Starting phenix.real_space_refine on Thu Feb 22 02:14:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x80_22088/02_2024/6x80_22088_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x80_22088/02_2024/6x80_22088.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x80_22088/02_2024/6x80_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_22088/02_2024/6x80_22088_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x80_22088/02_2024/6x80_22088_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x80_22088/02_2024/6x80_22088.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x80_22088/02_2024/6x80_22088.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x80_22088/02_2024/6x80_22088_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x80_22088/02_2024/6x80_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-dev-5238/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: 41.78, per 1000 atoms: 0.43 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: 33.05 Conformation dependent library (CDL) restraints added in 13.7 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: 14.71 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: 39.87 Time building geometry restraints manager: 35.96 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: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 16.660 Check model and map are aligned: 1.110 Set scattering table: 0.720 Process input model: 215.540 Find NCS groups from input model: 6.280 Set up NCS constraints: 1.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 246.800 ------------------------------------------------------------------------------- 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 : 8.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8079 (t70) cc_final: 0.7833 (t0) REVERT: A 334 LYS cc_start: 0.8945 (tttt) cc_final: 0.8705 (tttt) REVERT: A 383 ASN cc_start: 0.8560 (p0) cc_final: 0.8325 (p0) REVERT: B 502 GLN cc_start: 0.8713 (tp40) cc_final: 0.8423 (tp40) REVERT: B 539 ASP cc_start: 0.8199 (p0) cc_final: 0.7998 (p0) REVERT: C 102 ASP cc_start: 0.7998 (t70) cc_final: 0.7670 (t0) REVERT: D 13 ASN cc_start: 0.8537 (t0) cc_final: 0.8177 (t0) REVERT: D 357 MET cc_start: 0.8813 (mmt) cc_final: 0.8549 (mmt) REVERT: D 502 GLN cc_start: 0.8646 (tp40) cc_final: 0.8332 (tp-100) REVERT: D 576 GLN cc_start: 0.7971 (pt0) cc_final: 0.7767 (pp30) REVERT: E 334 LYS cc_start: 0.9212 (tttt) cc_final: 0.8839 (ttpp) REVERT: E 425 LEU cc_start: 0.9681 (mp) cc_final: 0.9460 (mt) REVERT: E 491 ASP cc_start: 0.8112 (m-30) cc_final: 0.7836 (m-30) REVERT: F 149 ILE cc_start: 0.9232 (pt) cc_final: 0.9029 (pt) REVERT: F 308 LYS cc_start: 0.9175 (tttt) cc_final: 0.8970 (ttpp) REVERT: F 352 MET cc_start: 0.8384 (mtt) cc_final: 0.8087 (mtt) REVERT: F 393 PHE cc_start: 0.8594 (m-10) cc_final: 0.8372 (m-10) REVERT: F 539 ASP cc_start: 0.8245 (p0) cc_final: 0.8037 (p0) REVERT: G 357 MET cc_start: 0.8810 (mmt) cc_final: 0.8524 (mmt) REVERT: G 431 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8472 (mp10) REVERT: H 357 MET cc_start: 0.8600 (mmt) cc_final: 0.8396 (mmt) REVERT: H 383 ASN cc_start: 0.8422 (p0) cc_final: 0.8218 (p0) REVERT: H 446 TYR cc_start: 0.9368 (m-80) cc_final: 0.9127 (m-80) REVERT: I 19 ASP cc_start: 0.8353 (t0) cc_final: 0.8099 (t0) REVERT: I 102 ASP cc_start: 0.8168 (t70) cc_final: 0.7404 (t0) REVERT: J 383 ASN cc_start: 0.8329 (p0) cc_final: 0.8108 (p0) REVERT: J 487 MET cc_start: 0.8560 (mtt) cc_final: 0.8349 (mtp) REVERT: K 357 MET cc_start: 0.8665 (mmt) cc_final: 0.8203 (mmt) REVERT: K 385 TYR cc_start: 0.8946 (p90) cc_final: 0.8506 (p90) REVERT: L 102 ASP cc_start: 0.7418 (t70) cc_final: 0.7212 (t0) REVERT: L 146 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7808 (mm-30) REVERT: L 561 MET cc_start: 0.8713 (mtp) cc_final: 0.8430 (mtp) REVERT: M 102 ASP cc_start: 0.8029 (t0) cc_final: 0.7771 (t0) REVERT: M 200 LYS cc_start: 0.9057 (mttt) cc_final: 0.8835 (mttm) REVERT: M 334 LYS cc_start: 0.9098 (tttt) cc_final: 0.8774 (tttt) REVERT: M 539 ASP cc_start: 0.8543 (p0) cc_final: 0.8339 (p0) REVERT: M 573 ARG cc_start: 0.8742 (ttm-80) cc_final: 0.7985 (ttt-90) REVERT: N 129 THR cc_start: 0.8647 (m) cc_final: 0.8439 (m) REVERT: N 336 ASP cc_start: 0.7960 (p0) cc_final: 0.7748 (p0) REVERT: N 383 ASN cc_start: 0.7947 (p0) cc_final: 0.7680 (p0) REVERT: N 393 PHE cc_start: 0.8654 (m-10) cc_final: 0.8248 (m-10) REVERT: N 436 ILE cc_start: 0.9074 (mt) cc_final: 0.8740 (pt) REVERT: O 102 ASP cc_start: 0.7802 (t70) cc_final: 0.7462 (t0) REVERT: O 502 GLN cc_start: 0.8592 (tp40) cc_final: 0.8217 (tm-30) REVERT: P 115 ASP cc_start: 0.8070 (t0) cc_final: 0.7796 (t0) REVERT: P 149 ILE cc_start: 0.9302 (pt) cc_final: 0.9053 (pt) REVERT: P 404 MET cc_start: 0.9391 (mtm) cc_final: 0.9179 (mtp) REVERT: P 431 GLN cc_start: 0.8377 (mm-40) cc_final: 0.8017 (mp10) REVERT: P 502 GLN cc_start: 0.8467 (tp40) cc_final: 0.7656 (tm-30) REVERT: Q 90 ASP cc_start: 0.8354 (t0) cc_final: 0.8141 (t0) REVERT: Q 502 GLN cc_start: 0.8683 (tp40) cc_final: 0.7833 (tm-30) REVERT: Q 573 ARG cc_start: 0.8872 (ttm-80) cc_final: 0.8331 (ptt180) REVERT: R 385 TYR cc_start: 0.8809 (p90) cc_final: 0.8606 (p90) REVERT: R 539 ASP cc_start: 0.8086 (p0) cc_final: 0.7807 (p0) REVERT: S 431 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8465 (mm110) REVERT: S 490 MET cc_start: 0.8765 (ttm) cc_final: 0.8522 (ttm) REVERT: T 102 ASP cc_start: 0.7831 (t70) cc_final: 0.7611 (t0) REVERT: T 532 GLU cc_start: 0.8539 (tt0) cc_final: 0.8312 (tt0) REVERT: U 124 ASP cc_start: 0.8085 (p0) cc_final: 0.7879 (p0) REVERT: U 149 ILE cc_start: 0.9276 (pt) cc_final: 0.9026 (pt) REVERT: U 431 GLN cc_start: 0.8285 (mm-40) cc_final: 0.8015 (mp10) REVERT: V 38 ILE cc_start: 0.9634 (pt) cc_final: 0.9379 (pt) REVERT: V 102 ASP cc_start: 0.7703 (t70) cc_final: 0.7435 (t0) REVERT: V 160 THR cc_start: 0.8741 (p) cc_final: 0.8517 (m) REVERT: V 235 ASP cc_start: 0.7818 (t0) cc_final: 0.7594 (t70) REVERT: V 385 TYR cc_start: 0.8842 (p90) cc_final: 0.8628 (p90) REVERT: V 502 GLN cc_start: 0.8518 (tp40) cc_final: 0.8154 (tp40) outliers start: 1 outliers final: 1 residues processed: 1108 average time/residue: 0.8232 time to fit residues: 1613.5156 Evaluate side-chains 805 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 804 time to evaluate : 8.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 ILE 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: 7.9990 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 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 13 ASN 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 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 H 527 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 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 502 GLN 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 154 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 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 98054 Z= 0.229 Angle : 0.801 12.208 132770 Z= 0.355 Chirality : 0.092 1.035 15312 Planarity : 0.002 0.019 16764 Dihedral : 32.185 150.105 23630 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.84 % Allowed : 12.05 % Favored : 86.11 % 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 : -2.47 (0.07), residues: 5500 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.001 PHE K 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 1151 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 969 time to evaluate : 8.236 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: A 334 LYS cc_start: 0.8935 (tttt) cc_final: 0.8709 (tttt) REVERT: A 383 ASN cc_start: 0.8320 (p0) cc_final: 0.8110 (p0) REVERT: A 518 ILE cc_start: 0.9478 (mt) cc_final: 0.9181 (mm) REVERT: B 502 GLN cc_start: 0.8651 (tp40) cc_final: 0.8340 (tp40) REVERT: C 309 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9157 (mp) REVERT: C 383 ASN cc_start: 0.8029 (OUTLIER) cc_final: 0.7771 (p0) REVERT: D 13 ASN cc_start: 0.8347 (t0) cc_final: 0.7981 (t0) REVERT: D 111 MET cc_start: 0.9034 (mtt) cc_final: 0.8830 (mtp) REVERT: D 502 GLN cc_start: 0.8532 (tp40) cc_final: 0.8175 (tm-30) REVERT: D 576 GLN cc_start: 0.7956 (pt0) cc_final: 0.7671 (pp30) REVERT: E 309 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9092 (mt) REVERT: E 491 ASP cc_start: 0.8074 (m-30) cc_final: 0.7846 (m-30) REVERT: F 13 ASN cc_start: 0.8074 (t0) cc_final: 0.7820 (t0) REVERT: F 242 TYR cc_start: 0.9139 (p90) cc_final: 0.8926 (p90) REVERT: F 308 LYS cc_start: 0.9193 (tttt) cc_final: 0.8992 (ttpp) REVERT: F 309 ILE cc_start: 0.9449 (OUTLIER) cc_final: 0.9130 (mt) REVERT: F 385 TYR cc_start: 0.8746 (p90) cc_final: 0.8501 (p90) REVERT: G 308 LYS cc_start: 0.9351 (tttt) cc_final: 0.9087 (tttp) REVERT: G 357 MET cc_start: 0.8955 (mmt) cc_final: 0.8573 (mmt) REVERT: G 393 PHE cc_start: 0.8795 (m-10) cc_final: 0.8569 (m-10) REVERT: H 276 SER cc_start: 0.9469 (t) cc_final: 0.9237 (m) REVERT: H 537 ASP cc_start: 0.7287 (m-30) cc_final: 0.6971 (m-30) REVERT: I 19 ASP cc_start: 0.8288 (t0) cc_final: 0.8063 (t0) REVERT: I 102 ASP cc_start: 0.8103 (t70) cc_final: 0.7488 (t0) REVERT: I 357 MET cc_start: 0.9087 (mmm) cc_final: 0.8622 (mmt) REVERT: I 393 PHE cc_start: 0.8723 (m-10) cc_final: 0.8447 (m-10) REVERT: J 334 LYS cc_start: 0.8871 (tttt) cc_final: 0.8471 (tttt) REVERT: J 383 ASN cc_start: 0.8175 (p0) cc_final: 0.7904 (p0) REVERT: J 502 GLN cc_start: 0.8692 (tp-100) cc_final: 0.8339 (tm-30) REVERT: K 120 MET cc_start: 0.8846 (ttm) cc_final: 0.8246 (mtp) REVERT: K 357 MET cc_start: 0.8771 (mmt) cc_final: 0.8541 (mmt) REVERT: L 13 ASN cc_start: 0.8251 (t0) cc_final: 0.7983 (t0) REVERT: L 129 THR cc_start: 0.8497 (m) cc_final: 0.8224 (m) REVERT: L 537 ASP cc_start: 0.7498 (m-30) cc_final: 0.7212 (m-30) REVERT: L 561 MET cc_start: 0.8722 (mtp) cc_final: 0.8433 (mtp) REVERT: M 56 SER cc_start: 0.9095 (t) cc_final: 0.8866 (p) REVERT: M 102 ASP cc_start: 0.8022 (t70) cc_final: 0.7646 (t0) REVERT: M 200 LYS cc_start: 0.9033 (mttt) cc_final: 0.8807 (mttm) REVERT: M 334 LYS cc_start: 0.9127 (tttt) cc_final: 0.8798 (ttpt) REVERT: M 336 ASP cc_start: 0.7983 (p0) cc_final: 0.7290 (p0) REVERT: M 539 ASP cc_start: 0.8622 (p0) cc_final: 0.8412 (p0) REVERT: M 573 ARG cc_start: 0.8769 (ttm-80) cc_final: 0.8037 (ttt-90) REVERT: N 303 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8350 (p0) REVERT: N 502 GLN cc_start: 0.8300 (tp40) cc_final: 0.7601 (tm-30) REVERT: O 102 ASP cc_start: 0.7792 (t70) cc_final: 0.7555 (t0) REVERT: O 235 ASP cc_start: 0.7984 (t0) cc_final: 0.7756 (t0) REVERT: O 385 TYR cc_start: 0.9095 (p90) cc_final: 0.8854 (p90) REVERT: O 396 ASN cc_start: 0.9178 (OUTLIER) cc_final: 0.8969 (p0) REVERT: O 502 GLN cc_start: 0.8431 (tp40) cc_final: 0.8092 (tm-30) REVERT: P 115 ASP cc_start: 0.8051 (t0) cc_final: 0.7769 (t0) REVERT: P 357 MET cc_start: 0.9059 (mmm) cc_final: 0.8715 (mmm) REVERT: P 446 TYR cc_start: 0.9449 (m-80) cc_final: 0.9110 (m-80) REVERT: P 502 GLN cc_start: 0.8377 (tp-100) cc_final: 0.7764 (tm-30) REVERT: P 539 ASP cc_start: 0.8227 (p0) cc_final: 0.7910 (p0) REVERT: Q 90 ASP cc_start: 0.8367 (t0) cc_final: 0.8130 (t0) REVERT: Q 502 GLN cc_start: 0.8558 (tp40) cc_final: 0.7676 (tm-30) REVERT: Q 573 ARG cc_start: 0.8842 (ttm-80) cc_final: 0.7964 (ttp80) REVERT: R 282 LYS cc_start: 0.9217 (ptmm) cc_final: 0.8992 (ptpp) REVERT: R 315 VAL cc_start: 0.8887 (t) cc_final: 0.8495 (p) REVERT: R 385 TYR cc_start: 0.8659 (p90) cc_final: 0.8344 (p90) REVERT: R 539 ASP cc_start: 0.8167 (p0) cc_final: 0.7928 (p0) REVERT: S 490 MET cc_start: 0.8608 (ttm) cc_final: 0.8388 (ttm) REVERT: S 561 MET cc_start: 0.8420 (mtp) cc_final: 0.8191 (mtp) REVERT: T 102 ASP cc_start: 0.7760 (t70) cc_final: 0.7475 (t0) REVERT: T 532 GLU cc_start: 0.8517 (tt0) cc_final: 0.8298 (tt0) REVERT: T 576 GLN cc_start: 0.7989 (pt0) cc_final: 0.7720 (pp30) REVERT: U 385 TYR cc_start: 0.8799 (p90) cc_final: 0.8592 (p90) REVERT: V 160 THR cc_start: 0.8636 (p) cc_final: 0.8410 (m) REVERT: V 235 ASP cc_start: 0.7987 (t0) cc_final: 0.7735 (t70) REVERT: V 385 TYR cc_start: 0.8807 (p90) cc_final: 0.8551 (p90) outliers start: 182 outliers final: 127 residues processed: 1104 average time/residue: 0.7875 time to fit residues: 1579.4575 Evaluate side-chains 957 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 824 time to evaluate : 8.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 383 ASN Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 539 ASP Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 401 SER Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 283 ASP Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain G residue 443 SER Chi-restraints excluded: chain G residue 469 THR Chi-restraints excluded: chain G residue 537 ASP Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 283 ASP Chi-restraints excluded: chain H residue 469 THR Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 290 SER Chi-restraints excluded: chain I residue 361 SER Chi-restraints excluded: chain I residue 419 VAL Chi-restraints excluded: chain I residue 469 THR Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 276 SER Chi-restraints excluded: chain J residue 448 VAL Chi-restraints excluded: chain J residue 469 THR Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 358 ILE Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain K residue 443 SER Chi-restraints excluded: chain K residue 469 THR Chi-restraints excluded: chain L residue 186 VAL Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 276 SER Chi-restraints excluded: chain L residue 320 LEU Chi-restraints excluded: chain L residue 469 THR Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 164 THR Chi-restraints excluded: chain M residue 188 LEU Chi-restraints excluded: chain M residue 205 VAL Chi-restraints excluded: chain M residue 283 ASP Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 290 SER Chi-restraints excluded: chain M residue 401 SER Chi-restraints excluded: chain M residue 469 THR Chi-restraints excluded: chain M residue 537 ASP Chi-restraints excluded: chain N residue 19 ASP Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 303 ASP Chi-restraints excluded: chain N residue 419 VAL Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain O residue 164 THR Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 396 ASN Chi-restraints excluded: chain O residue 443 SER Chi-restraints excluded: chain O residue 469 THR Chi-restraints excluded: chain P residue 164 THR Chi-restraints excluded: chain P residue 188 LEU Chi-restraints excluded: chain P residue 205 VAL Chi-restraints excluded: chain P residue 469 THR Chi-restraints excluded: chain Q residue 205 VAL Chi-restraints excluded: chain Q residue 342 ILE Chi-restraints excluded: chain Q residue 469 THR Chi-restraints excluded: chain Q residue 539 ASP Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 469 THR Chi-restraints excluded: chain S residue 19 ASP Chi-restraints excluded: chain S residue 112 LEU Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 188 LEU Chi-restraints excluded: