Starting phenix.real_space_refine on Sat Dec 16 09:30:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x80_22088/12_2023/6x80_22088_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x80_22088/12_2023/6x80_22088.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x80_22088/12_2023/6x80_22088_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x80_22088/12_2023/6x80_22088_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x80_22088/12_2023/6x80_22088_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x80_22088/12_2023/6x80_22088.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x80_22088/12_2023/6x80_22088.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x80_22088/12_2023/6x80_22088_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x80_22088/12_2023/6x80_22088_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 264 5.16 5 C 59092 2.51 5 N 16830 2.21 5 O 21296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 26": "OD1" <-> "OD2" Residue "A ASP 44": "OD1" <-> "OD2" Residue "A ASP 70": "OD1" <-> "OD2" Residue "A ASP 102": "OD1" <-> "OD2" Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 267": "OD1" <-> "OD2" Residue "A ASP 269": "OD1" <-> "OD2" Residue "A ASP 491": "OD1" <-> "OD2" Residue "A PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B ASP 102": "OD1" <-> "OD2" Residue "B PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "B ASP 336": "OD1" <-> "OD2" Residue "B PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 491": "OD1" <-> "OD2" Residue "B PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 26": "OD1" <-> "OD2" Residue "C ASP 44": "OD1" <-> "OD2" Residue "C ASP 102": "OD1" <-> "OD2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C ASP 124": "OD1" <-> "OD2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 269": "OD1" <-> "OD2" Residue "C ASP 312": "OD1" <-> "OD2" Residue "C ASP 339": "OD1" <-> "OD2" Residue "C PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 26": "OD1" <-> "OD2" Residue "D ASP 90": "OD1" <-> "OD2" Residue "D PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 220": "OE1" <-> "OE2" Residue "D ASP 235": "OD1" <-> "OD2" Residue "D TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 267": "OD1" <-> "OD2" Residue "D ASP 269": "OD1" <-> "OD2" Residue "D ASP 283": "OD1" <-> "OD2" Residue "D ASP 336": "OD1" <-> "OD2" Residue "D PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 26": "OD1" <-> "OD2" Residue "E ASP 44": "OD1" <-> "OD2" Residue "E ASP 102": "OD1" <-> "OD2" Residue "E ASP 124": "OD1" <-> "OD2" Residue "E PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 283": "OD1" <-> "OD2" Residue "E ASP 336": "OD1" <-> "OD2" Residue "E PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 491": "OD1" <-> "OD2" Residue "E PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 26": "OD1" <-> "OD2" Residue "F ASP 44": "OD1" <-> "OD2" Residue "F ASP 90": "OD1" <-> "OD2" Residue "F GLU 121": "OE1" <-> "OE2" Residue "F PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 267": "OD1" <-> "OD2" Residue "F ASP 269": "OD1" <-> "OD2" Residue "F ASP 336": "OD1" <-> "OD2" Residue "F GLU 367": "OE1" <-> "OE2" Residue "F PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 491": "OD1" <-> "OD2" Residue "F PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 26": "OD1" <-> "OD2" Residue "G ASP 44": "OD1" <-> "OD2" Residue "G ASP 79": "OD1" <-> "OD2" Residue "G ASP 102": "OD1" <-> "OD2" Residue "G ASP 115": "OD1" <-> "OD2" Residue "G PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 269": "OD1" <-> "OD2" Residue "G TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 336": "OD1" <-> "OD2" Residue "G PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 26": "OD1" <-> "OD2" Residue "H ASP 44": "OD1" <-> "OD2" Residue "H ASP 70": "OD1" <-> "OD2" Residue "H ASP 83": "OD1" <-> "OD2" Residue "H PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 269": "OD1" <-> "OD2" Residue "H PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 491": "OD1" <-> "OD2" Residue "H GLU 494": "OE1" <-> "OE2" Residue "H PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 19": "OD1" <-> "OD2" Residue "I ASP 79": "OD1" <-> "OD2" Residue "I ASP 102": "OD1" <-> "OD2" Residue "I PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 269": "OD1" <-> "OD2" Residue "I GLU 367": "OE1" <-> "OE2" Residue "I ASP 491": "OD1" <-> "OD2" Residue "I ASP 537": "OD1" <-> "OD2" Residue "I PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 44": "OD1" <-> "OD2" Residue "J ASP 90": "OD1" <-> "OD2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 235": "OD1" <-> "OD2" Residue "J TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 267": "OD1" <-> "OD2" Residue "J ASP 269": "OD1" <-> "OD2" Residue "J GLU 367": "OE1" <-> "OE2" Residue "J PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 26": "OD1" <-> "OD2" Residue "K ASP 44": "OD1" <-> "OD2" Residue "K GLU 121": "OE1" <-> "OE2" Residue "K PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 269": "OD1" <-> "OD2" Residue "K GLU 293": "OE1" <-> "OE2" Residue "K GLU 367": "OE1" <-> "OE2" Residue "K PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 491": "OD1" <-> "OD2" Residue "K PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 26": "OD1" <-> "OD2" Residue "L ASP 90": "OD1" <-> "OD2" Residue "L ASP 102": "OD1" <-> "OD2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "L ASP 124": "OD1" <-> "OD2" Residue "L PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 235": "OD1" <-> "OD2" Residue "L TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 269": "OD1" <-> "OD2" Residue "L ASP 491": "OD1" <-> "OD2" Residue "L PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 26": "OD1" <-> "OD2" Residue "M ASP 44": "OD1" <-> "OD2" Residue "M ASP 79": "OD1" <-> "OD2" Residue "M ASP 115": "OD1" <-> "OD2" Residue "M GLU 121": "OE1" <-> "OE2" Residue "M PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 269": "OD1" <-> "OD2" Residue "M ASP 339": "OD1" <-> "OD2" Residue "M ASP 378": "OD1" <-> "OD2" Residue "M PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 26": "OD1" <-> "OD2" Residue "N ASP 44": "OD1" <-> "OD2" Residue "N ASP 79": "OD1" <-> "OD2" Residue "N ASP 102": "OD1" <-> "OD2" Residue "N ASP 124": "OD1" <-> "OD2" Residue "N GLU 146": "OE1" <-> "OE2" Residue "N PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 539": "OD1" <-> "OD2" Residue "N PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 26": "OD1" <-> "OD2" Residue "O ASP 90": "OD1" <-> "OD2" Residue "O ASP 102": "OD1" <-> "OD2" Residue "O PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 235": "OD1" <-> "OD2" Residue "O TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 267": "OD1" <-> "OD2" Residue "O ASP 269": "OD1" <-> "OD2" Residue "O ASP 356": "OD1" <-> "OD2" Residue "O GLU 367": "OE1" <-> "OE2" Residue "O ASP 501": "OD1" <-> "OD2" Residue "O PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 26": "OD1" <-> "OD2" Residue "P ASP 44": "OD1" <-> "OD2" Residue "P ASP 115": "OD1" <-> "OD2" Residue "P PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 235": "OD1" <-> "OD2" Residue "P TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 491": "OD1" <-> "OD2" Residue "P ASP 501": "OD1" <-> "OD2" Residue "P PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 26": "OD1" <-> "OD2" Residue "Q ASP 79": "OD1" <-> "OD2" Residue "Q ASP 102": "OD1" <-> "OD2" Residue "Q ASP 115": "OD1" <-> "OD2" Residue "Q GLU 121": "OE1" <-> "OE2" Residue "Q ASP 124": "OD1" <-> "OD2" Residue "Q GLU 146": "OE1" <-> "OE2" Residue "Q PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 269": "OD1" <-> "OD2" Residue "Q GLU 293": "OE1" <-> "OE2" Residue "Q ASP 312": "OD1" <-> "OD2" Residue "Q GLU 367": "OE1" <-> "OE2" Residue "Q PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 26": "OD1" <-> "OD2" Residue "R PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 312": "OD1" <-> "OD2" Residue "R ASP 336": "OD1" <-> "OD2" Residue "R GLU 367": "OE1" <-> "OE2" Residue "R PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 44": "OD1" <-> "OD2" Residue "S ASP 70": "OD1" <-> "OD2" Residue "S ASP 102": "OD1" <-> "OD2" Residue "S GLU 121": "OE1" <-> "OE2" Residue "S GLU 146": "OE1" <-> "OE2" Residue "S PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 220": "OE1" <-> "OE2" Residue "S TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 269": "OD1" <-> "OD2" Residue "S TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 336": "OD1" <-> "OD2" Residue "S ASP 356": "OD1" <-> "OD2" Residue "S PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 501": "OD1" <-> "OD2" Residue "S PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 26": "OD1" <-> "OD2" Residue "T ASP 79": "OD1" <-> "OD2" Residue "T ASP 102": "OD1" <-> "OD2" Residue "T GLU 146": "OE1" <-> "OE2" Residue "T PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 235": "OD1" <-> "OD2" Residue "T TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 269": "OD1" <-> "OD2" Residue "T ASP 491": "OD1" <-> "OD2" Residue "T PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 26": "OD1" <-> "OD2" Residue "U ASP 44": "OD1" <-> "OD2" Residue "U ASP 79": "OD1" <-> "OD2" Residue "U ASP 102": "OD1" <-> "OD2" Residue "U ASP 124": "OD1" <-> "OD2" Residue "U GLU 146": "OE1" <-> "OE2" Residue "U PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 235": "OD1" <-> "OD2" Residue "U TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 269": "OD1" <-> "OD2" Residue "U TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 378": "OD1" <-> "OD2" Residue "U ASP 491": "OD1" <-> "OD2" Residue "U ASP 501": "OD1" <-> "OD2" Residue "U PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 26": "OD1" <-> "OD2" Residue "V ASP 70": "OD1" <-> "OD2" Residue "V ASP 102": "OD1" <-> "OD2" Residue "V GLU 121": "OE1" <-> "OE2" Residue "V PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 226": "OD1" <-> "OD2" Residue "V ASP 235": "OD1" <-> "OD2" Residue "V TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 269": "OD1" <-> "OD2" Residue "V PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 97482 Number of models: 1 Model: "" Number of chains: 44 Chain: "A" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4159 Classifications: {'peptide': 574} Modifications used: {'COO': 1} Link IDs: {'TRANS': 573} Chain: "B" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4159 Classifications: {'peptide': 574} Modifications used: {'COO': 1} Link IDs: {'TRANS': 573} Chain: "C" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4159 Classifications: {'peptide': 574} Modifications used: {'COO': 1} Link IDs: {'TRANS': 573} Chain: "D" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4159 Classifications: {'peptide': 574} Modifications used: {'COO': 1} Link IDs: {'TRANS': 573} Chain: "E" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4159 Classifications: {'peptide': 574} Modifications used: {'COO': 1} Link IDs: {'TRANS': 573} Chain: "F" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4159 Classifications: {'peptide': 574} Modifications used: {'COO': 1} Link IDs: {'TRANS': 573} Chain: "G" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4159 Classifications: {'peptide': 574} Modifications used: {'COO': 1} Link IDs: {'TRANS': 573} Chain: "H" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4159 Classifications: {'peptide': 574} Modifications used: {'COO': 1} Link IDs: {'TRANS': 573} Chain: "I" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4159 Classifications: {'peptide': 574} Modifications used: {'COO': 1} Link IDs: {'TRANS': 573} Chain: "J" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4159 Classifications: {'peptide': 574} Modifications used: {'COO': 1} Link IDs: {'TRANS': 573} Chain: "K" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4159 Classifications: {'peptide': 574} Modifications used: {'COO': 1} Link IDs: {'TRANS': 573} Chain: "L" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4159 Classifications: {'peptide': 574} Modifications used: {'COO': 1} Link IDs: {'TRANS': 573} Chain: "M" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4159 Classifications: {'peptide': 574} Modifications used: {'COO': 1} Link IDs: {'TRANS': 573} Chain: "N" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4159 Classifications: {'peptide': 574} Modifications used: {'COO': 1} Link IDs: {'TRANS': 573} Chain: "O" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4159 Classifications: {'peptide': 574} Modifications used: {'COO': 1} Link IDs: {'TRANS': 573} Chain: "P" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4159 Classifications: {'peptide': 574} Modifications used: {'COO': 1} Link IDs: {'TRANS': 573} Chain: "Q" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4159 Classifications: {'peptide': 574} Modifications used: {'COO': 1} Link IDs: {'TRANS': 573} Chain: "R" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4159 Classifications: {'peptide': 574} Modifications used: {'COO': 1} Link IDs: {'TRANS': 573} Chain: "S" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4159 Classifications: {'peptide': 574} Modifications used: {'COO': 1} Link IDs: {'TRANS': 573} Chain: "T" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4159 Classifications: {'peptide': 574} Modifications used: {'COO': 1} Link IDs: {'TRANS': 573} Chain: "U" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4159 Classifications: {'peptide': 574} Modifications used: {'COO': 1} Link IDs: {'TRANS': 573} Chain: "V" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4159 Classifications: {'peptide': 574} Modifications used: {'COO': 1} Link IDs: {'TRANS': 573} Chain: "A" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 272 Unusual residues: {'P8E': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 68 Chain: "B" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 272 Unusual residues: {'P8E': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 68 Chain: "C" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 272 Unusual residues: {'P8E': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 68 Chain: "D" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 272 Unusual residues: {'P8E': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 68 Chain: "E" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 272 Unusual residues: {'P8E': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 68 Chain: "F" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 272 Unusual residues: {'P8E': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 68 Chain: "G" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 272 Unusual residues: {'P8E': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 68 Chain: "H" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 272 Unusual residues: {'P8E': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 68 Chain: "I" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 272 Unusual residues: {'P8E': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 68 Chain: "J" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 272 Unusual residues: {'P8E': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 68 Chain: "K" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 272 Unusual residues: {'P8E': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 68 Chain: "L" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 272 Unusual residues: {'P8E': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 68 Chain: "M" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 272 Unusual residues: {'P8E': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 68 Chain: "N" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 272 Unusual residues: {'P8E': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 68 Chain: "O" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 272 Unusual residues: {'P8E': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 68 Chain: "P" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 272 Unusual residues: {'P8E': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 68 Chain: "Q" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 272 Unusual residues: {'P8E': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 68 Chain: "R" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 272 Unusual residues: {'P8E': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 68 Chain: "S" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 272 Unusual residues: {'P8E': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 68 Chain: "T" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 272 Unusual residues: {'P8E': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 68 Chain: "U" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 272 Unusual residues: {'P8E': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 68 Chain: "V" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 272 Unusual residues: {'P8E': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 68 Time building chain proxies: 36.78, per 1000 atoms: 0.38 Number of scatterers: 97482 At special positions: 0 Unit cell: (209.52, 212.76, 284.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 264 16.00 O 21296 8.00 N 16830 7.00 C 59092 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=371, symmetry=0 Number of additional bonds: simple=371, symmetry=0 Coordination: Other bonds: Time building additional restraints: 35.05 Conformation dependent library (CDL) restraints added in 15.6 seconds 25168 Ramachandran restraints generated. 12584 Oldfield, 0 Emsley, 12584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22660 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 312 helices and 87 sheets defined 43.7% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.84 Creating SS restraints... Processing helix chain 'A' and resid 9 through 34 removed outlier: 3.621A pdb=" N SER A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 99 removed outlier: 3.659A pdb=" N SER A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 83 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLU A 84 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 129 Processing helix chain 'A' and resid 214 through 223 removed outlier: 3.543A pdb=" N GLU A 220 " --> pdb=" O ALA A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 228 No H-bonds generated for 'chain 'A' and resid 225 through 228' Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.745A pdb=" N ILE A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ASP A 283 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 323 No H-bonds generated for 'chain 'A' and resid 321 through 323' Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 374 through 380 removed outlier: 3.696A pdb=" N ASP A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 479 through 481 No H-bonds generated for 'chain 'A' and resid 479 through 481' Processing helix chain 'A' and resid 483 through 536 removed outlier: 3.630A pdb=" N ASP A 491 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP A 506 " --> pdb=" O GLN A 502 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 575 removed outlier: 3.597A pdb=" N ALA A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLN A 569 " --> pdb=" O ASN A 565 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ASN A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL A 571 " --> pdb=" O SER A 567 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU A 572 " --> pdb=" O GLN A 568 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG A 573 " --> pdb=" O GLN A 569 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A 574 " --> pdb=" O ASN A 570 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 575 " --> pdb=" O VAL A 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 34 Processing helix chain 'B' and resid 45 through 99 removed outlier: 3.789A pdb=" N SER B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU B 84 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 129 Processing helix chain 'B' and resid 214 through 223 Processing helix chain 'B' and resid 225 through 228 No H-bonds generated for 'chain 'B' and resid 225 through 228' Processing helix chain 'B' and resid 273 through 285 removed outlier: 4.230A pdb=" N VAL B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ASP B 283 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N THR B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 374 through 380 Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 425 through 430 Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'B' and resid 479 through 481 No H-bonds generated for 'chain 'B' and resid 479 through 481' Processing helix chain 'B' and resid 483 through 536 removed outlier: 3.604A pdb=" N GLN B 513 " --> pdb=" O SER B 509 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 526 " --> pdb=" O THR B 522 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE B 535 " --> pdb=" O ALA B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 575 removed outlier: 3.569A pdb=" N ALA B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 566 " --> pdb=" O ALA B 562 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLN B 568 " --> pdb=" O ALA B 564 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N GLN B 569 " --> pdb=" O ASN B 565 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ASN B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL B 571 " --> pdb=" O SER B 567 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU B 572 " --> pdb=" O GLN B 568 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG B 573 " --> pdb=" O GLN B 569 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU B 574 " --> pdb=" O ASN B 570 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 575 " --> pdb=" O VAL B 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 34 Processing helix chain 'C' and resid 45 through 99 removed outlier: 3.726A pdb=" N SER C 66 " --> pdb=" O GLY C 62 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU C 84 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 129 Processing helix chain 'C' and resid 214 through 228 removed outlier: 3.985A pdb=" N SER C 224 " --> pdb=" O GLU C 220 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ASP C 226 " --> pdb=" O ASN C 222 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LYS C 227 " --> pdb=" O LYS C 223 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR C 228 " --> pdb=" O SER C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 285 removed outlier: 4.488A pdb=" N VAL C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS C 282 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASP C 283 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N THR C 284 " --> pdb=" O ALA C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 365 through 369 removed outlier: 3.576A pdb=" N LYS C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 369' Processing helix chain 'C' and resid 374 through 380 removed outlier: 3.743A pdb=" N ASP C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 405 removed outlier: 3.512A pdb=" N SER C 405 " --> pdb=" O SER C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 430 Processing helix chain 'C' and resid 479 through 481 No H-bonds generated for 'chain 'C' and resid 479 through 481' Processing helix chain 'C' and resid 483 through 536 removed outlier: 3.594A pdb=" N VAL C 526 " --> pdb=" O THR C 522 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE C 535 " --> pdb=" O ALA C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 575 removed outlier: 3.636A pdb=" N ALA C 545 " --> pdb=" O ALA C 541 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLN C 568 " --> pdb=" O ALA C 564 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLN C 569 " --> pdb=" O ASN C 565 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASN C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL C 571 " --> pdb=" O SER C 567 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU C 572 " --> pdb=" O GLN C 568 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG C 573 " --> pdb=" O GLN C 569 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU C 574 " --> pdb=" O ASN C 570 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 575 " --> pdb=" O VAL C 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 34 removed outlier: 3.727A pdb=" N SER D 24 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 99 removed outlier: 3.731A pdb=" N SER D 66 " --> pdb=" O GLY D 62 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 129 removed outlier: 3.605A pdb=" N LYS D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 223 Processing helix chain 'D' and resid 225 through 228 No H-bonds generated for 'chain 'D' and resid 225 through 228' Processing helix chain 'D' and resid 273 through 285 removed outlier: 4.118A pdb=" N VAL D 281 " --> pdb=" O ALA D 277 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS D 282 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ASP D 283 " --> pdb=" O ASN D 279 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 323 No H-bonds generated for 'chain 'D' and resid 321 through 323' Processing helix chain 'D' and resid 365 through 368 No H-bonds generated for 'chain 'D' and resid 365 through 368' Processing helix chain 'D' and resid 374 through 380 removed outlier: 3.731A pdb=" N ASP D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 405 Processing helix chain 'D' and resid 425 through 430 Processing helix chain 'D' and resid 479 through 481 No H-bonds generated for 'chain 'D' and resid 479 through 481' Processing helix chain 'D' and resid 483 through 536 removed outlier: 4.002A pdb=" N ASP D 491 " --> pdb=" O MET D 487 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN D 513 " --> pdb=" O SER D 509 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL D 526 " --> pdb=" O THR D 522 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE D 535 " --> pdb=" O ALA D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 575 removed outlier: 3.600A pdb=" N ALA D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLN D 568 " --> pdb=" O ALA D 564 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLN D 569 " --> pdb=" O ASN D 565 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASN D 570 " --> pdb=" O SER D 566 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL D 571 " --> pdb=" O SER D 567 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU D 572 " --> pdb=" O GLN D 568 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ARG D 573 " --> pdb=" O GLN D 569 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU D 574 " --> pdb=" O ASN D 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 34 Processing helix chain 'E' and resid 45 through 99 removed outlier: 3.698A pdb=" N SER E 66 " --> pdb=" O GLY E 62 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU E 84 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 129 removed outlier: 3.529A pdb=" N LYS E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 228 removed outlier: 4.017A pdb=" N SER E 224 " --> pdb=" O GLU E 220 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA E 225 " --> pdb=" O ILE E 221 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ASP E 226 " --> pdb=" O ASN E 222 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LYS E 227 " --> pdb=" O LYS E 223 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR E 228 " --> pdb=" O SER E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 285 removed outlier: 4.443A pdb=" N VAL E 281 " --> pdb=" O ALA E 277 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS E 282 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASP E 283 " --> pdb=" O ASN E 279 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 323 No H-bonds generated for 'chain 'E' and resid 321 through 323' Processing helix chain 'E' and resid 365 through 369 Processing helix chain 'E' and resid 374 through 380 Processing helix chain 'E' and resid 400 through 405 Processing helix chain 'E' and resid 425 through 430 Processing helix chain 'E' and resid 479 through 481 No H-bonds generated for 'chain 'E' and resid 479 through 481' Processing helix