraints excluded: chain k residue 185 LEU Chi-restraints excluded: chain k residue 193 ASP Chi-restraints excluded: chain k residue 196 PHE Chi-restraints excluded: chain l residue 40 LEU Chi-restraints excluded: chain l residue 176 LEU Chi-restraints excluded: chain l residue 193 ASP Chi-restraints excluded: chain m residue 50 THR Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 193 ASP Chi-restraints excluded: chain n residue 29 LEU Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 147 ILE Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 67 ILE Chi-restraints excluded: chain o residue 185 LEU Chi-restraints excluded: chain o residue 193 ASP Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 108 LEU Chi-restraints excluded: chain p residue 185 LEU Chi-restraints excluded: chain p residue 193 ASP Chi-restraints excluded: chain q residue 40 LEU Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain q residue 176 LEU Chi-restraints excluded: chain q residue 185 LEU Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 108 LEU Chi-restraints excluded: chain s residue 50 THR Chi-restraints excluded: chain s residue 67 ILE Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain s residue 185 LEU Chi-restraints excluded: chain s residue 196 PHE Chi-restraints excluded: chain t residue 50 THR Chi-restraints excluded: chain t residue 67 ILE Chi-restraints excluded: chain t residue 196 PHE Chi-restraints excluded: chain u residue 80 ASP Chi-restraints excluded: chain u residue 193 ASP Chi-restraints excluded: chain u residue 196 PHE Chi-restraints excluded: chain v residue 33 LEU Chi-restraints excluded: chain v residue 40 LEU Chi-restraints excluded: chain v residue 117 GLN Chi-restraints excluded: chain w residue 29 LEU Chi-restraints excluded: chain w residue 196 PHE Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 36 MET Chi-restraints excluded: chain x residue 50 THR Chi-restraints excluded: chain x residue 81 ARG Chi-restraints excluded: chain x residue 147 ILE Chi-restraints excluded: chain x residue 152 ILE Chi-restraints excluded: chain x residue 193 ASP Chi-restraints excluded: chain y residue 28 LEU Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain y residue 100 HIS Chi-restraints excluded: chain y residue 165 SER Chi-restraints excluded: chain y residue 176 LEU Chi-restraints excluded: chain y residue 193 ASP Chi-restraints excluded: chain z residue 33 LEU Chi-restraints excluded: chain z residue 45 ARG Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain z residue 193 ASP Chi-restraints excluded: chain 0 residue 36 MET Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 45 ARG Chi-restraints excluded: chain 1 residue 212 MET Chi-restraints excluded: chain 2 residue 40 LEU Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 2 residue 67 ILE Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 152 ILE Chi-restraints excluded: chain 2 residue 154 GLU Chi-restraints excluded: chain 2 residue 176 LEU Chi-restraints excluded: chain 2 residue 196 PHE Chi-restraints excluded: chain 3 residue 40 LEU Chi-restraints excluded: chain 3 residue 50 THR Chi-restraints excluded: chain 3 residue 176 LEU Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 5 residue 167 LEU Chi-restraints excluded: chain 6 residue 27 ASP Chi-restraints excluded: chain 6 residue 38 LEU Chi-restraints excluded: chain 6 residue 40 LEU Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 154 GLU Chi-restraints excluded: chain 6 residue 176 LEU Chi-restraints excluded: chain 6 residue 196 PHE Chi-restraints excluded: chain 7 residue 91 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 999 optimal weight: 3.9990 chunk 1052 optimal weight: 1.9990 chunk 960 optimal weight: 0.9990 chunk 1023 optimal weight: 0.0060 chunk 616 optimal weight: 6.9990 chunk 446 optimal weight: 4.9990 chunk 804 optimal weight: 0.4980 chunk 314 optimal weight: 3.9990 chunk 925 optimal weight: 0.5980 chunk 968 optimal weight: 9.9990 chunk 1020 optimal weight: 2.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 137 ASN X 161 ASN a 203 GLN ** e 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 137 ASN y 137 ASN ** 6 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 97320 Z= 0.161 Angle : 0.617 11.806 130980 Z= 0.268 Chirality : 0.031 0.183 14400 Planarity : 0.002 0.034 17160 Dihedral : 5.185 80.081 13624 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.46 % Allowed : 19.96 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 5.55 (0.07), residues: 11640 helix: 3.95 (0.05), residues: 10260 sheet: None (None), residues: 0 loop : 0.78 (0.20), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP H 199 HIS 0.001 0.000 HIS f 100 PHE 0.007 0.000 PHE n 196 TYR 0.006 0.001 TYR o 129 ARG 0.009 0.000 ARG c 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 9780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 467 time to evaluate : 8.