chain S residue 205 VAL Chi-restraints excluded: chain S residue 276 SER Chi-restraints excluded: chain S residue 469 THR Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain T residue 205 VAL Chi-restraints excluded: chain T residue 267 ASP Chi-restraints excluded: chain T residue 276 SER Chi-restraints excluded: chain T residue 283 ASP Chi-restraints excluded: chain T residue 303 ASP Chi-restraints excluded: chain T residue 469 THR Chi-restraints excluded: chain U residue 19 ASP Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 267 ASP Chi-restraints excluded: chain U residue 276 SER Chi-restraints excluded: chain U residue 309 ILE Chi-restraints excluded: chain U residue 397 VAL Chi-restraints excluded: chain U residue 469 THR Chi-restraints excluded: chain U residue 537 ASP Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 469 THR Chi-restraints excluded: chain V residue 477 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1254 random chunks: chunk 632 optimal weight: 10.0000 chunk 353 optimal weight: 3.9990 chunk 947 optimal weight: 20.0000 chunk 775 optimal weight: 20.0000 chunk 314 optimal weight: 7.9990 chunk 1140 optimal weight: 10.0000 chunk 1232 optimal weight: 20.0000 chunk 1016 optimal weight: 6.9990 chunk 1131 optimal weight: 6.9990 chunk 388 optimal weight: 8.9990 chunk 915 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 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 383 ASN C 527 ASN D 154 ASN ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN D 407 GLN ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN ** 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** ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 21 ASN ** K 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** N 407 GLN 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** ** R 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 251 GLN S 407 GLN ** T 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 98054 Z= 0.389 Angle : 0.778 11.396 132770 Z= 0.364 Chirality : 0.084 0.933 15312 Planarity : 0.003 0.023 16764 Dihedral : 31.011 148.881 23630 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.09 % Favored : 91.77 % Rotamer: Outliers : 3.03 % Allowed : 14.94 % Favored : 82.03 % 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: -0.56 (0.08), residues: 12584 helix: 2.15 (0.07), residues: 5500 sheet: -2.86 (0.12), residues: 1474 loop : -2.38 (0.08), residues: 5610 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.001 PHE U 393 TYR 0.048 0.002 TYR R 242 ARG 0.009 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 1107 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 807 time to evaluate : 8.322 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: A 334 LYS cc_start: 0.8980 (tttt) cc_final: 0.8644 (ttpt) REVERT: A 383 ASN cc_start: 0.8386 (p0) cc_final: 0.8135 (p0) REVERT: A 518 ILE cc_start: 0.9476 (mt) cc_final: 0.9211 (mm) REVERT: B 357 MET cc_start: 0.8976 (mmm) cc_final: 0.8639 (mmm) REVERT: B 502 GLN cc_start: 0.8683 (tp40) cc_final: 0.8373 (tp40) REVERT: C 309 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.9197 (mp) REVERT: D 13 ASN cc_start: 0.8541 (t0) cc_final: 0.8119 (t0) REVERT: D 38 ILE cc_start: 0.9704 (OUTLIER) cc_final: 0.9410 (pt) REVERT: D 120 MET cc_start: 0.8728 (ttp) cc_final: 0.8200 (ttm) REVERT: D 502 GLN cc_start: 0.8588 (tp40) cc_final: 0.8195 (tm-30) REVERT: E 309 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9104 (mt) REVERT: E 334 LYS cc_start: 0.9280 (tttt) cc_final: 0.8933 (ttpp) REVERT: E 502 GLN cc_start: 0.8678 (tp-100) cc_final: 0.8172 (tp-100) REVERT: F 13 ASN cc_start: 0.8329 (t0) cc_final: 0.8014 (t0) REVERT: F 308 LYS cc_start: 0.9209 (tttt) cc_final: 0.8999 (ttpp) REVERT: F 537 ASP cc_start: 0.7573 (m-30) cc_final: 0.7039 (m-30) REVERT: G 357 MET cc_start: 0.8912 (mmt) cc_final: 0.8473 (mmt) REVERT: H 537 ASP cc_start: 0.7567 (m-30) cc_final: 0.7211 (m-30) REVERT: I 13 ASN cc_start: 0.8534 (t0) cc_final: 0.8135 (t0) REVERT: I 19 ASP cc_start: 0.8314 (t0) cc_final: 0.8062 (t0) REVERT: I 124 ASP cc_start: 0.8403 (m-30) cc_final: 0.8153 (m-30) REVERT: I 146 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7320 (mm-30) REVERT: J 385 TYR cc_start: 0.8875 (p90) cc_final: 0.8667 (p90) REVERT: J 502 GLN cc_start: 0.8754 (tp-100) cc_final: 0.8390 (tm-30) REVERT: K 357 MET cc_start: 0.8744 (mmt) cc_final: 0.8217 (mmt) REVERT: K 385 TYR cc_start: 0.8784 (p90) cc_final: 0.8273 (p90) REVERT: L 13 ASN cc_start: 0.8428 (t0) cc_final: 0.8203 (t0) REVERT: L 102 ASP cc_start: 0.7371 (t0) cc_final: 0.7045 (t0) REVERT: L 129 THR cc_start: 0.8521 (m) cc_final: 0.8261 (m) REVERT: L 146 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7520 (mm-30) REVERT: L 537 ASP cc_start: 0.7287 (m-30) cc_final: 0.6890 (m-30) REVERT: M 13 ASN cc_start: 0.8694 (t0) cc_final: 0.8492 (t0) REVERT: M 102 ASP cc_start: 0.8083 (t70) cc_final: 0.7561 (t0) REVERT: M 334 LYS cc_start: 0.9126 (tttt) cc_final: 0.8759 (ttpt) REVERT: M 539 ASP cc_start: 0.8807 (p0) cc_final: 0.8409 (p0) REVERT: M 573 ARG cc_start: 0.8756 (ttm-80) cc_final: 0.8083 (ttt-90) REVERT: N 303 ASP cc_start: 0.8850 (OUTLIER) cc_final: 0.8347 (p0) REVERT: N 502 GLN cc_start: 0.8406 (tp40) cc_final: 0.7758 (tm-30) REVERT: O 102 ASP cc_start: 0.7822 (t70) cc_final: 0.7619 (t0) REVERT: O 502 GLN cc_start: 0.8468 (tp40) cc_final: 0.8211 (tm-30) REVERT: P 115 ASP cc_start: 0.8162 (t0) cc_final: 0.7868 (t0) REVERT: P 446 TYR cc_start: 0.9459 (m-80) cc_final: 0.9098 (m-80) REVERT: P 502 GLN cc_start: 0.8620 (tp-100) cc_final: 0.8036 (tm-30) REVERT: Q 90 ASP cc_start: 0.8383 (t0) cc_final: 0.8152 (t0) REVERT: Q 573 ARG cc_start: 0.8880 (ttm-80) cc_final: 0.7915 (ttt-90) REVERT: R 282 LYS cc_start: 0.9249 (ptmm) cc_final: 0.8980 (ptpp) REVERT: R 357 MET cc_start: 0.9160 (mmm) cc_final: 0.8843 (mmm) REVERT: R 385 TYR cc_start: 0.8631 (p90) cc_final: 0.8355 (p90) REVERT: R 539 ASP cc_start: 0.8318 (p0) cc_final: 0.8071 (p0) REVERT: S 431 GLN cc_start: 0.8717 (mm110) cc_final: 0.8208 (mm-40) REVERT: S 490 MET cc_start: 0.8822 (ttm) cc_final: 0.8611 (ttm) REVERT: T 102 ASP cc_start: 0.7691 (t70) cc_final: 0.7370 (t0) REVERT: T 532 GLU cc_start: 0.8550 (tt0) cc_final: 0.8343 (tt0) REVERT: U 235 ASP cc_start: 0.8150 (t0) cc_final: 0.7872 (t70) REVERT: U 396 ASN cc_start: 0.9360 (OUTLIER) cc_final: 0.9155 (p0) REVERT: U 431 GLN cc_start: 0.8206 (mp10) cc_final: 0.7978 (mp10) REVERT: V 160 THR cc_start: 0.8697 (p) cc_final: 0.8426 (m) REVERT: V 385 TYR cc_start: 0.8803 (p90) cc_final: 0.8563 (p90) outliers start: 300 outliers final: 229 residues processed: 1059 average time/residue: 0.7822 time to fit residues: 1511.9467 Evaluate side-chains 997 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 763 time to evaluate : 8.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 537 ASP Chi-restraints excluded: chain E residue 539 ASP Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 164 THR Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 283 ASP Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain G residue 443 SER Chi-restraints excluded: chain G residue 469 THR Chi-restraints excluded: chain G residue 537 ASP Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 283 ASP Chi-restraints excluded: chain H residue 322 ASN Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 469 THR Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 186 VAL Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 290 SER Chi-restraints excluded: chain I residue 419 VAL Chi-restraints excluded: chain I residue 443 SER Chi-restraints excluded: chain I residue 469 THR Chi-restraints excluded: chain I residue 537 ASP Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 276 SER Chi-restraints excluded: chain J residue 320 LEU Chi-restraints excluded: chain J residue 419 VAL Chi-restraints excluded: chain J residue 443 SER Chi-restraints excluded: chain J residue 448 VAL Chi-restraints excluded: chain J residue 469 THR Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 239 THR Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 342 ILE Chi-restraints excluded: chain K residue 358 ILE Chi-restraints excluded: chain K residue 401 SER Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain K residue 443 SER Chi-restraints excluded: chain K residue 469 THR Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 186 VAL Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 276 SER Chi-restraints excluded: chain L residue 320 LEU Chi-restraints excluded: chain L residue 397 VAL Chi-restraints excluded: chain L residue 443 SER Chi-restraints excluded: chain L residue 469 THR Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 164 THR Chi-restraints excluded: chain M residue 202 ASP Chi-restraints excluded: chain M residue 205 VAL Chi-restraints excluded: chain M residue 276 SER Chi-restraints excluded: chain M residue 283 ASP Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 290 SER Chi-restraints excluded: chain M residue 358 ILE Chi-restraints excluded: chain M residue 397 VAL Chi-restraints excluded: chain M residue 401 SER Chi-restraints excluded: chain M residue 443 SER Chi-restraints excluded: chain M residue 477 THR Chi-restraints excluded: chain M residue 518 ILE Chi-restraints excluded: chain M residue 537 ASP Chi-restraints excluded: chain N residue 19 ASP Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain N residue 283 ASP Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 303 ASP Chi-restraints excluded: chain N residue 309 ILE Chi-restraints excluded: chain N residue 419 VAL Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 164 THR Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 239 THR Chi-restraints excluded: chain O residue 258 VAL Chi-restraints excluded: chain O residue 276 SER Chi-restraints excluded: chain O residue 447 VAL Chi-restraints excluded: chain P residue 28 SER Chi-restraints excluded: chain P residue 164 THR Chi-restraints excluded: chain P residue 186 VAL Chi-restraints excluded: chain P residue 205 VAL Chi-restraints excluded: chain P residue 258 VAL Chi-restraints excluded: chain P residue 397 VAL Chi-restraints excluded: chain P residue 469 THR Chi-restraints excluded: chain Q residue 105 SER Chi-restraints excluded: chain Q residue 164 THR Chi-restraints excluded: chain Q residue 205 VAL Chi-restraints excluded: chain Q residue 283 ASP Chi-restraints excluded: chain Q residue 361 SER Chi-restraints excluded: chain Q residue 401 SER Chi-restraints excluded: chain Q residue 469 THR Chi-restraints excluded: chain Q residue 537 ASP Chi-restraints excluded: chain Q residue 539 ASP Chi-restraints excluded: chain R residue 19 ASP Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 419 VAL Chi-restraints excluded: chain R residue 469 THR Chi-restraints excluded: chain S residue 19 ASP Chi-restraints excluded: chain S residue 112 LEU Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 188 LEU Chi-restraints excluded: chain S residue 205 VAL Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 267 ASP Chi-restraints excluded: chain S residue 276 SER Chi-restraints excluded: chain S residue 342 ILE Chi-restraints excluded: chain S residue 419 VAL Chi-restraints excluded: chain S residue 443 SER Chi-restraints excluded: chain S residue 469 THR Chi-restraints excluded: chain S residue 537 ASP Chi-restraints excluded: chain T residue 149 ILE Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 186 VAL Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain T residue 205 VAL Chi-restraints excluded: chain T residue 239 THR Chi-restraints excluded: chain T residue 267 ASP Chi-restraints excluded: chain T residue 276 SER Chi-restraints excluded: chain T residue 303 ASP Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 469 THR Chi-restraints excluded: chain U residue 19 ASP Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain U residue 205 VAL Chi-restraints excluded: chain U residue 267 ASP Chi-restraints excluded: chain U residue 276 SER Chi-restraints excluded: chain U residue 290 SER Chi-restraints excluded: chain U residue 303 ASP Chi-restraints excluded: chain U residue 309 ILE Chi-restraints excluded: chain U residue 342 ILE Chi-restraints excluded: chain U residue 358 ILE Chi-restraints excluded: chain U residue 396 ASN Chi-restraints excluded: chain U residue 397 VAL Chi-restraints excluded: chain U residue 469 THR Chi-restraints excluded: chain U residue 537 ASP Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 186 VAL Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 285 THR Chi-restraints excluded: chain V residue 469 THR Chi-restraints excluded: chain V residue 477 THR 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: 9.9990 chunk 592 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 544 optimal weight: 20.0000 chunk 766 optimal weight: 9.9990 chunk 1144 optimal weight: 8.9990 chunk 1212 optimal weight: 10.0000 chunk 598 optimal weight: 4.9990 chunk 1085 optimal weight: 9.9990 chunk 326 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 13 ASN ** 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 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 527 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 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 294 ASN ** R 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 154 ASN ** T 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 98054 Z= 0.403 Angle : 0.759 10.710 132770 Z= 0.359 Chirality : 0.079 0.886 15312 Planarity : 0.003 0.021 16764 Dihedral : 30.449 146.235 23630 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.03 % Favored : 91.82 % Rotamer: Outliers : 3.95 % Allowed : 16.63 % Favored : 79.42 % 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: -0.38 (0.08), residues: 12584 helix: 2.27 (0.07), residues: 5500 sheet: -2.71 (0.13), residues: 1474 loop : -2.27 (0.08), residues: 5610 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.001 PHE K 393 TYR 0.049 0.002 TYR R 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 1176 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 391 poor density : 785 time to evaluate : 8.227 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: A 334 LYS cc_start: 0.9002 (tttt) cc_final: 0.8743 (ttpt) REVERT: A 383 ASN cc_start: 0.8267 (p0) cc_final: 0.8052 (p0) REVERT: B 90 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8134 (t0) REVERT: B 357 MET cc_start: 0.8913 (mmm) cc_final: 0.8513 (mmm) REVERT: B 502 GLN cc_start: 0.8695 (tp40) cc_final: 0.8371 (tp40) REVERT: C 532 GLU cc_start: 0.8512 (tt0) cc_final: 0.8265 (tt0) REVERT: D 13 ASN cc_start: 0.8601 (t0) cc_final: 0.8180 (t0) REVERT: D 38 ILE cc_start: 0.9703 (OUTLIER) cc_final: 0.9392 (pt) REVERT: D 502 GLN cc_start: 0.8601 (tp40) cc_final: 0.8229 (tm-30) REVERT: E 309 ILE cc_start: 0.9371 (OUTLIER) cc_final: 0.8961 (mt) REVERT: E 502 GLN cc_start: 0.8704 (tp-100) cc_final: 0.8160 (tp-100) REVERT: F 13 ASN cc_start: 0.8264 (t0) cc_final: 