chain 'E' and resid 483 through 536 removed outlier: 3.802A pdb=" N ASP E 491 " --> pdb=" O MET E 487 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP E 506 " --> pdb=" O GLN E 502 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL E 526 " --> pdb=" O THR E 522 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE E 535 " --> pdb=" O ALA E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 575 removed outlier: 3.715A pdb=" N ALA E 545 " --> pdb=" O ALA E 541 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLN E 568 " --> pdb=" O ALA E 564 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLN E 569 " --> pdb=" O ASN E 565 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASN E 570 " --> pdb=" O SER E 566 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL E 571 " --> pdb=" O SER E 567 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU E 572 " --> pdb=" O GLN E 568 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG E 573 " --> pdb=" O GLN E 569 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU E 574 " --> pdb=" O ASN E 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 34 removed outlier: 3.693A pdb=" N SER F 24 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 99 removed outlier: 3.685A pdb=" N SER F 66 " --> pdb=" O GLY F 62 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU F 84 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN F 85 " --> pdb=" O ALA F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 129 Processing helix chain 'F' and resid 214 through 223 Processing helix chain 'F' and resid 225 through 228 No H-bonds generated for 'chain 'F' and resid 225 through 228' Processing helix chain 'F' and resid 273 through 285 removed outlier: 3.761A pdb=" N ILE F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL F 281 " --> pdb=" O ALA F 277 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS F 282 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASP F 283 " --> pdb=" O ASN F 279 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR F 284 " --> pdb=" O ALA F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 349 No H-bonds generated for 'chain 'F' and resid 347 through 349' Processing helix chain 'F' and resid 365 through 369 Processing helix chain 'F' and resid 374 through 380 Processing helix chain 'F' and resid 400 through 405 Processing helix chain 'F' and resid 425 through 430 Processing helix chain 'F' and resid 479 through 481 No H-bonds generated for 'chain 'F' and resid 479 through 481' Processing helix chain 'F' and resid 483 through 536 removed outlier: 3.792A pdb=" N ASP F 491 " --> pdb=" O MET F 487 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE F 510 " --> pdb=" O ASP F 506 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN F 513 " --> pdb=" O SER F 509 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL F 526 " --> pdb=" O THR F 522 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE F 535 " --> pdb=" O ALA F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 566 removed outlier: 3.591A pdb=" N ALA F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER F 566 " --> pdb=" O ALA F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 575 Processing helix chain 'G' and resid 9 through 34 removed outlier: 3.709A pdb=" N SER G 24 " --> pdb=" O LEU G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 99 removed outlier: 3.509A pdb=" N ALA G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER G 66 " --> pdb=" O GLY G 62 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU G 84 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 129 Processing helix chain 'G' and resid 214 through 223 Processing helix chain 'G' and resid 225 through 228 No H-bonds generated for 'chain 'G' and resid 225 through 228' Processing helix chain 'G' and resid 273 through 285 removed outlier: 4.498A pdb=" N VAL G 281 " --> pdb=" O ALA G 277 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS G 282 " --> pdb=" O ILE G 278 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASP G 283 " --> pdb=" O ASN G 279 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR G 284 " --> pdb=" O ALA G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 323 No H-bonds generated for 'chain 'G' and resid 321 through 323' Processing helix chain 'G' and resid 347 through 349 No H-bonds generated for 'chain 'G' and resid 347 through 349' Processing helix chain 'G' and resid 365 through 369 Processing helix chain 'G' and resid 374 through 380 removed outlier: 3.502A pdb=" N ASP G 378 " --> pdb=" O ALA G 374 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 405 removed outlier: 3.844A pdb=" N SER G 405 " --> pdb=" O SER G 401 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 430 Processing helix chain 'G' and resid 461 through 463 No H-bonds generated for 'chain 'G' and resid 461 through 463' Processing helix chain 'G' and resid 479 through 481 No H-bonds generated for 'chain 'G' and resid 479 through 481' Processing helix chain 'G' and resid 483 through 536 removed outlier: 3.750A pdb=" N ASP G 491 " --> pdb=" O MET G 487 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR G 498 " --> pdb=" O GLU G 494 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN G 513 " --> pdb=" O SER G 509 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL G 526 " --> pdb=" O THR G 522 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE G 535 " --> pdb=" O ALA G 531 " (cutoff:3.500A) Processing helix chain 'G' and resid 540 through 575 removed outlier: 3.616A pdb=" N ALA G 545 " --> pdb=" O ALA G 541 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLN G 568 " --> pdb=" O ALA G 564 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLN G 569 " --> pdb=" O ASN G 565 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ASN G 570 " --> pdb=" O SER G 566 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL G 571 " --> pdb=" O SER G 567 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU G 572 " --> pdb=" O GLN G 568 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ARG G 573 " --> pdb=" O GLN G 569 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU G 574 " --> pdb=" O ASN G 570 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 34 Processing helix chain 'H' and resid 45 through 99 removed outlier: 3.709A pdb=" N SER H 66 " --> pdb=" O GLY H 62 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU H 84 " --> pdb=" O LYS H 80 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN H 85 " --> pdb=" O ALA H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 129 Processing helix chain 'H' and resid 214 through 223 removed outlier: 3.542A pdb=" N GLU H 220 " --> pdb=" O ALA H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 228 No H-bonds generated for 'chain 'H' and resid 225 through 228' Processing helix chain 'H' and resid 273 through 285 removed outlier: 4.407A pdb=" N VAL H 281 " --> pdb=" O ALA H 277 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS H 282 " --> pdb=" O ILE H 278 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASP H 283 " --> pdb=" O ASN H 279 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR H 284 " --> pdb=" O ALA H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 369 Processing helix chain 'H' and resid 374 through 380 Processing helix chain 'H' and resid 400 through 405 removed outlier: 3.664A pdb=" N SER H 405 " --> pdb=" O SER H 401 " (cutoff:3.500A) Processing helix chain 'H' and resid 426 through 430 Processing helix chain 'H' and resid 461 through 463 No H-bonds generated for 'chain 'H' and resid 461 through 463' Processing helix chain 'H' and resid 479 through 481 No H-bonds generated for 'chain 'H' and resid 479 through 481' Processing helix chain 'H' and resid 483 through 536 removed outlier: 3.770A pdb=" N ASP H 491 " --> pdb=" O MET H 487 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR H 498 " --> pdb=" O GLU H 494 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL H 523 " --> pdb=" O ASN H 519 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL H 526 " --> pdb=" O THR H 522 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE H 535 " --> pdb=" O ALA H 531 " (cutoff:3.500A) Processing helix chain 'H' and resid 540 through 575 removed outlier: 3.641A pdb=" N ALA H 545 " --> pdb=" O ALA H 541 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLN H 568 " --> pdb=" O ALA H 564 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLN H 569 " --> pdb=" O ASN H 565 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ASN H 570 " --> pdb=" O SER H 566 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL H 571 " --> pdb=" O SER H 567 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU H 572 " --> pdb=" O GLN H 568 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG H 573 " --> pdb=" O GLN H 569 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU H 574 " --> pdb=" O ASN H 570 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 34 removed outlier: 3.667A pdb=" N SER I 24 " --> pdb=" O LEU I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 99 removed outlier: 3.743A pdb=" N SER I 66 " --> pdb=" O GLY I 62 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU I 84 " --> pdb=" O LYS I 80 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN I 85 " --> pdb=" O ALA I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 129 Processing helix chain 'I' and resid 214 through 223 Processing helix chain 'I' and resid 225 through 228 No H-bonds generated for 'chain 'I' and resid 225 through 228' Processing helix chain 'I' and resid 273 through 285 removed outlier: 3.826A pdb=" N ILE I 278 " --> pdb=" O LEU I 274 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL I 281 " --> pdb=" O ALA I 277 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS I 282 " --> pdb=" O ILE I 278 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASP I 283 " --> pdb=" O ASN I 279 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR I 284 " --> pdb=" O ALA I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 323 No H-bonds generated for 'chain 'I' and resid 321 through 323' Processing helix chain 'I' and resid 365 through 369 Processing helix chain 'I' and resid 374 through 380 Processing helix chain 'I' and resid 400 through 405 removed outlier: 3.542A pdb=" N SER I 405 " --> pdb=" O SER I 401 " (cutoff:3.500A) Processing helix chain 'I' and resid 425 through 430 Processing helix chain 'I' and resid 461 through 463 No H-bonds generated for 'chain 'I' and resid 461 through 463' Processing helix chain 'I' and resid 479 through 481 No H-bonds generated for 'chain 'I' and resid 479 through 481' Processing helix chain 'I' and resid 483 through 536 removed outlier: 3.521A pdb=" N ILE I 507 " --> pdb=" O ILE I 503 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL I 526 " --> pdb=" O THR I 522 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE I 535 " --> pdb=" O ALA I 531 " (cutoff:3.500A) Processing helix chain 'I' and resid 540 through 566 removed outlier: 3.567A pdb=" N ALA I 545 " --> pdb=" O ALA I 541 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER I 566 " --> pdb=" O ALA I 562 " (cutoff:3.500A) Processing helix chain 'I' and resid 569 through 575 Processing helix chain 'J' and resid 9 through 34 removed outlier: 3.723A pdb=" N SER J 24 " --> pdb=" O LEU J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 99 removed outlier: 3.736A pdb=" N SER J 66 " --> pdb=" O GLY J 62 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU J 84 " --> pdb=" O LYS J 80 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN J 85 " --> pdb=" O ALA J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 129 Processing helix chain 'J' and resid 214 through 223 Processing helix chain 'J' and resid 225 through 228 No H-bonds generated for 'chain 'J' and resid 225 through 228' Processing helix chain 'J' and resid 273 through 285 removed outlier: 4.315A pdb=" N VAL J 281 " --> pdb=" O ALA J 277 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS J 282 " --> pdb=" O ILE J 278 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASP J 283 " --> pdb=" O ASN J 279 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR J 284 " --> pdb=" O ALA J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 368 No H-bonds generated for 'chain 'J' and resid 365 through 368' Processing helix chain 'J' and resid 374 through 380 Processing helix chain 'J' and resid 400 through 405 Processing helix chain 'J' and resid 425 through 430 Processing helix chain 'J' and resid 479 through 481 No H-bonds generated for 'chain 'J' and resid 479 through 481' Processing helix chain 'J' and resid 483 through 536 removed outlier: 4.009A pdb=" N ASP J 491 " --> pdb=" O MET J 487 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP J 506 " --> pdb=" O GLN J 502 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL J 526 " --> pdb=" O THR J 522 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE J 535 " --> pdb=" O ALA J 531 " (cutoff:3.500A) Processing helix chain 'J' and resid 540 through 566 removed outlier: 3.650A pdb=" N ALA J 545 " --> pdb=" O ALA J 541 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER J 566 " --> pdb=" O ALA J 562 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 575 Processing helix chain 'K' and resid 9 through 34 removed outlier: 3.735A pdb=" N SER K 24 " --> pdb=" O LEU K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 99 removed outlier: 3.766A pdb=" N SER K 66 " --> pdb=" O GLY K 62 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU K 84 " --> pdb=" O LYS K 80 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN K 85 " --> pdb=" O ALA K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 129 removed outlier: 3.518A pdb=" N LYS K 118 " --> pdb=" O ALA K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 228 removed outlier: 3.928A pdb=" N SER K 224 " --> pdb=" O GLU K 220 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA K 225 " --> pdb=" O ILE K 221 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASP K 226 " --> pdb=" O ASN K 