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 72 TYR cc_start: 0.8468 (t80) cc_final: 0.8136 (t80) REVERT: A 62 ASP cc_start: 0.8119 (m-30) cc_final: 0.7772 (m-30) REVERT: A 212 MET cc_start: 0.7164 (tpt) cc_final: 0.6884 (tpt) REVERT: B 185 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7519 (tt) REVERT: C 200 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8257 (mm-30) REVERT: E 66 LEU cc_start: 0.9003 (tp) cc_final: 0.8700 (tt) REVERT: F 79 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7924 (pp) REVERT: F 185 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7655 (mt) REVERT: I 29 LEU cc_start: 0.6660 (OUTLIER) cc_final: 0.6294 (tt) REVERT: I 40 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7689 (tt) REVERT: I 199 TRP cc_start: 0.8864 (t60) cc_final: 0.8363 (t60) REVERT: L 29 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6998 (tt) REVERT: M 29 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7555 (tt) REVERT: M 40 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8182 (tt) REVERT: N 81 ARG cc_start: 0.7989 (mpt180) cc_final: 0.6999 (tmm-80) REVERT: Q 36 MET cc_start: 0.8106 (tmm) cc_final: 0.7616 (tmm) REVERT: Y 163 SER cc_start: 0.6134 (m) cc_final: 0.5479 (p) REVERT: Y 206 GLU cc_start: 0.8404 (pp20) cc_final: 0.8077 (pp20) REVERT: Z 40 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6954 (tp) REVERT: c 62 ASP cc_start: 0.8692 (m-30) cc_final: 0.8262 (m-30) REVERT: d 62 ASP cc_start: 0.8587 (m-30) cc_final: 0.8343 (t0) REVERT: d 212 MET cc_start: 0.6727 (ptt) cc_final: 0.5498 (tmm) REVERT: f 45 ARG cc_start: 0.8368 (ttp80) cc_final: 0.8102 (ttp80) REVERT: f 62 ASP cc_start: 0.7936 (m-30) cc_final: 0.7594 (m-30) REVERT: h 199 TRP cc_start: 0.8682 (t60) cc_final: 0.8461 (t60) REVERT: i 185 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8126 (tt) REVERT: j 114 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8066 (mp) REVERT: k 126 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7421 (tp30) REVERT: k 176 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8268 (mp) REVERT: l 81 ARG cc_start: 0.8862 (mtp180) cc_final: 0.8605 (mmp80) REVERT: n 212 MET cc_start: 0.9077 (ttp) cc_final: 0.8703 (tpt) REVERT: p 62 ASP cc_start: 0.8078 (m-30) cc_final: 0.7698 (m-30) REVERT: q 40 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8508 (tp) REVERT: r 36 MET cc_start: 0.7713 (tmm) cc_final: 0.7153 (tmm) REVERT: r 62 ASP cc_start: 0.8498 (m-30) cc_final: 0.8020 (m-30) REVERT: s 196 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.7408 (m-80) REVERT: t 196 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7194 (t80) REVERT: t 197 GLU cc_start: 0.8570 (pp20) cc_final: 0.8296 (pp20) REVERT: v 40 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8124 (tt) REVERT: w 212 MET cc_start: 0.9352 (tmm) cc_final: 0.9022 (tpp) REVERT: x 81 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7586 (ttp80) REVERT: y 80 ASP cc_start: 0.6391 (p0) cc_final: 0.6190 (p0) REVERT: z 45 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7159 (ttm-80) REVERT: 1 42 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7523 (mm-30) REVERT: 1 45 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7956 (ttp-110) REVERT: 2 154 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8803 (pp20) REVERT: 2 196 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8664 (m-80) REVERT: 3 40 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6925 (tp) REVERT: 3 152 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7259 (mt) REVERT: 3 212 MET cc_start: 0.8416 (ppp) cc_final: 0.7883 (ppp) REVERT: 4 137 ASN cc_start: 0.7706 (p0) cc_final: 0.7434 (p0) REVERT: 5 37 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7319 (tm-30) REVERT: 6 126 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8153 (tm-30) REVERT: 6 154 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8007 (tm-30) REVERT: 6 196 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.8144 (m-80) REVERT: 6 206 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8914 (pt0) REVERT: 7 212 MET cc_start: 0.8442 (tpt) cc_final: 0.8164 (tpt) outliers start: 241 outliers final: 184 residues processed: 663 average time/residue: 0.7372 time to fit residues: 894.9026 Evaluate side-chains 649 residues out of total 9780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 439 time to evaluate : 8.