0.7934 (t0) REVERT: F 235 ASP cc_start: 0.7878 (t0) cc_final: 0.7661 (t70) REVERT: F 308 LYS cc_start: 0.9197 (tttt) cc_final: 0.8997 (ttpp) REVERT: F 385 TYR cc_start: 0.8745 (p90) cc_final: 0.8490 (p90) REVERT: F 537 ASP cc_start: 0.7572 (m-30) cc_final: 0.6969 (m-30) REVERT: G 129 THR cc_start: 0.8540 (m) cc_final: 0.8298 (m) REVERT: G 308 LYS cc_start: 0.9409 (tttt) cc_final: 0.9157 (tttp) REVERT: G 357 MET cc_start: 0.8897 (mmt) cc_final: 0.8477 (mmt) REVERT: H 537 ASP cc_start: 0.7416 (m-30) cc_final: 0.6993 (m-30) REVERT: I 13 ASN cc_start: 0.8578 (t0) cc_final: 0.8168 (t0) REVERT: I 19 ASP cc_start: 0.8331 (t0) cc_final: 0.8119 (t0) REVERT: I 124 ASP cc_start: 0.8398 (m-30) cc_final: 0.8153 (m-30) REVERT: I 146 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7293 (mm-30) REVERT: I 357 MET cc_start: 0.9117 (mmm) cc_final: 0.8666 (mmt) REVERT: J 385 TYR cc_start: 0.8914 (p90) cc_final: 0.8645 (p90) REVERT: J 502 GLN cc_start: 0.8796 (tp-100) cc_final: 0.8417 (tm-30) REVERT: K 357 MET cc_start: 0.8741 (mmt) cc_final: 0.8222 (mmt) REVERT: K 385 TYR cc_start: 0.8868 (p90) cc_final: 0.8430 (p90) REVERT: K 539 ASP cc_start: 0.8727 (p0) cc_final: 0.8481 (p0) REVERT: L 13 ASN cc_start: 0.8426 (t0) cc_final: 0.8217 (t0) REVERT: L 129 THR cc_start: 0.8527 (m) cc_final: 0.8282 (m) REVERT: L 537 ASP cc_start: 0.7335 (m-30) cc_final: 0.6841 (m-30) REVERT: M 102 ASP cc_start: 0.8182 (t70) cc_final: 0.7518 (t0) REVERT: M 334 LYS cc_start: 0.9132 (tttt) cc_final: 0.8878 (ttpt) REVERT: M 336 ASP cc_start: 0.7994 (p0) cc_final: 0.7446 (p0) REVERT: M 573 ARG cc_start: 0.8765 (ttm-80) cc_final: 0.8069 (ttt-90) REVERT: N 303 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8375 (p0) REVERT: N 502 GLN cc_start: 0.8431 (tp40) cc_final: 0.7794 (tm-30) REVERT: O 502 GLN cc_start: 0.8475 (tp40) cc_final: 0.8211 (tm-30) REVERT: O 573 ARG cc_start: 0.8697 (ttm-80) cc_final: 0.8056 (ttt180) REVERT: P 115 ASP cc_start: 0.8200 (t0) cc_final: 0.7933 (t0) REVERT: P 404 MET cc_start: 0.9108 (mtp) cc_final: 0.8733 (mtp) REVERT: P 446 TYR cc_start: 0.9465 (m-80) cc_final: 0.9082 (m-80) REVERT: P 502 GLN cc_start: 0.8629 (tp-100) cc_final: 0.8039 (tm-30) REVERT: Q 90 ASP cc_start: 0.8363 (t0) cc_final: 0.8159 (t0) REVERT: Q 573 ARG cc_start: 0.8885 (ttm-80) cc_final: 0.7925 (ttt-90) REVERT: R 282 LYS cc_start: 0.9281 (ptmm) cc_final: 0.9005 (ptpp) REVERT: R 385 TYR cc_start: 0.8631 (p90) cc_final: 0.8388 (p90) REVERT: R 539 ASP cc_start: 0.8376 (p0) cc_final: 0.8141 (p0) REVERT: S 283 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8389 (p0) REVERT: S 431 GLN cc_start: 0.8682 (mm110) cc_final: 0.8178 (mm-40) REVERT: S 490 MET cc_start: 0.8881 (ttm) cc_final: 0.8658 (ttm) REVERT: T 102 ASP cc_start: 0.7661 (t70) cc_final: 0.7253 (t0) REVERT: T 537 ASP cc_start: 0.7399 (m-30) cc_final: 0.7177 (m-30) REVERT: U 235 ASP cc_start: 0.8196 (t0) cc_final: 0.7869 (t70) REVERT: V 160 THR cc_start: 0.8684 (p) cc_final: 0.8426 (m) REVERT: V 235 ASP cc_start: 0.8042 (t0) cc_final: 0.7779 (t70) REVERT: V 385 TYR cc_start: 0.8800 (p90) cc_final: 0.8508 (p90) REVERT: V 487 MET cc_start: 0.8723 (mmm) cc_final: 0.8506 (mmt) outliers start: 391 outliers final: 300 residues processed: 1125 average time/residue: 0.7731 time to fit residues: 1592.1140 Evaluate side-chains 1053 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 748 time to evaluate : 8.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 537 ASP Chi-restraints excluded: chain E residue 539 ASP Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 164 THR Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 401 SER Chi-restraints excluded: chain F residue 443 SER Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 283 ASP Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain G residue 443 SER Chi-restraints excluded: chain G residue 469 THR Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain G residue 537 ASP Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 283 ASP Chi-restraints excluded: chain H residue 322 ASN Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 469 THR Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 186 VAL Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 290 SER Chi-restraints excluded: chain I residue 382 PHE Chi-restraints excluded: chain I residue 419 VAL Chi-restraints excluded: chain I residue 443 SER Chi-restraints excluded: chain I residue 469 THR Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain I residue 537 ASP Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 276 SER Chi-restraints excluded: chain J residue 320 LEU Chi-restraints excluded: chain J residue 419 VAL Chi-restraints excluded: chain J residue 427 VAL Chi-restraints excluded: chain J residue 443 SER Chi-restraints excluded: chain J residue 448 VAL Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain K residue 164 THR Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 239 THR Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 283 ASP Chi-restraints excluded: chain K residue 342 ILE Chi-restraints excluded: chain K residue 358 ILE Chi-restraints excluded: chain K residue 401 SER Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain K residue 443 SER Chi-restraints excluded: chain K residue 469 THR Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 186 VAL Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 239 THR Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 276 SER Chi-restraints excluded: chain L residue 283 ASP Chi-restraints excluded: chain L residue 320 LEU Chi-restraints excluded: chain L residue 397 VAL Chi-restraints excluded: chain L residue 443 SER Chi-restraints excluded: chain L residue 469 THR Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 164 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 188 LEU Chi-restraints excluded: chain M residue 202 ASP Chi-restraints excluded: chain M residue 276 SER Chi-restraints excluded: chain M residue 283 ASP Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 290 SER Chi-restraints excluded: chain M residue 309 ILE Chi-restraints excluded: chain M residue 358 ILE Chi-restraints excluded: chain M residue 397 VAL Chi-restraints excluded: chain M residue 401 SER Chi-restraints excluded: chain M residue 443 SER Chi-restraints excluded: chain M residue 469 THR Chi-restraints excluded: chain M residue 477 THR Chi-restraints excluded: chain M residue 537 ASP Chi-restraints excluded: chain N residue 19 ASP Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain N residue 283 ASP Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 303 ASP Chi-restraints excluded: chain N residue 309 ILE Chi-restraints excluded: chain N residue 401 SER Chi-restraints excluded: chain N residue 419 VAL Chi-restraints excluded: chain N residue 509 SER Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 164 THR Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 202 ASP Chi-restraints excluded: chain O residue 239 THR Chi-restraints excluded: chain O residue 258 VAL Chi-restraints excluded: chain O residue 276 SER Chi-restraints excluded: chain O residue 303 ASP Chi-restraints excluded: chain O residue 385 TYR Chi-restraints excluded: chain O residue 443 SER Chi-restraints excluded: chain O residue 447 VAL Chi-restraints excluded: chain O residue 469 THR Chi-restraints excluded: chain O residue 537 ASP Chi-restraints excluded: chain P residue 28 SER Chi-restraints excluded: chain P residue 164 THR Chi-restraints excluded: chain P residue 186 VAL Chi-restraints excluded: chain P residue 205 VAL Chi-restraints excluded: chain P residue 258 VAL Chi-restraints excluded: chain P residue 358 ILE Chi-restraints excluded: chain P residue 397 VAL Chi-restraints excluded: chain P residue 469 THR Chi-restraints excluded: chain Q residue 105 SER Chi-restraints excluded: chain Q residue 164 THR Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 205 VAL Chi-restraints excluded: chain Q residue 239 THR Chi-restraints excluded: chain Q residue 283 ASP Chi-restraints excluded: chain Q residue 401 SER Chi-restraints excluded: chain Q residue 443 SER Chi-restraints excluded: chain Q residue 469 THR Chi-restraints excluded: chain Q residue 537 ASP Chi-restraints excluded: chain Q residue 539 ASP Chi-restraints excluded: chain R residue 19 ASP Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain R residue 172 THR Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 239 THR Chi-restraints excluded: chain R residue 290 SER Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 419 VAL Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 469 THR Chi-restraints excluded: chain S residue 19 ASP Chi-restraints excluded: chain S residue 112 LEU Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain S residue 188 LEU Chi-restraints excluded: chain S residue 205 VAL Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 267 ASP Chi-restraints excluded: chain S residue 276 SER Chi-restraints excluded: chain S residue 283 ASP Chi-restraints excluded: chain S residue 285 THR Chi-restraints excluded: chain S residue 290 SER Chi-restraints excluded: chain S residue 309 ILE Chi-restraints excluded: chain S residue 342 ILE Chi-restraints excluded: chain S residue 419 VAL Chi-restraints excluded: chain S residue 443 SER Chi-restraints excluded: chain S residue 469 THR Chi-restraints excluded: chain S residue 477 THR Chi-restraints excluded: chain S residue 481 THR Chi-restraints excluded: chain S residue 537 ASP Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 149 ILE Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 186 VAL Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain T residue 202 ASP Chi-restraints excluded: chain T residue 205 VAL Chi-restraints excluded: chain T residue 239 THR Chi-restraints excluded: chain T residue 255 ILE Chi-restraints excluded: chain T residue 267 ASP Chi-restraints excluded: chain T residue 276 SER Chi-restraints excluded: chain T residue 303 ASP Chi-restraints excluded: chain T residue 397 VAL Chi-restraints excluded: chain T residue 401 SER Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 469 THR Chi-restraints excluded: chain U residue 19 ASP Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 186 VAL Chi-restraints excluded: chain U residue 188 LEU Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain U residue 205 VAL Chi-restraints excluded: chain U residue 267 ASP Chi-restraints excluded: chain U residue 276 SER Chi-restraints excluded: chain U residue 290 SER Chi-restraints excluded: chain U residue 303 ASP Chi-restraints excluded: chain U residue 309 ILE Chi-restraints excluded: chain U residue 342 ILE Chi-restraints excluded: chain U residue 358 ILE Chi-restraints excluded: chain U residue 427 VAL Chi-restraints excluded: chain U residue 469 THR Chi-restraints excluded: chain U residue 537 ASP Chi-restraints excluded: chain V residue 149 ILE Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 186 VAL Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 283 ASP Chi-restraints excluded: chain V residue 285 THR Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 469 THR Chi-restraints excluded: chain V residue 477 THR Chi-restraints excluded: chain V residue 537 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1254 random chunks: chunk 1009 optimal weight: 6.9990 chunk 688 optimal weight: 10.0000 chunk 17 optimal weight: 0.0020 chunk 902 optimal weight: 3.9990 chunk 500 optimal weight: 9.9990 chunk 1034 optimal weight: 0.9990 chunk 837 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 618 optimal weight: 9.9990 chunk 1087 optimal weight: 10.0000 chunk 305 optimal weight: 10.0000 overall best weight: 3.5996 ------------------------------------------------------------------------------- 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 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 21 ASN ** K 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 ASN M 154 ASN ** 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 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 21 ASN ** R 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 520 ASN ** T 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 431 GLN ** 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 98054 Z= 0.226 Angle : 0.682 9.486 132770 Z= 0.317 Chirality : 0.074 0.810 15312 Planarity : 0.002 0.021 16764 Dihedral : 29.035 139.372 23630 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.61 % Allowed : 17.81 % Favored : 78.59 % 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: 0.09 (0.08), residues: 12584 helix: 2.70 (0.07), residues: 5500 sheet: -2.48 (0.13), residues: 1562 loop : -2.04 (0.08), residues: 5522 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.001 PHE V 382 TYR 0.047 0.002 TYR S 242 ARG 0.003 0.000 ARG R 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 1208 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 357 poor density : 851 time to evaluate : 9.448 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: A 334 LYS cc_start: 0.8907 (tttt) cc_final: 0.8661 (ttpt) REVERT: C 309 ILE cc_start: 0.9442 (OUTLIER) cc_final: 0.9218 (mp) REVERT: C 532 GLU cc_start: 0.8536 (tt0) cc_final: 0.8284 (tt0) REVERT: D 13 ASN cc_start: 0.8427 (t0) cc_final: 0.7971 (t0) REVERT: D 38 ILE cc_start: 0.9701 (OUTLIER) cc_final: 0.9479 (pt) REVERT: D 145 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8311 (mm-40) REVERT: D 502 GLN cc_start: 0.8526 (tp40) cc_final: 0.8203 (tm-30) REVERT: E 309 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.8961 (mt) REVERT: E 502 GLN cc_start: 0.8682 (tp-100) cc_final: 0.8140 (tp-100) REVERT: E 532 GLU cc_start: 0.8581 (tt0) cc_final: 0.8350 (tt0) REVERT: F 235 ASP cc_start: 0.7813 (t0) cc_final: 0.7604 (t70) REVERT: F 385 TYR cc_start: 0.8816 (p90) cc_final: 0.8567 (p90) REVERT: F 537 ASP cc_start: 0.6944 (m-30) cc_final: 0.6235 (m-30) REVERT: G 129 THR cc_start: 0.8473 (m) cc_final: 0.8248 (m) REVERT: G 308 LYS cc_start: 0.9385 (tttt) cc_final: 0.9145 (tttp) REVERT: G 357 MET cc_start: 0.8878 (mmt) cc_final: 0.8389 (mmt) REVERT: I 19 ASP cc_start: 0.8213 (t0) cc_final: 0.7978 (t0) REVERT: I 124 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8079 (m-30) REVERT: I 357 MET cc_start: 0.9056 (mmm) cc_final: 0.8574 (mmt) REVERT: J 385 TYR cc_start: 0.8897 (p90) cc_final: 0.8608 (p90) REVERT: J 502 GLN cc_start: 0.8739 (tp-100) cc_final: 0.8382 (tm-30) REVERT: K 309 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.9131 (mp) REVERT: K 357 MET cc_start: 0.8749 (mmt) cc_final: 0.8218 (mmt) REVERT: K 385 TYR cc_start: 0.8836 (p90) cc_final: 0.8326 (p90) REVERT: K 539 ASP cc_start: 0.8657 (p0) cc_final: 0.8455 (p0) REVERT: L 13 ASN cc_start: 0.8171 (t0) cc_final: 0.7920 (t0) REVERT: L 129 THR cc_start: 0.8482 (m) cc_final: 0.8230 (m) REVERT: L 537 ASP cc_start: 0.7364 (m-30) cc_final: 0.7072 (m-30) REVERT: M 102 ASP cc_start: 0.8154 (t70) cc_final: 0.7524 (t0) REVERT: M 334 LYS cc_start: 0.9111 (tttt) cc_final: 0.8854 (ttpt) REVERT: M 336 ASP cc_start: 0.7852 (p0) cc_final: 0.7345 (p0) REVERT: M 573 ARG cc_start: 0.8733 (ttm-80) cc_final: 0.8048 (ttt-90) REVERT: N 303 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8433 (p0) REVERT: N 502 GLN cc_start: 0.8330 (tp40) cc_final: 0.7644 (tm-30) REVERT: O 102 ASP cc_start: 0.7739 (t0) cc_final: 0.7425 (t0) REVERT: O 502 GLN cc_start: 0.8400 (tp40) cc_final: 0.8115 (tm-30) REVERT: O 573 ARG cc_start: 0.8642 (ttm-80) cc_final: 0.8016 (ttt180) REVERT: P 115 ASP cc_start: 0.8167 (t0) cc_final: 0.7853 (t0) REVERT: P 308 LYS cc_start: 0.9366 (tttt) cc_final: 0.9108 (tttm) REVERT: P 357 MET cc_start: 0.9128 (mmm) cc_final: 0.8613 (mmm) REVERT: P 404 MET cc_start: 0.9074 (mtp) cc_final: 0.8689 (mtp) REVERT: P 446 TYR cc_start: 0.9419 (m-80) cc_final: 0.9039 (m-80) REVERT: P 502 GLN cc_start: 0.8466 (tp-100) cc_final: 0.7829 (tm-30) REVERT: P 539 ASP cc_start: 0.8417 (p0) cc_final: 0.8177 (p0) REVERT: Q 90 ASP cc_start: 0.8389 (t0) cc_final: 0.8161 (t0) REVERT: Q 502 GLN cc_start: 0.8609 (tp40) cc_final: 0.7831 (tm-30) REVERT: Q 573 ARG cc_start: 0.8851 (ttm-80) cc_final: 0.7974 (ttp-170) REVERT: R 282 LYS cc_start: 0.9261 (ptmm) cc_final: 0.9012 (ptpp) REVERT: R 315 VAL cc_start: 0.8753 (t) cc_final: 0.8384 (p) REVERT: R 385 TYR cc_start: 0.8591 (p90) cc_final: 0.8335 (p90) REVERT: R 539 ASP cc_start: 0.8366 (p0) cc_final: 0.8154 (p0) REVERT: S 283 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8319 (p0) REVERT: S 431 GLN cc_start: 0.8668 (mm110) cc_final: 0.8414 (mm-40) REVERT: S 490 MET cc_start: 0.8638 (ttm) cc_final: 0.8333 (ttm) REVERT: T 102 ASP cc_start: 0.7227 (t70) cc_final: 0.6973 (t0) REVERT: U 146 GLU cc_start: 0.5943 (pt0) cc_final: 0.5635 (pt0) REVERT: U 234 TYR cc_start: 0.9225 (p90) cc_final: 0.8689 (p90) REVERT: V 235 ASP cc_start: 0.7967 (t0) cc_final: 0.7656 (t70) REVERT: V 385 TYR cc_start: 0.8787 (p90) cc_final: 0.8555 (p90) REVERT: V 487 MET cc_start: 0.8766 (mmm) cc_final: 0.8433 (mmt) outliers start: 357 outliers final: 275 residues processed: 1160 average time/residue: 0.7807 time to fit residues: 1657.6988 Evaluate side-chains 1059 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 777 time to evaluate : 8.