222 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS K 227 " --> pdb=" O LYS K 223 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR K 228 " --> pdb=" O SER K 224 " (cutoff:3.500A) Processing helix chain 'K' and resid 273 through 285 removed outlier: 4.447A pdb=" N VAL K 281 " --> pdb=" O ALA K 277 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS K 282 " --> pdb=" O ILE K 278 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ASP K 283 " --> pdb=" O ASN K 279 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR K 284 " --> pdb=" O ALA K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 365 through 369 Processing helix chain 'K' and resid 374 through 380 removed outlier: 3.744A pdb=" N ASP K 378 " --> pdb=" O ALA K 374 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA K 379 " --> pdb=" O THR K 375 " (cutoff:3.500A) Processing helix chain 'K' and resid 400 through 405 Processing helix chain 'K' and resid 426 through 430 Processing helix chain 'K' and resid 479 through 481 No H-bonds generated for 'chain 'K' and resid 479 through 481' Processing helix chain 'K' and resid 483 through 536 removed outlier: 3.696A pdb=" N ASP K 491 " --> pdb=" O MET K 487 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR K 498 " --> pdb=" O GLU K 494 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL K 526 " --> pdb=" O THR K 522 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE K 535 " --> pdb=" O ALA K 531 " (cutoff:3.500A) Processing helix chain 'K' and resid 540 through 575 removed outlier: 3.702A pdb=" N ALA K 545 " --> pdb=" O ALA K 541 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLN K 568 " --> pdb=" O ALA K 564 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLN K 569 " --> pdb=" O ASN K 565 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASN K 570 " --> pdb=" O SER K 566 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL K 571 " --> pdb=" O SER K 567 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU K 572 " --> pdb=" O GLN K 568 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ARG K 573 " --> pdb=" O GLN K 569 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU K 574 " --> pdb=" O ASN K 570 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU K 575 " --> pdb=" O VAL K 571 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 34 removed outlier: 3.727A pdb=" N SER L 24 " --> pdb=" O LEU L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 100 removed outlier: 3.690A pdb=" N SER L 66 " --> pdb=" O GLY L 62 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU L 84 " --> pdb=" O LYS L 80 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN L 85 " --> pdb=" O ALA L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 129 removed outlier: 3.572A pdb=" N MET L 111 " --> pdb=" O LYS L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 223 Processing helix chain 'L' and resid 225 through 228 No H-bonds generated for 'chain 'L' and resid 225 through 228' Processing helix chain 'L' and resid 273 through 285 removed outlier: 4.282A pdb=" N VAL L 281 " --> pdb=" O ALA L 277 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS L 282 " --> pdb=" O ILE L 278 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ASP L 283 " --> pdb=" O ASN L 279 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR L 284 " --> pdb=" O ALA L 280 " (cutoff:3.500A) Processing helix chain 'L' and resid 365 through 369 Processing helix chain 'L' and resid 374 through 380 removed outlier: 3.655A pdb=" N ASP L 378 " --> pdb=" O ALA L 374 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 405 removed outlier: 3.797A pdb=" N SER L 405 " --> pdb=" O SER L 401 " (cutoff:3.500A) Processing helix chain 'L' and resid 425 through 430 Processing helix chain 'L' and resid 479 through 481 No H-bonds generated for 'chain 'L' and resid 479 through 481' Processing helix chain 'L' and resid 483 through 536 removed outlier: 3.680A pdb=" N ASP L 491 " --> pdb=" O MET L 487 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR L 498 " --> pdb=" O GLU L 494 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL L 526 " --> pdb=" O THR L 522 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE L 535 " --> pdb=" O ALA L 531 " (cutoff:3.500A) Processing helix chain 'L' and resid 540 through 575 removed outlier: 3.603A pdb=" N ALA L 545 " --> pdb=" O ALA L 541 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLN L 568 " --> pdb=" O ALA L 564 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLN L 569 " --> pdb=" O ASN L 565 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ASN L 570 " --> pdb=" O SER L 566 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL L 571 " --> pdb=" O SER L 567 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEU L 572 " --> pdb=" O GLN L 568 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ARG L 573 " --> pdb=" O GLN L 569 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU L 574 " --> pdb=" O ASN L 570 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 34 removed outlier: 3.642A pdb=" N SER M 24 " --> pdb=" O LEU M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 99 removed outlier: 3.723A pdb=" N SER M 66 " --> pdb=" O GLY M 62 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU M 84 " --> pdb=" O LYS M 80 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN M 85 " --> pdb=" O ALA M 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 129 removed outlier: 3.558A pdb=" N MET M 111 " --> pdb=" O LYS M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 223 removed outlier: 3.597A pdb=" N GLU M 220 " --> pdb=" O ALA M 216 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 228 No H-bonds generated for 'chain 'M' and resid 225 through 228' Processing helix chain 'M' and resid 273 through 285 removed outlier: 4.620A pdb=" N VAL M 281 " --> pdb=" O ALA M 277 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS M 282 " --> pdb=" O ILE M 278 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASP M 283 " --> pdb=" O ASN M 279 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR M 284 " --> pdb=" O ALA M 280 " (cutoff:3.500A) Processing helix chain 'M' and resid 367 through 369 No H-bonds generated for 'chain 'M' and resid 367 through 369' Processing helix chain 'M' and resid 374 through 380 removed outlier: 3.625A pdb=" N ASP M 378 " --> pdb=" O ALA M 374 " (cutoff:3.500A) Processing helix chain 'M' and resid 400 through 405 Processing helix chain 'M' and resid 425 through 430 Processing helix chain 'M' and resid 479 through 481 No H-bonds generated for 'chain 'M' and resid 479 through 481' Processing helix chain 'M' and resid 483 through 536 removed outlier: 3.993A pdb=" N ASP M 491 " --> pdb=" O MET M 487 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN M 513 " --> pdb=" O SER M 509 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE M 535 " --> pdb=" O ALA M 531 " (cutoff:3.500A) Processing helix chain 'M' and resid 540 through 566 removed outlier: 3.597A pdb=" N ALA M 545 " --> pdb=" O ALA M 541 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER M 566 " --> pdb=" O ALA M 562 " (cutoff:3.500A) Processing helix chain 'M' and resid 569 through 575 Processing helix chain 'N' and resid 9 through 34 Processing helix chain 'N' and resid 45 through 100 removed outlier: 3.657A pdb=" N SER N 66 " --> pdb=" O GLY N 62 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP N 83 " --> pdb=" O ASP N 79 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLU N 84 " --> pdb=" O LYS N 80 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN N 85 " --> pdb=" O ALA N 81 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 129 Processing helix chain 'N' and resid 214 through 223 Processing helix chain 'N' and resid 225 through 228 No H-bonds generated for 'chain 'N' and resid 225 through 228' Processing helix chain 'N' and resid 273 through 285 removed outlier: 4.305A pdb=" N VAL N 281 " --> pdb=" O ALA N 277 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS N 282 " --> pdb=" O ILE N 278 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ASP N 283 " --> pdb=" O ASN N 279 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR N 284 " --> pdb=" O ALA N 280 " (cutoff:3.500A) Processing helix chain 'N' and resid 365 through 368 No H-bonds generated for 'chain 'N' and resid 365 through 368' Processing helix chain 'N' and resid 374 through 380 removed outlier: 3.573A pdb=" N ASP N 378 " --> pdb=" O ALA N 374 " (cutoff:3.500A) Processing helix chain 'N' and resid 400 through 405 Processing helix chain 'N' and resid 425 through 430 Processing helix chain 'N' and resid 479 through 481 No H-bonds generated for 'chain 'N' and resid 479 through 481' Processing helix chain 'N' and resid 483 through 536 removed outlier: 3.915A pdb=" N ASP N 491 " --> pdb=" O MET N 487 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE N 535 " --> pdb=" O ALA N 531 " (cutoff:3.500A) Processing helix chain 'N' and resid 540 through 575 removed outlier: 3.694A pdb=" N ALA N 545 " --> pdb=" O ALA N 541 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLN N 568 " --> pdb=" O ALA N 564 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLN N 569 " --> pdb=" O ASN N 565 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ASN N 570 " --> pdb=" O SER N 566 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL N 571 " --> pdb=" O SER N 567 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU N 572 " --> pdb=" O GLN N 568 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG N 573 " --> pdb=" O GLN N 569 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU N 574 " --> pdb=" O ASN N 570 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU N 575 " --> pdb=" O VAL N 571 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 34 removed outlier: 3.713A pdb=" N SER O 24 " --> pdb=" O LEU O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 100 removed outlier: 3.739A pdb=" N SER O 66 " --> pdb=" O GLY O 62 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU O 84 " --> pdb=" O LYS O 80 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN O 85 " --> pdb=" O ALA O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 129 Processing helix chain 'O' and resid 214 through 223 removed outlier: 3.551A pdb=" N GLU O 220 " --> pdb=" O ALA O 216 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 228 No H-bonds generated for 'chain 'O' and resid 225 through 228' Processing helix chain 'O' and resid 273 through 285 removed outlier: 4.478A pdb=" N VAL O 281 " --> pdb=" O ALA O 277 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS O 282 " --> pdb=" O ILE O 278 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ASP O 283 " --> pdb=" O ASN O 279 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR O 284 " --> pdb=" O ALA O 280 " (cutoff:3.500A) Processing helix chain 'O' and resid 321 through 323 No H-bonds generated for 'chain 'O' and resid 321 through 323' Processing helix chain 'O' and resid 348 through 350 No H-bonds generated for 'chain 'O' and resid 348 through 350' Processing helix chain 'O' and resid 365 through 369 Processing helix chain 'O' and resid 374 through 380 Processing helix chain 'O' and resid 400 through 405 removed outlier: 3.697A pdb=" N SER O 405 " --> pdb=" O SER O 401 " (cutoff:3.500A) Processing helix chain 'O' and resid 425 through 430 Processing helix chain 'O' and resid 479 through 481 No H-bonds generated for 'chain 'O' and resid 479 through 481' Processing helix chain 'O' and resid 483 through 536 removed outlier: 3.679A pdb=" N ILE O 535 " --> pdb=" O ALA O 531 " (cutoff:3.500A) Processing helix chain 'O' and resid 540 through 575 removed outlier: 3.672A pdb=" N ALA O 545 " --> pdb=" O ALA O 541 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN O 568 " --> pdb=" O ALA O 564 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLN O 569 " --> pdb=" O ASN O 565 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASN O 570 " --> pdb=" O SER O 566 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL O 571 " --> pdb=" O SER O 567 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU O 572 " --> pdb=" O GLN O 568 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG O 573 " --> pdb=" O GLN O 569 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU O 574 " --> pdb=" O ASN O 570 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 34 removed outlier: 3.746A pdb=" N SER P 24 " --> pdb=" O LEU P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 99 removed outlier: 3.773A pdb=" N SER P 66 " --> pdb=" O GLY P 62 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU P 84 " --> pdb=" O LYS P 80 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN P 85 " --> pdb=" O ALA P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 129 Processing helix chain 'P' and resid 214 through 223 Processing helix chain 'P' and resid 225 through 228 No H-bonds generated for 'chain 'P' and resid 225 through 228' Processing helix chain 'P' and resid 273 through 285 removed outlier: 3.647A pdb=" N ILE P 278 " --> pdb=" O LEU P 274 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL P 281 " --> pdb=" O ALA P 277 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS P 282 " --> pdb=" O ILE P 278 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ASP P 283 " --> pdb=" O ASN P 279 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR P 284 " --> pdb=" O ALA P 280 " (cutoff:3.500A) Processing helix chain 'P' and resid 365 through 369 Processing helix chain 'P' and resid 374 through 380 removed outlier: 3.602A pdb=" N ASP P 378 " --> pdb=" O ALA P 374 " (cutoff:3.500A) Processing helix chain 'P' and resid 400 through 405 Processing helix chain 'P' and resid 425 through 430 Processing helix chain 'P' and resid 461 through 463 No H-bonds generated for 'chain 'P' and resid 461 through 463' Processing helix chain 'P' and resid 479 through 481 No H-bonds generated for 'chain 'P' and resid 479 through 481' Processing helix chain 'P' and resid 483 through 536 removed outlier: 3.609A pdb=" N GLN P 513 " --> pdb=" O SER