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 193 ASP Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain K residue 193 ASP Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 193 ASP Chi-restraints excluded: chain N residue 29 LEU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 196 PHE Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 152 ILE Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 193 ASP Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain S residue 193 ASP Chi-restraints excluded: chain S residue 196 PHE Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 152 ILE Chi-restraints excluded: chain T residue 193 ASP Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 176 LEU Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 80 ASP Chi-restraints excluded: chain V residue 193 ASP Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain Y residue 40 LEU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 152 ILE Chi-restraints excluded: chain Y residue 176 LEU Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain b residue 27 ASP Chi-restraints excluded: chain c residue 27 ASP Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 196 PHE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 152 ILE Chi-restraints excluded: chain e residue 158 ASN Chi-restraints excluded: chain e residue 193 ASP Chi-restraints excluded: chain f residue 36 MET Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 165 SER Chi-restraints excluded: chain f residue 176 LEU Chi-restraints excluded: chain f residue 185 LEU Chi-restraints excluded: chain f residue 193 ASP Chi-restraints excluded: chain g residue 173 THR Chi-restraints excluded: chain g residue 176 LEU Chi-restraints excluded: chain g residue 193 ASP Chi-restraints excluded: chain h residue 176 LEU Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 176 LEU Chi-restraints excluded: chain i residue 185 LEU Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain j residue 114 LEU Chi-restraints excluded: chain j residue 185 LEU Chi-restraints excluded: chain j residue 193 ASP Chi-restraints excluded: chain k residue 36 MET Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain k residue 126 GLU Chi-restraints excluded: chain k residue 176 LEU Chi-restraints excluded: chain k residue 185 LEU Chi-restraints excluded: chain k residue 193 ASP Chi-restraints excluded: chain k residue 196 PHE Chi-restraints excluded: chain l residue 40 LEU Chi-restraints excluded: chain l residue 176 LEU Chi-restraints excluded: chain l residue 193 ASP Chi-restraints excluded: chain m residue 50 THR Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 193 ASP Chi-restraints excluded: chain n residue 147 ILE Chi-restraints excluded: chain n residue 160 ASP Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 67 ILE Chi-restraints excluded: chain o residue 185 LEU Chi-restraints excluded: chain o residue 193 ASP Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 185 LEU Chi-restraints excluded: chain p residue 193 ASP Chi-restraints excluded: chain q residue 40 LEU Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain q residue 176 LEU Chi-restraints excluded: chain q residue 185 LEU Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 108 LEU Chi-restraints excluded: chain s residue 38 LEU Chi-restraints excluded: chain s residue 50 THR Chi-restraints excluded: chain s residue 67 ILE Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain s residue 185 LEU Chi-restraints excluded: chain s residue 196 PHE Chi-restraints excluded: chain t residue 50 THR Chi-restraints excluded: chain t residue 67 ILE Chi-restraints excluded: chain t residue 196 PHE Chi-restraints excluded: chain u residue 80 ASP Chi-restraints excluded: chain u residue 193 ASP Chi-restraints excluded: chain u residue 196 PHE Chi-restraints excluded: chain v residue 33 LEU Chi-restraints excluded: chain v residue 40 LEU Chi-restraints excluded: chain v residue 117 GLN Chi-restraints excluded: chain w residue 29 LEU Chi-restraints excluded: chain w residue 196 PHE Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 36 MET Chi-restraints excluded: chain x residue 50 THR Chi-restraints excluded: chain x residue 81 ARG Chi-restraints excluded: chain x residue 147 ILE Chi-restraints excluded: chain x residue 152 ILE Chi-restraints excluded: chain x residue 193 ASP Chi-restraints excluded: chain y residue 28 LEU Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain y residue 100 HIS Chi-restraints excluded: chain y residue 165 SER Chi-restraints excluded: chain y residue 176 LEU Chi-restraints excluded: chain y residue 193 ASP Chi-restraints excluded: chain z residue 33 LEU Chi-restraints excluded: chain z residue 45 ARG Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain z residue 193 ASP Chi-restraints excluded: chain 0 residue 36 MET Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 45 ARG Chi-restraints excluded: chain 1 residue 212 MET Chi-restraints excluded: chain 2 residue 40 LEU Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 2 residue 67 ILE Chi-restraints excluded: chain 2 residue 152 ILE Chi-restraints excluded: chain 2 residue 154 GLU Chi-restraints excluded: chain 2 residue 176 LEU Chi-restraints excluded: chain 2 residue 196 PHE Chi-restraints excluded: chain 3 residue 40 LEU Chi-restraints excluded: chain 3 residue 50 THR Chi-restraints excluded: chain 3 residue 152 ILE Chi-restraints excluded: chain 3 residue 176 LEU Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 165 SER Chi-restraints excluded: chain 5 residue 29 LEU Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 5 residue 167 LEU Chi-restraints excluded: chain 6 residue 27 ASP Chi-restraints excluded: chain 6 residue 29 LEU Chi-restraints excluded: chain 6 residue 38 LEU Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 154 GLU Chi-restraints excluded: chain 6 residue 176 LEU Chi-restraints excluded: chain 6 residue 196 PHE Chi-restraints excluded: chain 7 residue 91 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 672 optimal weight: 0.8980 chunk 1082 optimal weight: 6.9990 chunk 660 optimal weight: 7.9990 chunk 513 optimal weight: 0.0370 chunk 752 optimal weight: 2.9990 chunk 1135 optimal weight: 9.9990 chunk 1045 optimal weight: 0.7980 chunk 904 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 698 optimal weight: 4.9990 chunk 554 optimal weight: 1.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 137 ASN M 100 HIS ** e 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 137 ASN ** 6 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 97320 Z= 0.165 Angle : 0.623 11.995 130980 Z= 0.271 Chirality : 0.031 0.185 14400 Planarity : 0.002 0.034 17160 Dihedral : 5.105 78.373 13622 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.25 % Allowed : 20.35 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 5.51 (0.07), residues: 11640 helix: 3.93 (0.05), residues: 10260 sheet: None (None), residues: 0 loop : 0.71 (0.19), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP i 199 HIS 0.002 0.000 HIS I 100 PHE 0.006 0.000 PHE 2 54 TYR 0.018 0.001 TYR b 129 ARG 0.010 0.000 ARG c 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 9780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 459 time to evaluate : 8.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 72 TYR cc_start: 0.8456 (t80) cc_final: 0.8116 (t80) REVERT: A 62 ASP cc_start: 0.8125 (m-30) cc_final: 0.7776 (m-30) REVERT: B 185 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7492 (tt) REVERT: C 200 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8259 (mm-30) REVERT: C 208 THR cc_start: 0.9522 (t) cc_final: 0.9240 (p) REVERT: E 66 LEU cc_start: 0.9012 (tp) cc_final: 0.8706 (tt) REVERT: F 79 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7930 (pp) REVERT: I 29 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.6306 (tt) REVERT: I 40 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7733 (tt) REVERT: L 29 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.7004 (tt) REVERT: M 29 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7547 (tt) REVERT: M 40 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8187 (tt) REVERT: N 81 ARG cc_start: 0.7972 (mpt180) cc_final: 0.7634 (mmp80) REVERT: O 36 MET cc_start: 0.8202 (tmm) cc_final: 0.7944 (tmm) REVERT: Q 36 MET cc_start: 0.8115 (tmm) cc_final: 0.7619 (tmm) REVERT: Y 163 SER cc_start: 0.6199 (m) cc_final: 0.5531 (p) REVERT: Y 206 GLU cc_start: 0.8391 (pp20) cc_final: 0.8068 (pp20) REVERT: Z 40 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6967 (tp) REVERT: c 62 ASP cc_start: 0.8664 (m-30) cc_final: 0.8264 (m-30) REVERT: d 62 ASP cc_start: 0.8582 (m-30) cc_final: 0.8344 (t0) REVERT: d 212 MET cc_start: 0.6728 (ptt) cc_final: 0.5492 (tmm) REVERT: f 45 ARG cc_start: 0.8399 (ttp80) cc_final: 0.8132 (ttp80) REVERT: f 62 ASP cc_start: 0.7931 (m-30) cc_final: 0.7588 (m-30) REVERT: h 199 TRP cc_start: 0.8737 (t60) cc_final: 0.8506 (t60) REVERT: i 185 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8134 (tt) REVERT: i 199 TRP cc_start: 0.8228 (t60) cc_final: 0.8014 (t60) REVERT: j 114 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8071 (mp) REVERT: k 126 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7428 (tp30) REVERT: k 176 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8253 (mp) REVERT: l 81 ARG cc_start: 0.8914 (mtp180) cc_final: 0.8622 (mmp80) REVERT: n 212 MET cc_start: 0.8990 (ttp) cc_final: 0.8676 (tpt) REVERT: p 62 ASP cc_start: 0.8082 (m-30) cc_final: 0.7703 (m-30) REVERT: q 40 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8486 (tp) REVERT: r 36 MET cc_start: 0.7593 (tmm) cc_final: 