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 576 GLN Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 537 ASP Chi-restraints excluded: chain E residue 576 GLN Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 164 THR Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 401 SER Chi-restraints excluded: chain F residue 443 SER Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 283 ASP Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 303 ASP Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 437 SER Chi-restraints excluded: chain G residue 443 SER Chi-restraints excluded: chain G residue 537 ASP Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 283 ASP Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 469 THR Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 186 VAL Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain I residue 290 SER Chi-restraints excluded: chain I residue 401 SER Chi-restraints excluded: chain I residue 419 VAL Chi-restraints excluded: chain I residue 443 SER Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain I residue 537 ASP Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 239 THR Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 276 SER Chi-restraints excluded: chain J residue 320 LEU Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 401 SER Chi-restraints excluded: chain J residue 419 VAL Chi-restraints excluded: chain J residue 443 SER Chi-restraints excluded: chain J residue 448 VAL Chi-restraints excluded: chain J residue 469 THR Chi-restraints excluded: chain K residue 19 ASP Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 239 THR Chi-restraints excluded: chain K residue 283 ASP Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 342 ILE Chi-restraints excluded: chain K residue 358 ILE Chi-restraints excluded: chain K residue 401 SER Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain K residue 469 THR Chi-restraints excluded: chain L residue 186 VAL Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 276 SER Chi-restraints excluded: chain L residue 397 VAL Chi-restraints excluded: chain L residue 443 SER Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 38 ILE Chi-restraints excluded: chain M residue 164 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 205 VAL Chi-restraints excluded: chain M residue 276 SER Chi-restraints excluded: chain M residue 283 ASP Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 290 SER Chi-restraints excluded: chain M residue 309 ILE Chi-restraints excluded: chain M residue 397 VAL Chi-restraints excluded: chain M residue 426 SER Chi-restraints excluded: chain M residue 443 SER Chi-restraints excluded: chain M residue 469 THR Chi-restraints excluded: chain M residue 477 THR Chi-restraints excluded: chain M residue 518 ILE Chi-restraints excluded: chain M residue 537 ASP Chi-restraints excluded: chain N residue 19 ASP Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 198 ASP Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 303 ASP Chi-restraints excluded: chain N residue 309 ILE Chi-restraints excluded: chain N residue 401 SER Chi-restraints excluded: chain N residue 419 VAL Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 498 THR Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 164 THR Chi-restraints excluded: chain O residue 202 ASP Chi-restraints excluded: chain O residue 239 THR Chi-restraints excluded: chain O residue 276 SER Chi-restraints excluded: chain O residue 385 TYR Chi-restraints excluded: chain O residue 443 SER Chi-restraints excluded: chain O residue 447 VAL Chi-restraints excluded: chain O residue 469 THR Chi-restraints excluded: chain O residue 537 ASP Chi-restraints excluded: chain P residue 28 SER Chi-restraints excluded: chain P residue 186 VAL Chi-restraints excluded: chain P residue 358 ILE Chi-restraints excluded: chain P residue 397 VAL Chi-restraints excluded: chain P residue 460 ASN Chi-restraints excluded: chain Q residue 105 SER Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 205 VAL Chi-restraints excluded: chain Q residue 239 THR Chi-restraints excluded: chain Q residue 283 ASP Chi-restraints excluded: chain Q residue 401 SER Chi-restraints excluded: chain Q residue 443 SER Chi-restraints excluded: chain Q residue 537 ASP Chi-restraints excluded: chain Q residue 539 ASP Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain R residue 172 THR Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 239 THR Chi-restraints excluded: chain R residue 258 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 419 VAL Chi-restraints excluded: chain R residue 460 ASN Chi-restraints excluded: chain R residue 498 THR Chi-restraints excluded: chain S residue 19 ASP Chi-restraints excluded: chain S residue 112 LEU Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain S residue 188 LEU Chi-restraints excluded: chain S residue 205 VAL Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 276 SER Chi-restraints excluded: chain S residue 283 ASP Chi-restraints excluded: chain S residue 285 THR Chi-restraints excluded: chain S residue 290 SER Chi-restraints excluded: chain S residue 309 ILE Chi-restraints excluded: chain S residue 342 ILE Chi-restraints excluded: chain S residue 419 VAL Chi-restraints excluded: chain S residue 426 SER Chi-restraints excluded: chain S residue 443 SER Chi-restraints excluded: chain S residue 477 THR Chi-restraints excluded: chain S residue 481 THR Chi-restraints excluded: chain S residue 537 ASP Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 149 ILE Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 186 VAL Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain T residue 205 VAL Chi-restraints excluded: chain T residue 239 THR Chi-restraints excluded: chain T residue 267 ASP Chi-restraints excluded: chain T residue 276 SER Chi-restraints excluded: chain T residue 283 ASP Chi-restraints excluded: chain T residue 303 ASP Chi-restraints excluded: chain T residue 358 ILE Chi-restraints excluded: chain T residue 401 SER Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain U residue 19 ASP Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain U residue 186 VAL Chi-restraints excluded: chain U residue 188 LEU Chi-restraints excluded: chain U residue 205 VAL Chi-restraints excluded: chain U residue 276 SER Chi-restraints excluded: chain U residue 290 SER Chi-restraints excluded: chain U residue 303 ASP Chi-restraints excluded: chain U residue 309 ILE Chi-restraints excluded: chain U residue 358 ILE Chi-restraints excluded: chain U residue 396 ASN Chi-restraints excluded: chain U residue 397 VAL Chi-restraints excluded: chain U residue 427 VAL Chi-restraints excluded: chain U residue 443 SER Chi-restraints excluded: chain U residue 455 SER Chi-restraints excluded: chain U residue 537 ASP Chi-restraints excluded: chain V residue 149 ILE Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 186 VAL Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 283 ASP Chi-restraints excluded: chain V residue 358 ILE Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 477 THR Chi-restraints excluded: chain V residue 537 ASP 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: 1.9990 chunk 239 optimal weight: 2.9990 chunk 711 optimal weight: 6.9990 chunk 299 optimal weight: 7.9990 chunk 1213 optimal weight: 10.0000 chunk 1007 optimal weight: 9.9990 chunk 561 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 401 optimal weight: 10.0000 chunk 636 optimal weight: 5.9990 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 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 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 39 ASN ** T 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 145 GLN ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 98054 Z= 0.282 Angle : 0.699 10.351 132770 Z= 0.328 Chirality : 0.073 0.801 15312 Planarity : 0.002 0.024 16764 Dihedral : 28.939 136.968 23630 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.70 % Favored : 92.28 % Rotamer: Outliers : 4.18 % Allowed : 17.95 % Favored : 77.87 % 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: 0.17 (0.08), residues: 12584 helix: 2.70 (0.07), residues: 5500 sheet: -2.08 (0.13), residues: 1628 loop : -2.02 (0.08), residues: 5456 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.001 PHE K 393 TYR 0.054 0.002 TYR R 242 ARG 0.004 0.000 ARG R 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 1197 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 414 poor density : 783 time to evaluate : 8.267 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 LYS cc_start: 0.8953 (tttt) cc_final: 0.8634 (ttpt) REVERT: B 90 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8181 (t0) REVERT: B 357 MET cc_start: 0.9039 (mmm) cc_final: 0.8227 (mmm) REVERT: C 112 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9024 (mm) REVERT: C 532 GLU cc_start: 0.8545 (tt0) cc_final: 0.8288 (tt0) REVERT: D 13 ASN cc_start: 0.8472 (t0) cc_final: 0.8007 (t0) REVERT: D 502 GLN cc_start: 0.8540 (tp40) cc_final: 0.8237 (tm-30) REVERT: E 309 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.8928 (mt) REVERT: E 502 GLN cc_start: 0.8679 (tp-100) cc_final: 0.8127 (tp-100) REVERT: E 532 GLU cc_start: 0.8589 (tt0) cc_final: 0.8347 (tt0) REVERT: F 235 ASP cc_start: 0.7845 (t0) cc_final: 0.7632 (t70) REVERT: F 385 TYR cc_start: 0.8829 (p90) cc_final: 0.8594 (p90) REVERT: G 129 THR cc_start: 0.8476 (m) cc_final: 0.8227 (m) REVERT: G 308 LYS cc_start: 0.9420 (tttt) cc_final: 0.9160 (tttp) REVERT: G 357 MET cc_start: 0.8876 (mmt) cc_final: 0.8433 (mmt) REVERT: I 124 ASP cc_start: 0.8354 (m-30) cc_final: 0.8103 (m-30) REVERT: J 385 TYR cc_start: 0.8894 (p90) cc_final: 0.8608 (p90) REVERT: J 502 GLN cc_start: 0.8688 (tp-100) cc_final: 0.8338 (tm-30) REVERT: K 357 MET cc_start: 0.8744 (mmt) cc_final: 0.8251 (mmt) REVERT: K 385 TYR cc_start: 0.8838 (p90) cc_final: 0.8369 (p90) REVERT: K 539 ASP cc_start: 0.8727 (p0) cc_final: 0.8467 (p0) REVERT: L 13 ASN cc_start: 0.8342 (t0) cc_final: 0.8105 (t0) REVERT: L 129 THR cc_start: 0.8470 (m) cc_final: 0.8234 (m) REVERT: L 537 ASP cc_start: 0.7383 (m-30) cc_final: 0.6849 (m-30) REVERT: M 56 SER cc_start: 0.9092 (t) cc_final: 0.8802 (p) REVERT: M 102 ASP cc_start: 0.8132 (t70) cc_final: 0.7496 (t0) REVERT: M 539 ASP cc_start: 0.8750 (p0) cc_final: 0.8418 (p0) REVERT: M 573 ARG cc_start: 0.8747 (ttm-80) cc_final: 0.8055 (ttt-90) REVERT: N 303 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8422 (p0) REVERT: N 502 GLN cc_start: 0.8360 (tp40) cc_final: 0.7637 (tm-30) REVERT: O 102 ASP cc_start: 0.7927 (t0) cc_final: 0.7524 (t0) REVERT: O 502 GLN cc_start: 0.8409 (tp40) cc_final: 0.8184 (tm-30) REVERT: O 573 ARG cc_start: 0.8648 (ttm-80) cc_final: 0.8032 (ttt180) REVERT: P 115 ASP cc_start: 0.8141 (t0) cc_final: 0.7825 (t0) REVERT: P 404 MET cc_start: 0.9163 (mtp) cc_final: 0.8827 (mtp) REVERT: P 446 TYR cc_start: 0.9438 (m-80) cc_final: 0.9022 (m-80) REVERT: P 502 GLN cc_start: 0.8584 (tp-100) cc_final: 0.8003 (tm-30) REVERT: Q 90 ASP cc_start: 0.8392 (t0) cc_final: 0.8163 (t0) REVERT: Q 502 GLN cc_start: 0.8609 (tp40) cc_final: 0.7823 (tm-30) REVERT: Q 573 ARG cc_start: 0.8870 (ttm-80) cc_final: 0.8002 (ttp-170) REVERT: R 282 LYS cc_start: 0.9286 (ptmm) cc_final: 0.8998 (ptpp) REVERT: R 315 VAL cc_start: 0.8802 (t) cc_final: 0.8432 (p) REVERT: R 385 TYR cc_start: 0.8572 (p90) cc_final: 0.8344 (p90) REVERT: R 539 ASP cc_start: 0.8411 (p0) cc_final: 0.8205 (p0) REVERT: S 283 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8351 (p0) REVERT: S 431 GLN cc_start: 0.8686 (mm110) cc_final: 0.8432 (mm-40) REVERT: S 490 MET cc_start: 0.8708 (ttm) cc_final: 0.8444 (ttm) REVERT: T 102 ASP cc_start: 0.7018 (t70) cc_final: 0.6812 (t0) REVERT: U 146 GLU cc_start: 0.6028 (pt0) cc_final: 0.5715 (pt0) REVERT: U 234 TYR cc_start: 0.9219 (p90) cc_final: 0.8636 (p90) REVERT: V 235 ASP cc_start: 0.8063 (t0) cc_final: 0.7752 (t70) REVERT: V 385 TYR cc_start: 0.8780 (p90) cc_final: 0.8527 (p90) REVERT: V 487 MET cc_start: 0.8775 (mmm) cc_final: 0.8462 (mmt) outliers start: 414 outliers final: 336 residues processed: 1150 average time/residue: 0.7653 time to fit residues: 1615.8155 Evaluate side-chains 1101 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 341 poor density : 760 time to evaluate : 8.