P 509 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL P 526 " --> pdb=" O THR P 522 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE P 535 " --> pdb=" O ALA P 531 " (cutoff:3.500A) Processing helix chain 'P' and resid 540 through 566 removed outlier: 3.568A pdb=" N ALA P 545 " --> pdb=" O ALA P 541 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER P 566 " --> pdb=" O ALA P 562 " (cutoff:3.500A) Processing helix chain 'P' and resid 569 through 575 Processing helix chain 'Q' and resid 9 through 34 Processing helix chain 'Q' and resid 45 through 99 removed outlier: 3.753A pdb=" N SER Q 66 " --> pdb=" O GLY Q 62 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP Q 83 " --> pdb=" O ASP Q 79 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLU Q 84 " --> pdb=" O LYS Q 80 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLN Q 85 " --> pdb=" O ALA Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 129 Processing helix chain 'Q' and resid 214 through 228 removed outlier: 4.205A pdb=" N SER Q 224 " --> pdb=" O GLU Q 220 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA Q 225 " --> pdb=" O ILE Q 221 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ASP Q 226 " --> pdb=" O ASN Q 222 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS Q 227 " --> pdb=" O LYS Q 223 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR Q 228 " --> pdb=" O SER Q 224 " (cutoff:3.500A) Processing helix chain 'Q' and resid 273 through 285 removed outlier: 3.764A pdb=" N ILE Q 278 " --> pdb=" O LEU Q 274 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL Q 281 " --> pdb=" O ALA Q 277 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS Q 282 " --> pdb=" O ILE Q 278 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ASP Q 283 " --> pdb=" O ASN Q 279 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR Q 284 " --> pdb=" O ALA Q 280 " (cutoff:3.500A) Processing helix chain 'Q' and resid 321 through 323 No H-bonds generated for 'chain 'Q' and resid 321 through 323' Processing helix chain 'Q' and resid 348 through 350 No H-bonds generated for 'chain 'Q' and resid 348 through 350' Processing helix chain 'Q' and resid 367 through 369 No H-bonds generated for 'chain 'Q' and resid 367 through 369' Processing helix chain 'Q' and resid 374 through 380 Processing helix chain 'Q' and resid 400 through 405 Processing helix chain 'Q' and resid 425 through 430 Processing helix chain 'Q' and resid 479 through 481 No H-bonds generated for 'chain 'Q' and resid 479 through 481' Processing helix chain 'Q' and resid 483 through 536 removed outlier: 3.796A pdb=" N GLN Q 513 " --> pdb=" O SER Q 509 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL Q 526 " --> pdb=" O THR Q 522 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE Q 535 " --> pdb=" O ALA Q 531 " (cutoff:3.500A) Processing helix chain 'Q' and resid 540 through 575 removed outlier: 3.628A pdb=" N ALA Q 545 " --> pdb=" O ALA Q 541 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER Q 566 " --> pdb=" O ALA Q 562 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLN Q 568 " --> pdb=" O ALA Q 564 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N GLN Q 569 " --> pdb=" O ASN Q 565 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASN Q 570 " --> pdb=" O SER Q 566 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL Q 571 " --> pdb=" O SER Q 567 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LEU Q 572 " --> pdb=" O GLN Q 568 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG Q 573 " --> pdb=" O GLN Q 569 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU Q 574 " --> pdb=" O ASN Q 570 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU Q 575 " --> pdb=" O VAL Q 571 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 34 removed outlier: 3.755A pdb=" N SER R 24 " --> pdb=" O LEU R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 99 removed outlier: 3.650A pdb=" N SER R 66 " --> pdb=" O GLY R 62 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP R 83 " --> pdb=" O ASP R 79 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLU R 84 " --> pdb=" O LYS R 80 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN R 85 " --> pdb=" O ALA R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 129 removed outlier: 3.536A pdb=" N LYS R 118 " --> pdb=" O ALA R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 223 Processing helix chain 'R' and resid 225 through 228 No H-bonds generated for 'chain 'R' and resid 225 through 228' Processing helix chain 'R' and resid 273 through 285 removed outlier: 4.291A pdb=" N VAL R 281 " --> pdb=" O ALA R 277 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ASP R 283 " --> pdb=" O ASN R 279 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR R 284 " --> pdb=" O ALA R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 348 through 350 No H-bonds generated for 'chain 'R' and resid 348 through 350' Processing helix chain 'R' and resid 365 through 369 Processing helix chain 'R' and resid 374 through 380 removed outlier: 3.634A pdb=" N ASP R 378 " --> pdb=" O ALA R 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 400 through 405 removed outlier: 3.566A pdb=" N SER R 405 " --> pdb=" O SER R 401 " (cutoff:3.500A) Processing helix chain 'R' and resid 425 through 430 Processing helix chain 'R' and resid 479 through 481 No H-bonds generated for 'chain 'R' and resid 479 through 481' Processing helix chain 'R' and resid 483 through 536 removed outlier: 3.664A pdb=" N ASP R 491 " --> pdb=" O MET R 487 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE R 535 " --> pdb=" O ALA R 531 " (cutoff:3.500A) Processing helix chain 'R' and resid 540 through 575 removed outlier: 3.558A pdb=" N ALA R 545 " --> pdb=" O ALA R 541 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN R 568 " --> pdb=" O ALA R 564 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLN R 569 " --> pdb=" O ASN R 565 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASN R 570 " --> pdb=" O SER R 566 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL R 571 " --> pdb=" O SER R 567 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU R 572 " --> pdb=" O GLN R 568 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG R 573 " --> pdb=" O GLN R 569 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU R 574 " --> pdb=" O ASN R 570 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 34 Processing helix chain 'S' and resid 45 through 99 removed outlier: 3.816A pdb=" N SER S 66 " --> pdb=" O GLY S 62 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU S 84 " --> pdb=" O LYS S 80 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN S 85 " --> pdb=" O ALA S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 129 removed outlier: 3.542A pdb=" N LYS S 118 " --> pdb=" O ALA S 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 214 through 223 Processing helix chain 'S' and resid 225 through 228 No H-bonds generated for 'chain 'S' and resid 225 through 228' Processing helix chain 'S' and resid 273 through 285 removed outlier: 4.228A pdb=" N VAL S 281 " --> pdb=" O ALA S 277 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS S 282 " --> pdb=" O ILE S 278 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASP S 283 " --> pdb=" O ASN S 279 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR S 284 " --> pdb=" O ALA S 280 " (cutoff:3.500A) Processing helix chain 'S' and resid 374 through 380 removed outlier: 3.524A pdb=" N ALA S 379 " --> pdb=" O THR S 375 " (cutoff:3.500A) Processing helix chain 'S' and resid 400 through 405 Processing helix chain 'S' and resid 425 through 430 Processing helix chain 'S' and resid 479 through 481 No H-bonds generated for 'chain 'S' and resid 479 through 481' Processing helix chain 'S' and resid 483 through 536 removed outlier: 3.922A pdb=" N ASP S 491 " --> pdb=" O MET S 487 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL S 526 " --> pdb=" O THR S 522 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE S 535 " --> pdb=" O ALA S 531 " (cutoff:3.500A) Processing helix chain 'S' and resid 540 through 575 removed outlier: 3.717A pdb=" N ALA S 545 " --> pdb=" O ALA S 541 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER S 566 " --> pdb=" O ALA S 562 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLN S 568 " --> pdb=" O ALA S 564 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N GLN S 569 " --> pdb=" O ASN S 565 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ASN S 570 " --> pdb=" O SER S 566 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL S 571 " --> pdb=" O SER S 567 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU S 572 " --> pdb=" O GLN S 568 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ARG S 573 " --> pdb=" O GLN S 569 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU S 574 " --> pdb=" O ASN S 570 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU S 575 " --> pdb=" O VAL S 571 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 34 Processing helix chain 'T' and resid 45 through 99 removed outlier: 3.848A pdb=" N SER T 66 " --> pdb=" O GLY T 62 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU T 84 " --> pdb=" O LYS T 80 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN T 85 " --> pdb=" O ALA T 81 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 129 Processing helix chain 'T' and resid 214 through 228 removed outlier: 3.972A pdb=" N SER T 224 " --> pdb=" O GLU T 220 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA T 225 " --> pdb=" O ILE T 221 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ASP T 226 " --> pdb=" O ASN T 222 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LYS T 227 " --> pdb=" O LYS T 223 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR T 228 " --> pdb=" O SER T 224 " (cutoff:3.500A) Processing helix chain 'T' and resid 273 through 285 removed outlier: 4.479A pdb=" N VAL T 281 " --> pdb=" O ALA T 277 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS T 282 " --> pdb=" O ILE T 278 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ASP T 283 " --> pdb=" O ASN T 279 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR T 284 " --> pdb=" O ALA T 280 " (cutoff:3.500A) Processing helix chain 'T' and resid 321 through 323 No H-bonds generated for 'chain 'T' and resid 321 through 323' Processing helix chain 'T' and resid 347 through 349 No H-bonds generated for 'chain 'T' and resid 347 through 349' Processing helix chain 'T' and resid 367 through 369 No H-bonds generated for 'chain 'T' and resid 367 through 369' Processing helix chain 'T' and resid 374 through 380 removed outlier: 3.642A pdb=" N ASP T 378 " --> pdb=" O ALA T 374 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA T 379 " --> pdb=" O THR T 375 " (cutoff:3.500A) Processing helix chain 'T' and resid 400 through 405 Processing helix chain 'T' and resid 425 through 430 Processing helix chain 'T' and resid 461 through 463 No H-bonds generated for 'chain 'T' and resid 461 through 463' Processing helix chain 'T' and resid 479 through 481 No H-bonds generated for 'chain 'T' and resid 479 through 481' Processing helix chain 'T' and resid 483 through 536 removed outlier: 3.746A pdb=" N ASP T 491 " --> pdb=" O MET T 487 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN T 513 " --> pdb=" O SER T 509 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL T 526 " --> pdb=" O THR T 522 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE T 535 " --> pdb=" O ALA T 531 " (cutoff:3.500A) Processing helix chain 'T' and resid 540 through 566 removed outlier: 3.638A pdb=" N ALA T 545 " --> pdb=" O ALA T 541 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER T 566 " --> pdb=" O ALA T 562 " (cutoff:3.500A) Processing helix chain 'T' and resid 569 through 575 Processing helix chain 'U' and resid 9 through 34 removed outlier: 3.737A pdb=" N SER U 24 " --> pdb=" O LEU U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 99 removed outlier: 3.860A pdb=" N SER U 66 " --> pdb=" O GLY U 62 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU U 84 " --> pdb=" O LYS U 80 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN U 85 " --> pdb=" O ALA U 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 106 through 129 Processing helix chain 'U' and resid 214 through 223 Processing helix chain 'U' and resid 225 through 228 No H-bonds generated for 'chain 'U' and resid 225 through 228' Processing helix chain 'U' and resid 273 through 285 removed outlier: 4.154A pdb=" N VAL U 281 " --> pdb=" O ALA U 277 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS U 282 " --> pdb=" O ILE U 278 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP U 283 " --> pdb=" O ASN U 279 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR U 284 " --> pdb=" O ALA U 280 " (cutoff:3.500A) Processing helix chain 'U' and resid 347 through 349 No H-bonds generated for 'chain 'U' and resid 347 through 349' Processing helix chain 'U' and resid 365 through 368 No H-bonds generated for 'chain 'U' and resid 365 through 368' Processing helix chain 'U' and resid 374 through 380 Processing helix chain 'U' and resid 400 through 405 removed outlier: 3.744A pdb=" N SER U 405 " --> pdb=" O SER U 401 " (cutoff:3.500A) Processing helix chain 'U' and resid 426 through 430 Processing helix chain 'U' and resid 479 through 481 No H-bonds generated for 'chain 'U' and resid 479 through 481' Processing helix chain 'U' and resid 483 through 536 removed outlier: 3.688A pdb=" N ASP U 491 " --> pdb=" O MET U 487 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR U 498 " --> pdb=" O GLU U 494 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL U 523 " --> pdb=" O ASN U 519 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL U 526 " --> pdb=" O THR U 522 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 540 through 566 removed outlier: 3.527A pdb=" N ALA U 545 " --> pdb=" O ALA U 541 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER U 566 " --> pdb=" O ALA U 562 " (cutoff:3.500A) Processing helix chain 'U' and