0.7161 (tmm) REVERT: r 62 ASP cc_start: 0.8504 (m-30) cc_final: 0.8019 (m-30) REVERT: s 196 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.7399 (m-80) REVERT: t 196 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.7210 (t80) REVERT: t 197 GLU cc_start: 0.8581 (pp20) cc_final: 0.8303 (pp20) REVERT: v 40 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8131 (tt) REVERT: w 212 MET cc_start: 0.9399 (tmm) cc_final: 0.8975 (tpp) REVERT: x 81 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7594 (ttp80) REVERT: z 45 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7160 (ttm-80) REVERT: 1 42 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7661 (mm-30) REVERT: 1 45 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8058 (ttp-110) REVERT: 2 154 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8807 (pp20) REVERT: 2 196 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8704 (m-80) REVERT: 3 40 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6925 (tp) REVERT: 3 212 MET cc_start: 0.8422 (ppp) cc_final: 0.7880 (ppp) REVERT: 4 137 ASN cc_start: 0.7709 (p0) cc_final: 0.7435 (p0) REVERT: 5 37 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7279 (tm-30) REVERT: 6 126 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8146 (tm-30) REVERT: 6 154 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8012 (tm-30) REVERT: 6 196 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.8153 (m-80) REVERT: 7 212 MET cc_start: 0.8438 (tpt) cc_final: 0.8166 (tpt) outliers start: 220 outliers final: 187 residues processed: 634 average time/residue: 0.7220 time to fit residues: 840.8844 Evaluate side-chains 648 residues out of total 9780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 437 time to evaluate : 8.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 193 ASP Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain K residue 193 ASP Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 193 ASP Chi-restraints excluded: chain N residue 29 LEU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 196 PHE Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 152 ILE Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 193 ASP Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain S residue 193 ASP Chi-restraints excluded: chain S residue 196 PHE Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 152 ILE Chi-restraints excluded: chain T residue 193 ASP Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 176 LEU Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 80 ASP Chi-restraints excluded: chain V residue 193 ASP Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain Y residue 40 LEU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 152 ILE Chi-restraints excluded: chain Y residue 176 LEU Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain b residue 27 ASP Chi-restraints excluded: chain c residue 27 ASP Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 196 PHE Chi-restraints excluded: chain e residue 152 ILE Chi-restraints excluded: chain e residue 158 ASN Chi-restraints excluded: chain e residue 193 ASP Chi-restraints excluded: chain f residue 36 MET Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 165 SER Chi-restraints excluded: chain f residue 176 LEU Chi-restraints excluded: chain f residue 185 LEU Chi-restraints excluded: chain f residue 193 ASP Chi-restraints excluded: chain g residue 173 THR Chi-restraints excluded: chain g residue 176 LEU Chi-restraints excluded: chain g residue 193 ASP Chi-restraints excluded: chain h residue 176 LEU Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 176 LEU Chi-restraints excluded: chain i residue 185 LEU Chi-restraints excluded: chain i residue 193 ASP Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain j residue 114 LEU Chi-restraints excluded: chain j residue 185 LEU Chi-restraints excluded: chain j residue 193 ASP Chi-restraints excluded: chain k residue 36 MET Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain k residue 126 GLU Chi-restraints excluded: chain k residue 176 LEU Chi-restraints excluded: chain k residue 185 LEU Chi-restraints excluded: chain k residue 193 ASP Chi-restraints excluded: chain k residue 196 PHE Chi-restraints excluded: chain l residue 40 LEU Chi-restraints excluded: chain l residue 176 LEU Chi-restraints excluded: chain l residue 193 ASP Chi-restraints excluded: chain m residue 50 THR Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 193 ASP Chi-restraints excluded: chain n residue 147 ILE Chi-restraints excluded: chain n residue 160 ASP Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 67 ILE Chi-restraints excluded: chain o residue 185 LEU Chi-restraints excluded: chain o residue 193 