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 537 ASP Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 164 THR Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 401 SER Chi-restraints excluded: chain F residue 443 SER Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 283 ASP Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 303 ASP Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 437 SER Chi-restraints excluded: chain G residue 443 SER Chi-restraints excluded: chain G residue 469 THR Chi-restraints excluded: chain G residue 537 ASP Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 283 ASP Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 468 THR Chi-restraints excluded: chain H residue 469 THR Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 186 VAL Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain I residue 290 SER Chi-restraints excluded: chain I residue 401 SER Chi-restraints excluded: chain I residue 419 VAL Chi-restraints excluded: chain I residue 443 SER Chi-restraints excluded: chain I residue 469 THR Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain I residue 537 ASP Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 239 THR Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 276 SER Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 401 SER Chi-restraints excluded: chain J residue 419 VAL Chi-restraints excluded: chain J residue 427 VAL Chi-restraints excluded: chain J residue 443 SER Chi-restraints excluded: chain J residue 448 VAL Chi-restraints excluded: chain J residue 469 THR Chi-restraints excluded: chain K residue 19 ASP Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 239 THR Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 283 ASP Chi-restraints excluded: chain K residue 315 VAL Chi-restraints excluded: chain K residue 342 ILE Chi-restraints excluded: chain K residue 358 ILE Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain K residue 426 SER Chi-restraints excluded: chain K residue 443 SER Chi-restraints excluded: chain K residue 469 THR Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 186 VAL Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 276 SER Chi-restraints excluded: chain L residue 283 ASP Chi-restraints excluded: chain L residue 320 LEU Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 397 VAL Chi-restraints excluded: chain L residue 443 SER Chi-restraints excluded: chain L residue 469 THR Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 38 ILE Chi-restraints excluded: chain M residue 164 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 188 LEU Chi-restraints excluded: chain M residue 205 VAL Chi-restraints excluded: chain M residue 249 THR Chi-restraints excluded: chain M residue 276 SER Chi-restraints excluded: chain M residue 283 ASP Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 290 SER Chi-restraints excluded: chain M residue 309 ILE Chi-restraints excluded: chain M residue 397 VAL Chi-restraints excluded: chain M residue 401 SER Chi-restraints excluded: chain M residue 426 SER Chi-restraints excluded: chain M residue 443 SER Chi-restraints excluded: chain M residue 469 THR Chi-restraints excluded: chain M residue 477 THR Chi-restraints excluded: chain M residue 518 ILE Chi-restraints excluded: chain M residue 537 ASP Chi-restraints excluded: chain N residue 19 ASP Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 198 ASP Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain N residue 283 ASP Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 303 ASP Chi-restraints excluded: chain N residue 309 ILE Chi-restraints excluded: chain N residue 345 THR Chi-restraints excluded: chain N residue 397 VAL Chi-restraints excluded: chain N residue 401 SER Chi-restraints excluded: chain N residue 419 VAL Chi-restraints excluded: chain N residue 426 SER Chi-restraints excluded: chain N residue 433 ILE Chi-restraints excluded: chain N residue 443 SER Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 498 THR Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 164 THR Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 202 ASP Chi-restraints excluded: chain O residue 239 THR Chi-restraints excluded: chain O residue 258 VAL Chi-restraints excluded: chain O residue 276 SER Chi-restraints excluded: chain O residue 385 TYR Chi-restraints excluded: chain O residue 407 GLN Chi-restraints excluded: chain O residue 443 SER Chi-restraints excluded: chain O residue 447 VAL Chi-restraints excluded: chain O residue 469 THR Chi-restraints excluded: chain O residue 537 ASP Chi-restraints excluded: chain P residue 28 SER Chi-restraints excluded: chain P residue 164 THR Chi-restraints excluded: chain P residue 186 VAL Chi-restraints excluded: chain P residue 205 VAL Chi-restraints excluded: chain P residue 358 ILE Chi-restraints excluded: chain P residue 397 VAL Chi-restraints excluded: chain P residue 401 SER Chi-restraints excluded: chain P residue 460 ASN Chi-restraints excluded: chain P residue 469 THR Chi-restraints excluded: chain Q residue 105 SER Chi-restraints excluded: chain Q residue 164 THR Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 205 VAL Chi-restraints excluded: chain Q residue 239 THR Chi-restraints excluded: chain Q residue 283 ASP Chi-restraints excluded: chain Q residue 285 THR Chi-restraints excluded: chain Q residue 401 SER Chi-restraints excluded: chain Q residue 426 SER Chi-restraints excluded: chain Q residue 443 SER Chi-restraints excluded: chain Q residue 469 THR Chi-restraints excluded: chain Q residue 537 ASP Chi-restraints excluded: chain Q residue 539 ASP Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain R residue 172 THR Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 239 THR Chi-restraints excluded: chain R residue 258 VAL Chi-restraints excluded: chain R residue 290 SER Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 419 VAL Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 460 ASN Chi-restraints excluded: chain R residue 469 THR Chi-restraints excluded: chain R residue 498 THR Chi-restraints excluded: chain S residue 19 ASP Chi-restraints excluded: chain S residue 112 LEU Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain S residue 188 LEU Chi-restraints excluded: chain S residue 205 VAL Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 255 ILE Chi-restraints excluded: chain S residue 267 ASP Chi-restraints excluded: chain S residue 276 SER Chi-restraints excluded: chain S residue 283 ASP Chi-restraints excluded: chain S residue 285 THR Chi-restraints excluded: chain S residue 290 SER Chi-restraints excluded: chain S residue 309 ILE Chi-restraints excluded: chain S residue 342 ILE Chi-restraints excluded: chain S residue 419 VAL Chi-restraints excluded: chain S residue 426 SER Chi-restraints excluded: chain S residue 443 SER Chi-restraints excluded: chain S residue 469 THR Chi-restraints excluded: chain S residue 477 THR Chi-restraints excluded: chain S residue 481 THR Chi-restraints excluded: chain S residue 537 ASP Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 149 ILE Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 186 VAL Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain T residue 205 VAL Chi-restraints excluded: chain T residue 239 THR Chi-restraints excluded: chain T residue 255 ILE Chi-restraints excluded: chain T residue 267 ASP Chi-restraints excluded: chain T residue 276 SER Chi-restraints excluded: chain T residue 283 ASP Chi-restraints excluded: chain T residue 303 ASP Chi-restraints excluded: chain T residue 358 ILE Chi-restraints excluded: chain T residue 401 SER Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 460 ASN Chi-restraints excluded: chain T residue 469 THR Chi-restraints excluded: chain U residue 19 ASP Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 105 SER Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 186 VAL Chi-restraints excluded: chain U residue 188 LEU Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain U residue 205 VAL Chi-restraints excluded: chain U residue 276 SER Chi-restraints excluded: chain U residue 290 SER Chi-restraints excluded: chain U residue 303 ASP Chi-restraints excluded: chain U residue 309 ILE Chi-restraints excluded: chain U residue 342 ILE Chi-restraints excluded: chain U residue 358 ILE Chi-restraints excluded: chain U residue 397 VAL Chi-restraints excluded: chain U residue 427 VAL Chi-restraints excluded: chain U residue 443 SER Chi-restraints excluded: chain U residue 455 SER Chi-restraints excluded: chain U residue 469 THR Chi-restraints excluded: chain U residue 537 ASP Chi-restraints excluded: chain V residue 149 ILE Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 186 VAL Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 283 ASP Chi-restraints excluded: chain V residue 358 ILE Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 469 THR Chi-restraints excluded: chain V residue 477 THR Chi-restraints excluded: chain V residue 537 ASP 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: 0.6980 chunk 691 optimal weight: 2.9990 chunk 886 optimal weight: 1.9990 chunk 686 optimal weight: 6.9990 chunk 1021 optimal weight: 7.9990 chunk 677 optimal weight: 9.9990 chunk 1208 optimal weight: 2.9990 chunk 756 optimal weight: 9.9990 chunk 736 optimal weight: 3.9990 chunk 558 optimal weight: 0.0370 overall best weight: 1.7464 ------------------------------------------------------------------------------- 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** C 551 ASN D 85 GLN ** 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 ** H 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 527 ASN H 551 ASN I 13 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 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 21 ASN O 98 GLN O 104 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 Q 288 GLN R 128 ASN 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 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 136 GLN ** V 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 98054 Z= 0.164 Angle : 0.663 9.419 132770 Z= 0.305 Chirality : 0.070 0.741 15312 Planarity : 0.002 0.025 16764 Dihedral : 27.698 129.969 23630 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.18 % Allowed : 19.45 % Favored : 77.36 % 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: 0.48 (0.08), residues: 12584 helix: 2.92 (0.07), residues: 5588 sheet: -1.88 (0.13), residues: 1716 loop : -1.91 (0.08), residues: 5280 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.001 PHE K 393 TYR 0.048 0.002 TYR R 242 ARG 0.004 0.000 ARG R 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 1251 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 936 time to evaluate : 8.438 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 LYS cc_start: 0.8905 (tttt) cc_final: 0.8653 (ttpt) REVERT: C 532 GLU cc_start: 0.8483 (tt0) cc_final: 0.8227 (tt0) REVERT: D 13 ASN cc_start: 0.8229 (t0) cc_final: 0.7777 (t0) REVERT: D 38 ILE cc_start: 0.9436 (pt) cc_final: 0.9217 (pt) REVERT: D 145 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8266 (mm-40) REVERT: D 502 GLN cc_start: 0.8492 (tp40) cc_final: 0.8204 (tm-30) REVERT: E 102 ASP cc_start: 0.7637 (t0) cc_final: 0.7183 (t0) REVERT: E 309 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8995 (mt) REVERT: E 502 GLN cc_start: 0.8660 (tp-100) cc_final: 0.8132 (tp-100) REVERT: F 102 ASP cc_start: 0.7463 (t70) cc_final: 0.7240 (t0) REVERT: F 235 ASP cc_start: 0.7814 (t0) cc_final: 0.7580 (t70) REVERT: F 242 TYR cc_start: 0.9034 (p90) cc_final: 0.8694 (p90) REVERT: F 385 TYR cc_start: 0.8785 (p90) cc_final: 0.8569 (p90) REVERT: F 537 ASP cc_start: 0.7036 (m-30) cc_final: 0.6350 (m-30) REVERT: G 102 ASP cc_start: 0.8023 (t0) cc_final: 0.7767 (t0) REVERT: G 129 THR cc_start: 0.8408 (m) cc_final: 0.8208 (m) REVERT: G 357 MET cc_start: 0.8791 (mmt) cc_final: 0.8325 (mmt) REVERT: H 276 SER cc_start: 0.9464 (t) cc_final: 0.9263 (m) REVERT: H 380 MET cc_start: 0.8547 (mmm) cc_final: 0.7910 (mtt) REVERT: I 19 ASP cc_start: 0.8160 (t0) cc_final: 0.7952 (t0) REVERT: I 124 ASP cc_start: 0.8343 (m-30) cc_final: 0.8071 (m-30) REVERT: I 357 MET cc_start: 0.9167 (mmm) cc_final: 0.8917 (mmm) REVERT: J 385 TYR cc_start: 0.8897 (p90) cc_final: 0.8613 (p90) REVERT: J 502 GLN cc_start: 0.8616 (tp-100) cc_final: 0.8274 (tm-30) REVERT: K 357 MET cc_start: 0.8721 (mmt) cc_final: 0.8241 (mmt) REVERT: K 385 TYR cc_start: 0.8718 (p90) cc_final: 0.8252 (p90) REVERT: L 13 ASN cc_start: 0.8003 (t0) cc_final: 0.7727 (t0) REVERT: L 129 THR cc_start: 0.8386 (m) cc_final: 0.8161 (m) REVERT: L 537 ASP cc_start: 0.7333 (m-30) cc_final: 0.6972 (m-30) REVERT: M 539 ASP cc_start: 0.8760 (p0) cc_final: 0.8512 (p0) REVERT: M 573 ARG cc_start: 0.8702 (ttm-80) cc_final: 0.8065 (ttt-90) REVERT: N 120 MET cc_start: 0.8672 (ttm) cc_final: 0.8303 (mtp) REVERT: N 146 GLU cc_start: 0.8019 (mp0) cc_final: 0.7794 (mp0) REVERT: N 502 GLN cc_start: 0.8186 (tp40) cc_final: 0.7451 (tm-30) REVERT: O 102 ASP cc_start: 0.7681 (t0) cc_final: 0.7202 (t0) REVERT: O 309 ILE cc_start: 0.9442 (OUTLIER) cc_final: 0.9207 (mt) REVERT: O 491 ASP cc_start: 0.8582 (m-30) cc_final: 0.8287 (m-30) REVERT: P 115 ASP cc_start: 0.8082 (t0) cc_final: 0.7743 (t0) REVERT: P 308 LYS cc_start: 0.9384 (tttt) cc_final: 0.9164 (tttm) REVERT: P 404 MET cc_start: 0.8993 (mtp) cc_final: 0.8591 (mtp) REVERT: P 446 TYR cc_start: 0.9395 (m-80) cc_final: 0.8914 (m-80) REVERT: P 502 GLN cc_start: 0.8408 (tp-100) cc_final: 0.7784 (tm-30) REVERT: P 539 ASP cc_start: 0.8490 (p0) cc_final: 0.8288 (p0) REVERT: Q 393 PHE cc_start: 0.8632 (m-10) cc_final: 0.8428 (m-10) REVERT: Q 502 GLN cc_start: 0.8509 (tp40) cc_final: 0.7698 (tm-30) REVERT: Q 573 ARG cc_start: 0.8840 (ttm-80) cc_final: 0.8005 (ttp-170) REVERT: R 282 LYS cc_start: 0.9251 (ptmm) cc_final: 0.8997 (ptpp) REVERT: R 315 VAL cc_start: 0.8452 (t) cc_final: 0.8063 (p) REVERT: R 385 TYR cc_start: 0.8473 (p90) cc_final: 0.8250 (p90) REVERT: R 561 MET cc_start: 0.7990 (mtt) cc_final: 0.7775 (mtt) REVERT: S 82 MET cc_start: 0.8842 (mmm) cc_final: 0.8626 (mtm) REVERT: S 283 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8226 (p0) REVERT: S 431 GLN cc_start: 0.8652 (mm110) cc_final: 0.8313 (mm-40) REVERT: S 490 MET cc_start: 0.8407 (ttm) cc_final: 0.8148 (ttm) REVERT: U 146 GLU cc_start: 0.5823 (pt0) cc_final: 0.5432 (pt0) REVERT: U 234 TYR cc_start: 0.9132 (p90) cc_final: 0.8707 (p90) REVERT: U 357 MET cc_start: 0.9225 (mmm) cc_final: 0.8899 (mmt) REVERT: U 385 TYR cc_start: 0.8551 (p90) cc_final: 0.8281 (p90) REVERT: U 431 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8497 (pm20) REVERT: V 235 ASP cc_start: 0.7949 (t0) cc_final: 0.7649 (t70) REVERT: V 487 MET cc_start: 0.8734 (mmm) cc_final: 0.8506 (mmt) outliers start: 315 outliers final: 243 residues processed: 1218 average time/residue: 0.7722 time to fit residues: 1723.3381 Evaluate side-chains 1073 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 826 time to evaluate : 8.