resid 569 through 575 removed outlier: 3.595A pdb=" N LEU U 572 " --> pdb=" O GLN U 569 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 34 removed outlier: 3.757A pdb=" N SER V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 99 removed outlier: 4.004A pdb=" N SER V 66 " --> pdb=" O GLY V 62 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY V 73 " --> pdb=" O ASN V 69 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU V 84 " --> pdb=" O LYS V 80 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN V 85 " --> pdb=" O ALA V 81 " (cutoff:3.500A) Processing helix chain 'V' and resid 106 through 127 removed outlier: 3.688A pdb=" N LYS V 118 " --> pdb=" O ALA V 114 " (cutoff:3.500A) Processing helix chain 'V' and resid 214 through 223 Processing helix chain 'V' and resid 225 through 228 No H-bonds generated for 'chain 'V' and resid 225 through 228' Processing helix chain 'V' and resid 273 through 285 removed outlier: 3.624A pdb=" N ILE V 278 " --> pdb=" O LEU V 274 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N VAL V 281 " --> pdb=" O ALA V 277 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS V 282 " --> pdb=" O ILE V 278 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASP V 283 " --> pdb=" O ASN V 279 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR V 284 " --> pdb=" O ALA V 280 " (cutoff:3.500A) Processing helix chain 'V' and resid 321 through 323 No H-bonds generated for 'chain 'V' and resid 321 through 323' Processing helix chain 'V' and resid 347 through 349 No H-bonds generated for 'chain 'V' and resid 347 through 349' Processing helix chain 'V' and resid 365 through 369 Processing helix chain 'V' and resid 374 through 380 removed outlier: 3.726A pdb=" N ASP V 378 " --> pdb=" O ALA V 374 " (cutoff:3.500A) Processing helix chain 'V' and resid 400 through 405 removed outlier: 3.608A pdb=" N SER V 405 " --> pdb=" O SER V 401 " (cutoff:3.500A) Processing helix chain 'V' and resid 426 through 430 Processing helix chain 'V' and resid 479 through 481 No H-bonds generated for 'chain 'V' and resid 479 through 481' Processing helix chain 'V' and resid 483 through 536 removed outlier: 3.507A pdb=" N ALA V 488 " --> pdb=" O LYS V 484 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR V 498 " --> pdb=" O GLU V 494 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP V 506 " --> pdb=" O GLN V 502 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL V 523 " --> pdb=" O ASN V 519 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL V 526 " --> pdb=" O THR V 522 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE V 535 " --> pdb=" O ALA V 531 " (cutoff:3.500A) Processing helix chain 'V' and resid 540 through 575 removed outlier: 3.552A pdb=" N ALA V 545 " --> pdb=" O ALA V 541 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN V 555 " --> pdb=" O ASN V 551 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER V 566 " --> pdb=" O ALA V 562 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLN V 568 " --> pdb=" O ALA V 564 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLN V 569 " --> pdb=" O ASN V 565 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ASN V 570 " --> pdb=" O SER V 566 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL V 571 " --> pdb=" O SER V 567 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU V 572 " --> pdb=" O GLN V 568 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG V 573 " --> pdb=" O GLN V 569 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU V 574 " --> pdb=" O ASN V 570 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU V 575 " --> pdb=" O VAL V 571 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 145 through 148 removed outlier: 3.674A pdb=" N VAL A 157 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 172 through 176 Processing sheet with id= C, first strand: chain 'A' and resid 231 through 235 Processing sheet with id= D, first strand: chain 'A' and resid 237 through 239 Processing sheet with id= E, first strand: chain 'B' and resid 145 through 148 removed outlier: 3.670A pdb=" N VAL B 157 " --> pdb=" O PHE B 147 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 172 through 176 Processing sheet with id= G, first strand: chain 'B' and resid 231 through 235 Processing sheet with id= H, first strand: chain 'B' and resid 237 through 239 Processing sheet with id= I, first strand: chain 'C' and resid 145 through 148 removed outlier: 3.597A pdb=" N PHE C 147 " --> pdb=" O VAL C 157 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 157 " --> pdb=" O PHE C 147 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 171 through 176 Processing sheet with id= K, first strand: chain 'C' and resid 231 through 235 Processing sheet with id= L, first strand: chain 'C' and resid 287 through 291 Processing sheet with id= M, first strand: chain 'D' and resid 145 through 148 Processing sheet with id= N, first strand: chain 'D' and resid 172 through 176 Processing sheet with id= O, first strand: chain 'D' and resid 231 through 235 Processing sheet with id= P, first strand: chain 'D' and resid 237 through 239 Processing sheet with id= Q, first strand: chain 'E' and resid 145 through 148 removed outlier: 3.546A pdb=" N VAL E 157 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 172 through 176 Processing sheet with id= S, first strand: chain 'E' and resid 231 through 235 Processing sheet with id= T, first strand: chain 'E' and resid 237 through 239 Processing sheet with id= U, first strand: chain 'E' and resid 391 through 393 removed outlier: 3.535A pdb=" N PHE E 393 " --> pdb=" O GLN E 434 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 145 through 148 removed outlier: 3.627A pdb=" N VAL F 157 " --> pdb=" O PHE F 147 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 172 through 176 Processing sheet with id= X, first strand: chain 'F' and resid 231 through 235 removed outlier: 3.830A pdb=" N ASP F 235 " --> pdb=" O ARG F 329 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 237 through 239 Processing sheet with id= Z, first strand: chain 'G' and resid 145 through 148 removed outlier: 3.524A pdb=" N VAL G 157 " --> pdb=" O PHE G 147 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 172 through 176 Processing sheet with id= AB, first strand: chain 'G' and resid 231 through 235 removed outlier: 3.513A pdb=" N ASP G 235 " --> pdb=" O ARG G 329 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 237 through 239 Processing sheet with id= AD, first strand: chain 'H' and resid 145 through 148 removed outlier: 3.662A pdb=" N VAL H 157 " --> pdb=" O PHE H 147 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 359 through 363 removed outlier: 3.984A pdb=" N ARG H 173 " --> pdb=" O LYS H 334 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 237 through 239 Processing sheet with id= AG, first strand: chain 'H' and resid 391 through 393 Processing sheet with id= AH, first strand: chain 'I' and resid 145 through 148 removed outlier: 3.560A pdb=" N VAL I 157 " --> pdb=" O PHE I 147 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'I' and resid 172 through 176 Processing sheet with id= AJ, first strand: chain 'I' and resid 231 through 235 Processing sheet with id= AK, first strand: chain 'I' and resid 237 through 239 Processing sheet with id= AL, first strand: chain 'J' and resid 145 through 148 removed outlier: 3.564A pdb=" N VAL J 157 " --> pdb=" O PHE J 147 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'J' and resid 172 through 176 Processing sheet with id= AN, first strand: chain 'J' and resid 231 through 235 Processing sheet with id= AO, first strand: chain 'J' and resid 237 through 239 Processing sheet with id= AP, first strand: chain 'K' and resid 145 through 148 Processing sheet with id= AQ, first strand: chain 'K' and resid 172 through 176 Processing sheet with id= AR, first strand: chain 'K' and resid 231 through 235 Processing sheet with id= AS, first strand: chain 'K' and resid 237 through 239 Processing sheet with id= AT, first strand: chain 'K' and resid 391 through 393 Processing sheet with id= AU, first strand: chain 'L' and resid 145 through 148 removed outlier: 3.524A pdb=" N VAL L 157 " --> pdb=" O PHE L 147 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'L' and resid 172 through 176 Processing sheet with id= AW, first strand: chain 'L' and resid 231 through 235 Processing sheet with id= AX, first strand: chain 'L' and resid 237 through 239 Processing sheet with id= AY, first strand: chain 'M' and resid 145 through 148 Processing sheet with id= AZ, first strand: chain 'M' and resid 359 through 363 removed outlier: 3.598A pdb=" N ARG M 173 " --> pdb=" O LYS M 334 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'M' and resid 237 through 239 Processing sheet with id= BB, first strand: chain 'M' and resid 391 through 393 Processing sheet with id= BC, first strand: chain 'N' and resid 145 through 148 removed outlier: 3.544A pdb=" N VAL N 157 " --> pdb=" O PHE N 147 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'N' and resid 172 through 176 Processing sheet with id= BE, first strand: chain 'N' and resid 231 through 235 removed outlier: 3.712A pdb=" N ASP N 235 " --> pdb=" O ARG N 329 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'N' and resid 237 through 239 Processing sheet with id= BG, first strand: chain 'O' and resid 145 through 148 removed outlier: 3.533A pdb=" N VAL O 157 " --> pdb=" O PHE O 147 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'O' and resid 359 through 363 Processing sheet with id= BI, first strand: chain 'O' and resid 237 through 239 Processing sheet with id= BJ, first strand: chain 'P' and resid 145 through 148 removed outlier: 3.531A pdb=" N VAL P 157 " --> pdb=" O PHE P 147 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'P' and resid 172 through 176 Processing sheet with id= BL, first strand: chain 'P' and resid 231 through 235 removed outlier: 3.562A pdb=" N ASP P 235 " --> pdb=" O ARG P 329 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'P' and resid 237 through 239 Processing sheet with id= BN, first strand: chain 'Q' and resid 145 through 148 removed outlier: 3.607A pdb=" N VAL Q 157 " --> pdb=" O PHE Q 147 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'Q' and resid 359 through 363 Processing sheet with id= BP, first strand: chain 'Q' and resid 237 through 239 Processing sheet with id= BQ, first strand: chain 'Q' and resid 391 through 393 Processing sheet with id= BR, first strand: chain 'R' and resid 145 through 148 Processing sheet with id= BS, first strand: chain 'R' and resid 359 through 363 removed outlier: 3.705A pdb=" N ASP R 235 " --> pdb=" O ARG R 329 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'R' and resid 237 through 239 removed outlier: 3.635A pdb=" N THR R 300 " --> pdb=" O GLN R 288 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'S' and resid 145 through 148 removed outlier: 3.525A pdb=" N PHE S 147 " --> pdb=" O VAL S 157 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL S 157 " --> pdb=" O PHE S 147 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'S' and resid 359 through 363 Processing sheet with id= BW, first strand: chain 'S' and resid 237 through 239 Processing sheet with id= BX, first strand: chain 'T' and resid 145 through 148 Processing sheet with id= BY, first strand: chain 'T' and resid 172 through 176 Processing sheet with id= BZ, first strand: chain 'T' and resid 231 through 235 Processing sheet with id= CA, first strand: chain 'T' and resid 237 through 239 Processing sheet with id= CB, first strand: chain 'U' and resid 145 through 148 Processing sheet with id= CC, first strand: chain 'U' and resid 359 through 363 removed outlier: 3.704A pdb=" N ARG U 173 " --> pdb=" O LYS U 334 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'U' and resid 237 through 239 Processing sheet with id= CE, first strand: chain 'U' and resid 391 through 393 Processing sheet with id= CF, first strand: chain 'V' and resid 145 through 148 Processing sheet with id= CG, first strand: chain 'V' and resid 172 through 176 Processing sheet with id= CH, first strand: chain 'V' and resid 231 through 235 removed outlier: 3.597A pdb=" N SER V 331 " --> pdb=" O THR V 233 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'V' and resid 237 through 239 4352 hydrogen bonds defined for protein. 12648 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: 36.74 Time building geometry restraints manager: 37.