ASP Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 185 LEU Chi-restraints excluded: chain p residue 193 ASP Chi-restraints excluded: chain q residue 40 LEU Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain q residue 176 LEU Chi-restraints excluded: chain q residue 185 LEU Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 108 LEU Chi-restraints excluded: chain s residue 38 LEU Chi-restraints excluded: chain s residue 50 THR Chi-restraints excluded: chain s residue 67 ILE Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain s residue 185 LEU Chi-restraints excluded: chain s residue 196 PHE Chi-restraints excluded: chain t residue 50 THR Chi-restraints excluded: chain t residue 67 ILE Chi-restraints excluded: chain t residue 196 PHE Chi-restraints excluded: chain u residue 80 ASP Chi-restraints excluded: chain u residue 193 ASP Chi-restraints excluded: chain u residue 196 PHE Chi-restraints excluded: chain v residue 33 LEU Chi-restraints excluded: chain v residue 40 LEU Chi-restraints excluded: chain v residue 117 GLN Chi-restraints excluded: chain w residue 29 LEU Chi-restraints excluded: chain w residue 196 PHE Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 36 MET Chi-restraints excluded: chain x residue 50 THR Chi-restraints excluded: chain x residue 81 ARG Chi-restraints excluded: chain x residue 147 ILE Chi-restraints excluded: chain x residue 152 ILE Chi-restraints excluded: chain x residue 193 ASP Chi-restraints excluded: chain y residue 28 LEU Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain y residue 100 HIS Chi-restraints excluded: chain y residue 165 SER Chi-restraints excluded: chain y residue 176 LEU Chi-restraints excluded: chain y residue 193 ASP Chi-restraints excluded: chain z residue 33 LEU Chi-restraints excluded: chain z residue 45 ARG Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain z residue 193 ASP Chi-restraints excluded: chain 0 residue 36 MET Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 0 residue 67 ILE Chi-restraints excluded: chain 1 residue 45 ARG Chi-restraints excluded: chain 1 residue 212 MET Chi-restraints excluded: chain 2 residue 40 LEU Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 2 residue 67 ILE Chi-restraints excluded: chain 2 residue 152 ILE Chi-restraints excluded: chain 2 residue 154 GLU Chi-restraints excluded: chain 2 residue 176 LEU Chi-restraints excluded: chain 2 residue 196 PHE Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 3 residue 40 LEU Chi-restraints excluded: chain 3 residue 50 THR Chi-restraints excluded: chain 3 residue 176 LEU Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 165 SER Chi-restraints excluded: chain 5 residue 29 LEU Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 5 residue 167 LEU Chi-restraints excluded: chain 6 residue 27 ASP Chi-restraints excluded: chain 6 residue 29 LEU Chi-restraints excluded: chain 6 residue 38 LEU Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 154 GLU Chi-restraints excluded: chain 6 residue 176 LEU Chi-restraints excluded: chain 6 residue 196 PHE Chi-restraints excluded: chain 7 residue 91 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 718 optimal weight: 3.9990 chunk 963 optimal weight: 0.1980 chunk 277 optimal weight: 0.7980 chunk 833 optimal weight: 0.0870 chunk 133 optimal weight: 0.7980 chunk 251 optimal weight: 6.9990 chunk 905 optimal weight: 0.9980 chunk 379 optimal weight: 2.9990 chunk 930 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 100 HIS N 137 ASN P 137 ASN U 137 ASN V 203 GLN e 85 GLN ** e 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 137 ASN t 137 ASN x 137 ASN ** 6 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 161 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.111627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.084946 restraints weight = 272934.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.088457 restraints weight = 171777.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.088506 restraints weight = 120627.101| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 97320 Z= 0.151 Angle : 0.612 12.046 130980 Z= 0.264 Chirality : 0.030 0.186 14400 Planarity : 0.002 0.036 17160 Dihedral : 5.013 76.313 13622 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.93 % Allowed : 20.79 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 5.65 (0.07), residues: 11640 helix: 4.03 (0.05), residues: 10260 sheet: None (None), residues: 0 loop : 0.65 (0.19), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP I 199 HIS 0.001 0.000 HIS a 100 PHE 0.006 0.000 PHE 2 54 TYR 0.009 0.000 TYR c 129 ARG 0.008 0.000 ARG T 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15576.60 seconds wall clock time: 278 minutes 15.02 seconds (16695.02 seconds total)