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain F residue 164 THR Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 401 SER Chi-restraints excluded: chain F residue 443 SER Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 283 ASP Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 303 ASP Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 437 SER Chi-restraints excluded: chain G residue 443 SER Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 469 THR Chi-restraints excluded: chain G residue 537 ASP Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 468 THR Chi-restraints excluded: chain H residue 469 THR Chi-restraints excluded: chain I residue 186 VAL Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 401 SER Chi-restraints excluded: chain I residue 443 SER Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 239 THR Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 276 SER Chi-restraints excluded: chain J residue 401 SER Chi-restraints excluded: chain J residue 421 SER Chi-restraints excluded: chain J residue 427 VAL Chi-restraints excluded: chain J residue 443 SER Chi-restraints excluded: chain J residue 448 VAL Chi-restraints excluded: chain J residue 469 THR Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 283 ASP Chi-restraints excluded: chain K residue 315 VAL Chi-restraints excluded: chain K residue 358 ILE Chi-restraints excluded: chain K residue 401 SER Chi-restraints excluded: chain K residue 426 SER Chi-restraints excluded: chain K residue 443 SER Chi-restraints excluded: chain K residue 469 THR Chi-restraints excluded: chain L residue 186 VAL Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 276 SER Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 397 VAL Chi-restraints excluded: chain L residue 443 SER Chi-restraints excluded: chain M residue 164 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 205 VAL Chi-restraints excluded: chain M residue 249 THR Chi-restraints excluded: chain M residue 283 ASP Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 309 ILE Chi-restraints excluded: chain M residue 397 VAL Chi-restraints excluded: chain M residue 401 SER Chi-restraints excluded: chain M residue 426 SER Chi-restraints excluded: chain M residue 443 SER Chi-restraints excluded: chain M residue 469 THR Chi-restraints excluded: chain M residue 477 THR Chi-restraints excluded: chain M residue 518 ILE Chi-restraints excluded: chain M residue 537 ASP Chi-restraints excluded: chain N residue 19 ASP Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain N residue 283 ASP Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 309 ILE Chi-restraints excluded: chain N residue 397 VAL Chi-restraints excluded: chain N residue 426 SER Chi-restraints excluded: chain N residue 443 SER Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 498 THR Chi-restraints excluded: chain O residue 164 THR Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 205 VAL Chi-restraints excluded: chain O residue 239 THR Chi-restraints excluded: chain O residue 309 ILE Chi-restraints excluded: chain O residue 443 SER Chi-restraints excluded: chain O residue 447 VAL Chi-restraints excluded: chain O residue 469 THR Chi-restraints excluded: chain P residue 186 VAL Chi-restraints excluded: chain P residue 205 VAL Chi-restraints excluded: chain P residue 287 VAL Chi-restraints excluded: chain P residue 397 VAL Chi-restraints excluded: chain P residue 401 SER Chi-restraints excluded: chain P residue 460 ASN Chi-restraints excluded: chain P residue 469 THR Chi-restraints excluded: chain Q residue 205 VAL Chi-restraints excluded: chain Q residue 239 THR Chi-restraints excluded: chain Q residue 283 ASP Chi-restraints excluded: chain Q residue 401 SER Chi-restraints excluded: chain Q residue 426 SER Chi-restraints excluded: chain Q residue 443 SER Chi-restraints excluded: chain Q residue 469 THR Chi-restraints excluded: chain Q residue 539 ASP Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 258 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 469 THR Chi-restraints excluded: chain R residue 498 THR Chi-restraints excluded: chain S residue 19 ASP Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain S residue 188 LEU Chi-restraints excluded: chain S residue 205 VAL Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 276 SER Chi-restraints excluded: chain S residue 283 ASP Chi-restraints excluded: chain S residue 290 SER Chi-restraints excluded: chain S residue 309 ILE Chi-restraints excluded: chain S residue 419 VAL Chi-restraints excluded: chain S residue 426 SER Chi-restraints excluded: chain S residue 443 SER Chi-restraints excluded: chain S residue 477 THR Chi-restraints excluded: chain S residue 481 THR Chi-restraints excluded: chain S residue 537 ASP Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 48 MET Chi-restraints excluded: chain T residue 149 ILE Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 186 VAL Chi-restraints excluded: chain T residue 205 VAL Chi-restraints excluded: chain T residue 358 ILE Chi-restraints excluded: chain T residue 401 SER Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 186 VAL Chi-restraints excluded: chain U residue 205 VAL Chi-restraints excluded: chain U residue 303 ASP Chi-restraints excluded: chain U residue 342 ILE Chi-restraints excluded: chain U residue 355 THR Chi-restraints excluded: chain U residue 397 VAL Chi-restraints excluded: chain U residue 427 VAL Chi-restraints excluded: chain U residue 431 GLN Chi-restraints excluded: chain U residue 443 SER Chi-restraints excluded: chain U residue 455 SER Chi-restraints excluded: chain U residue 469 THR Chi-restraints excluded: chain U residue 537 ASP Chi-restraints excluded: chain V residue 149 ILE Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 186 VAL Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 283 ASP Chi-restraints excluded: chain V residue 355 THR Chi-restraints excluded: chain V residue 358 ILE Chi-restraints excluded: chain V residue 401 SER Chi-restraints excluded: chain V residue 443 SER Chi-restraints excluded: chain V residue 469 THR Chi-restraints excluded: chain V residue 477 THR Chi-restraints excluded: chain V residue 537 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1254 random chunks: chunk 747 optimal weight: 9.9990 chunk 482 optimal weight: 4.9990 chunk 721 optimal weight: 0.3980 chunk 364 optimal weight: 0.3980 chunk 237 optimal weight: 9.9990 chunk 234 optimal weight: 6.9990 chunk 768 optimal weight: 0.9990 chunk 823 optimal weight: 0.0970 chunk 597 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 950 optimal weight: 4.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 GLN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 ASN ** 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** G 407 GLN 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** J 462 GLN ** 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** ** O 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 128 ASN ** R 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 128 ASN ** T 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 154 ASN V 527 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 98054 Z= 0.157 Angle : 0.663 9.744 132770 Z= 0.304 Chirality : 0.069 0.699 15312 Planarity : 0.002 0.038 16764 Dihedral : 27.210 128.746 23628 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.02 % Allowed : 19.94 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: 0.66 (0.08), residues: 12584 helix: 3.04 (0.07), residues: 5588 sheet: -1.67 (0.13), residues: 1716 loop : -1.82 (0.08), residues: 5280 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.001 PHE K 393 TYR 0.049 0.001 TYR J 242 ARG 0.003 0.000 ARG K 504 *********************** 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 1232 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 933 time to evaluate : 9.525 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 REVERT: A 334 LYS cc_start: 0.8833 (tttt) cc_final: 0.8599 (ttpt) REVERT: A 502 GLN cc_start: 0.8648 (tp-100) cc_final: 0.8319 (tp40) REVERT: B 39 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7758 (m-40) REVERT: C 532 GLU cc_start: 0.8414 (tt0) cc_final: 0.8164 (tt0) REVERT: D 13 ASN cc_start: 0.8147 (t0) cc_final: 0.7762 (t0) REVERT: D 502 GLN cc_start: 0.8486 (tp40) cc_final: 0.8194 (tm-30) REVERT: E 102 ASP cc_start: 0.7705 (t0) cc_final: 0.7248 (t0) REVERT: E 309 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.8972 (mt) REVERT: E 502 GLN cc_start: 0.8613 (tp-100) cc_final: 0.8088 (tp-100) REVERT: F 102 ASP cc_start: 0.7382 (t70) cc_final: 0.7152 (t0) REVERT: F 235 ASP cc_start: 0.7758 (t0) cc_final: 0.7535 (t70) REVERT: F 242 TYR cc_start: 0.8940 (p90) cc_final: 0.8708 (p90) REVERT: F 309 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9072 (mt) REVERT: F 393 PHE cc_start: 0.8799 (m-10) cc_final: 0.8569 (m-10) REVERT: F 537 ASP cc_start: 0.6975 (m-30) cc_final: 0.6218 (m-30) REVERT: G 129 THR cc_start: 0.8401 (m) cc_final: 0.8193 (m) REVERT: G 308 LYS cc_start: 0.9333 (tttt) cc_final: 0.9081 (tttp) REVERT: G 357 MET cc_start: 0.8763 (mmt) cc_final: 0.8378 (mmt) REVERT: G 385 TYR cc_start: 0.8550 (p90) cc_final: 0.8230 (p90) REVERT: I 19 ASP cc_start: 0.8166 (t0) cc_final: 0.7953 (t0) REVERT: I 124 ASP cc_start: 0.8326 (m-30) cc_final: 0.8074 (m-30) REVERT: I 352 MET cc_start: 0.8924 (mtt) cc_final: 0.8600 (mtt) REVERT: J 82 MET cc_start: 0.8466 (mtm) cc_final: 0.8168 (mtp) REVERT: J 385 TYR cc_start: 0.8875 (p90) cc_final: 0.8610 (p90) REVERT: J 502 GLN cc_start: 0.8583 (tp-100) cc_final: 0.8261 (tm-30) REVERT: K 129 THR cc_start: 0.8429 (m) cc_final: 0.8210 (m) REVERT: L 13 ASN cc_start: 0.7937 (t0) cc_final: 0.7678 (t0) REVERT: L 129 THR cc_start: 0.8355 (m) cc_final: 0.8152 (m) REVERT: L 537 ASP cc_start: 0.7324 (m-30) cc_final: 0.6995 (m-30) REVERT: M 573 ARG cc_start: 0.8704 (ttm-80) cc_final: 0.8073 (ttt-90) REVERT: N 146 GLU cc_start: 0.7970 (mp0) cc_final: 0.7767 (mp0) REVERT: N 502 GLN cc_start: 0.8118 (tp40) cc_final: 0.7343 (tm-30) REVERT: N 534 GLN cc_start: 0.8885 (mm-40) cc_final: 0.8661 (tp40) REVERT: O 102 ASP cc_start: 0.7633 (t0) cc_final: 0.7180 (t0) REVERT: O 309 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.9190 (mt) REVERT: O 491 ASP cc_start: 0.8537 (m-30) cc_final: 0.8290 (m-30) REVERT: P 115 ASP cc_start: 0.8073 (t0) cc_final: 0.7744 (t0) REVERT: P 308 LYS cc_start: 0.9396 (tttt) cc_final: 0.9152 (tttm) REVERT: P 446 TYR cc_start: 0.9375 (m-80) cc_final: 0.8978 (m-80) REVERT: P 502 GLN cc_start: 0.8415 (tp-100) cc_final: 0.7803 (tm-30) REVERT: Q 573 ARG cc_start: 0.8830 (ttm-80) cc_final: 0.8185 (ptt180) REVERT: R 48 MET cc_start: 0.8466 (ttp) cc_final: 0.8217 (ttp) REVERT: R 282 LYS cc_start: 0.9197 (ptmm) cc_final: 0.8983 (ptpp) REVERT: R 315 VAL cc_start: 0.8386 (t) cc_final: 0.8013 (p) REVERT: S 283 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8233 (p0) REVERT: S 431 GLN cc_start: 0.8631 (mm110) cc_final: 0.8305 (mm-40) REVERT: T 357 MET cc_start: 0.9068 (mmm) cc_final: 0.8841 (mmp) REVERT: T 534 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8372 (mm-40) REVERT: U 146 GLU cc_start: 0.5839 (pt0) cc_final: 0.5453 (pt0) REVERT: U 234 TYR cc_start: 0.9141 (p90) cc_final: 0.8789 (p90) REVERT: U 357 MET cc_start: 0.9176 (mmm) cc_final: 0.8868 (mmt) REVERT: U 385 TYR cc_start: 0.8474 (p90) cc_final: 0.8193 (p90) REVERT: V 235 ASP cc_start: 0.8019 (t0) cc_final: 0.7703 (t70) REVERT: V 487 MET cc_start: 0.8678 (mmm) cc_final: 0.8458 (mmt) outliers start: 299 outliers final: 245 residues processed: 1192 average time/residue: 0.7737 time to fit residues: 1684.0354 Evaluate side-chains 1095 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 845 time to evaluate : 8.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain F residue 164 THR Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 401 SER Chi-restraints excluded: chain F residue 443 SER Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 283 ASP Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 303 ASP Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 437 SER Chi-restraints excluded: chain G residue 443 SER Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 469 THR Chi-restraints excluded: chain G residue 537 ASP Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 283 ASP Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 468 THR Chi-restraints excluded: chain H residue 469 THR Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 186 VAL Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 401 SER Chi-restraints excluded: chain I residue 443 SER Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 239 THR Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 401 SER Chi-restraints excluded: chain J residue 421 SER Chi-restraints excluded: chain J residue 427 VAL Chi-restraints excluded: chain J residue 448 VAL Chi-restraints excluded: chain J residue 469 THR Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 283 ASP Chi-restraints excluded: chain K residue 315 VAL Chi-restraints excluded: chain K residue 358 ILE Chi-restraints excluded: chain K residue 401 SER Chi-restraints excluded: chain K residue 443 SER Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 186 VAL Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 397 VAL Chi-restraints excluded: chain L residue 443 SER Chi-restraints excluded: chain L residue 477 THR Chi-restraints excluded: chain M residue 164 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 188 LEU Chi-restraints excluded: chain M residue 205 VAL Chi-restraints excluded: chain M residue 249 THR Chi-restraints excluded: chain M residue 276 SER Chi-restraints excluded: chain M residue 283 ASP Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 309 ILE Chi-restraints excluded: chain M residue 397 VAL Chi-restraints excluded: chain M residue 401 SER Chi-restraints excluded: chain M residue 443 SER Chi-restraints excluded: chain M residue 469 THR Chi-restraints excluded: chain M residue 518 ILE Chi-restraints excluded: chain M residue 537 ASP Chi-restraints excluded: chain N residue 19 ASP Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 198 ASP Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain N residue 283 ASP Chi-restraints excluded: chain N residue 309 ILE Chi-restraints excluded: chain N residue 355 THR Chi-restraints excluded: chain N residue 397 VAL Chi-restraints excluded: chain N residue 401 SER Chi-restraints excluded: chain N residue 426 SER Chi-restraints excluded: chain N residue 443 SER Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 498 THR Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 205 VAL Chi-restraints excluded: chain O residue 239 THR Chi-restraints excluded: chain O residue 258 VAL Chi-restraints excluded: chain O residue 309 ILE Chi-restraints excluded: chain O residue 419 VAL Chi-restraints excluded: chain O residue 443 SER Chi-restraints excluded: chain O residue 447 VAL Chi-restraints excluded: chain O residue 469 THR Chi-restraints excluded: chain P residue 186 VAL Chi-restraints excluded: chain P residue 205 VAL Chi-restraints excluded: chain P residue 287 VAL Chi-restraints excluded: chain P residue 401 SER Chi-restraints excluded: chain P residue 426 SER Chi-restraints excluded: chain P residue 443 SER Chi-restraints excluded: chain P residue 460 ASN Chi-restraints excluded: chain Q residue 205 VAL Chi-restraints excluded: chain Q residue 239 THR Chi-restraints excluded: chain Q residue 283 ASP Chi-restraints excluded: chain Q residue 401 SER Chi-restraints excluded: chain Q residue 426 SER Chi-restraints excluded: chain Q residue 443 SER Chi-restraints excluded: chain Q residue 469 THR Chi-restraints excluded: chain Q residue 537 ASP Chi-restraints excluded: chain R residue 19 ASP Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain R residue 239 THR Chi-restraints excluded: chain R residue 258 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 469 THR Chi-restraints excluded: chain R residue 498 THR Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain S residue 188 LEU Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 258 VAL Chi-restraints excluded: chain S residue 276 SER Chi-restraints excluded: chain S residue 283 ASP Chi-restraints excluded: chain S residue 290 SER Chi-restraints excluded: chain S residue 309 ILE Chi-restraints excluded: chain S residue 419 VAL Chi-restraints excluded: chain S residue 426 SER Chi-restraints excluded: chain S residue 443 SER Chi-restraints excluded: chain S residue 469 THR Chi-restraints excluded: chain S residue 481 THR Chi-restraints excluded: chain S residue 537 ASP Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 149 ILE Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 186 VAL Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain T residue 205 VAL Chi-restraints excluded: chain T residue 255 ILE Chi-restraints excluded: chain T residue 276 SER Chi-restraints excluded: chain T residue 358 ILE Chi-restraints excluded: chain T residue 401 SER Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 448 VAL Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 186 VAL Chi-restraints excluded: chain U residue 188 LEU Chi-restraints excluded: chain U residue 205 VAL Chi-restraints excluded: chain U residue 303 ASP Chi-restraints excluded: chain U residue 342 ILE Chi-restraints excluded: chain U residue 355 THR Chi-restraints excluded: chain U residue 427 VAL Chi-restraints excluded: chain U residue 443 SER Chi-restraints excluded: chain U residue 469 THR Chi-restraints excluded: chain V residue 149 ILE Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 186 VAL Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 355 THR Chi-restraints excluded: chain V residue 358 ILE Chi-restraints excluded: chain V residue 401 SER Chi-restraints excluded: chain V residue 443 SER Chi-restraints excluded: chain V residue 477 THR Chi-restraints excluded: chain V residue 537 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1254 random chunks: chunk 1099 optimal weight: 0.0980 chunk 1157 optimal weight: 9.9990 chunk 1056 optimal weight: 5.9990 chunk 1126 optimal weight: 10.0000 chunk 677 optimal weight: 6.9990 chunk 490 optimal weight: 2.9990 chunk 884 optimal weight: 9.9990 chunk 345 optimal weight: 9.9990 chunk 1017 optimal weight: 5.9990 chunk 1065 optimal weight: 5.9990 chunk 1122 optimal weight: 20.0000 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 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** ** E 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 ASN ** G 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 371 GLN ** I 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 462 GLN ** K 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 444 ASN L 371 GLN L 407 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** ** O 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 128 ASN ** R 499 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2762 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= 0.256 Angle : 0.692 10.498 132770 Z= 0.324 Chirality : 0.070 0.702 15312 Planarity : 0.002 0.037 16764 Dihedral : 27.671 131.166 23628 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.20 % Allowed : 20.15 % Favored : 76.65 % 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: 0.65 (0.08), residues: 12584 helix: 3.00 (0.07), residues: 5500 sheet: -1.66 (0.13), residues: 1716 loop : -1.71 (0.08), residues: 5368 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.001 PHE O 393 TYR 0.051 0.002 TYR S 242 ARG 0.004 0.000 ARG E 504 *********************** 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 1115 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 317 poor density : 798 time to evaluate : 8.388 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 LYS cc_start: 0.8907 (tttt) cc_final: 0.8642 (ttpt) REVERT: B 39 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.7883 (m-40) REVERT: C 532 GLU cc_start: 0.8526 (tt0) cc_final: 0.8248 (tt0) REVERT: D 13 ASN cc_start: 0.8411 (t0) cc_final: 0.7957 (t0) REVERT: D 502 GLN cc_start: 0.8561 (tp40) cc_final: 0.8255 (tm-30) REVERT: E 82 MET cc_start: 0.8615 (mtp) cc_final: 0.8404 (mtm) REVERT: E 102 ASP cc_start: 0.7741 (t0) cc_final: 0.7236 (t0) REVERT: E 502 GLN cc_start: 0.8609 (tp-100) cc_final: 0.8081 (tp-100) REVERT: E 532 GLU cc_start: 0.8578 (tt0) cc_final: 0.8304 (tt0) REVERT: F 102 ASP cc_start: 0.7685 (t70) cc_final: 0.7319 (t0) REVERT: F 235 ASP cc_start: 0.7851 (t0) cc_final: 0.7635 (t70) REVERT: F 242 TYR cc_start: 0.8992 (p90) cc_final: 0.8656 (p90) REVERT: F 334 LYS cc_start: 0.8390 (tttt) cc_final: 0.8145 (tttt) REVERT: G 308 LYS cc_start: 0.9398 (tttt) cc_final: 0.9143 (tttp) REVERT: G 357 MET cc_start: 0.8769 (mmt) cc_final: 0.8385 (mmt) REVERT: I 19 ASP cc_start: 0.8208 (t0) cc_final: 0.7989 (t0) REVERT: I 124 ASP cc_start: 0.8338 (m-30) cc_final: 0.8093 (m-30) REVERT: I 385 TYR cc_start: 0.8536 (p90) cc_final: 0.8216 (p90) REVERT: J 385 TYR cc_start: 0.8755 (p90) cc_final: 0.8468 (p90) REVERT: J 502 GLN cc_start: 0.8618 (tp-100) cc_final: 0.8287 (tm-30) REVERT: K 122 GLU cc_start: 0.8851 (tp30) cc_final: 0.8628 (tp30) REVERT: K 537 ASP cc_start: 0.8663 (p0) cc_final: 0.8397 (p0) REVERT: L 13 ASN cc_start: 0.8227 (t0) cc_final: 0.7977 (t0) REVERT: L 129 THR cc_start: 0.8407 (m) cc_final: 0.8172 (m) REVERT: L 537 ASP cc_start: 0.7361 (m-30) cc_final: 0.6967 (m-30) REVERT: M 385 TYR cc_start: 0.8526 (p90) cc_final: 0.8127 (p90) REVERT: M 573 ARG cc_start: 0.8737 (ttm-80) cc_final: 0.8052 (ttt-90) REVERT: N 502 GLN cc_start: 0.8316 (tp40) cc_final: 0.7619 (tm-30) REVERT: O 102 ASP cc_start: 0.7862 (t0) cc_final: 0.7459 (t0) REVERT: O 491 ASP cc_start: 0.8567 (m-30) cc_final: 0.8329 (m-30) REVERT: P 115 ASP cc_start: 0.8160 (t0) cc_final: 0.7844 (t0) REVERT: P 308 LYS cc_start: 0.9400 (tttt) cc_final: 0.9130 (tttm) REVERT: P 446 TYR cc_start: 0.9424 (m-80) cc_final: 0.9017 (m-80) REVERT: P 502 GLN cc_start: 0.8488 (tp-100) cc_final: 0.7861 (tm-30) REVERT: Q 502 GLN cc_start: 0.8347 (tp40) cc_final: 0.7301 (tm-30) REVERT: Q 573 ARG cc_start: 0.8872 (ttm-80) cc_final: 0.7893 (ttt-90) REVERT: R 48 MET cc_start: 0.8508 (ttp) cc_final: 0.8194 (ttm) REVERT: R 315 VAL cc_start: 0.8642 (t) cc_final: 0.8258 (p) REVERT: R 561 MET cc_start: 0.8186 (mtt) cc_final: 0.7814 (mtt) REVERT: S 283 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8308 (p0) REVERT: S 490 MET cc_start: 0.8664 (ttm) cc_final: 0.8388 (ttm) REVERT: U 146 GLU cc_start: 0.5996 (pt0) cc_final: 0.5664 (pt0) REVERT: U 234 TYR cc_start: 0.9209 (p90) cc_final: 0.8754 (p90) REVERT: U 357 MET cc_start: 0.9154 (mmm) cc_final: 0.8590 (mmm) REVERT: U 385 TYR cc_start: 0.8427 (p90) cc_final: 0.8112 (p90) REVERT: U 431 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8610 (pm20) REVERT: U 487 MET cc_start: 0.8713 (mmm) cc_final: 0.7804 (mmm) REVERT: V 235 ASP cc_start: 0.8073 (t0) cc_final: 0.7755 (t70) REVERT: V 487 MET cc_start: 0.8781 (mmm) cc_final: 0.8536 (mmt) outliers start: 317 outliers final: 288 residues processed: 1077 average time/residue: 0.7667 time to fit residues: 1515.2508 Evaluate side-chains 1071 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 780 time to evaluate : 8.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 352 MET Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 164 THR Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 401 SER Chi-restraints excluded: chain F residue 443 SER Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 283 ASP Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 303 ASP Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 437 SER Chi-restraints excluded: chain G residue 443 SER Chi-restraints excluded: chain G residue 469 THR Chi-restraints excluded: chain G residue 537 ASP Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 283 ASP Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 468 THR Chi-restraints excluded: chain H residue 469 THR Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 186 VAL Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 401 SER Chi-restraints excluded: chain I residue 443 SER Chi-restraints excluded: chain I residue 469 THR Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 239 THR Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 401 SER Chi-restraints excluded: chain J residue 421 SER Chi-restraints excluded: chain J residue 427 VAL Chi-restraints excluded: chain J residue 443 SER Chi-restraints excluded: chain J residue 448 VAL Chi-restraints excluded: chain J residue 455 SER Chi-restraints excluded: chain J residue 469 THR Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 239 THR Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 283 ASP Chi-restraints excluded: chain K residue 315 VAL Chi-restraints excluded: chain K residue 358 ILE Chi-restraints excluded: chain K residue 401 SER Chi-restraints excluded: chain K residue 426 SER Chi-restraints excluded: chain K residue 427 VAL Chi-restraints excluded: chain K residue 443 SER Chi-restraints excluded: chain K residue 469 THR Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 186 VAL Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 276 SER Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 397 VAL Chi-restraints excluded: chain L residue 443 SER Chi-restraints excluded: chain L residue 469 THR Chi-restraints excluded: chain L residue 477 THR Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 164 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 188 LEU Chi-restraints excluded: chain M residue 205 VAL Chi-restraints excluded: chain M residue 249 THR Chi-restraints excluded: chain M residue 276 SER Chi-restraints excluded: chain M residue 283 ASP Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 309 ILE Chi-restraints excluded: chain M residue 397 VAL Chi-restraints excluded: chain M residue 401 SER Chi-restraints excluded: chain M residue 421 SER Chi-restraints excluded: chain M residue 426 SER Chi-restraints excluded: chain M residue 443 SER Chi-restraints excluded: chain M residue 469 THR Chi-restraints excluded: chain M residue 518 ILE Chi-restraints excluded: chain M residue 537 ASP Chi-restraints excluded: chain N residue 19 ASP Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 198 ASP Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain N residue 283 ASP Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 309 ILE Chi-restraints excluded: chain N residue 355 THR Chi-restraints excluded: chain N residue 397 VAL Chi-restraints excluded: chain N residue 401 SER Chi-restraints excluded: chain N residue 426 SER Chi-restraints excluded: chain N residue 443 SER Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 498 THR Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 164 THR Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 202 ASP Chi-restraints excluded: chain O residue 205 VAL Chi-restraints excluded: chain O residue 239 THR Chi-restraints excluded: chain O residue 258 VAL Chi-restraints excluded: chain O residue 385 TYR Chi-restraints excluded: chain O residue 419 VAL Chi-restraints excluded: chain O residue 443 SER Chi-restraints excluded: chain O residue 447 VAL Chi-restraints excluded: chain O residue 469 THR Chi-restraints excluded: chain P residue 105 SER Chi-restraints excluded: chain P residue 164 THR Chi-restraints excluded: chain P residue 186 VAL Chi-restraints excluded: chain P residue 205 VAL Chi-restraints excluded: chain P residue 287 VAL Chi-restraints excluded: chain P residue 358 ILE Chi-restraints excluded: chain P residue 401 SER Chi-restraints excluded: chain P residue 426 SER Chi-restraints excluded: chain P residue 443 SER Chi-restraints excluded: chain P residue 460 ASN Chi-restraints excluded: chain P residue 469 THR Chi-restraints excluded: chain Q residue 105 SER Chi-restraints excluded: chain Q residue 164 THR Chi-restraints excluded: chain Q residue 205 VAL Chi-restraints excluded: chain Q residue 239 THR Chi-restraints excluded: chain Q residue 283 ASP Chi-restraints excluded: chain Q residue 401 SER Chi-restraints excluded: chain Q residue 426 SER Chi-restraints excluded: chain Q residue 443 SER Chi-restraints excluded: chain Q residue 469 THR Chi-restraints excluded: chain Q residue 537 ASP Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 258 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 426 SER Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 469 THR Chi-restraints excluded: chain R residue 498 THR Chi-restraints excluded: chain S residue 112 LEU Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain S residue 188 LEU Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 258 VAL Chi-restraints excluded: chain S residue 276 SER Chi-restraints excluded: chain S residue 283 ASP Chi-restraints excluded: chain S residue 290 SER Chi-restraints excluded: chain S residue 309 ILE Chi-restraints excluded: chain S residue 342 ILE Chi-restraints excluded: chain S residue 419 VAL Chi-restraints excluded: chain S residue 426 SER Chi-restraints excluded: chain S residue 443 SER Chi-restraints excluded: chain S residue 469 THR Chi-restraints excluded: chain S residue 481 THR Chi-restraints excluded: chain S residue 537 ASP Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 149 ILE Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 186 VAL Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain T residue 205 VAL Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain T residue 255 ILE Chi-restraints excluded: chain T residue 276 SER Chi-restraints excluded: chain T residue 358 ILE Chi-restraints excluded: chain T residue 401 SER Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 448 VAL Chi-restraints excluded: chain T residue 469 THR Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 186 VAL Chi-restraints excluded: chain U residue 188 LEU Chi-restraints excluded: chain U residue 205 VAL Chi-restraints excluded: chain U residue 303 ASP Chi-restraints excluded: chain U residue 342 ILE Chi-restraints excluded: chain U residue 355 THR Chi-restraints excluded: chain U residue 358 ILE Chi-restraints excluded: chain U residue 397 VAL Chi-restraints excluded: chain U residue 427 VAL Chi-restraints excluded: chain U residue 431 GLN Chi-restraints excluded: chain U residue 443 SER Chi-restraints excluded: chain U residue 469 THR Chi-restraints excluded: chain V residue 149 ILE Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 186 VAL Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 355 THR Chi-restraints excluded: chain V residue 358 ILE Chi-restraints excluded: chain V residue 401 SER Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 443 SER Chi-restraints excluded: chain V residue 469 THR Chi-restraints excluded: chain V residue 537 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1254 random chunks: chunk 739 optimal weight: 4.9990 chunk 1191 optimal weight: 6.9990 chunk 726 optimal weight: 8.9990 chunk 565 optimal weight: 1.9990 chunk 827 optimal weight: 10.0000 chunk 1249 optimal weight: 5.9990 chunk 1149 optimal weight: 6.9990 chunk 994 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 768 optimal weight: 3.9990 chunk 610 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** B 444 ASN ** 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** ** E 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 527 ASN ** 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** J 462 GLN ** 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** O 98 GLN O 104 GLN ** O 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 499 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 98054 Z= 0.221 Angle : 0.682 13.657 132770 Z= 0.318 Chirality : 0.069 0.695 15312 Planarity : 0.002 0.031 16764 Dihedral : 27.529 130.652 23628 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.13 % Allowed : 20.24 % Favored : 76.63 % 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: 0.70 (0.08), residues: 12584 helix: 3.02 (0.07), residues: 5500 sheet: -1.59 (0.13), residues: 1716 loop : -1.67 (0.08), residues: 5368 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.001 PHE K 393 TYR 0.055 0.002 TYR R 242 ARG 0.003 0.000 ARG R 413 ********************** REFINEMENT MACRO_CYCLE 10 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 1107 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 797 time to evaluate : 8.315 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 LYS cc_start: 0.8908 (tttt) cc_final: 0.8659 (ttpt) REVERT: B 39 ASN cc_start: 0.8226 (OUTLIER) cc_final: 0.7848 (m-40) REVERT: C 532 GLU cc_start: 0.8521 (tt0) cc_final: 0.8244 (tt0) REVERT: D 13 ASN cc_start: 0.8382 (t0) cc_final: 0.7914 (t0) REVERT: D 502 GLN cc_start: 0.8544 (tp40) cc_final: 0.8196 (tm-30) REVERT: E 102 ASP cc_start: 0.7763 (t0) cc_final: 0.7256 (t0) REVERT: E 502 GLN cc_start: 0.8610 (tp-100) cc_final: 0.8077 (tp-100) REVERT: E 532 GLU cc_start: 0.8582 (tt0) cc_final: 0.8277 (tt0) REVERT: F 102 ASP cc_start: 0.7664 (t70) cc_final: 0.7245 (t0) REVERT: F 235 ASP cc_start: 0.7823 (t0) cc_final: 0.7585 (t70) REVERT: F 242 TYR cc_start: 0.8954 (p90) cc_final: 0.8666 (p90) REVERT: F 309 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.9052 (mt) REVERT: G 357 MET cc_start: 0.8793 (mmt) cc_final: 0.8412 (mmt) REVERT: I 19 ASP cc_start: 0.8187 (t0) cc_final: 0.7967 (t0) REVERT: I 124 ASP cc_start: 0.8336 (m-30) cc_final: 0.8082 (m-30) REVERT: J 385 TYR cc_start: 0.8777 (p90) cc_final: 0.8499 (p90) REVERT: J 502 GLN cc_start: 0.8632 (tp-100) cc_final: 0.8309 (tm-30) REVERT: K 122 GLU cc_start: 0.8828 (tp30) cc_final: 0.8595 (tp30) REVERT: L 13 ASN cc_start: 0.8180 (t0) cc_final: 0.7932 (t0) REVERT: L 129 THR cc_start: 0.8379 (m) cc_final: 0.8170 (m) REVERT: L 537 ASP cc_start: 0.7372 (m-30) cc_final: 0.7002 (m-30) REVERT: M 385 TYR cc_start: 0.8522 (p90) cc_final: 0.8131 (p90) REVERT: M 573 ARG cc_start: 0.8731 (ttm-80) cc_final: 0.8097 (ttt-90) REVERT: N 202 ASP cc_start: 0.8260 (t0) cc_final: 0.8046 (t70) REVERT: N 502 GLN cc_start: 0.8274 (tp40) cc_final: 0.7548 (tm-30) REVERT: O 102 ASP cc_start: 0.7804 (t0) cc_final: 0.7289 (t0) REVERT: O 283 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.7796 (p0) REVERT: O 491 ASP cc_start: 0.8602 (m-30) cc_final: 0.8364 (m-30) REVERT: P 48 MET cc_start: 0.8513 (ttp) cc_final: 0.8292 (tpp) REVERT: P 115 ASP cc_start: 0.8111 (t0) cc_final: 0.7801 (t0) REVERT: P 308 LYS cc_start: 0.9414 (tttt) cc_final: 0.9132 (tttm) REVERT: P 446 TYR cc_start: 0.9399 (m-80) cc_final: 0.8918 (m-80) REVERT: P 502 GLN cc_start: 0.8495 (tp-100) cc_final: 0.7864 (tm-30) REVERT: Q 502 GLN cc_start: 0.8288 (tp40) cc_final: 0.7360 (tm-30) REVERT: Q 573 ARG cc_start: 0.8866 (ttm-80) cc_final: 0.7888 (ttt-90) REVERT: R 48 MET cc_start: 0.8475 (ttp) cc_final: 0.8198 (ttm) REVERT: R 315 VAL cc_start: 0.8525 (t) cc_final: 0.8139 (p) REVERT: R 561 MET cc_start: 0.8232 (mtt) cc_final: 0.7903 (mtt) REVERT: S 283 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8291 (p0) REVERT: S 431 GLN cc_start: 0.8642 (mm110) cc_final: 0.8306 (mm-40) REVERT: S 490 MET cc_start: 0.8648 (ttm) cc_final: 0.8356 (ttm) REVERT: U 146 GLU cc_start: 0.6117 (pt0) cc_final: 0.5805 (pt0) REVERT: U 234 TYR cc_start: 0.9204 (p90) cc_final: 0.8757 (p90) REVERT: U 357 MET cc_start: 0.9146 (mmm) cc_final: 0.8562 (mmm) REVERT: U 431 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8566 (pm20) REVERT: U 487 MET cc_start: 0.8698 (mmm) cc_final: 0.7866 (mmm) REVERT: V 487 MET cc_start: 0.8778 (mmm) cc_final: 0.8545 (mmt) outliers start: 310 outliers final: 296 residues processed: 1074 average time/residue: 0.7648 time to fit residues: 1506.9641 Evaluate side-chains 1086 residues out of total 9900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 785 time to evaluate : 8.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 352 MET Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 164 THR Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 401 SER Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain F residue 443 SER Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 283 ASP Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 303 ASP Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 437 SER Chi-restraints excluded: chain G residue 443 SER Chi-restraints excluded: chain G residue 469 THR Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 537 ASP Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 283 ASP Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 468 THR Chi-restraints excluded: chain H residue 469 THR Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 186 VAL Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 290 SER Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 401 SER Chi-restraints excluded: chain I residue 443 SER Chi-restraints excluded: chain I residue 469 THR Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 239 THR Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 401 SER Chi-restraints excluded: chain J residue 421 SER Chi-restraints excluded: chain J residue 427 VAL Chi-restraints excluded: chain J residue 443 SER Chi-restraints excluded: chain J residue 448 VAL Chi-restraints excluded: chain J residue 455 SER Chi-restraints excluded: chain J residue 469 THR Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 239 THR Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 283 ASP Chi-restraints excluded: chain K residue 315 VAL Chi-restraints excluded: chain K residue 358 ILE Chi-restraints excluded: chain K residue 401 SER Chi-restraints excluded: chain K residue 426 SER Chi-restraints excluded: chain K residue 443 SER Chi-restraints excluded: chain K residue 469 THR Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 186 VAL Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 320 LEU Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 397 VAL Chi-restraints excluded: chain L residue 443 SER Chi-restraints excluded: chain L residue 469 THR Chi-restraints excluded: chain L residue 477 THR Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 164 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 186 VAL Chi-restraints excluded: chain M residue 188 LEU Chi-restraints excluded: chain M residue 249 THR Chi-restraints excluded: chain M residue 276 SER Chi-restraints excluded: chain M residue 283 ASP Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 309 ILE Chi-restraints excluded: chain M residue 397 VAL Chi-restraints excluded: chain M residue 401 SER Chi-restraints excluded: chain M residue 421 SER Chi-restraints excluded: chain M residue 426 SER Chi-restraints excluded: chain M residue 443 SER Chi-restraints excluded: chain M residue 469 THR Chi-restraints excluded: chain M residue 518 ILE Chi-restraints excluded: chain M residue 537 ASP Chi-restraints excluded: chain N residue 19 ASP Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 198 ASP Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain N residue 283 ASP Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 309 ILE Chi-restraints excluded: chain N residue 355 THR Chi-restraints excluded: chain N residue 358 ILE Chi-restraints excluded: chain N residue 397 VAL Chi-restraints excluded: chain N residue 401 SER Chi-restraints excluded: chain N residue 426 SER Chi-restraints excluded: chain N residue 443 SER Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 498 THR Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 164 THR Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 202 ASP Chi-restraints excluded: chain O residue 239 THR Chi-restraints excluded: chain O residue 258 VAL Chi-restraints excluded: chain O residue 283 ASP Chi-restraints excluded: chain O residue 385 TYR Chi-restraints excluded: chain O residue 419 VAL Chi-restraints excluded: chain O residue 443 SER Chi-restraints excluded: chain O residue 447 VAL Chi-restraints excluded: chain O residue 469 THR Chi-restraints excluded: chain P residue 105 SER Chi-restraints excluded: chain P residue 164 THR Chi-restraints excluded: chain P residue 186 VAL Chi-restraints excluded: chain P residue 205 VAL Chi-restraints excluded: chain P residue 287 VAL Chi-restraints excluded: chain P residue 358 ILE Chi-restraints excluded: chain P residue 401 SER Chi-restraints excluded: chain P residue 426 SER Chi-restraints excluded: chain P residue 443 SER Chi-restraints excluded: chain P residue 460 ASN Chi-restraints excluded: chain P residue 469 THR Chi-restraints excluded: chain Q residue 164 THR Chi-restraints excluded: chain Q residue 205 VAL Chi-restraints excluded: chain Q residue 239 THR Chi-restraints excluded: chain Q residue 283 ASP Chi-restraints excluded: chain Q residue 401 SER Chi-restraints excluded: chain Q residue 426 SER Chi-restraints excluded: chain Q residue 443 SER Chi-restraints excluded: chain Q residue 469 THR Chi-restraints excluded: chain Q residue 537 ASP Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 258 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 426 SER Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 469 THR Chi-restraints excluded: chain R residue 498 THR Chi-restraints excluded: chain S residue 112 LEU Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain S residue 188 LEU Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 258 VAL Chi-restraints excluded: chain S residue 276 SER Chi-restraints excluded: chain S residue 283 ASP Chi-restraints excluded: chain S residue 290 SER Chi-restraints excluded: chain S residue 309 ILE Chi-restraints excluded: chain S residue 342 ILE Chi-restraints excluded: chain S residue 419 VAL Chi-restraints excluded: chain S residue 426 SER Chi-restraints excluded: chain S residue 443 SER Chi-restraints excluded: chain S residue 469 THR Chi-restraints excluded: chain S residue 481 THR Chi-restraints excluded: chain S residue 537 ASP Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 149 ILE Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 186 VAL Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain T residue 205 VAL Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain T residue 255 ILE Chi-restraints excluded: chain T residue 276 SER Chi-restraints excluded: chain T residue 358 ILE Chi-restraints excluded: chain T residue 401 SER Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 448 VAL Chi-restraints excluded: chain T residue 469 THR Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 105 SER Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 186 VAL Chi-restraints excluded: chain U residue 188 LEU Chi-restraints excluded: chain U residue 205 VAL Chi-restraints excluded: chain U residue 290 SER Chi-restraints excluded: chain U residue 303 ASP Chi-restraints excluded: chain U residue 342 ILE Chi-restraints excluded: chain U residue 355 THR Chi-restraints excluded: chain U residue 358 ILE Chi-restraints excluded: chain U residue 397 VAL Chi-restraints excluded: chain U residue 426 SER Chi-restraints excluded: chain U residue 427 VAL Chi-restraints excluded: chain U residue 431 GLN Chi-restraints excluded: chain U residue 443 SER Chi-restraints excluded: chain U residue 469 THR Chi-restraints excluded: chain V residue 149 ILE Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 186 VAL Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 355 THR Chi-restraints excluded: chain V residue 358 ILE Chi-restraints excluded: chain V residue 401 SER Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 443 SER Chi-restraints excluded: chain V residue 469 THR Chi-restraints excluded: chain V residue 477 THR Chi-restraints excluded: chain V residue 537 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1254 random chunks: chunk 790 optimal weight: 10.0000 chunk 1059 optimal weight: 9.9990 chunk 304 optimal weight: 5.9990 chunk 917 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 276 optimal weight: 9.9990 chunk 996 optimal weight: 2.9990 chunk 417 optimal weight: 0.0170 chunk 1023 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 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** ** E 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 ASN I 179 GLN ** I 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 462 GLN ** 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** O 98 GLN O 104 GLN ** O 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 424 ASN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.084352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.071157 restraints weight = 210865.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.073502 restraints weight = 88343.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.074951 restraints weight = 47486.546| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 98054 Z= 0.206 Angle : 0.677 13.008 132770 Z= 0.315 Chirality : 0.069 0.682 15312 Planarity : 0.002 0.031 16764 Dihedral : 27.395 130.295 23628 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.24 % Allowed : 20.22 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: 0.77 (0.08), residues: 12584 helix: 3.07 (0.07), residues: 5500 sheet: -1.51 (0.13), residues: 1716 loop : -1.64 (0.08), residues: 5368 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.001 PHE K 393 TYR 0.054 0.002 TYR R 242 ARG 0.003 0.000 ARG R 413 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23379.99 seconds wall clock time: 413 minutes 22.78 seconds (24802.78 seconds total)