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 32668 1.34 - 1.45: 10615 1.45 - 1.57: 54243 1.57 - 1.69: 0 1.69 - 1.80: 528 Bond restraints: 98054 Sorted by residual: bond pdb=" C1 P8E E 606 " pdb=" C2 P8E E 606 " ideal model delta sigma weight residual 1.490 1.531 -0.041 2.00e-02 2.50e+03 4.19e+00 bond pdb=" C1 P8E A 606 " pdb=" C2 P8E A 606 " ideal model delta sigma weight residual 1.490 1.530 -0.040 2.00e-02 2.50e+03 3.97e+00 bond pdb=" C1 P8E I 606 " pdb=" C2 P8E I 606 " ideal model delta sigma weight residual 1.490 1.529 -0.039 2.00e-02 2.50e+03 3.84e+00 bond pdb=" C1 P8E F 604 " pdb=" C2 P8E F 604 " ideal model delta sigma weight residual 1.490 1.529 -0.039 2.00e-02 2.50e+03 3.83e+00 bond pdb=" C1 P8E Q 604 " pdb=" C2 P8E Q 604 " ideal model delta sigma weight residual 1.490 1.529 -0.039 2.00e-02 2.50e+03 3.83e+00 ... (remaining 98049 not shown) Histogram of bond angle deviations from ideal: 98.07 - 104.79: 264 104.79 - 111.51: 49083 111.51 - 118.22: 30449 118.22 - 124.94: 52951 124.94 - 131.66: 23 Bond angle restraints: 132770 Sorted by residual: angle pdb=" N GLY N 316 " pdb=" CA GLY N 316 " pdb=" C GLY N 316 " ideal model delta sigma weight residual 114.48 107.96 6.52 1.19e+00 7.06e-01 3.00e+01 angle pdb=" N GLY B 316 " pdb=" CA GLY B 316 " pdb=" C GLY B 316 " ideal model delta sigma weight residual 113.58 108.08 5.50 1.07e+00 8.73e-01 2.64e+01 angle pdb=" N GLY K 316 " pdb=" CA GLY K 316 " pdb=" C GLY K 316 " ideal model delta sigma weight residual 114.48 108.81 5.67 1.19e+00 7.06e-01 2.27e+01 angle pdb=" N GLY U 316 " pdb=" CA GLY U 316 " pdb=" C GLY U 316 " ideal model delta sigma weight residual 114.85 108.48 6.37 1.35e+00 5.49e-01 2.23e+01 angle pdb=" N GLY D 316 " pdb=" CA GLY D 316 " pdb=" C GLY D 316 " ideal model delta sigma weight residual 113.79 108.28 5.51 1.17e+00 7.31e-01 2.22e+01 ... (remaining 132765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 61554 36.00 - 71.99: 2590 71.99 - 107.99: 1299 107.99 - 143.98: 576 143.98 - 179.98: 223 Dihedral angle restraints: 66242 sinusoidal: 30778 harmonic: 35464 Sorted by residual: dihedral pdb=" CA TYR V 242 " pdb=" C TYR V 242 " pdb=" N ALA V 243 " pdb=" CA ALA V 243 " ideal model delta harmonic sigma weight residual -180.00 -140.08 -39.92 0 5.00e+00 4.00e-02 6.37e+01 dihedral pdb=" CA TYR U 242 " pdb=" C TYR U 242 " pdb=" N ALA U 243 " pdb=" CA ALA U 243 " ideal model delta harmonic sigma weight residual -180.00 -140.32 -39.68 0 5.00e+00 4.00e-02 6.30e+01 dihedral pdb=" CA TYR T 242 " pdb=" C TYR T 242 " pdb=" N ALA T 243 " pdb=" CA ALA T 243 " ideal model delta harmonic sigma weight residual -180.00 -140.90 -39.10 0 5.00e+00 4.00e-02 6.12e+01 ... (remaining 66239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.067: 14938 1.067 - 2.134: 0 2.134 - 3.201: 0 3.201 - 4.268: 0 4.268 - 5.335: 374 Chirality restraints: 15312 Sorted by residual: chirality pdb=" C2 P8E C 610 " pdb=" C1 P8E C 610 " pdb=" C3 P8E C 610 " pdb=" O6 P8E C 610 " both_signs ideal model delta sigma weight residual False -2.55 2.78 -5.33 2.00e-01 2.50e+01 7.12e+02 chirality pdb=" C2 P8E H 610 " pdb=" C1 P8E H 610 " pdb=" C3 P8E H 610 " pdb=" O6 P8E H 610 " both_signs ideal model delta sigma weight residual False -2.55 2.78 -5.33 2.00e-01 2.50e+01 7.11e+02 chirality pdb=" C2 P8E D 610 " pdb=" C1 P8E D 610 " pdb=" C3 P8E D 610 " pdb=" O6 P8E D 610 " both_signs ideal model delta sigma weight residual False -2.55 2.78 -5.33 2.00e-01 2.50e+01 7.10e+02 ... (remaining 15309 not shown) Planarity restraints: 16764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 242 " 0.006 2.00e-02 2.50e+03 1.04e-02 2.16e+00 pdb=" CG TYR R 242 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR R 242 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR R 242 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR R 242 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR R 242 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR R 242 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR R 242 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 160 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C THR C 160 " 0.025 2.00e-02 2.50e+03 pdb=" O THR C 160 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE C 161 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 382 " -0.006 2.00e-02 2.50e+03 1.05e-02 1.92e+00 pdb=" CG PHE L 382 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE L 382 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE L 382 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE L 382 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE L 382 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE L 382 " -0.002 2.00e-02 2.50e+03 ... (remaining 16761 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 6 2.03 - 2.75: 17130 2.75 - 3.46: 145136 3.46 - 4.18: 221771 4.18 - 4.90: 404721 Nonbonded interactions: 788764 Sorted by model distance: nonbonded pdb=" OG SER K 455 " pdb=" O6 P8E K 615 " model vdw 1.310 2.440 nonbonded pdb=" OG SER P 455 " pdb=" O6 P8E P 615 " model vdw 1.368 2.440 nonbonded pdb=" OG SER A 455 " pdb=" O6 P8E A 615 " model vdw 1.396 2.440 nonbonded pdb=" OG SER P 455 " pdb=" C2 P8E P 615 " model vdw 1.426 3.370 nonbonded pdb=" OG SER K 455 " pdb=" C2 P8E K 615 " model vdw 1.428 3.370 ... (remaining 788759 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.840 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: 0.070 Extract box with map and model: 16.060 Check model and map are aligned: 1.130 Set scattering table: 0.690 Process input model: 206.560 Find NCS groups from input model: 5.820 Set up NCS constraints: 1.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 236.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 98054 Z= 0.411 Angle : 0.638 6.524 132770 Z= 0.359 Chirality : 0.812 5.335 15312 Planarity : 0.002 0.015 16764 Dihedral : 29.599 179.977 43582 Min Nonbonded Distance : 1.310 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.49 % Favored : 91.33 % Rotamer: Outliers : 0.01 % Allowed : 7.20 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.07), residues: 12584 helix: 0.33 (0.06), residues: 5566 sheet: -3.59 (0.11), residues: 1474 loop : -3.00 (0.07), residues: 5544 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.001 PHE L 382 TYR 0.025 0.002 TYR R 242 ARG 0.005 0.000 ARG P 109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25168 Ramachandran restraints generated. 12584 Oldfield, 0 Emsley, 12584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25168 Ramachandran restraints generated. 12584 Oldfield, 0 Emsley, 12584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1107 time to evaluate : 7.964 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1108 average time/residue: 0.8472 time to fit residues: 1655.6366 Evaluate side-chains 787 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 786 time to evaluate : 10.117 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7738 time to fit residues: 14.2780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1254 random chunks: chunk 1058 optimal weight: 9.9990 chunk 950 optimal weight: 5.9990 chunk 527 optimal weight: 10.0000 chunk 324 optimal weight: 6.9990 chunk 641 optimal weight: 5.9990 chunk 507 optimal weight: 2.9990 chunk 982 optimal weight: 5.9990 chunk 380 optimal weight: 9.9990 chunk 597 optimal weight: 8.9990 chunk 731 optimal weight: 0.1980 chunk 1138 optimal weight: 0.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 21 ASN A 39 ASN A 63 GLN A 98 GLN A 104 GLN A 113 GLN A 145 GLN A 154 ASN A 155 GLN A 165 GLN A 179 GLN A 407 GLN A 502 GLN A 511 GLN A 519 ASN A 568 GLN B 21 ASN B 63 GLN B 85 GLN B 98 GLN B 104 GLN B 113 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 GLN B 519 ASN B 527 ASN B 568 GLN C 13 ASN C 17 ASN C 98 GLN C 113 GLN C 154 ASN C 155 GLN C 165 GLN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 ASN C 407 GLN ** C 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 GLN C 519 ASN C 527 ASN C 568 GLN D 63 GLN D 98 GLN D 104 GLN D 113 GLN D 128 ASN D 141 ASN D 155 GLN ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN D 251 GLN D 511 GLN D 519 ASN D 520 ASN E 13 ASN E 21 ASN E 63 GLN E 98 GLN E 104 GLN E 113 GLN E 154 ASN E 155 GLN ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 ASN E 502 GLN E 511 GLN E 519 ASN E 527 ASN F 13 ASN F 63 GLN F 98 GLN F 104 GLN F 113 GLN F 155 GLN ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 ASN F 519 ASN F 520 ASN F 568 GLN G 13 ASN G 63 GLN G 98 GLN G 104 GLN G 113 GLN G 155 GLN G 165 GLN G 511 GLN G 519 ASN G 520 ASN G 527 ASN H 21 ASN H 63 GLN H 85 GLN H 98 GLN H 104 GLN H 113 GLN H 154 ASN H 179 GLN H 288 GLN ** H 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 519 ASN H 520 ASN I 13 ASN I 21 ASN I 63 GLN I 85 GLN I 98 GLN I 113 GLN I 154 ASN I 155 GLN I 179 GLN ** I 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 511 GLN I 519 ASN I 568 GLN J 98 GLN J 113 GLN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 154 ASN J 165 GLN J 407 GLN J 502 GLN J 511 GLN J 519 ASN J 520 ASN J 568 GLN K 21 ASN K 39 ASN K 98 GLN K 113 GLN K 136 GLN K 155 GLN ** K 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 407 GLN K 511 GLN K 519 ASN K 520 ASN K 527 ASN L 98 GLN L 104 GLN L 113 GLN L 145 GLN L 155 GLN L 294 ASN L 511 GLN L 519 ASN L 520 ASN L 527 ASN L 568 GLN M 21 ASN M 85 GLN M 98 GLN M 104 GLN M 113 GLN M 145 GLN M 155 GLN M 294 ASN M 371 GLN ** M 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 511 GLN M 519 ASN M 568 GLN N 63 GLN N 98 GLN N 104 GLN N 113 GLN N 154 ASN N 155 GLN ** N 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 294 ASN N 407 GLN N 511 GLN N 519 ASN N 527 ASN N 551 ASN O 113 GLN O 136 GLN O 145 GLN O 155 GLN O 179 GLN ** O 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 396 ASN O 407 GLN ** O 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 511 GLN O 519 ASN P 21 ASN P 63 GLN P 98 GLN P 104 GLN P 113 GLN P 136 GLN P 141 ASN P 154 ASN P 155 GLN P 407 GLN P 424 ASN P 511 GLN P 519 ASN P 520 ASN P 527 ASN P 568 GLN Q 104 GLN Q 113 GLN Q 128 ASN Q 154 ASN Q 179 GLN ** Q 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 407 GLN Q 511 GLN Q 519 ASN Q 568 GLN R 63 GLN R 98 GLN R 104 GLN R 113 GLN R 128 ASN R 141 ASN R 155 GLN R 179 GLN R 407 GLN ** R 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 511 GLN R 519 ASN R 527 ASN S 63 GLN S 98 GLN S 104 GLN S 113 GLN S 145 GLN S 154 ASN S 155 GLN S 511 GLN S 519 ASN S 568 GLN T 21 ASN T 63 GLN T 85 GLN T 98 GLN T 104 GLN T 113 GLN T 145 GLN T 155 GLN T 271 ASN T 407 GLN T 431 GLN ** T 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 511 GLN T 519 ASN T 527 ASN T 568 GLN U 21 ASN U 63 GLN U 98 GLN U 104 GLN U 113 GLN U 155 GLN ** U 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 396 ASN U 407 GLN U 511 GLN U 519 ASN U 568 GLN V 63 GLN V 98 GLN V 104 GLN V 113 GLN V 128 ASN V 155 GLN V 288 GLN V 511 GLN V 519 ASN V 520 ASN V 568 GLN Total number of N/Q/H flips: 258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 98054 Z= 0.238 Angle : 0.802 12.157 132770 Z= 0.357 Chirality : 0.091 1.020 15312 Planarity : 0.002 0.019 16764 Dihedral : 31.732 149.215 23628 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.89 % Allowed : 12.02 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.07), residues: 12584 helix: 1.86 (0.07), residues: 5522 sheet: -3.06 (0.12), residues: 1562 loop : -2.48 (0.07), residues: 5500 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.001 PHE L 393 TYR 0.041 0.002 TYR S 242 ARG 0.002 0.000 ARG B 305 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25168 Ramachandran restraints generated. 12584 Oldfield, 0 Emsley, 12584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25168 Ramachandran restraints generated. 12584 Oldfield, 0 Emsley, 12584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1157 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 970 time to evaluate : 8.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 187 outliers final: 123 residues processed: 1107 average time/residue: 0.8119 time to fit residues: 1625.9716 Evaluate side-chains 938 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 815 time to evaluate : 7.971 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 123 outliers final: 24 residues processed: 123 average time/residue: 0.6829 time to fit residues: 173.0665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1254 random chunks: chunk 632 optimal weight: 9.9990 chunk 353 optimal weight: 5.9990 chunk 947 optimal weight: 10.0000 chunk 775 optimal weight: 5.9990 chunk 314 optimal weight: 10.0000 chunk 1140 optimal weight: 10.0000 chunk 1232 optimal weight: 20.0000 chunk 1016 optimal weight: 8.9990 chunk 1131 optimal weight: 10.0000 chunk 388 optimal weight: 6.9990 chunk 915 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 85 GLN A 145 GLN ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 GLN B 407 GLN B 534 GLN C 85 GLN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 527 ASN D 154 ASN ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN D 407 GLN D 502 GLN ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 407 GLN G 527 ASN H 179 GLN H 251 GLN H 407 GLN ** H 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 179 GLN ** I 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 431 GLN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 21 ASN ** K 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 ASN ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 407 GLN ** M 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 145 GLN ** O 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 396 ASN ** O 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 502 GLN ** R 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 251 GLN S 407 GLN T 145 GLN T 154 ASN ** T 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 154 ASN ** U 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 396 ASN V 85 GLN V 407 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 98054 Z= 0.418 Angle : 0.789 10.638 132770 Z= 0.371 Chirality : 0.084 0.931 15312 Planarity : 0.003 0.027 16764 Dihedral : 31.095 145.862 23628 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.30 % Favored : 91.54 % Rotamer: Outliers : 2.36 % Allowed : 15.57 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.08), residues: 12584 helix: 2.10 (0.07), residues: 5500 sheet: -2.87 (0.12), residues: 1474 loop : -2.39 (0.08), residues: 5610 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.002 PHE U 393 TYR 0.048 0.002 TYR R 242 ARG 0.006 0.000 ARG R 413 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25168 Ramachandran restraints generated. 12584 Oldfield, 0 Emsley, 12584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25168 Ramachandran restraints generated. 12584 Oldfield, 0 Emsley, 12584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1029 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 795 time to evaluate : 8.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 234 outliers final: 165 residues processed: 996 average time/residue: 0.8251 time to fit residues: 1496.3786 Evaluate side-chains 911 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 746 time to evaluate : 8.298 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 165 outliers final: 30 residues processed: 165 average time/residue: 0.7134 time to fit residues: 238.7934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1254 random chunks: chunk 1127 optimal weight: 10.0000 chunk 857 optimal weight: 8.9990 chunk 592 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 544 optimal weight: 7.9990 chunk 766 optimal weight: 10.0000 chunk 1144 optimal weight: 5.9990 chunk 1212 optimal weight: 10.0000 chunk 598 optimal weight: 8.9990 chunk 1085 optimal weight: 8.9990 chunk 326 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 ASN C 21 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 ASN ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN ** I 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 431 GLN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 ASN L 376 ASN ** M 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 407 GLN O 98 GLN ** O 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 396 ASN ** O 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 21 ASN R 294 ASN ** R 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 21 ASN U 128 ASN ** U 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 396 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 98054 Z= 0.365 Angle : 0.737 9.659 132770 Z= 0.348 Chirality : 0.078 0.869 15312 Planarity : 0.002 0.030 16764 Dihedral : 30.106 140.134 23628 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.60 % Favored : 92.26 % Rotamer: Outliers : 2.21 % Allowed : 17.75 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.08), residues: 12584 helix: 2.34 (0.07), residues: 5500 sheet: -2.70 (0.13), residues: 1474 loop : -2.26 (0.08), residues: 5610 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.001 PHE K 393 TYR 0.047 0.002 TYR S 242 ARG 0.005 0.000 ARG R 413 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25168 Ramachandran restraints generated. 12584 Oldfield, 0 Emsley, 12584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25168 Ramachandran restraints generated. 12584 Oldfield, 0 Emsley, 12584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 789 time to evaluate : 8.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 219 outliers final: 126 residues processed: 976 average time/residue: 0.8354 time to fit residues: 1463.4960 Evaluate side-chains 861 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 735 time to evaluate : 8.206 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 126 outliers final: 37 residues processed: 126 average time/residue: 0.7403 time to fit residues: 189.2121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1254 random chunks: chunk 1009 optimal weight: 4.9990 chunk 688 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 902 optimal weight: 0.0980 chunk 500 optimal weight: 9.9990 chunk 1034 optimal weight: 0.9980 chunk 837 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 618 optimal weight: 9.9990 chunk 1087 optimal weight: 7.9990 chunk 305 optimal weight: 20.0000 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN B 165 GLN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 527 ASN ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 ASN G 128 ASN ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 527 ASN ** I 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 527 ASN K 21 ASN ** K 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 551 ASN N 128 ASN ** N 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 407 GLN N 520 ASN ** O 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 407 GLN ** O 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 520 ASN ** T 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 396 ASN V 136 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 98054 Z= 0.228 Angle : 0.680 11.048 132770 Z= 0.317 Chirality : 0.074 0.803 15312 Planarity : 0.002 0.023 16764 Dihedral : 28.857 134.274 23628 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 1.78 % Allowed : 18.90 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.08), residues: 12584 helix: 2.73 (0.07), residues: 5500 sheet: -2.15 (0.12), residues: 1694 loop : -2.14 (0.08), residues: 5390 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.001 PHE V 382 TYR 0.046 0.002 TYR S 242 ARG 0.004 0.000 ARG M 413 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25168 Ramachandran restraints generated. 12584 Oldfield, 0 Emsley, 12584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25168 Ramachandran restraints generated. 12584 Oldfield, 0 Emsley, 12584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1035 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 859 time to evaluate : 8.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 176 outliers final: 101 residues processed: 1016 average time/residue: 0.8265 time to fit residues: 1526.2342 Evaluate side-chains 885 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 784 time to evaluate : 8.077 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 44 residues processed: 101 average time/residue: 0.7665 time to fit residues: 161.0227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1254 random chunks: chunk 407 optimal weight: 7.9990 chunk 1091 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 711 optimal weight: 5.9990 chunk 299 optimal weight: 9.9990 chunk 1213 optimal weight: 2.9990 chunk 1007 optimal weight: 8.9990 chunk 561 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 401 optimal weight: 10.0000 chunk 636 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 ASN ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 ASN ** M 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN O 104 GLN ** O 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 407 GLN ** O 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 396 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 98054 Z= 0.283 Angle : 0.697 9.981 132770 Z= 0.328 Chirality : 0.073 0.797 15312 Planarity : 0.002 0.029 16764 Dihedral : 28.771 134.504 23628 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.46 % Favored : 92.52 % Rotamer: Outliers : 1.87 % Allowed : 19.45 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.08), residues: 12584 helix: 2.70 (0.07), residues: 5500 sheet: -1.85 (0.12), residues: 1848 loop : -2.07 (0.08), residues: 5236 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.001 PHE K 393 TYR 0.052 0.002 TYR R 242 ARG 0.008 0.000 ARG M 413 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25168 Ramachandran restraints generated. 12584 Oldfield, 0 Emsley, 12584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25168 Ramachandran restraints generated. 12584 Oldfield, 0 Emsley, 12584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 971 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 786 time to evaluate : 8.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 185 outliers final: 118 residues processed: 947 average time/residue: 0.8486 time to fit residues: 1459.4470 Evaluate side-chains 878 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 760 time to evaluate : 8.130 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 118 outliers final: 50 residues processed: 118 average time/residue: 0.7209 time to fit residues: 174.6171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1254 random chunks: chunk 1169 optimal weight: 9.9990 chunk 136 optimal weight: 0.0070 chunk 691 optimal weight: 2.9990 chunk 886 optimal weight: 0.9990 chunk 686 optimal weight: 8.9990 chunk 1021 optimal weight: 7.9990 chunk 677 optimal weight: 10.0000 chunk 1208 optimal weight: 1.9990 chunk 756 optimal weight: 7.9990 chunk 736 optimal weight: 2.9990 chunk 558 optimal weight: 7.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 ASN ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 527 ASN D 551 ASN ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 551 ASN ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 ASN G 527 ASN ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 551 ASN I 179 GLN ** I 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 520 ASN I 551 ASN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 551 ASN ** K 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 444 ASN K 551 ASN ** M 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN ** O 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 551 ASN P 551 ASN ** Q 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 407 GLN ** R 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 551 ASN ** T 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 551 ASN U 21 ASN ** U 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 98054 Z= 0.168 Angle : 0.668 11.885 132770 Z= 0.307 Chirality : 0.071 0.747 15312 Planarity : 0.002 0.028 16764 Dihedral : 27.559 130.012 23628 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.16 % Allowed : 20.25 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.08), residues: 12584 helix: 2.90 (0.07), residues: 5588 sheet: -1.92 (0.12), residues: 1716 loop : -1.90 (0.08), residues: 5280 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.001 PHE K 393 TYR 0.050 0.002 TYR P 242 ARG 0.008 0.000 ARG M 413 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25168 Ramachandran restraints generated. 12584 Oldfield, 0 Emsley, 12584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25168 Ramachandran restraints generated. 12584 Oldfield, 0 Emsley, 12584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 931 time to evaluate : 8.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 79 residues processed: 1032 average time/residue: 0.8260 time to fit residues: 1553.1710 Evaluate side-chains 883 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 804 time to evaluate : 8.170 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 54 residues processed: 79 average time/residue: 0.7116 time to fit residues: 119.5865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1254 random chunks: chunk 747 optimal weight: 4.9990 chunk 482 optimal weight: 6.9990 chunk 721 optimal weight: 20.0000 chunk 364 optimal weight: 0.0870 chunk 237 optimal weight: 10.0000 chunk 234 optimal weight: 4.9990 chunk 768 optimal weight: 0.9990 chunk 823 optimal weight: 6.9990 chunk 597 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 950 optimal weight: 7.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 ASN G 527 ASN ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 371 GLN ** H 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 179 GLN ** I 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 444 ASN ** M 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 534 GLN ** T 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 154 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 98054 Z= 0.231 Angle : 0.680 10.223 132770 Z= 0.318 Chirality : 0.071 0.753 15312 Planarity : 0.002 0.030 16764 Dihedral : 27.705 130.025 23628 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.30 % Allowed : 20.84 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.08), residues: 12584 helix: 2.85 (0.07), residues: 5588 sheet: -1.85 (0.12), residues: 1716 loop : -1.85 (0.08), residues: 5280 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.001 PHE K 393 TYR 0.054 0.002 TYR R 242 ARG 0.007 0.000 ARG M 413 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25168 Ramachandran restraints generated. 12584 Oldfield, 0 Emsley, 12584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25168 Ramachandran restraints generated. 12584 Oldfield, 0 Emsley, 12584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 823 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 129 outliers final: 99 residues processed: 930 average time/residue: 0.8846 time to fit residues: 1512.9809 Evaluate side-chains 890 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 791 time to evaluate : 8.092 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 53 residues processed: 99 average time/residue: 0.7490 time to fit residues: 153.7920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1254 random chunks: chunk 1099 optimal weight: 3.9990 chunk 1157 optimal weight: 8.9990 chunk 1056 optimal weight: 9.9990 chunk 1126 optimal weight: 8.9990 chunk 677 optimal weight: 10.0000 chunk 490 optimal weight: 5.9990 chunk 884 optimal weight: 8.9990 chunk 345 optimal weight: 7.9990 chunk 1017 optimal weight: 3.9990 chunk 1065 optimal weight: 4.9990 chunk 1122 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 371 GLN ** M 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 128 ASN ** R 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 98054 Z= 0.312 Angle : 0.713 10.873 132770 Z= 0.338 Chirality : 0.072 0.771 15312 Planarity : 0.002 0.031 16764 Dihedral : 28.183 132.171 23628 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 1.00 % Allowed : 21.15 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.08), residues: 12584 helix: 2.66 (0.07), residues: 5588 sheet: -1.86 (0.12), residues: 1716 loop : -1.85 (0.08), residues: 5280 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.001 PHE K 393 TYR 0.055 0.002 TYR R 242 ARG 0.007 0.000 ARG M 413 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25168 Ramachandran restraints generated. 12584 Oldfield, 0 Emsley, 12584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25168 Ramachandran restraints generated. 12584 Oldfield, 0 Emsley, 12584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 770 time to evaluate : 8.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 85 residues processed: 858 average time/residue: 0.8405 time to fit residues: 1312.4659 Evaluate side-chains 841 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 756 time to evaluate : 8.255 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 52 residues processed: 85 average time/residue: 0.7449 time to fit residues: 134.3718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1254 random chunks: chunk 739 optimal weight: 10.0000 chunk 1191 optimal weight: 8.9990 chunk 726 optimal weight: 9.9990 chunk 565 optimal weight: 4.9990 chunk 827 optimal weight: 3.9990 chunk 1249 optimal weight: 8.9990 chunk 1149 optimal weight: 6.9990 chunk 994 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 768 optimal weight: 6.9990 chunk 610 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 407 GLN ** M 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2636 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: